Merge branch 'main' into default_mass_charge

mbuild/bond_graph.py

@@ -147,7 +147,7 @@ def compose(self, graph):
         adj = self._adj
         for node, neighbors in graph._adj.items():
             if self.has_node(node):
-                (adj[node].add(neighbor) for neighbor in neighbors)
+                [adj[node].add(neighbor) for neighbor in neighbors]
             else:
                 # Add new node even if it has no bond/neighbor
                 adj[node] = neighbors

mbuild/tests/test_coordinate_transform.py

@@ -448,3 +448,16 @@ def test_z_axis_transform(self, h2o):
         for i in range(4):
             z_axis_transform(h2o)
         assert np.allclose(h2o.xyz, init_xyz, atol=1e-4)
+
+    def test_bondgraph(self, ch3):
+        ch3_2 = mb.clone(ch3)
+        mb.force_overlap(ch3_2, ch3_2["up"], ch3["up"])
+        ch3.add(ch3_2)
+        bgraph = ch3.bond_graph
+        for edge0, edge1 in bgraph.edges():
+            assert bgraph.has_edge(edge0, edge1)
+            assert bgraph.has_edge(edge1, edge0)
+        neighbors = {"C": 4, "H": 1}
+        for node in bgraph.nodes():
+            x = map(lambda node: node.name, bgraph._adj[node])
+            assert neighbors[node.name] == len(list(x))