implement isomerism bug fixes plus tests

cgsmiles/graph_utils.py

@@ -91,10 +91,16 @@ def sort_nodes_by_attr(graph,
         attr_dict = nx.get_node_attributes(new_graph, attr)
         new_dict = {}
         for key, values in attr_dict.items():
+            try:
+                iter(values)
+            except TypeError:
+                is_list = False
+            else:
+                is_list = not isinstance(values, str)
             if is_list:
                 new_values = [mapping[value] for value in values]
             else:
-               new_values = mapping[values]
+                new_values = mapping[values]
             new_dict[key] = new_values
         if new_dict:
             nx.set_node_attributes(new_graph, new_dict, attr)

cgsmiles/pysmiles_utils.py

@@ -63,7 +63,7 @@ def annotate_ez_isomers(molecule):
     Parameters
     ----------
     molecule: nx.Graph
-        The molecule of intrest, which must of ez_isomer_pairs
+        The molecule of interest, which must of ez_isomer_pairs
         and ez_isomer_class set as node attributes
     """
     ez_isomer_atoms = nx.get_node_attributes(molecule, 'ez_isomer_atoms')

cgsmiles/tests/test_molecule_resolve.py

@@ -236,14 +236,14 @@ def test_all_atom_resolve_molecule(smile, ref_frags, elements, ref_edges, chiral
     meta_mol, molecule = MoleculeResolver.from_string(smile).resolve()
 
     # loop and compare fragments first
-    counter=0
+    counter = 0
     for node, ref in zip(meta_mol.nodes, ref_frags):
         assert meta_mol.nodes[node]['fragname'] ==  ref[0]
         block_graph = meta_mol.nodes[node]['graph']
         target_elements = nx.get_node_attributes(block_graph, 'element')
         sorted_elements =  [target_elements[key] for key in sorted(target_elements)]
         print("-->", sorted_elements)
-        print("-->",ref[1].split())
+        print("-->", ref[1].split())
         assert sorted_elements == ref[1].split()
         print(counter)
         counter += 1