Prevent resonance structure generation from making charged adsorbates.

The problem was that O=X (where X is the surface site) was forming [O+]#X
which has a net charge.

Not sure if this is the best way to solve the problem, but it solves the problem.

Closes cfgoldsmith#43

rmgpy/molecule/resonance.py

@@ -502,7 +502,10 @@ def generate_adj_lone_pair_multiple_bond_resonance_structures(mol):
             except AtomTypeError:
                 pass  # Don't append resonance structure if it creates an undefined atomType
             else:
-                structures.append(structure)
+                if structure.getNetCharge() and structure.containsSurfaceSite():
+                    pass
+                else:
+                    structures.append(structure)
     return structures
 
 

rmgpy/molecule/resonanceTest.py

@@ -1332,3 +1332,12 @@ def testExocyclicDB(self):
         newmol = generate_clar_structures(mol)
 
         self.assertEquals(len(newmol), 0)
+
+    def testSurfaceO(self):
+        """Test resonance structure generation for surface adsorbed O=X
+
+        Should not crash."""
+        # See https://github.com/cfgoldsmith/RMG-Py/issues/43
+        mol_list = generate_resonance_structures(Molecule().fromAdjacencyList("""OX
+1 X u0 p0 c0 {2,D}
+2 O u0 p2 c0 {1,D}"""))