modify max_heavy_atoms constraint

Author: bjkreitz

rmgpy/constraints.py

@@ -113,7 +113,7 @@ def fails_species_constraints(species):
 
     max_heavy_atoms = species_constraints.get('maximumHeavyAtoms', -1)
     if max_heavy_atoms != -1:
-        heavy_atoms = struct.get_num_atoms() - struct.get_num_atoms('H')
+        heavy_atoms = struct.get_num_atoms() - struct.get_num_atoms('H') - struct.get_num_atoms('X')
         if heavy_atoms > max_heavy_atoms:
             return f"Exceeded maximumHeavyAtoms: {heavy_atoms} > {max_heavy_atoms}"