More performance improvements - moving calculation of bonds next to atoms to a single place (so we don't loop over the bonds in a molecule multiple times), and removing some integer parsing that was un-needed
Using TryGetValue instead of ContainsKey and lookup
Fixed more ContiansKey + lookups to use TryGetValue
Merge pull request #3 from NonlinearDynamics/Performance

More performance improvements - moving calculation of bonds next to atom...