Minor bug fixes and improvements

A small bug for writing molecule file headers snuck through with the first release and has been fixed.

A syntax bug for finding missing atoms was fixed. This is not likely to have caused problems and no maps will need to be rerun. The bug would only cause problems if mapping reactions with lots of atoms changing bonds between the pre and post reaction.

AutoMapper now prints a comment once the tool has finished running.

Improvements made to tutorial documentation and inline code comments.