Added sup and super links.
Simplifies naming for top level molecule.
Added resources for functional groups.
changed code layout.
Fixes from review

Added most the fixes suggested by Volker.
Deleted ComponentPositions as this is being dealt with in a separate
branch.
Fixes suggested by Volker

Added .this prefixes
Renamed some variables
Removed AddNeighbour and PrintNeighbour as no longer needed
Added exception to getSubScript
Fix for molecules with no atom sets
Merge with master

Resolved conflicts and merged with master
Merge pull request #1 from egonw/utility-class

Utility class
Added addneighbours and pass boolean instead of cli

addNeighbours added to deal with functional groups
No longer passing cli to StucturalFormula, passing boolean instead.
Merged with master