Utility Class update 1

Very minor implementation of the StructuralFormula class
Added subscript method

Added a method to work out the subscript of a number for more clarity
when printing structural formulas.
Javadoc

Updated some javadoc / comments
Fixed bug

Null was showing up, fixed
Update

Added some changes to address some issues with the utility class
Reformat

Reformatted a lot of code, also tried new heuristics  and approach
Removed unused code

Got rid of some dead code
Update

General update
Merge branch 'master' into utility-class
Delete files
Dirty implementation

Messy implementation but functional for StructuralFormula
Delete files

Deleting some dead files
Tidy up

Tidied up the code for StrucuralFormula
Tidy Up
Code Comments

Commented some code and added some frame for new code
Code Refactor / Comments

Refactored some code in StructuralFormula / added comments
Further reduction to code
Add Neighbours work

Made some changes to AddNeighbours
Added command line interface for StructuralFormula

-sf to compute the formula
-sf -sub to use subscripts
Removed duplicate prints

Found something that was printing duplicate atoms, fixed.