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.
Removed duplicate atom set printing
Fixed bug with isolated atoms

Null pointers were being observed. Fixed.
Edited some permissions
gitignore update
Merged utility-class into component-positions

Merged some changes from utility-class into component-positions. Needed
to get more accurate results / cli.