Added color and scale customization properties for secondary structures
Added a secondary structure class to help us iterate over secondary structures instead of only the amino acids. This also allowed us to implement secondary structure selection and the highlighting of secondary structure
Added the ability to spawn  the hydrogen bonds that connect beta sheets
Fixed a problem that caused parts of the backbone to not look right when moving an amino acid because they were no being updated
minor modifications to make the program run on cooked mode
edited resolution settings so that the application no longer looks like crap
Merge branch 'features/secondary_structure_builder' into features/UI/test