Parameter file is implemented, completely.
Minor changes
Minor changes.
Test fucntion has been changed.
Add Makefile.
Create Makefile and project file.
Generic dihedral checking condition has been changed.
Prep file reader is refactored.
Create make file
TODO:
	Implement printing functions
	Test
Prep file reading has been refactored.
Test program has been implemented.
TODO:
	GetIndexByName has some issues
Prep file has been tested.
Errors have been fixed.
Test program has been implemented.
Library file reader has been refactored
Coordinate file reader refactoring and test function
Add make file and test files
Documentation and commentary
Fully documented compatible with doxygen
Set the default output stream for Print functions
Default output stream for Print functions fixed
Remove unused files for gems and other layers
Accessors and Mutators