Add first steps for dictionary funtionality to read XYZ coordinates
Added get Trp Coordinate and write to dictionary function
Fix get trpCoordfromPDB make it more concise/clearer to read
Fix get hemeCoordfromPDB make it more concise/clearer to read
Replace coordinates used in estimation of k^2 function, now call from dictionary
Fix typo, should be Fe not HemeFe to read from dictionary. Fixed for other heme dictionary calls
fix typo of Fe to FE, replace coordinates with calls from the atomXYZ coordinate library
removed several print functions used for debugging
Read from dictionary for coordinates in kappaSquaredRoutine
Read from dictionary for coordinates calling trp and heme coordinates
Added getTrp and getHeme coordinate functions to kappaSquared routine
Remove all globals for coordinates, using dictionary of atomXYZ for coordinates instead