Reworked CalculateProjectSASA.py 

Basically it doesn't make sense to save a single file for an entire dataset because the result of mdtraj.geometry.sasa.shrake_rupley is an array with SASA for each ATOM in the trajectory. So the script will save a file for each trajectory in an input range. Additionally, I removed the atom indices flag because I think most people will use it incorrectly.