Adding all previous functionality to SmogCalpha
Added models function to read in contact_parameters from .dat or .params files
Deprecated many options in check_options. Made SmogCalpha the only model class created.
Debugging loading models with SmogCalpha
Cleaning up model generation.
Added SMOG citation to SmogCalpha.py
Preliminary testing update. dryrun works.
Correctly saves clean_pdb without Hydrogens in subdir
Changed all gmx commands to _sbm in shadow map calc