def initialize_protein_dict():
    rtn_dict = dict()
    rtn_dict['Vif'] = 0
    rtn_dict['Vpr'] = 1
    rtn_dict['Tat'] = 2
    rtn_dict['Env'] = 3
    rtn_dict['Rev'] = 4
    rtn_dict['Nef'] = 5
    rtn_dict['Gag'] = 6
    rtn_dict['GagProPol'] = 7
    rtn_dict['Gag_dimers'] = 8
    return rtn_dict     