code: def remove_files(self):
          
          file_list = ["molecule.svg","lig.pdb","HIS.pdb","PHE.pdb","TRP.pdb","TYR.pdb","lig.mol","test.xtc"]
          for residue in self.topol_data.dict_of_plotted_res.keys():
              file_list.append(residue[1]+residue[2]+".svg")
          for f in file_list:
              if os.path.isfile(f)==True:
                  os.remove(f)
docs: Removes intermediate files.