old_contents: # Some utility classes to represent a PDB structure
  
  class Atom:
      """
      A simple class for an amino acid residue
      """
  
      def __init__(self, type):
          self.type = type
          self.coords = (0.0, 0.0, 0.0)
  
      # Overload the __repr__ operator to make printing simpler.
      def __repr__(self):
          return self.type
  
  class Residue:
      """
      A simple class for an amino acid residue
      """
  
      def __init__(self, type, number):
          self.type = type
          self.number = number
          self.atoms = []
  
      # Overload the __repr__ operator to make printing simpler.
      def __repr__(self):
          return self.type + " " + self.number
  
  class ActiveSite:
      """
      A simple class for an active site
      """
  
      def __init__(self, name):
          self.name = name
          self.residues = []
  
      # Overload the __repr__ operator to make printing simpler.
      def __repr__(self):
          return self.name
  
new_contents: # Some utility classes to represent a PDB structure
  
  class Atom:
      """
      A simple class for an amino acid residue
      """
  
      def __init__(self, type):
          self.type = type
          self.coords = (0.0, 0.0, 0.0)
  
      # Overload the __repr__ operator to make printing simpler.
      def __repr__(self):
          return self.type
  
  class Residue:
      """
      A simple class for an amino acid residue
      """
  
      def __init__(self, type, number):
          self.type = type
          self.number = number
          self.atoms = []
  
      # Overload the __repr__ operator to make printing simpler.
      def __repr__(self):
          return "{0} {1}".format(self.type, self.number)
  
  class ActiveSite:
      """
      A simple class for an active site
      """
  
      def __init__(self, name):
          self.name = name
          self.residues = []
  
      # Overload the __repr__ operator to make printing simpler.
      def __repr__(self):
          return self.name
  
subject: use new string formatting to get around missing conversion