added fragment

      Each entry in this list should be an RdkitAtom

    """

    self.atoms = [AtomShim(x.GetAtomicNum(), get_partial_charge(x)) for x in atoms]

    #self.atoms = atoms 

  def GetAtoms(self):

    """Returns the list of atoms

  keep_inds = [sorted(list(keep)) for keep in keep_inds]

  return keep_inds

  # Now extract atoms

  #atoms_to_keep = []

  #for i, frag_keep_inds in enumerate(keep_inds):

  #  frag = fragments[i]

  #  mol = frag[1]

  #  atoms = mol.GetAtoms()

  #  frag_keep = [atoms[keep_ind] for keep_ind in frag_keep_inds]

  #  atoms_to_keep.append(frag_keep)

  #return atoms_to_keep

def reduce_molecular_complex_to_contacts(fragments, cutoff=4.5):

  """Reduce a molecular complex to only those atoms near a contact.