docs: def topology_mdtraj(traj):
      '''Generate topology spec for the MolecularViewer from mdtraj.
  
      :param mdtraj.Trajectory traj: the trajectory
      :return: A chemview-compatible dictionary corresponding to the topology defined in mdtraj.
  
      '''
      import mdtraj as md
  
      top = {}
      top['atom_types'] = [a.element.symbol for a in traj.topology.atoms]
      top['atom_names'] = [a.name for a in traj.topology.atoms]
      top['bonds'] = [(a.index, b.index) for a, b in traj.topology.bonds]
      top['secondary_structure'] = md.compute_dssp(traj[0])[0]
      top['residue_types'] = [r.name for r in traj.topology.residues ]
      top['residue_indices'] = [ [a.index for a in r.atoms] for r in traj.topology.residues ]
  
      return top