code: def to_trajectory(self, show_ports=False, chains=None,
                        residues=None, box=None):
          
          atom_list = [particle for particle in self.particles(show_ports)]
  
          top = self._to_topology(atom_list, chains, residues)
  
          # Coordinates.
          xyz = np.ndarray(shape=(1, top.n_atoms, 3), dtype='float')
          for idx, atom in enumerate(atom_list):
              xyz[0, idx] = atom.pos
  
          # Unitcell information.
          unitcell_angles = [90.0, 90.0, 90.0]
          if box is None:
              unitcell_lengths = np.empty(3)
              for dim, val in enumerate(self.periodicity):
                  if val:
                      unitcell_lengths[dim] = val
                  else:
                      unitcell_lengths[dim] = self.boundingbox.lengths[dim] + 0.5
          else:
              unitcell_lengths = box.lengths
              unitcell_angles = box.angles
  
          return md.Trajectory(xyz, top, unitcell_lengths=unitcell_lengths,
                               unitcell_angles=unitcell_angles)
docs: Convert to an md.Trajectory and flatten the compound.
  
          Parameters
          ----------
          show_ports : bool, optional, default=False
              Include all port atoms when converting to trajectory.
          chains : mb.Compound or list of mb.Compound
              Chain types to add to the topology
          residues : str of list of str
              Labels of residues in the Compound. Residues are assigned by
              checking against Compound.name.
          box : mb.Box, optional, default=self.boundingbox (with buffer)
              Box information to be used when converting to a `Trajectory`.
              If 'None', a bounding box is used with a 0.5nm buffer in each
              dimension. to avoid overlapping atoms, unless `self.periodicity`
              is not None, in which case those values are used for the
              box lengths.
  
          Returns
          -------
          trajectory : md.Trajectory
  
          See also
          --------
          _to_topology