def partial_transform(self, traj):
        """Featurize an MD trajectory into a vector space via distance
        after superposition

        Parameters
        ----------
        traj : mdtraj.Trajectory
            A molecular dynamics trajectory to featurize.

        Returns
        -------
        features : np.ndarray, shape=(n_frames, n_ref_frames)
            The RMSD value of each frame of the input trajectory to be
            featurized versus each frame in the reference trajectory. The
            number of features is the number of reference frames.

        See Also
        --------
        transform : simultaneously featurize a collection of MD trajectories
        """
        if self.atom_indices is not None:
            sliced_traj = traj.atom_slice(self.atom_indices)
        else:
            sliced_traj = traj
        result = libdistance.cdist(
            sliced_traj, self.sliced_reference_traj, 'rmsd'
        )
        return self._transform(result)