def partial_transform(self, traj):
        """Featurize an MD trajectory into a vector space with the raw
        cartesian coordinates.

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

        Returns
        -------
        features : np.ndarray, dtype=float, shape=(n_samples, n_features)
            A featurized trajectory is a 2D array of shape
            `(length_of_trajectory x n_features)` where each `features[i]`
            vector is computed by applying the featurization function
            to the `i`th snapshot of the input trajectory.

        Notes
        -----
        If you requested superposition (gave `ref_traj` in __init__) the
        input trajectory will be modified.

        See Also
        --------
        transform : simultaneously featurize a collection of MD trajectories
        """
        # Optionally take only certain atoms
        if self.atom_indices is not None:
            p_traj = traj.atom_slice(self.atom_indices)
        else:
            p_traj = traj

        # Optionally superpose to a reference trajectory.
        if self.ref_traj is not None:
            p_traj.superpose(self.ref_traj, parallel=False)

        # Get the positions and reshape.
        value = p_traj.xyz.reshape(len(p_traj), -1)
        return value