SuperposeFeaturizer

class SuperposeFeaturizer(Featurizer):
    """Featurizer based on euclidian atom distances to reference structure.

    This featurizer transforms a dataset containing MD trajectories into
    a vector dataset by representing each frame in each of the MD trajectories
    by a vector containing the distances from a specified set of atoms to
    the 'reference position' of those atoms, in ``reference_traj``.

    Parameters
    ----------
    atom_indices : np.ndarray, shape=(n_atoms,), dtype=int
        The indices of the atoms to superpose and compute the distances with
    reference_traj : md.Trajectory
        The reference conformation to superpose each frame with respect to
        (only the first frame in reference_traj is used)
    superpose_atom_indices : np.ndarray, shape=(n_atoms,), dtype=int
        If not None, these atom_indices are used for the superposition
    """