mdtraj.compute_drid¶
- mdtraj.compute_drid(traj, atom_indices=None)¶
Distribution of reciprocal interatomic distances (DRID) representation of an MD trajectory
- Parameters:
traj (md.Trajectory) – A trajectory
atom_indices (np.ndarray, dtype=int, shape=(n_atom_indices,) or None) – The indices (zero-based) of the atoms to use in the DRID representation. If None, all atoms will be used.
- Returns:
X – A rotationally invariant vector representation of each frame in the simulation. The DRID vector contains the mean, second, and third central moments of the reciprocal interatomic distances (with 1-2 interactions excluded).
- Return type:
np.ndarray, shape=(n_frames, n_atom_indices*3), dtype=np.double
References
[1]Zhou, Caflisch; Distribution of Reciprocal of Interatomic Distances: A Fast Structural Metric. JCTC 2012 doi:10.1021/ct3003145