jbellamycarter

def all_atom_rmsd(ref, traj):
    """Calculate the all-atom RMSD for a trajectory against reference.
    Assumes that the same structure is being compared with all atoms
    in the same order. `traj` can be a single frame or a full trajectory.
    
    Parameters
    ----------
    ref : list or ndarray
        xyz coordinates for the reference positions (Nx3)
    traj : list or ndarray