msmbuilder.metrics.RMSD.one_to_many¶
- RMSD.one_to_many(prepared_traj1, prepared_traj2, index1, indices2)¶
Calculate a vector of distances from one frame of the first trajectory to many frames of the second trajectory
The distances calculated are from the index1`th frame of `prepared_traj1 to the frames in prepared_traj2 with indices indices2
Parameters: prepared_traj1 : rmsd.TheoData
First prepared trajectory
prepared_traj2 : rmsd.TheoData
Second prepared trajectory
index1 : int
index in prepared_trajectory
indices2 : ndarray
list of indices in prepared_traj2 to calculate the distances to
Returns: Vector of distances of length len(indices2) :
Notes
If the omp_parallel optional argument is True, we use shared-memory parallelization in C to do this faster. Using omp_parallel = False is advised if indices2 is a short list and you are paralellizing your algorithm (say via mpi) at a different level.