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.