msmbuilder.metrics.RMSD.__init__

RMSD.__init__(atomindices=None, omp_parallel=True)

Initalize an RMSD calculator

Parameters:

atomindices : array_like, optional

List of the indices of the atoms that you want to use for the RMSD calculation. For example, if your trajectory contains the coordinates of all the atoms, but you only want to compute the RMSD on the C-alpha atoms, then you can supply a reduced set of atom_indices. If unsupplied, all of the atoms will be used.

omp_parallel : bool, optional

Use OpenMP parallelized C code under the hood to take advantage of multicore architectures. If you’re using another parallelization scheme (e.g. MPI), you might consider turning off this flag.

Notes

You can also control the degree of parallelism with the OMP_NUM_THREADS envirnoment variable