Python GPURMSD Examples

Example #1

File: test_gpurmsd.py Project: jimsnyderjr/msmbuilder

def test_gpurmsd():
    traj = Trajectory.load_trajectory_file(trj_path)

    gpurmsd = GPURMSD()
    ptraj = gpurmsd.prepare_trajectory(traj)
    gpurmsd._gpurmsd.print_params()
    gpu_distances = gpurmsd.one_to_all(ptraj, ptraj, 0)

    cpurmsd = RMSD()
    ptraj = cpurmsd.prepare_trajectory(traj)
    cpu_distances = cpurmsd.one_to_all(ptraj, ptraj, 0)

    npt.assert_array_almost_equal(cpu_distances, gpu_distances, decimal=4)

Example #2

File: test_gpurmsd.py Project: AgnesHH/msmbuilder

def test_gpurmsd():
    traj = Trajectory.load_trajectory_file(trj_path)    

    gpurmsd = GPURMSD()
    ptraj = gpurmsd.prepare_trajectory(traj)
    gpurmsd._gpurmsd.print_params()
    gpu_distances = gpurmsd.one_to_all(ptraj, ptraj, 0)

    cpurmsd = RMSD()
    ptraj = cpurmsd.prepare_trajectory(traj)
    cpu_distances = cpurmsd.one_to_all(ptraj, ptraj, 0)
    
    npt.assert_array_almost_equal(cpu_distances, gpu_distances, decimal=4)

Example #3

File: test_gpurmsd.py Project: jimsnyderjr/msmbuilder

 def gpudist(t):
     gpurmsd = GPURMSD()
     pt = gpurmsd.prepare_trajectory(t)
     gpurmsd._gpurmsd.print_params()
     return gpurmsd.one_to_all(pt, pt, 0)

Example #4

File: test_gpurmsd.py Project: AgnesHH/msmbuilder

 def gpudist(t):
     gpurmsd = GPURMSD()
     pt = gpurmsd.prepare_trajectory(t)
     gpurmsd._gpurmsd.print_params()
     return gpurmsd.one_to_all(pt, pt, 0)