def save_container(filename, dtype):
s = Serializer({
'Data': np.array(minus_ones, dtype=dtype),
'completed_vtrajs': np.zeros((n_vtrajs), dtype=np.bool),
'hashes': hashes
})
s.save_to_hdf(filename)
def draw_index(probs, n_picks=1, UseFastMethod=True):
"""Draw a number (or many numbers, controlled by n_picks), weighted by the probabilities probs."""
if UseFastMethod:
t = np.cumsum(probs)
s = sum(probs)
return np.searchsorted(t, np.random.rand(n_picks) * s)
tcounts = mmread(
'/Users/tud51931/projects/MSM/msm/ff03-hybridkcenter/RMSDCluster4.2/lagtime50/tCounts.UnMapped.mtx'
)
Assignment = Serializer.LoadFromHDF(
'/Users/tud51931/projects/MSM/msm/ff03-hybridkcenter/RMSDCluster4.2/lagtime50/Assignments.Fixed.h5'
)
trajnum = 100
frames = Assignment['Data'].shape[1]
a = Serializer()
a['Data'] = -1 * np.ones((trajnum, frames))
for traj in range(trajnum):
print '%d of %d Trajectories' % (traj, trajnum)
startstate = 126
a['Data'][traj, 0] = startstate
for step in range(1, frames):
probs = tcounts.data[tcounts.row == startstate] / sum(
tcounts.data[tcounts.row == startstate])
a['Data'][traj, step] = tcounts.col[tcounts.row == startstate][
draw_index(probs)[0]]
startstate = a['Data'][traj, step]
a.SaveToHDF('Assignments.rmsd4.2.faked.h5')
