def main():
"""Parse command line inputs, load up files, and build a movie."""
parser = arglib.ArgumentParser(description="""
Create an MSM movie by sampling a sequence of states and sampling a
random conformation from each state in the sequence.
""")
parser.add_argument('project')
parser.add_argument('assignments', default='Data/Assignments.Fixed.h5')
parser.add_argument('tprob', default='Data/tProb.mtx')
parser.add_argument('num_steps')
parser.add_argument('starting_state', type=int, help='''Which state to start trajectory from.''')
parser.add_argument('output', default='sample_traj.pdb', help="""The filename of your output trajectory. The filetype suffix will be used to select the output file format.""")
args = parser.parse_args()
try:
assignments = io.loadh(args.assignments, 'arr_0')
except KeyError:
assignments = io.loadh(args.assignments, 'Data')
num_steps = int(args.num_steps)
starting_state = int(args.starting_state)
project = Project.load_from(args.project)
T = scipy.io.mmread(args.tprob).tocsr()
state_traj = msm_analysis.sample(T, starting_state, num_steps)
sampled_traj = project.get_random_confs_from_states(assignments, state_traj, 1)
traj = sampled_traj[0]
traj["XYZList"] = np.array([t["XYZList"][0] for t in sampled_traj])
traj.save(args.output)
def run( tProb, start_state, steps, project, out_pdb, out_xtc ):
state_traj = msm_analysis.sample( tProb, start_state, steps )
print "Sampled tProb."
state_sizes = np.bincount( assignments[np.where(assignments!=-1)] ) # size of each state.
which_ind_traj = [ np.random.randint( state_sizes[i] ) for i in state_traj ] # Random integer in each state in the traj
uniq_states = np.unique( state_traj )
state_lookup = dict(zip(uniq_states, np.arange(uniq_states.shape[0])))
print "Translating to trajectory, frame pairs..."
which_states = [ np.array( np.where( assignments == i ) ).T for i in uniq_states ]
# The (traj,frame) list for each state
which_traj = np.array([which_states[state_lookup[uniq_states[state_lookup[state]]]][i]
for state, i in zip(state_traj, which_ind_traj)])
# Grab a random (traj,frame) for each state visited in the trajectory
print "Loading frames from the Trajectory."
traj = project.load_frame(which_traj[0][0], which_traj[0][1])
for i in range(1, len(which_traj)):
traj += project.load_frame(which_traj[i][0], which_traj[i][1])
print i
traj[0].save_to_pdb(out_pdb)
traj.save_to_xtc(out_xtc)
print "Saved output to %s and %s" % (out_pdb, out_xtc)
return
def __init__(self):
self.epsilon = 1E-7
self.alpha = 0.001 # Confidence for uncertainty estimate
# Testing is stochastic; we expect errors 0.1 % of the time.
self.max_lag = 100
self.times = np.arange(self.max_lag)
self.num_steps = 100000
self.C = np.array([[500, 2], [2, 50]])
self.T = MSMLib.estimate_transition_matrix(self.C)
self.state_traj = np.array(msm_analysis.sample(self.T, 0, self.num_steps))
def main(modeldir, start, type):
start=int(start)
data=dict()
project=Project.load_from('%s/ProjectInfo.yaml' % modeldir.split('Data')[0])
files=glob.glob('%s/fkbp*xtal.pdb' % modeldir.split('Data')[0])
pdb=files[0]
unbound=numpy.loadtxt('%s/tpt-%s/unbound_%s_states.txt' % (modeldir, type, type), dtype=int)
T=mmread('%s/tProb.mtx' % modeldir)
startstate=unbound[start]
ass=io.loadh('%s/Assignments.Fixed.h5' % modeldir)
steps=100000
print "on start state %s" % startstate
if os.path.exists('%s/tpt-%s/movie_state%s_1millisec.states.dat' % (modeldir, type, startstate)):
print "loading from states"
traj=numpy.loadtxt('%s/tpt-%s/movie_state%s_1millisec.states.dat' % (modeldir, type, startstate))
else:
traj=msm_analysis.sample(T, int(startstate),int(steps))
numpy.savetxt('%s/tpt-%s/movie_state%s_1millisec.states.dat' % (modeldir, type, startstate), traj)
print "checking for chkpt file"
checkfile=glob.glob('%s/tpt-%s/movie_state%s_*chkpt' % (modeldir, type, startstate))
if len(checkfile) > 0:
movie=Trajectory.load_from_xtc(checkfile[0], PDBFilename=pdb)
n=int(checkfile[0].split('xtc.state')[1].split('chkpt')[0])
os.system('mv %s %s.chkpt.cp' % (checkfile[0], checkfile[0].split('.xtc')[0]))
print "checkpointing at state index %s out of %s" % (n, len(traj))
checkfile=checkfile[0]
restart=True
else:
restart=False
n=0
movie=project.empty_traj()
while n < len(traj):
print "on state %s" % n
state=int(traj[n])
t=project.get_random_confs_from_states(ass['arr_0'], [int(state),], 10)
if n==0:
movie['XYZList']=t[0]['XYZList']
n+=1
continue
elif n % 100==0:
movie['XYZList']=numpy.vstack((movie['XYZList'], t[0]['XYZList']))
if restart==True:
os.system('mv %s %s.chkpt.cp' % (checkfile, checkfile.split('.xtc')[0]))
movie.save_to_xtc('%s/tpt-%s/movie_state%s_1millisec.xtc.state%schkpt' % (modeldir, type, startstate, n))
checkfile='%s/tpt-%s/movie_state%s_1millisec.xtc.state%schkpt' % (modeldir, type, startstate, n)
n+=1
continue
elif n!=0:
movie['XYZList']=numpy.vstack((movie['XYZList'], t[0]['XYZList']))
n+=1
continue
movie.save_to_xtc('%s/tpt-%s/movie_state%s_1millisec.xtc' % (modeldir, type, startstate))
def raw_msm_correlation(trans_matrix,
observable,
assignments,
n_steps=10000,
starting_state=0):
"""Calculate an autocorrelation function from an MSM.
Parameters
----------
trans_matrix : sparse or dense matrix
Transition matrix
observable : np.ndarray, shape=[n_trajs, max_n_frames]
Value of the observable in each conf
assignments : np.ndarray, shape=[n_trajs, max_n_frames]
State membership for each conf
n_steps : int
Number of steps to simulate
starting_state : int
State to start the trajectory from
Notes
-----
This function works by first generating a 'sample' trajectory from the MSM. This
approach is necessary as it allows treatment of intra-state dynamics.
Returns
-------
correlation : np.ndarray, shape=[n_steps]
The autocorrelation of the observable
traj : np.ndarray, shape=[n_steps]
The simulated trajectory, represented as a sequence of states
obs_traj : np.ndarray, shape=[n_steps]
The observable signal, as a sequence of values from traj
"""
traj = msm_analysis.sample(trans_matrix, starting_state, n_steps)
# NOTE: I'm not sure if this MaxInt is right. (RTM 9/6)
MaxInt = np.ones(assignments.shape).sum()
obs_traj = np.array([
observable[np.where(assignments == State)].take(
[np.random.randint(MaxInt)], mode='wrap') for State in traj
])
corr = fft_acf(obs_traj)
return corr, traj, obs_traj
def raw_msm_correlation(trans_matrix, observable, assignments, n_steps=10000, starting_state=0):
"""Calculate an autocorrelation function from an MSM.
Parameters
----------
trans_matrix : sparse or dense matrix
Transition matrix
observable : np.ndarray, shape=[n_trajs, max_n_frames]
Value of the observable in each conf
assignments : np.ndarray, shape=[n_trajs, max_n_frames]
State membership for each conf
n_steps : int
Number of steps to simulate
starting_state : int
State to start the trajectory from
Notes
-----
This function works by first generating a 'sample' trajectory from the MSM. This
approach is necessary as it allows treatment of intra-state dynamics.
Returns
-------
correlation : np.ndarray, shape=[n_steps]
The autocorrelation of the observable
traj : np.ndarray, shape=[n_steps]
The simulated trajectory, represented as a sequence of states
obs_traj : np.ndarray, shape=[n_steps]
The observable signal, as a sequence of values from traj
"""
traj = msm_analysis.sample(trans_matrix, starting_state, n_steps)
# NOTE: I'm not sure if this MaxInt is right. (RTM 9/6)
MaxInt = np.ones(assignments.shape).sum()
obs_traj = np.array( [observable[ np.where( assignments == State ) ].take( [ np.random.randint( MaxInt ) ], mode='wrap' ) for State in traj ] )
corr = fft_acf(obs_traj)
return corr, traj, obs_traj
def main():
"""Parse command line inputs, load up files, and build a movie."""
args = parser.parse_args()
try:
assignments = io.loadh(args.assignments, 'arr_0')
except KeyError:
assignments = io.loadh(args.assignments, 'Data')
num_steps = int(args.num_steps)
starting_state = int(args.starting_state)
project = Project.load_from(args.project)
T = scipy.io.mmread(args.tprob).tocsr()
state_traj = msm_analysis.sample(T, starting_state, num_steps)
sampled_traj = project.get_random_confs_from_states(
assignments, state_traj, 1)
traj = sampled_traj[0]
traj["XYZList"] = np.array([t["XYZList"][0] for t in sampled_traj])
traj.save(args.output)
def entry_point():
"""Parse command line inputs, load up files, and build a movie."""
args = parser.parse_args()
try:
assignments = io.loadh(args.assignments, 'arr_0')
except KeyError:
assignments = io.loadh(args.assignments, 'Data')
num_steps = int(args.num_steps)
starting_state = int(args.starting_state)
project = Project.load_from(args.project)
T = scipy.io.mmread(args.tprob).tocsr()
state_traj = msm_analysis.sample(T, starting_state, num_steps)
sampled_traj = project.get_random_confs_from_states(
assignments, state_traj, 1)
traj = sampled_traj[0]
traj["XYZList"] = np.array([t["XYZList"][0] for t in sampled_traj])
traj.save(args.output)
triples = [
(0, 1, 2), # (waypoint, source, sink) to test
(0, 1, 3),
(0, 1, 4)
]
# load in the transition matrx
N = 11
T = np.transpose(np.genfromtxt('mat_1.dat')[:, :-3])
print(T)
print(T.shape)
print(T.sum(1))
# sample from it
print("Making a len: %d traj" % steps)
traj = msm_analysis.sample(T, np.random.randint(11), steps, force_dense=True)
print("Generated traj")
# count the fraction visits
n_visited_waypoint = 0
n_notvisited_waypoint = 0
started = False
visited = False
for (waypoint, source, sink) in triples:
for n, i in enumerate(traj):
if n % 10000 == 0:
steps = 10**6 # sample steps
triples = [ (0, 1, 2), # (waypoint, source, sink) to test
(0, 1, 3),
(0, 1, 4) ]
# load in the transition matrx
N = 11
T = np.transpose( np.genfromtxt('mat_1.dat')[:,:-3] )
print T
print T.shape
print T.sum(1)
# sample from it
print "Making a len: %d traj" % steps
traj = msm_analysis.sample(T, np.random.randint(11), steps, force_dense=True)
print "Generated traj"
# count the fraction visits
n_visited_waypoint = 0
n_notvisited_waypoint = 0
started = False
visited = False
for (waypoint, source, sink) in triples:
for n,i in enumerate(traj):
if n % 10000 == 0:
"""
import os
import sys
import numpy as np
import scipy.sparse
from msmbuilder import io, msm_analysis, MSMLib
from bayesmutant import SimpleMutantSampler
P = np.loadtxt('base_transition_matrix.dat')
mutant_transition_matrix = P + 0.2*scipy.sparse.rand(P.shape[0], P.shape[1], density=0.1).todense()
mutant_transition_matrix /= np.sum(mutant_transition_matrix, axis=1)
trajectory = np.array(msm_analysis.sample(P, 0, 5000))
base_counts = MSMLib.get_counts_from_traj(trajectory).todense()
print 'base counts'
print base_counts
ms = SimpleMutantSampler(base_counts, mutant_transition_matrix)
ms.step(5000)
print 'observed counts'
print ms.counts
io.saveh('sampling.h5', base_counts=base_counts, samples=ms.samples,
observed_counts=ms.counts, scores=ms.scores,
transition_matrix=mutant_transition_matrix)
print "Cannot load msm data."
tProb = mmread(args.tProb)
try:
raw_data = io.loadh(args.raw_data)["arr_0"]
except:
raw_data = io.loadh(args.raw_data)["Data"]
num_frames = raw_data.shape[1]
num_lagtimes = num_frames / args.lagtime
# msm_acf = msm_analysis.msm_acf(tProb, msm_data, np.arange(num_lagtimes),
# num_modes=args.num_modes)
sampled_traj = msm_analysis.sample(tProb, np.random.randint(tProb.shape[0]), num_lagtimes)
data_traj = msm_data[sampled_traj]
msm_acf = autocorrelate.fft_autocorrelate(data_traj)
raw_acfs = []
for i in xrange(np.max([raw_data.shape[0], 10])):
max_non_neg = np.where(raw_data[i] != -1)[0].max()
row = raw_data[i][: max_non_neg + 1]
raw_acfs.append(autocorrelate.fft_autocorrelate(row))
figure()
axes((0.18, 0.18, 0.72, 0.72))
raw_label = "Raw Data"
def _run_trial(arg_dict):
# inject the arg_dict into the local namespace - may be a bad idea...
for key in arg_dict.keys():
exec(key + " = arg_dict['" + key + "']")
# initialize data structures to hold output
distance_to_target = np.zeros(rounds_of_sampling)
obs_distance = np.zeros(rounds_of_sampling)
# the assignments array will hold all of the output of all simulations
assignments = -1.0 * np.ones((rounds_of_sampling * simultaneous_samplers + 1,
max(size_of_intial_data, length_of_sampling_trajs+1) ))
# initialize the "true" transition matrix
if not transition_matrix:
assert num_states > 0
C_rand = np.random.randint( 0, 100, (num_states, num_states) )
C_rand += C_rand.T
T = MSMLib.estimate_transition_matrix( C_rand )
else:
T = transition_matrix
num_states = T.shape[0]
T = sparse.csr_matrix(T)
msm_analysis.check_transition(T)
if observable_function:
try:
obs_goal = observable_function(T)
except Exception as e:
print >> sys.stderr, e
raise Exception("Error evaluating function: %s" % observable_function.__name__)
assignments[0,:size_of_intial_data] = msm_analysis.sample(T, None, size_of_intial_data)
# iterate, adding simulation time
for sampling_round in range(rounds_of_sampling):
# apply the adaptive sampling method - we need to be true to what a
# real simulation would actually see for the counts matrix
mod_assignments = assignments.copy()
mapping = MSMLib.renumber_states( mod_assignments )
C_mod = MSMLib.get_count_matrix_from_assignments( mod_assignments )
T_mod = MSMLib.estimate_transition_matrix(C_mod)
adaptive_sampling_multivariate = SamplerObject.sample(C_mod)
# choose the states to sample from (in the original indexing)
state_inds = np.arange(len(adaptive_sampling_multivariate))
sampler = stats.rv_discrete(name='sampler',
values=[state_inds, adaptive_sampling_multivariate])
starting_states = sampler.rvs( size=simultaneous_samplers )
starting_states = mapping[starting_states]
# start new 'simulations' in each of those states
for i,init_state in enumerate(starting_states):
a_ind = sampling_round * simultaneous_samplers + i + 1
s_ind = length_of_sampling_trajs + 1
assignments[a_ind,:s_ind] = msm_analysis.sample(T, init_state, s_ind)
# build a new MSM from all the simulation so far
C_raw = MSMLib.get_count_matrix_from_assignments( assignments, n_states=num_states )
C_raw = C_raw + C_raw.T # might want to add trimming, etc.
T_pred = MSMLib.estimate_transition_matrix(C_raw)
# calculate the error between the real transition matrix and our best prediction
assert T.shape == T_pred.shape
distance_to_target[sampling_round] = np.sqrt( ((T_pred - T).data ** 2).sum() ) \
/ float(num_states)
if observable_function:
obs_distance[sampling_round] = np.abs(observable_function(T_mod) - obs_goal)
return distance_to_target, obs_distance