def set_initial(posterior, pklfile, burnin=-10, max_distance=80):
"""Prepare input for refinement. """
samples = load(pklfile)
coords = samples['coordinates'].reshape(len(samples), -1, 3)[burnin:]
coords = coords.reshape(-1, 3)
norm = np.linalg.norm(coords, axis=1)
coords = coords[norm < max_distance]
n_particles = len(posterior.params['coordinates'].get()) // 3
new_coords = coords[-n_particles:].copy()
new_coords += np.random.randn(*new_coords.shape)
posterior.params['coordinates'].set(new_coords)
posterior.update()
cc = []
for image in posterior.likelihoods:
for param in (image.mock._rotation, image.mock._scale,
image.mock._background):
param.set(samples[param.name][-1])
image.update()
image.precision.set(1 / np.var(image.data - image.mock.get()))
cc.append(isd.crosscorr(image.data, image.mock.get()))
print(np.min(cc), np.max(cc), np.mean(cc))
def load(self, aa, f_name):
"""
Load set of expansion coefficients from isd+.
@param aa: Amino acid type
@param f_name: File containing ramachandran definition
"""
import os
from numpy import reshape, array
from csb.io import load
f_name = os.path.expanduser(f_name)
params, _energies = load(f_name)
params = params[self._n]
a, b, c, d = params[aa]
a, b, c, d = reshape(array(a), (self._n, self._n)).astype('d'), \
reshape(array(b), (self._n, self._n)).astype('d'), \
reshape(array(c), (self._n, self._n)).astype('d'), \
reshape(array(d), (self._n, self._n)).astype('d')
# Not a typo, I accidently swichted cos*sin and sin*cos
self._cc, self._cs, self._sc, self._ss = -a, -c, -b, -d
def load(self, aa, f_name):
"""
Load set of expansion coefficients from isd+.
@param aa: Amino acid type
@param f_name: File containing ramachandran definition
"""
import os
from numpy import reshape, array
from csb.io import load
f_name = os.path.expanduser(f_name)
params, _energies = load(f_name)
params = params[self._n]
a, b, c, d = params[aa]
a, b, c, d = reshape(array(a), (self._n, self._n)).astype('d'), \
reshape(array(b), (self._n, self._n)).astype('d'), \
reshape(array(c), (self._n, self._n)).astype('d'), \
reshape(array(d), (self._n, self._n)).astype('d')
# Not a typo, I accidently swichted cos*sin and sin*cos
self._cc, self._cs, self._sc, self._ss = -a, -c, -b, -d
if not 'rex' in globals():
with open('./run_parallel.py') as script:
exec script
def calc_energy(state, rex):
E = []
for x, s in zip(state,rex.samplers):
s.set_replica_params()
#s.model.params['coordinates'].set(x.positions)
s.parameter.set(x.positions)
E.append(-s.model.log_prob())
return E
samples = load('/tmp/samples{}.pkl'.format(['',2][0]))
E = np.array([[s.potential_energy for s in S] for S in samples])
X = np.array([[s.positions for s in S] for S in samples])
EE = []
for x in X:
e = []
for k, y in enumerate(x):
sampler = rex[k]
sampler.parameter.set(y)
sampler.set_replica_params()
e.append(-sampler.model.log_prob())
EE.append(e)
EE = np.array(EE)
prior = simulation.create_prior()
posterior = isd.PosteriorCoordinates('ribosome',
likelihoods=likelihoods,
priors=[prior])
# predict radius of gyration
Rg = 2.74 * (n_atoms / 10.)**0.34
# create prior term
rgyr = simulation.create_radius_of_gyration(1., 'exponential')
rgyr.rate = 10.
# force Rg term to be treated as prior
posterior.priors.append(rgyr)
# spherical initial structure
params['coordinates'].set(isd.random_sphere(n_particles, Rg))
pklfile = '../simulations/posterior_ribosome_200.pkl'
if False and os.path.exists(pklfile):
print('loading {}'.format(pklfile))
ensemble = load(pklfile)
gibbs.set_params(posterior, ensemble)
coords = params['coordinates'].get().reshape(-1, 3)
coords += np.random.standard_normal(coords.shape) * diameter / 4.
posterior.params['coordinates'].set(coords)
else:
print('{} not found'.format(pklfile))
posterior.update()
samples.append(rex.next())
if __name__ == '__main__':
from csb.io import load, dump
import os
n_replicas = 50
schedule = np.transpose([
np.logspace(0., np.log10(1.06), n_replicas),
np.linspace(1., 0.1, n_replicas)
])
try:
schedule = load(
os.path.expanduser('~/tmp/geo_rosetta_contacts_Rg_6_schedule.pkl'))
except:
schedule = load(
'/space/users/mhabeck/tmp/geo_rosetta_contacts_Rg_6_schedule.pkl')
schedule[0, :] = 1.
posterior = create_posterior()
replicas = [create_replica(q, beta, posterior) for q, beta in schedule]
rex = ParallelReplicaExchange(replicas, n_cpus=25)
samples = []
if False:
Test pickling of c-wrappers
"""
from csb.io import load, dump
from isdhic import NBList
resolution = 500
with open('../scripts/chrX_cell1_{}kb.py'.format(resolution)) as script:
exec script
forcefield = posterior['tsallis'].forcefield
nblist = forcefield.nblist
dump(nblist, '/tmp/nblist.pkl')
nblist2 = load('/tmp/nblist.pkl')
print nblist.ctype.update(posterior.params['coordinates'].get().reshape(-1, 3),
1)
print nblist2.ctype.update(
posterior.params['coordinates'].get().reshape(-1, 3), 1)
dump(forcefield, '/tmp/forcefield.pkl')
forcefield2 = load('/tmp/forcefield.pkl')
print forcefield.energy(posterior.params['coordinates'].get().reshape(-1, 3))
print forcefield2.energy(posterior.params['coordinates'].get().reshape(-1, 3))
posterior['tsallis'].q = 1.03
posterior['rog'].beta = 0.2
posterior['contacts'].beta = 0.2