"""
Testing functionality of the Universe class
"""
import numpy as np
from isdhic import utils
pymol = utils.ChainViewer()
universe = utils.create_universe(n_particles=1e4 - 1, diameter=4.)
for counter, particle in enumerate(universe):
if counter % 100: continue
print particle, np.round(universe.coords[particle.serial])
posterior, contacts = create_isd_posterior()
L_intra = posterior.likelihoods['contacts']
L_bbone = posterior.likelihoods['backbone']
L_rog = posterior.likelihoods['Rg']
prior = posterior.conformational_priors['tsallis_prior']
beadsize = L_bbone.data.values[0]
## make isdhic classes
n_particles = len(posterior.universe.atoms)
params = isdhic.Parameters()
universe = utils.create_universe(n_particles, beadsize)
coords = isdhic.Coordinates(universe)
forces = isdhic.Forces(universe)
forcefield = isdhic.ForcefieldFactory.create_forcefield(
'rosetta', universe)
forcefield.d = np.array([[beadsize]])
forcefield.k = np.array([[0.0486]])
contacts = isdhic.ModelDistances(contacts, 'contacts')
logistic = isdhic.Logistic(contacts.name,
L_intra.data.values,
contacts,
params=params)
connectivity = zip(range(n_particles - 1), range(1, n_particles))
return list(pairs)
def numpy_distances(distances, universe):
return np.sum((universe.coords[distances.first_index] -
universe.coords[distances.second_index])**2, 1)**0.5
if __name__ == '__main__':
n_particles = int(1e4) - 1
n_distances = 10000
diameter = 4.
universe = utils.create_universe(n_particles, diameter)
precision = isdhic.Precision('lowerupper')
coords = isdhic.Coordinates(universe)
pairs = random_pairs(n_particles, n_distances)
connectivity = zip(np.arange(1, n_particles), np.arange(n_particles - 1))
contacts = isdhic.ModelDistances(pairs, 'contacts')
chain = isdhic.ModelDistances(connectivity, 'chain')
distances = isdhic.ModelDistances(connectivity + pairs, 'all')
params = isdhic.Parameters()
for param in (precision, coords, distances):
params.add(param)
print 'Getting/setting of Cartesian coordinates works? -',