occ.set_weight(1.5)
occ.write_distances('')
rmf_restraints.append(occ)
output_objects.append(occ)
print('nuisances:', occ.get_particles_to_sample())
dof.get_nuisances_from_restraint(occ)
socc = occ.get_output()
print(socc)
##############################
# Shuffle
##############################
IMP.pmi.tools.shuffle_configuration(hier, max_translation=50)
dof.optimize_flexible_beads(200)
############################# SAMPLING ##############################
# Run replica exchange Monte Carlo sampling
num_frames = 50000
if '--mmcif' in sys.argv or '--test' in sys.argv:
num_frames = 5
rex = IMP.pmi.macros.ReplicaExchange0(
mdl,
root_hier=hier,
crosslink_restraints=rmf_restraints,
monte_carlo_sample_objects=dof.get_movers(),
replica_exchange_maximum_temperature=3.0,
global_output_directory="output/",
cr = IMP.pmi.restraints.stereochemistry.ConnectivityRestraint(mol)
cr.add_to_model()
output_objects.append(cr)
crs.append(cr)
# Excluded volume - automatically more efficient due to rigid bodies
evr = IMP.pmi.restraints.stereochemistry.ExcludedVolumeSphere(included_objects = mols)
evr.add_to_model()
output_objects.append(evr)
###################### SAMPLING #####################
# First shuffle the system
IMP.pmi.tools.shuffle_configuration(root_hier,
max_translation=30)
# Quickly move all flexible beads into place
dof.optimize_flexible_beads(100)
# Run replica exchange Monte Carlo sampling
rex=IMP.pmi.macros.ReplicaExchange0(mdl,
root_hier=root_hier, # pass the root hierarchy
crosslink_restraints=crs, # will display like XLs
monte_carlo_sample_objects=dof.get_movers(), # pass MC movers
global_output_directory='multiscale_output/',
output_objects=output_objects,
monte_carlo_steps=10,
number_of_best_scoring_models=0, # set >0 to store best PDB files (but this is slow to do online)
number_of_frames=1) # increase number of frames to get better results!
rex.execute_macro()
