2 """This script shows how to represent a system at multiple scales and do
6 from __future__
import print_function
20 print(
"This example is too slow to test in debug mode - run without")
21 print(
"internal tests enabled, or without the --run-quick-test flag")
27 components = [
"Rpb1",
"Rpb2",
"Rpb3",
"Rpb4"]
28 colors = [
'medium purple',
'goldenrod',
'orchid',
'olive drab']
39 for n
in range(len(components)):
40 print(
'PMI: setting up', components[n],
'1WCM:'+chains[n])
41 mol = st.create_molecule(
43 sequence=seqs[
'1WCM:'+chains[n]],
45 atomic = mol.add_structure(
47 chain_id=chains[n], offset=0)
48 mol.add_representation(atomic,
51 mol.add_representation(mol[:]-atomic,
52 resolutions=[beadsize],
73 dof.create_rigid_body(mol,
74 nonrigid_parts=mol.get_non_atomic_residues(),
77 nonrigid_max_trans=0.1)
92 output_objects.append(cr)
97 included_objects=mols)
99 output_objects.append(evr)
107 dof.optimize_flexible_beads(100)
115 monte_carlo_sample_objects=dof.get_movers(),
116 global_output_directory=
'multiscale_output/',
117 output_objects=output_objects,
118 monte_carlo_steps=10,
120 number_of_best_scoring_models=0,