IMP  2.0.0
The Integrative Modeling Platform
rmf/simulation.py

This example shows writing a brownian dynamics simulation to a rmf file. It includes a bounding box, restraints and a hierarchy of particles.

1 ## \example rmf/simulation.py
2 ## This example shows writing a brownian dynamics simulation to a rmf file. It includes a bounding box, restraints and a hierarchy of particles.
3 
4 import IMP.atom
5 import IMP.rmf
6 import RMF
7 import IMP.container
8 import IMP.display
9 
10 k=10.0
11 np=10
12 frames=10
13 
14 m= IMP.Model()
15 bb= IMP.algebra.BoundingBox3D(IMP.algebra.Vector3D(0,0,0),
16  IMP.algebra.Vector3D(10,10,10))
17 
18 ps= [IMP.core.XYZR.setup_particle(IMP.Particle(m)) for i in range(0,np)]
19 h= IMP.atom.Hierarchy.setup_particle(IMP.Particle(m, "root"))
20 for p in ps:
21  p.set_radius(1)
22  p.set_coordinates_are_optimized(True)
23  IMP.atom.Mass.setup_particle(p, 30)
24  IMP.atom.Diffusion.setup_particle(p)
25  p.set_coordinates(IMP.algebra.get_random_vector_in(bb))
26 rs=[]
27 link= IMP.core.HarmonicUpperBoundSphereDistancePairScore(0,k)
28 pl=[]
29 for i in range(0, len(ps)/2):
30  pp=(ps[2*i], ps[2*i+1])
31  pl.append(pp)
32  # create OK staring position
33  pp[1].set_coordinates(IMP.algebra.get_random_vector_on(pp[0].get_sphere()))
34  IMP.display.Colored.setup_particle(pp[0], IMP.display.get_display_color(i))
35  IMP.display.Colored.setup_particle(pp[1], IMP.display.get_display_color(i))
36  hr= IMP.atom.Hierarchy.setup_particle(IMP.Particle(m, "molecule "+str(i)))
37  hr.add_child(IMP.atom.Hierarchy.setup_particle(pp[0]))
38  hr.add_child(IMP.atom.Hierarchy.setup_particle(pp[1]))
39  h.add_child(hr)
40 r= IMP.container.PairsRestraint(link, pl, "Bonds")
41 rs.append(r)
42 
43 ev= IMP.core.ExcludedVolumeRestraint(ps, k, 1, "EV")
44 rs.append(ev)
45 
46 bbss= IMP.core.BoundingBox3DSingletonScore(IMP.core.HarmonicUpperBound(0,k), bb)
47 bbr= IMP.container.SingletonsRestraint(bbss, ps)
48 rs.append(bbr)
49 
50 sf= IMP.core.RestraintsScoringFunction(rs, "SF")
51 
52 bd= IMP.atom.BrownianDynamics(m)
53 bd.set_log_level(IMP.base.SILENT)
54 bd.set_scoring_function(sf)
55 
56 bd.set_maximum_time_step(10)
57 
58 name= IMP.base.create_temporary_file_name("brownian", ".rmf")
59 rmf= RMF.create_rmf_file(name)
60 rmf.set_description("Brownian dyanmics trajectory with 10fs timestep.\n")
61 IMP.rmf.add_hierarchy(rmf, h)
62 IMP.rmf.add_restraints(rmf, rs)
63 IMP.rmf.add_geometry(rmf, IMP.display.BoundingBoxGeometry(bb))
64 
65 os= IMP.rmf.SaveOptimizerState(rmf)
66 os.update_always("initial conformation")
67 os.set_log_level(IMP.base.SILENT)
68 os.set_simulator(bd)
69 bd.add_optimizer_state(os)
70 
71 bd.optimize(frames)
72 
73 print "file is", rmf.get_name()