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IMP Reference Guide  2.8.0
The Integrative Modeling Platform
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atom/rigid_brownian_dynamics.py

This example shows how to run brownian dynamics with rigid bodies.

1 ## \example atom/rigid_brownian_dynamics.py
2 # This example shows how to run brownian dynamics with rigid bodies.
3 
4 import IMP.atom
5 import IMP.core
6 import IMP.algebra
7 import IMP.display
8 import sys
9 
10 IMP.setup_from_argv(sys.argv, "rigid brownian dynamics")
11 
12 
13 def create_rigid_body(m, name):
14  prb = IMP.core.RigidBody.setup_particle(
15  IMP.Particle(m), IMP.algebra.ReferenceFrame3D())
16  prb.set_coordinates_are_optimized(True)
17  prb.set_name(name + " rb")
18  ph = IMP.atom.Molecule.setup_particle(IMP.Particle(m))
19  ph.set_name(name)
20  for i in range(0, 2):
21  for j in range(0, 2):
22  for k in range(0, 2):
23  d = IMP.core.XYZR.setup_particle(IMP.Particle(m),
24  IMP.algebra.Sphere3D(
25  IMP.algebra.Vector3D(
26  i, j, k) * 10.0,
27  10))
28  ph.add_child(IMP.atom.Fragment.setup_particle(d))
29  IMP.atom.Mass.setup_particle(d, 1000)
30  prb.add_member(d)
31  d.set_name(name + str(i) + str(j) + str(k))
32  d = IMP.atom.RigidBodyDiffusion.setup_particle(prb)
33  d.set_rotational_diffusion_coefficient(
34  d.get_rotational_diffusion_coefficient() * 100)
35  return prb, ph
36 
37 
38 def display(i, w, hs):
39  w.set_frame(i)
40  for h in hs:
41  g = IMP.atom.HierarchyGeometry(h)
42  w.add_geometry(g)
43 
44 m = IMP.Model()
45 IMP.set_log_level(IMP.SILENT)
46 
47 rb0, h0 = create_rigid_body(m, "first")
48 rb1, h1 = create_rigid_body(m, "second")
49 rb1.set_reference_frame(IMP.algebra.ReferenceFrame3D(
50  IMP.algebra.Transformation3D(IMP.algebra.Vector3D(30, 0, 0))))
51 
52 ev = IMP.core.ExcludedVolumeRestraint(
53  IMP.container.ListSingletonContainer(
54  m, rb0.get_rigid_members() + rb1.get_rigid_members()), 1, 3)
55 
56 #h= IMP.core.Harmonic(0,1)
57 #s= IMP.core.DistanceToSingletonScore(h, IMP.algebra.Vector3D(0,0,0))
58 #r= IMP.core.SingletonRestraint(s, rb0.get_member(0))
59 # m.add_restraint(r)
60 cr = IMP.atom.create_distance_restraint(
61  IMP.atom.Selection(h0), IMP.atom.Selection(h1), 0, 1)
62 
63 sf = IMP.core.RestraintsScoringFunction([ev, cr])
64 
65 bd = IMP.atom.BrownianDynamics(m)
66 bd.set_scoring_function(sf)
67 bd.set_time_step(10000)
68 
69 nm = IMP.create_temporary_file_name("rigid_bd", ".pym")
70 nm = "rigid.pym"
71 w = IMP.display.PymolWriter(nm)
72 for i in range(0, 100):
73  display(i, w, [h0, h1])
74  bd.optimize(10)