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rigid_brownian_dynamics.py
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## \example atom/rigid_brownian_dynamics.py
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## This example shows how to run brownian dynamics with rigid bodies.
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4
import
IMP.atom
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import
IMP.core
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import
IMP.algebra
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import
IMP.display
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def
create_rigid_body
(m, name):
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prb=
IMP.core.RigidBody.setup_particle
(
IMP.Particle
(m),
IMP.algebra.ReferenceFrame3D
())
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prb.set_coordinates_are_optimized(
True
)
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prb.set_name(name+
" rb"
)
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ph=
IMP.atom.Molecule.setup_particle
(
IMP.Particle
(m))
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ph.set_name(name)
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for
i
in
range(0,2):
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for
j
in
range(0,2):
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for
k
in
range(0,2):
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d=
IMP.core.XYZR.setup_particle
(
IMP.Particle
(m),
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IMP.algebra.Sphere3D
(
IMP.algebra.Vector3D
(i,j,k)*10.0,
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10))
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ph.add_child(
IMP.atom.Fragment.setup_particle
(d))
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IMP.atom.Mass.setup_particle
(d, 1000)
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prb.add_member(d)
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d.set_name(name+str(i)+str(j)+str(k))
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d=
IMP.atom.RigidBodyDiffusion.setup_particle
(prb)
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d.set_rotational_diffusion_coefficient(d.get_rotational_diffusion_coefficient()*100)
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return
prb, ph
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def
display(i, w, hs):
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w.set_frame(i)
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for
h
in
hs:
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g=
IMP.atom.HierarchyGeometry
(h)
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w.add_geometry(g)
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m=
IMP.Model
()
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IMP.base.set_log_level
(IMP.base.SILENT)
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rb0, h0=
create_rigid_body
(m,
"first"
)
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rb1, h1=
create_rigid_body
(m,
"second"
)
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rb1.set_reference_frame(
IMP.algebra.ReferenceFrame3D
(
IMP.algebra.Transformation3D
(
IMP.algebra.Vector3D
(30,0,0))))
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ev=
IMP.core.ExcludedVolumeRestraint
(
IMP.container.ListSingletonContainer
(rb0.get_members()+rb1.get_members()),
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1, 3)
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m.add_restraint(ev)
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#h= IMP.core.Harmonic(0,1)
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#s= IMP.core.DistanceToSingletonScore(h, IMP.algebra.Vector3D(0,0,0))
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#r= IMP.core.SingletonRestraint(s, rb0.get_member(0))
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#m.add_restraint(r)
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cr=
IMP.atom.create_distance_restraint
(
IMP.atom.Selection
(h0),
IMP.atom.Selection
(h1), 0, 1)
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m.add_restraint(cr)
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bd=
IMP.atom.BrownianDynamics
(m)
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bd.set_time_step(10000)
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nm=
IMP.base.create_temporary_file_name
(
"rigid_bd"
,
".pym"
)
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nm=
"rigid.pym"
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w=
IMP.display.PymolWriter
(nm)
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for
i
in
range(0,100):
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display(i, w, [h0, h1])
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bd.optimize(10)