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IMP Reference Guide  develop.63b38c487d,2024/12/22
The Integrative Modeling Platform
rigid_brownian_dynamics.py
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 
45 m = IMP.Model()
46 IMP.set_log_level(IMP.SILENT)
47 
48 rb0, h0 = create_rigid_body(m, "first")
49 rb1, h1 = create_rigid_body(m, "second")
50 rb1.set_reference_frame(IMP.algebra.ReferenceFrame3D(
51  IMP.algebra.Transformation3D(IMP.algebra.Vector3D(30, 0, 0))))
52 
53 ev = IMP.core.ExcludedVolumeRestraint(
54  IMP.container.ListSingletonContainer(
55  m, rb0.get_rigid_members() + rb1.get_rigid_members()), 1, 3)
56 
57 cr = IMP.atom.create_distance_restraint(
58  IMP.atom.Selection(h0), IMP.atom.Selection(h1), 0, 1)
59 
60 sf = IMP.core.RestraintsScoringFunction([ev, cr])
61 
62 bd = IMP.atom.BrownianDynamics(m)
63 bd.set_scoring_function(sf)
64 bd.set_time_step(10000)
65 
66 nm = IMP.create_temporary_file_name("rigid_bd", ".pym")
67 nm = "rigid.pym"
68 w = IMP.display.PymolWriter(nm)
69 for i in range(0, 100):
70  display(i, w, [h0, h1])
71  bd.optimize(10)
IMP::algebra::Transformation3D
Simple 3D transformation class.
Definition: Transformation3D.h:37
IMP::atom::RigidBodyDiffusion::setup_particle
static RigidBodyDiffusion setup_particle(Model *m, ParticleIndex pi)
Definition: Diffusion.h:157
IMP::setup_from_argv
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
IMP::atom::Fragment::setup_particle
static Fragment setup_particle(Model *m, ParticleIndex pi)
Definition: Fragment.h:67
IMP::core::XYZR::setup_particle
static XYZR setup_particle(Model *m, ParticleIndex pi)
Definition: XYZR.h:48
IMP::core::RestraintsScoringFunction
Create a scoring function on a list of restraints.
Definition: RestraintsScoringFunction.h:23
IMP::algebra::ReferenceFrame3D
A reference frame in 3D.
Definition: ReferenceFrame3D.h:22
IMP::atom::Molecule::setup_particle
static Molecule setup_particle(Model *m, ParticleIndex pi)
Definition: Molecule.h:37
IMP::Model
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:86
IMP::atom::BrownianDynamics
Simple Brownian dynamics simulator.
Definition: BrownianDynamics.h:80
IMP::container::ListSingletonContainer
Store a list of ParticleIndexes.
Definition: ListSingletonContainer.h:35
IMP::atom::Mass::setup_particle
static Mass setup_particle(Model *m, ParticleIndex pi, Float mass)
Definition: Mass.h:48
IMP::set_log_level
void set_log_level(LogLevel l)
Set the current global log level.
IMP::core
Basic functionality that is expected to be used by a wide variety of IMP users.
IMP::algebra
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
IMP::algebra::Vector3D
VectorD< 3 > Vector3D
Definition: VectorD.h:408
IMP::core::ExcludedVolumeRestraint
Prevent a set of particles and rigid bodies from inter-penetrating.
Definition: ExcludedVolumeRestraint.h:40
IMP::Particle
Class to handle individual particles of a Model object.
Definition: Particle.h:43
IMP::display::PymolWriter
Write a CGO file with the geometry.
Definition: PymolWriter.h:34
IMP::atom::create_distance_restraint
Restraint * create_distance_restraint(const Selection &n0, const Selection &n1, double x0, double k, std::string name="Distance%1%")
IMP::display
Output IMP model data in various file formats.
IMP::atom
Functionality for loading, creating, manipulating and scoring atomic structures.
IMP::atom::create_rigid_body
IMP::core::RigidBody create_rigid_body(const Hierarchies &h, std::string name=std::string("created rigid body"))
Rigidify a molecule or collection of molecules.
IMP::atom::Selection
Select hierarchy particles identified by the biological name.
Definition: Selection.h:70
IMP::core::RigidBody::setup_particle
static RigidBody setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor ps)
Definition: rigid_bodies.h:180
IMP::atom::HierarchyGeometry
Display an IMP::atom::Hierarchy particle as balls.
Definition: hierarchy_tools.h:180
IMP::create_temporary_file_name
std::string create_temporary_file_name(std::string prefix="imp_temp", std::string suffix="")
Create a temporary file.