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IMP Reference Guide  develop.63b38c487d,2024/12/22
The Integrative Modeling Platform
simulation.py
1 ## \example rmf/simulation.py
2 # This example shows writing a brownian dynamics simulation to a rmf file.
3 # It includes a bounding box, restraints and a hierarchy of particles.
4 
5 import IMP.atom
6 import IMP.rmf
7 import RMF
8 import IMP.container
9 import IMP.display
10 import sys
11 
12 IMP.setup_from_argv(sys.argv, "simulation")
13 
14 k = 10.0
15 np = 10
16 frames = 10
17 
18 m = IMP.Model()
19 bb = IMP.algebra.BoundingBox3D(IMP.algebra.Vector3D(0, 0, 0),
20  IMP.algebra.Vector3D(10, 10, 10))
21 
22 ps = [IMP.core.XYZR.setup_particle(IMP.Particle(m))
23  for i in range(0, np)]
24 h = IMP.atom.Hierarchy.setup_particle(IMP.Particle(m, "root"))
25 for p in ps:
26  p.set_radius(1)
27  p.set_coordinates_are_optimized(True)
28  IMP.atom.Mass.setup_particle(p, 30)
29  IMP.atom.Diffusion.setup_particle(p)
30  p.set_coordinates(IMP.algebra.get_random_vector_in(bb))
31 rs = []
32 link = IMP.core.HarmonicUpperBoundSphereDistancePairScore(0, k)
33 pl = []
34 for i in range(0, len(ps) // 2):
35  pp = (ps[2 * i], ps[2 * i + 1])
36  pl.append(pp)
37  # create OK staring position
38  pp[1].set_coordinates(IMP.algebra.get_random_vector_on(pp[0].get_sphere()))
39  IMP.display.Colored.setup_particle(pp[0], IMP.display.get_display_color(i))
40  IMP.display.Colored.setup_particle(pp[1], IMP.display.get_display_color(i))
41  hr = IMP.atom.Hierarchy.setup_particle(
42  IMP.Particle(m, "molecule " + str(i)))
43  hr.add_child(IMP.atom.Hierarchy.setup_particle(pp[0]))
44  hr.add_child(IMP.atom.Hierarchy.setup_particle(pp[1]))
45  h.add_child(hr)
46 r = IMP.container.PairsRestraint(link, pl, "Bonds")
47 rs.append(r)
48 
49 ev = IMP.core.ExcludedVolumeRestraint(ps, k, 1, "EV")
50 rs.append(ev)
51 
52 bbss = IMP.core.BoundingBox3DSingletonScore(
53  IMP.core.HarmonicUpperBound(0, k), bb)
54 bbr = IMP.container.SingletonsRestraint(bbss, ps)
55 rs.append(bbr)
56 
57 sf = IMP.core.RestraintsScoringFunction(rs, "SF")
58 
59 bd = IMP.atom.BrownianDynamics(m)
60 bd.set_log_level(IMP.SILENT)
61 bd.set_scoring_function(sf)
62 
63 bd.set_maximum_time_step(10)
64 
65 rmf = RMF.create_rmf_file("brownian.rmf")
66 rmf.set_description("Brownian dynamics trajectory with 10fs timestep.\n")
67 IMP.rmf.add_hierarchy(rmf, h)
68 IMP.rmf.add_restraints(rmf, rs)
69 IMP.rmf.add_geometry(rmf, IMP.display.BoundingBoxGeometry(bb))
70 
71 os = IMP.rmf.SaveOptimizerState(m, rmf)
72 os.update_always("initial conformation")
73 os.set_log_level(IMP.SILENT)
74 os.set_simulator(bd)
75 bd.add_optimizer_state(os)
76 
77 bd.optimize(frames)
78 
79 print("file is", rmf.get_name())
IMP::container::SingletonsRestraint
Applies a SingletonScore to each Singleton in a list.
Definition: SingletonsRestraint.h:36
IMP::core::HarmonicUpperBoundSphereDistancePairScore
A harmonic upper bound on the distance between two spheres.
Definition: SphereDistancePairScore.h:58
IMP::setup_from_argv
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
IMP::container
Various classes to hold sets of particles.
IMP::core::HarmonicUpperBound
Upper bound harmonic function (non-zero when feature > mean)
Definition: core/HarmonicUpperBound.h:22
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::get_random_vector_in
Vector3D get_random_vector_in(const Cylinder3D &c)
Generate a random vector in a cylinder with uniform density.
IMP::Model
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:86
IMP::atom::Hierarchy::setup_particle
static Hierarchy setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor children=ParticleIndexesAdaptor())
Create a Hierarchy of level t by adding the needed attributes.
Definition: atom/Hierarchy.h:240
IMP::rmf::add_hierarchy
void add_hierarchy(RMF::FileHandle fh, atom::Hierarchy hs)
IMP::atom::BrownianDynamics
Simple Brownian dynamics simulator.
Definition: BrownianDynamics.h:80
IMP::atom::Mass::setup_particle
static Mass setup_particle(Model *m, ParticleIndex pi, Float mass)
Definition: Mass.h:48
IMP::display::get_display_color
Color get_display_color(unsigned int i)
IMP::display::Colored::setup_particle
static Colored setup_particle(Model *m, ParticleIndex pi, Color color)
Definition: Colored.h:62
IMP::rmf::add_restraints
void add_restraints(RMF::NodeHandle fh, const Restraints &hs)
IMP::rmf::SaveOptimizerState
Periodically dump the state of all associated objects into the RMF file.
Definition: SaveOptimizerState.h:26
IMP::atom::Diffusion::setup_particle
static Diffusion setup_particle(Model *m, ParticleIndex pi, Float D)
Setup the particle with the specified diffusion coefficient.
Definition: Diffusion.h:76
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::algebra::get_random_vector_on
VectorD< D > get_random_vector_on(const UnitSimplexD< D > &s)
Generate a random vector on a unit simplex with uniform density.
Definition: vector_generators.h:145
IMP::rmf::add_geometry
void add_geometry(RMF::FileHandle file, display::Geometry *r)
Add a single geometry to the file.
IMP::display
Output IMP model data in various file formats.
IMP::atom
Functionality for loading, creating, manipulating and scoring atomic structures.
IMP::rmf
Support for the RMF file format for storing hierarchical molecular data and markup.
IMP::container::PairsRestraint
Applies a PairScore to each Pair in a list.
Definition: PairsRestraint.h:36