IMP  2.2.1
The Integrative Modeling Platform
incremental_mc.py
1 ## \example core/incremental_mc.py
2 # This example shows how to do incremental scoring with Monte Carlo.
3 # Incremental scoring can be significantly faster than non-incremental
4 # scoring when using moves that only move a few particles at a time.
5 
6 import IMP.core
7 import IMP.container
8 import IMP.algebra
9 import IMP.display
10 import sys
11 
12 IMP.base.setup_from_argv(sys.argv, "Optimize balls example")
13 
15  num_balls = 2
16  num_mc_steps = 10
17 else:
18  num_balls = 20
19  num_mc_steps = 1000
20 
21 m = IMP.kernel.Model()
23  IMP.algebra.Vector3D(30, 30, 30))
24 ps = []
25 for i in range(0, num_balls):
26  ps.append(IMP.kernel.Particle(m))
28  d.set_radius(10)
29  d.set_coordinates(IMP.algebra.get_random_vector_in(bb))
30  d.set_coordinates_are_optimized(True)
31 
36  IMP.core.HarmonicUpperBound(0, 1), bb),
37  psl)
38 mc = IMP.core.MonteCarlo(m)
39 isf = IMP.core.IncrementalScoringFunction(ps, [r, rb])
40 mc.set_incremental_scoring_function(isf)
41 
42 mvs = [IMP.core.BallMover([p], 5) for p in ps]
43 sm = IMP.core.SerialMover(mvs)
44 mc.add_mover(sm)
45 IMP.base.set_log_level(IMP.base.SILENT)
46 print "initial", isf.evaluate(False)
47 after = mc.optimize(num_mc_steps)
48 print "final", after
49 name = IMP.base.create_temporary_file_name("incremental_mc", ".pym")
51 for p in ps:
53  w.add_geometry(g)
54 print "pymol", name
Applies a SingletonScore to each Singleton in a list.
bool get_is_quick_test()
Definition: base/flags.h:179
A Monte Carlo optimizer.
Definition: MonteCarlo.h:45
See IMP.container for more information.
Upper bound harmonic function (non-zero when feature > mean)
void set_log_level(LogLevel l)
Set the current global log level.
std::string create_temporary_file_name(std::string prefix="imp_temp", std::string suffix="")
Modify a set of continuous variables by perturbing them within a ball.
Score particles based on how far outside a box they are.
Vector3D get_random_vector_in(const Cylinder3D &c)
Generate a random vector in a cylinder with uniform density.
static XYZR setup_particle(kernel::Model *m, ParticleIndex pi)
Definition: XYZR.h:48
Store a kernel::ParticleIndexes.
Class to handle individual model particles.
See IMP.core for more information.
See IMP.algebra for more information.
VectorD< 3 > Vector3D
Definition: VectorD.h:395
Prevent a set of particles and rigid bodies from inter-penetrating.
Write a CGO file with the geometry.
Definition: PymolWriter.h:34
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
See IMP.display for more information.
Definition: ChimeraWriter.h:17
Apply a list of movers one at a time.
Definition: SerialMover.h:23
Class for storing model, its restraints, constraints, and particles.
Definition: kernel/Model.h:72
Display an IMP::core::XYZR particle as a ball.
Definition: XYZR.h:150