IMP  2.3.0
The Integrative Modeling Platform
decay.py
1 ## \example misc/decay.py
2 # Use the IMP::misc::DecayPairContainerOptimizerState to gradually break
3 # the bonds in a bd simulation.
4 
5 import IMP.atom
6 import IMP.container
7 import IMP.misc
8 import IMP.display
9 import IMP.example
10 import IMP.base
11 import sys
12 import IMP.rmf
13 #import IMP.benchmark
14 import RMF
15 import random
16 
18  sys.argv, "Use the IMP::misc::DecayPairContainerOptimizerState to gradually break the bonds in a bd simulation")
19 
20 if IMP.base.get_bool_flag("run_quick_test"):
21  np = 8
22  nb = 8
23  prob = .5
24  period = 2
25  steps = 10
26 else:
27  np = 20
28  nb = 40
29  prob = .9
30  period = 10
31  steps = 10000
32 
33 m = IMP.kernel.Model()
34 
36  IMP.algebra.Vector3D(100, 100, 100))
37 ps = []
38 for i in range(0, np):
39  p = IMP.kernel.Particle(m)
41  d.set_coordinates(IMP.algebra.Vector3D(10. * (i/10), 10. * (i%10), 10.))
42  d.set_radius(10)
43  d.set_coordinates_are_optimized(True)
47  ps.append(p)
49 
50 bds = []
51 for i in range(0, nb):
52  pp = random.sample(ps, 2)
53  if pp not in bds and [pp[1], pp[0]] not in bds:
54  bds.append(pp)
55 
57 dos = IMP.misc.DecayPairContainerOptimizerState(cf, bds, "decay")
58 dos.set_period(period)
59 dos.set_log_level(IMP.base.SILENT) # VERBOSE
60 
61 # create restraints
62 rs = []
64  IMP.core.HarmonicUpperBound(0, 10), bb)
65 rs.append(IMP.container.SingletonsRestraint(box_score, ps, "box"))
67 rs.append(IMP.container.PairsRestraint(bond_score,
68  dos.get_output_container(),
69  "bonds"))
70 ev = IMP.core.ExcludedVolumeRestraint(ps, 10, 10)
71 IMP.base.set_log_level(IMP.SILENT)
72 
73 # set up simulator
75 bd.set_maximum_time_step(1000)
76 bd.set_scoring_function(rs + [ev])
77 bd.add_optimizer_state(dos)
78 
79 # set up display
80 fn = IMP.base.create_temporary_file_name("decay", ".rmf")
81 rmf = RMF.create_rmf_file(fn)
82 print "setting up file"
84 IMP.rmf.add_restraints(rmf, rs + [ev])
86 IMP.rmf.add_geometries(rmf, [g])
87 os = IMP.rmf.SaveOptimizerState(m, rmf)
88 os.set_period(max(steps / 100, 1))
89 bd.add_optimizer_state(os)
90 
91 # actually optimize things
92 print "running"
93 bd.optimize(steps)
94 
95 print "see", fn
Applies a SingletonScore to each Singleton in a list.
A harmonic upper bound on the distance between two spheres.
void add_restraints(RMF::NodeHandle fh, const kernel::Restraints &hs)
Various classes to hold sets of particles.
Upper bound harmonic function (non-zero when feature > mean)
Miscellaneous functionality that is not expected to be used by many IMP users.
void set_log_level(LogLevel l)
Set the current global log level.
bool get_bool_flag(std::string name)
std::string create_temporary_file_name(std::string prefix="imp_temp", std::string suffix="")
Create a temporary file.
Maintain a pair container with a decaying list of pairs.
Low level functionality (logging, error handling, profiling, command line flags etc) that is used by ...
Score particles based on how far outside a box they are.
static XYZR setup_particle(kernel::Model *m, ParticleIndex pi)
Definition: XYZR.h:48
Simple Brownian dynamics simulator.
static Hierarchy setup_particle(kernel::Model *m, kernel::ParticleIndex pi, kernel::ParticleIndexesAdaptor children=kernel::ParticleIndexesAdaptor())
static Colored setup_particle(kernel::Model *m, ParticleIndex pi, Color color)
Definition: Colored.h:62
Color get_display_color(unsigned int i)
void add_hierarchies(RMF::NodeHandle fh, const atom::Hierarchies &hs)
Class to handle individual model particles.
void add_geometries(RMF::NodeHandle parent, const display::GeometriesTemp &r)
static Mass setup_particle(kernel::Model *m, ParticleIndex pi, Float mass)
Definition: Mass.h:44
Example module.
VectorD< 3 > Vector3D
Definition: VectorD.h:395
Prevent a set of particles and rigid bodies from inter-penetrating.
static Diffusion setup_particle(kernel::Model *m, ParticleIndex pi, Float D)
Definition: Diffusion.h:50
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for the RMF file format for storing hierarchical molecular data and markup.
Applies a PairScore to each Pair in a list.
Class for storing model, its restraints, constraints, and particles.
Definition: kernel/Model.h:73