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IMP Reference Guide  develop.d97d4ead1f,2024/11/21
The Integrative Modeling Platform
slab.py
1 import IMP.npctransport
2 import IMP
3 import RMF
4 import IMP.rmf
5 import IMP.atom
6 
7 height = 20
8 radius = 20
9 k = 100
10 
11 m = IMP.Model()
12 p_slab = IMP.Particle(m, "slab")
13 slab = IMP.npctransport.SlabWithCylindricalPore.setup_particle(
14  p_slab, height, radius)
15 p = IMP.Particle(m)
16 IMP.atom.Hierarchy.setup_particle(p)
17 d = IMP.core.XYZR.setup_particle(p)
18 d.set_radius(10)
19 d.set_coordinates_are_optimized(True)
20 IMP.atom.Diffusion.setup_particle(p)
21 IMP.atom.Mass.setup_particle(p, 1)
22 slabps = IMP.npctransport.SlabWithCylindricalPorePairScore(k)
23 r = IMP.core.PairRestraint(m, slabps, [p_slab.get_index(), p.get_index()],
24  "slab")
25 bb = IMP.algebra.BoundingBox3D(IMP.algebra.Vector3D(-100, -100, -100),
26  IMP.algebra.Vector3D(100, 100, 100))
27 bbss = IMP.core.BoundingBox3DSingletonScore(IMP.core.HarmonicUpperBound(0, 10),
28  bb)
29 bbr = IMP.core.SingletonRestraint(m, bbss, p.get_index(), "bb")
30 
31 nm = IMP.create_temporary_file_name("slab", ".rmf")
32 rmf = RMF.create_rmf_file(nm)
33 IMP.rmf.add_hierarchies(rmf, [p])
34 bbg = IMP.display.BoundingBoxGeometry(bb)
35 sg = IMP.npctransport.SlabWithCylindricalPoreWireGeometry(height, radius, 100)
36 sg.set_was_used(True)
37 sgs = sg.get_components()
38 # silliness we have to do for now
39 IMP.rmf.add_static_geometries(rmf, [bbg]+sgs)
40 IMP.rmf.add_restraints(rmf, [bbr, r])
41 
42 os = IMP.rmf.SaveOptimizerState(m, rmf)
43 
44 bd = IMP.atom.BrownianDynamics(m)
45 bd.set_scoring_function([bbr, r])
46 bd.set_log_level(IMP.SILENT)
47 bd.add_optimizer_state(os)
48 bd.set_maximum_time_step(2000)
49 
50 bd.optimize(100)
51 print("File is", nm)
IMP::npctransport
Simulation of transport through the Nuclear Pore Complex.
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::npctransport::SlabWithCylindricalPore::setup_particle
static SlabWithCylindricalPore setup_particle(Model *m, ParticleIndex pi, double thickness, double radius)
Definition: SlabWithCylindricalPore.h:67
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::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::rmf::add_hierarchies
void add_hierarchies(RMF::NodeHandle fh, const atom::Hierarchies &hs)
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::Particle
Class to handle individual particles of a Model object.
Definition: Particle.h:43
IMP::core::PairRestraint
Applies a PairScore to a Pair.
Definition: PairRestraint.h:31
IMP::rmf::add_static_geometries
void add_static_geometries(RMF::FileHandle parent, const display::GeometriesTemp &r)
Add geometries, assuming they do not move between frames.
IMP::atom
Functionality for loading, creating, manipulating and scoring atomic structures.
IMP::core::SingletonRestraint
Applies a SingletonScore to a Singleton.
Definition: SingletonRestraint.h:31
IMP::rmf
Support for the RMF file format for storing hierarchical molecular data and markup.
IMP::create_temporary_file_name
std::string create_temporary_file_name(std::string prefix="imp_temp", std::string suffix="")
Create a temporary file.