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IMP Reference Guide  develop.031dafb4d2,2024/05/16
The Integrative Modeling Platform
bounding_box_restraint.py
1 import IMP, IMP.core, IMP.algebra, IMP.container
2 
3 K_BB = 10.0 # bounding box force coefficient in kcal/mol/A^2
4 RADIUS = 1.0 # particle radius in A
5 
6 def create_particle(m, bb, radius = RADIUS):
7  p = IMP.Particle(m)
8  s = IMP.algebra.Sphere3D(
9  IMP.algebra.get_random_vector_in(bb), radius)
10  d = IMP.core.XYZR.setup_particle(p, s)
11  d.set_coordinates_are_optimized(True)
12  return p
13 
14 bb = IMP.algebra.BoundingBox3D(IMP.algebra.Vector3D(0, 0, 0),
15  IMP.algebra.Vector3D(10, 10, 10))
16 m = IMP.Model()
17 particles = []
18 for i in range(0,10):
19  particles.append(create_particle(m, bb))
20 hpb = IMP.core.HarmonicUpperBound(0, K_BB)
21 bbss = IMP.core.BoundingBox3DSingletonScore(hpb, bb)
22 bbr = IMP.container.SingletonsRestraint(bbss, particles)
IMP::container::SingletonsRestraint
Applies a SingletonScore to each Singleton in a list.
Definition: SingletonsRestraint.h:36
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::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::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::Particle
Class to handle individual particles of a Model object.
Definition: Particle.h:43