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IMP Reference Guide
develop.63b38c487d,2024/12/22
The Integrative Modeling Platform
IMP Manual
Reference Guide
Tutorial Index
Modules
Classes
Examples
doc
examples
core
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::core::GenericBoundingBox3DSingletonScore
Definition:
BoundingBox3DSingletonScore.h:64
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::algebra::BoundingBoxD< 3 >
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
IMP::algebra::SphereD< 3 >