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IMP Reference Guide
2.20.0
The Integrative Modeling Platform
IMP Manual
Reference Guide
Tutorial Index
Modules
Classes
Examples
version 2.20.0
core/excluded_volume.py
Setup an excluded volume restraint between a bunch of particles with radius.
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## \example core/excluded_volume.py
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# Setup an excluded volume restraint between a bunch of particles with radius.
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#
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5
import
IMP.container
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import
sys
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IMP.setup_from_argv
(sys.argv,
"excluded volume"
)
9
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# Make 100 particles randomly distributed in a cubic box
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m =
IMP.Model
()
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lsc =
IMP.container.ListSingletonContainer
(m)
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b =
IMP.algebra.BoundingBox3D
(
IMP.algebra.Vector3D
(0,0,0),
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IMP.algebra.Vector3D
(10,10,10))
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for
i
in
range(100):
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p = m.add_particle(
"p"
)
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lsc.add(p)
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d =
IMP.core.XYZR.setup_particle
(m, p,
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IMP.algebra.Sphere3D
(
IMP.algebra.get_random_vector_in
(b), 1))
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# this container lists all pairs that are close at the time of evaluation
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nbl =
IMP.container.ClosePairContainer
(lsc, 0, 2)
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h =
IMP.core.HarmonicLowerBound
(0, 1)
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sd =
IMP.core.SphereDistancePairScore
(h)
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# use the lower bound on the inter-sphere distance to push the spheres apart
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nbr =
IMP.container.PairsRestraint
(sd, nbl)
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# alternatively, one could just do
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r =
IMP.core.ExcludedVolumeRestraint
(lsc)
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# get the current score
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sf =
IMP.core.RestraintsScoringFunction
([nbr, r])
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print(sf.evaluate(
False
))