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IMP Reference Guide
2.6.1
The Integrative Modeling Platform
IMP Manual
Reference Guide
Modules
Classes
Examples
version 2.6.1
container/bipartite_nonbonded_interactions.py
This example shows how set up excluded volume interactions between two sets of particles.
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## \example container/bipartite_nonbonded_interactions.py
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# This example shows how set up excluded volume interactions between two
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# sets of particles.
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import
IMP
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import
IMP.core
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import
IMP.container
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import
sys
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IMP.setup_from_argv
(sys.argv,
"bipartite nonbonded interactions"
)
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# This example addes a restraint on bipartite nonbonded interactions
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# after excluding a set of bonded interactions.
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m =
IMP.Model
()
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# The set of particles
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ps0 =
IMP.container.ListSingletonContainer
(m,
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IMP.core.create_xyzr_particles
(m, 20, 1.0))
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ps1 =
IMP.container.ListSingletonContainer
(m,
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IMP.core.create_xyzr_particles
(m, 20, 2.0))
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# Set up the nonbonded list
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nbl =
IMP.container.CloseBipartitePairContainer
(ps0, ps1, 0, 1)
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# Set up excluded volume
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ps =
IMP.core.SphereDistancePairScore
(
IMP.core.HarmonicLowerBound
(0, 1))
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evr =
IMP.container.PairsRestraint
(ps, nbl)
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# Set up optimizer
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o =
IMP.core.ConjugateGradients
(m)
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o.set_scoring_function([evr])
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o.optimize(1000)