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nonbonded_interactions.py
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## \example container/nonbonded_interactions.py
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## This example shows how to set up an excluded volume restraint for a set of XYZRDecorator-style particles.
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import
IMP
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import
IMP.core
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import
IMP.atom
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import
IMP.container
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# This example addes a restraint on 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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ps =
IMP.container.ListSingletonContainer
(
IMP.core.create_xyzr_particles
(m, 20, 1.0))
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# create a bond between two particles
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bd0=
IMP.atom.Bonded.setup_particle
(ps.get_particle(0))
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bd1=
IMP.atom.Bonded.setup_particle
(ps.get_particle(1))
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IMP.atom.create_custom_bond
(bd0, bd1, 2.0)
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# Set up the nonbonded list for all pairs at are touching
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# and let things move 3 before updating the list
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nbl=
IMP.container.ClosePairContainer
(ps, 0.0, 3.0)
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nbl.add_pair_filter(
IMP.atom.BondedPairFilter
())
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# Set up excluded volume
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sdps=
IMP.core.SoftSpherePairScore
(1)
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evr=
IMP.container.PairsRestraint
(sdps, nbl)
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m.add_restraint(evr)
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# Set up optimizer
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o=
IMP.core.ConjugateGradients
()
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o.set_model(m)
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o.optimize(1000)