container/bipartite_nonbonded_interactions.py

This example shows how set up excluded volume interactions between two sets of particles.

## \example container/bipartite_nonbonded_interactions.py
# This example shows how set up excluded volume interactions between two
# sets of particles.

import IMP
import IMP.core
import IMP.container
import sys

IMP.setup_from_argv(sys.argv, "bipartite nonbonded interactions")

# This example addes a restraint on bipartite nonbonded interactions
# after excluding a set of bonded interactions.

m = IMP.Model()
# The set of particles
ps0 = IMP.container.ListSingletonContainer(m,
                         IMP.core.create_xyzr_particles(m, 20, 1.0))
ps1 = IMP.container.ListSingletonContainer(m,
                         IMP.core.create_xyzr_particles(m, 20, 2.0))

# Set up the nonbonded list
nbl = IMP.container.CloseBipartitePairContainer(ps0, ps1, 0, 1)

# Set up excluded volume
ps = IMP.core.SphereDistancePairScore(IMP.core.HarmonicLowerBound(0, 1))
evr = IMP.container.PairsRestraint(ps, nbl)

# Set up optimizer
o = IMP.core.ConjugateGradients(m)
o.set_scoring_function([evr])

o.optimize(1000)