container/nonbonded_interactions.py

This example shows how to set up an excluded volume restraint for a set of XYZRDecorator-style particles.

## \example container/nonbonded_interactions.py
# This example shows how to set up an excluded volume restraint for a set
# of XYZRDecorator-style particles.

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

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

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

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

# create a bond between two particles
bd0 = IMP.atom.Bonded.setup_particle(m, ps.get_indexes()[0])
bd1 = IMP.atom.Bonded.setup_particle(m, ps.get_indexes()[1])
IMP.atom.create_custom_bond(bd0, bd1, 2.0)

# Set up the nonbonded list for all pairs that are touching
# and let things move 3 before updating the list
nbl = IMP.container.ClosePairContainer(ps, 0.0, 3.0)
nbl.add_pair_filter(IMP.atom.BondedPairFilter())

# Set up excluded volume
sdps = IMP.core.SoftSpherePairScore(1)
evr = IMP.container.PairsRestraint(sdps, nbl)

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

o.optimize(1000)