core/rigid_collisions.py

Collision detection and building of a non-bonded list can be sped up when rigid bodies are used. To do this, use a RigidClosePairsFinder.

## \example core/rigid_collisions.py
# Collision detection and building of a non-bonded list can be sped up when rigid bodies are used.
# To do this, use a RigidClosePairsFinder.

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

# This example addes a restraint on nonbonded interactions
# Since it is between two rigid bodies, internal interactions are ignored

m = IMP.kernel.Model()
# The particles in the rigid bodies
rbps0 = IMP.core.create_xyzr_particles(m, 3, 1)
rbps1 = IMP.core.create_xyzr_particles(m, 3, 1)

rbp0 = IMP.kernel.Particle(m)
rbp1 = IMP.kernel.Particle(m)

rbss0 = IMP.core.RigidBody.setup_particle(rbp0, IMP.core.XYZs(rbps0))

rbss1 = IMP.core.RigidBody.setup_particle(rbp1, IMP.core.XYZs(rbps1))

lsc = IMP.container.ListSingletonContainer(m)
lsc.add_particles(rbps0)
lsc.add_particles(rbps1)

# Set up the nonbonded list
nbl = IMP.container.ClosePairContainer(
    lsc, 0, IMP.core.RigidClosePairsFinder(), 2.0)

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

# Set up optimizer
o = IMP.core.ConjugateGradients()
o.set_model(m)

done = False
while not done:
    try:
        o.optimize(1000)
    except IMP.base.ModelException:
        for d in [rbss0, rbss1]:
            d.set_transformation(
                IMP.algebra.Transformation3D(
                    IMP.algebra.get_random_rotation_3d(),
                    IMP.algebra.get_random_vector_in(
                        IMP.algebra.BoundingBox3D(
                            IMP.algebra.Vector3D(
                                0, 0, 0),
                            IMP.algebra.Vector3D(10, 10, 10)))))
    else:
        done = True