core/symmetry.py

Show how to use the code in core to enforce symmetry.

## \example core/symmetry.py
# Show how to use the code in core to enforce symmetry.

import IMP.core
import IMP.container

m = IMP.kernel.Model()
m.set_log_level(IMP.base.SILENT)
ps = []
# create 4 xyz particles
for i in range(0, 4):
    p = IMP.kernel.Particle(m)
    ps.append(p)
    d = IMP.core.XYZ.setup_particle(p, IMP.algebra.Vector3D(.5, 0, 0))
    IMP.core.XYZR.setup_particle(p, 1)

# set the 0 particle as the reference particle for the others as
# they will get their positions from it
for i, p in enumerate(ps[1:]):
    # the other 3 particles are all symmetric copies of the first
    IMP.core.Reference.setup_particle(p, ps[0])
    # the symmetry operation is rotation around the z axis
    tr = IMP.algebra.Transformation3D(
        IMP.algebra.get_rotation_about_axis(IMP.algebra.get_basis_vector_3d(2),
                                            3.14 / 2.0 * (
                                                i + 1)),
        IMP.algebra.Vector3D(0, 0, 0))
    sm = IMP.core.TransformationSymmetry(tr)
    # set up a constraint for the one particle, if you have more than one with the same symmetry
    # transform, you should use an IMP.container.SingletonsConstraint.
    c = IMP.core.SingletonConstraint(sm, None, p)
    m.add_score_state(c)
r = IMP.core.ExcludedVolumeRestraint(IMP.container.ListSingletonContainer(ps),
                                     1)
m.add_restraint(r)

d0 = IMP.core.XYZ(ps[0])
# print only optimize the main particle
d0.set_coordinates_are_optimized(True)

opt = IMP.core.ConjugateGradients(m)
opt.optimize(10)
print("score is ", m.evaluate(False))
for p in ps:
    print(p.get_name(), IMP.core.XYZ(p).get_coordinates())