gsl examples

simplex

The IMP::gsl::Simplex optimizer is a local optimizer that does not require derivatives.

import IMP, IMP.test import IMP.core import IMP.gsl import IMP.algebra m= IMP.Model() # create two particles to optimize d0= IMP.core.XYZ.setup_particle(IMP.Particle(m), IMP.algebra.Vector3D(0,0,0)) d1= IMP.core.XYZ.setup_particle(IMP.Particle(m), IMP.algebra.Vector3D(3,4,5)) d0.set_coordinates_are_optimized(True) d1.set_coordinates_are_optimized(True) # restrain their distance to be 1 dist= IMP.core.DistanceRestraint(IMP.core.Harmonic(1, 1), d0, d1) m.add_restraint(dist) opt = IMP.gsl.Simplex(m) opt.set_minimum_size(.000001) opt.set_initial_length(1) # probably more steps than are needed e = opt.optimize(1000000) print IMP.core.get_distance(d0, d1)

IMP::algebra::VectorD IMP::gsl::Simplex IMP::core::XYZ IMP::core::DistanceRestraint IMP::core::Harmonic