IMP  2.1.0
The Integrative Modeling Platform
simplex.py
1 ## \example gsl/simplex.py
2 # The IMP::gsl::Simplex optimizer is a local optimizer that does not
3 # require derivatives.
4 
5 import IMP
6 import IMP.test
7 import IMP.core
8 import IMP.gsl
9 import IMP.algebra
10 
11 
12 m = IMP.kernel.Model()
13 
14 # create two particles to optimize
19 d0.set_coordinates_are_optimized(True)
20 d1.set_coordinates_are_optimized(True)
21 
22 # restrain their distance to be 1
24 m.add_restraint(dist)
25 
26 opt = IMP.gsl.Simplex(m)
27 opt.set_minimum_size(.000001)
28 opt.set_initial_length(1)
29 
30 # probably more steps than are needed
31 e = opt.optimize(1000000)
32 print IMP.core.get_distance(d0, d1)
See IMP.test for more information.
Definition: test_config.h:107
static XYZ setup_particle(kernel::Model *m, ParticleIndex pi)
Definition: XYZ.h:53
See IMP.gsl for more information.
Distance restraint between two particles.
double get_distance(XYZR a, XYZR b)
Compute the sphere distance between a and b.
Definition: XYZR.h:88
A simplex optimizer taken from GSL.
Definition: Simplex.h:27
Class to handle individual model particles.
See IMP.core for more information.
See IMP.algebra for more information.
Class for storing model, its restraints, constraints, and particles.
Harmonic function (symmetric about the mean)
Definition: core/Harmonic.h:25