IMP
2.4.0
The Integrative Modeling Platform
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Modules
Classes
Examples
gsl/simplex.py
The
IMP::gsl::Simplex
optimizer is a local optimizer that does not require derivatives.
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## \example gsl/simplex.py
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# The IMP::gsl::Simplex optimizer is a local optimizer that does not
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# require derivatives.
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import
IMP
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import
IMP.test
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import
IMP.core
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import
IMP.gsl
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import
IMP.algebra
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m =
IMP.kernel.Model
()
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# create two particles to optimize
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d0 =
IMP.core.XYZ.setup_particle
(
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IMP.kernel.Particle
(m),
IMP.algebra.Vector3D
(0, 0, 0))
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d1 =
IMP.core.XYZ.setup_particle
(
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IMP.kernel.Particle
(m),
IMP.algebra.Vector3D
(3, 4, 5))
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d0.set_coordinates_are_optimized(
True
)
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d1.set_coordinates_are_optimized(
True
)
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# restrain their distance to be 1
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dist =
IMP.core.DistanceRestraint
(
IMP.core.Harmonic
(1, 1), d0, d1)
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m.add_restraint(dist)
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opt =
IMP.gsl.Simplex
(m)
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opt.set_minimum_size(.000001)
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opt.set_initial_length(1)
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# probably more steps than are needed
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e = opt.optimize(1000000)
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print(
IMP.core.get_distance
(d0, d1))