core::optimization::ParticleSwarmMinimizer Class Reference

Particle Swarm Optimization engine. More...

#include <ParticleSwarmMinimizer.hh>

Inheritance diagram for core::optimization::ParticleSwarmMinimizer:

Collaboration diagram for core::optimization::ParticleSwarmMinimizer:

Public Member Functions
	ParticleSwarmMinimizer (Multivec p_min, Multivec p_max)
virtual	~ParticleSwarmMinimizer ()
ParticleOPs	run (Size num_cycles, Multifunc &f_fitness, Size num_part=50)
ParticleOPs	run (Size num_cycles, Multifunc &f_fitness, Size num_part, Multivec init_values)
void	run (Size num_cycles, Multifunc &f_fitness, ParticleOPs &particles)
void	print_particles (ParticleOPs &particles, std::string header)
	helper function for displaying current particle information; calls the output operator on each particle More...

Protected Member Functions
virtual void	score_all_particles (Multifunc &f_fitness, ParticleOPs &particles)

Private Attributes
Size	size_
Real	C_inertia_start_
Real	C_inertia_end_
Real	C_pbest_
Real	C_lbest_
Real	C_gbest_
int	first_nbr_
int	last_nbr_
Multivec	p_min_
Multivec	p_max_
Multivec	p_range_
Multivec	v_max_

Detailed Description

Particle Swarm Optimization engine.

Algorithm details based heavily on

 Chen, Liu, Huang, Hwang, Ho (2006).
 "SODOCK:  Swarm Optimization for Highly Flexible Protein-Ligand Docking"
 J Comput Chem 28: 612-623, 2007

Also on http://en.wikipedia.org/wiki/Particle_swarm_optimization http://www.swarmintelligence.org/

One can imagine writing another version that distributed the work via MPI...

Definition at line 133 of file ParticleSwarmMinimizer.hh.

Constructor & Destructor Documentation

core::optimization::ParticleSwarmMinimizer::ParticleSwarmMinimizer	(	Multivec	p_min,
		Multivec	p_max
	)

Definition at line 53 of file ParticleSwarmMinimizer.cc.

References p_max_, p_min_, p_range_, size_, and v_max_.

core::optimization::ParticleSwarmMinimizer::~ParticleSwarmMinimizer ( )

virtual

Definition at line 79 of file ParticleSwarmMinimizer.cc.

Member Function Documentation

void core::optimization::ParticleSwarmMinimizer::print_particles	(	ParticleOPs &	particles,
		std::string	header
	)

helper function for displaying current particle information; calls the output operator on each particle

Definition at line 255 of file ParticleSwarmMinimizer.cc.

ParticleOPs core::optimization::ParticleSwarmMinimizer::run	(	Size	num_cycles,
		Multifunc &	f_fitness,
		Size	num_part = 50
	)

Definition at line 82 of file ParticleSwarmMinimizer.cc.

References my_RG(), p_min_, p_range_, and size_.

Referenced by protocols::optimize_weights::IterativeOptEDriver::optimize_weights(), and run().

ParticleOPs core::optimization::ParticleSwarmMinimizer::run	(	Size	num_cycles,
		Multifunc &	f_fitness,
		Size	num_part,
		Multivec	init_values
	)

Definition at line 103 of file ParticleSwarmMinimizer.cc.

References my_RG(), p_max_, p_min_, run(), and size_.

void core::optimization::ParticleSwarmMinimizer::run	(	Size	num_cycles,
		Multifunc &	f_fitness,
		ParticleOPs &	particles
	)

Definition at line 128 of file ParticleSwarmMinimizer.cc.

References C_gbest_, C_inertia_end_, C_inertia_start_, C_lbest_, C_pbest_, core::optimization::cmp_particles(), first_nbr_, last_nbr_, my_RG(), protocols::forge::build::SegmentInsertConnectionScheme::N, p_max_, p_min_, score_all_particles(), size_, and v_max_.

void core::optimization::ParticleSwarmMinimizer::score_all_particles ( Multifunc &  f_fitness, ParticleOPs &  particles  )

protectedvirtual

Reimplemented in protocols::pockets::DarcParticleSwarmMinimizer.

Definition at line 246 of file ParticleSwarmMinimizer.cc.

References protocols::forge::build::SegmentInsertConnectionScheme::N.

Referenced by run().

Member Data Documentation

Real core::optimization::ParticleSwarmMinimizer::C_gbest_

private

Definition at line 156 of file ParticleSwarmMinimizer.hh.

Referenced by run().

Real core::optimization::ParticleSwarmMinimizer::C_inertia_end_

private

Definition at line 153 of file ParticleSwarmMinimizer.hh.

Referenced by run().

Real core::optimization::ParticleSwarmMinimizer::C_inertia_start_

private

Definition at line 152 of file ParticleSwarmMinimizer.hh.

Referenced by run().

Real core::optimization::ParticleSwarmMinimizer::C_lbest_

private

Definition at line 155 of file ParticleSwarmMinimizer.hh.

Referenced by run().

Real core::optimization::ParticleSwarmMinimizer::C_pbest_

private

Definition at line 154 of file ParticleSwarmMinimizer.hh.

Referenced by run().

int core::optimization::ParticleSwarmMinimizer::first_nbr_

private

Definition at line 157 of file ParticleSwarmMinimizer.hh.

Referenced by run().

int core::optimization::ParticleSwarmMinimizer::last_nbr_

private

Definition at line 158 of file ParticleSwarmMinimizer.hh.

Referenced by run().

Multivec core::optimization::ParticleSwarmMinimizer::p_max_

private

Definition at line 160 of file ParticleSwarmMinimizer.hh.

Referenced by ParticleSwarmMinimizer(), and run().

Multivec core::optimization::ParticleSwarmMinimizer::p_min_

private

Definition at line 159 of file ParticleSwarmMinimizer.hh.

Referenced by ParticleSwarmMinimizer(), and run().

Multivec core::optimization::ParticleSwarmMinimizer::p_range_

private

Definition at line 161 of file ParticleSwarmMinimizer.hh.

Referenced by ParticleSwarmMinimizer(), and run().

Size core::optimization::ParticleSwarmMinimizer::size_

private

Definition at line 151 of file ParticleSwarmMinimizer.hh.

Referenced by ParticleSwarmMinimizer(), and run().

Multivec core::optimization::ParticleSwarmMinimizer::v_max_

private

Definition at line 162 of file ParticleSwarmMinimizer.hh.

Referenced by ParticleSwarmMinimizer(), and run().

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The documentation for this class was generated from the following files:

• src/core/optimization/ParticleSwarmMinimizer.hh
• src/core/optimization/ParticleSwarmMinimizer.cc