core::optimization::MinimizerOptions Class Reference

#include <MinimizerOptions.hh>

Inheritance diagram for core::optimization::MinimizerOptions:

Public Member Functions
	~MinimizerOptions () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
	MinimizerOptions (std::string const &min_type_in, Real const minimize_tolerance_in, bool const use_nblist_in, bool const deriv_check_in=false, bool const deriv_check_verbose_in=false)
MinimizerOptionsOP	clone () const
std::string const &	min_type () const
void	min_type (std::string min_type_in)
std::string &	min_type ()
void	deriv_check (bool deriv_check_in)
void	deriv_check_to_stdout (bool setting)
bool	deriv_check () const
bool	deriv_check_verbose () const
bool	deriv_check_to_stdout () const
Real	minimize_tolerance () const
Real &	minimize_tolerance ()
void	minimize_tolerance (Real minimize_tolerance_in)
bool	use_nblist () const
	Indicate whether or not a handful of optimizations regarding the neighbor list have been enabled. More...
void	use_nblist (bool use_nblist_in)
	Indicate whether or not a handful of optimizations regarding the neighbor list should be enabled. More...
bool	nblist_auto_update () const
void	nblist_auto_update (bool setting)
bool	silent () const
void	silent (bool silent_in)
Real	gmax_cutoff_for_convergence () const
void	gmax_cutoff_for_convergence (Real gmax_in)
Real	ax_init () const
Real	xx_init () const
Real	bx_init () const
Real	brent_abs_tolerance () const
Real	linmin_deriv_cutoff () const
	The derivative cutoff used for Brent. More...
void	linmin_deriv_cutoff (core::Real const &val)
	Set the derivative cutoff used for Brent. More...
int	max_iter () const
void	max_iter (int n)
Real	ga_mutation_probability () const
void	ga_mutation_probability (Real p)
Real	armijo_max_step_limit () const
void	armijo_max_step_limit (Real lim)

Private Attributes
int	max_iter_
std::string	min_type_
Real	minimize_tolerance_
bool	use_nblist_
bool	nblist_auto_update_
bool	deriv_check_
bool	deriv_check_verbose_
bool	deriv_check_to_stdout_
bool	silent_
Real	gmax_cutoff_for_convergence_
Real	ax_init_
Real	xx_init_
Real	bx_init_
Real	brent_abs_tolerance_
Real	linmin_deriv_cutoff_
Real	ga_mutation_probability_
Real	armijo_max_step_limit_

Constructor & Destructor Documentation

core::optimization::MinimizerOptions::~MinimizerOptions ( )

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

core::optimization::MinimizerOptions::MinimizerOptions	(	std::string const &	min_type_in,
		Real const	minimize_tolerance_in,
		bool const	use_nblist_in,
		bool const	deriv_check_in = false,
		bool const	deriv_check_verbose_in = false
	)

References max_iter_, and nblist_auto_update_.

Referenced by clone().

Member Function Documentation

Real core::optimization::MinimizerOptions::armijo_max_step_limit

(

)

const

References armijo_max_step_limit_.

Referenced by core::optimization::Minimizer::run().

void core::optimization::MinimizerOptions::armijo_max_step_limit

(

Real

lim

)

References armijo_max_step_limit_.

Real core::optimization::MinimizerOptions::ax_init

(

)

const

References ax_init_.

Real core::optimization::MinimizerOptions::brent_abs_tolerance

(

)

const

References brent_abs_tolerance_.

Real core::optimization::MinimizerOptions::bx_init

(

)

const

References bx_init_.

MinimizerOptionsOP core::optimization::MinimizerOptions::clone

(

)

const

References deriv_check_, deriv_check_to_stdout_, deriv_check_verbose_, min_type_, minimize_tolerance_, MinimizerOptions(), nblist_auto_update_, and use_nblist_.

void core::optimization::MinimizerOptions::deriv_check

(

bool

deriv_check_in

)

References deriv_check_.

Referenced by core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::optimization::AtomTreeMinimizer::run(), and core::optimization::CartesianMinimizer::run().

bool core::optimization::MinimizerOptions::deriv_check

(

)

const

References deriv_check_.

void core::optimization::MinimizerOptions::deriv_check_to_stdout

(

bool

setting

)

References deriv_check_to_stdout_.

Referenced by core::optimization::AtomTreeMinimizer::run(), and core::optimization::CartesianMinimizer::run().

bool core::optimization::MinimizerOptions::deriv_check_to_stdout

(

)

const

References deriv_check_to_stdout_.

bool core::optimization::MinimizerOptions::deriv_check_verbose

(

)

const

References deriv_check_verbose_.

Referenced by core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::optimization::AtomTreeMinimizer::run(), and core::optimization::CartesianMinimizer::run().

Real core::optimization::MinimizerOptions::ga_mutation_probability

(

)

const

References ga_mutation_probability_.

void core::optimization::MinimizerOptions::ga_mutation_probability

(

Real

p

)

References ga_mutation_probability_.

Real core::optimization::MinimizerOptions::gmax_cutoff_for_convergence

(

)

const

References gmax_cutoff_for_convergence_.

Referenced by core::optimization::Minimizer::dfpmin_armijo(), and core::optimization::Minimizer::lbfgs().

void core::optimization::MinimizerOptions::gmax_cutoff_for_convergence

(

Real

gmax_in

)

References gmax_cutoff_for_convergence_.

Real core::optimization::MinimizerOptions::linmin_deriv_cutoff

(

)

const

The derivative cutoff used for Brent.

References linmin_deriv_cutoff_.

Referenced by core::optimization::Minimizer::linmin_iterated().

void core::optimization::MinimizerOptions::linmin_deriv_cutoff

(

core::Real const &

val

)

Set the derivative cutoff used for Brent.

References linmin_deriv_cutoff_, and protocols::hybridization::val.

int core::optimization::MinimizerOptions::max_iter

(

)

const

References max_iter_.

Referenced by protocols::simple_moves::CombinePoseMover::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply(), protocols::md::CartesianMD::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::electron_density::VoxelSpacingRefinementMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::electron_density::BfactorFittingMover::apply(), protocols::relax::RangeRelaxMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::pose_creation::MakeJunctionsMover::assign_seq(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_cartligmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::idealize_and_repack_pose(), protocols::pose_creation::MergePDBatOverlapMover::merge_junction_sequence(), protocols::pose_creation::MergePDBatOverlapMover::minimize_overlap(), protocols::ddg::ddGMover::minimize_with_constraints(), protocols::relax::LocalRelax::optimization_loop(), protocols::ligand_docking::ga_ligand_dock::GridScorer::optimize(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::premin_ligand(), protocols::rna::movers::ErraserMinimizerMover::process_entire_pose(), protocols::mpi_refinement::ramp_minpack_loop(), protocols::mpi_refinement::WorkUnit_Sampler::ramp_minpack_loop2(), protocols::loop_grower::LoopGrower::refine_cycle(), core::pack::RTMin::rtmin(), core::optimization::NelderMeadSimplex::run(), protocols::mpi_refinement::WorkUnit_bbGauss::run(), protocols::mpi_refinement::WorkUnit_RamaPerturber::run(), and core::optimization::Minimizer::run().

void core::optimization::MinimizerOptions::max_iter

(

int

n

)

References max_iter_.

std::string const & core::optimization::MinimizerOptions::min_type

(

)

const

References min_type_.

Referenced by core::optimization::AtomTreeMinimizer::check_setup(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::minimize_sugar(), core::optimization::CartesianMinimizer::run(), and core::optimization::Minimizer::run().

void core::optimization::MinimizerOptions::min_type

(

std::string

min_type_in

)

References min_type_.

std::string & core::optimization::MinimizerOptions::min_type

(

)

References min_type_.

Real core::optimization::MinimizerOptions::minimize_tolerance

(

)

const

References minimize_tolerance_.

Referenced by protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::minimize_sugar(), and core::optimization::Minimizer::run().

Real & core::optimization::MinimizerOptions::minimize_tolerance

(

)

References minimize_tolerance_.

void core::optimization::MinimizerOptions::minimize_tolerance

(

Real

minimize_tolerance_in

)

References minimize_tolerance_.

bool core::optimization::MinimizerOptions::nblist_auto_update

(

)

const

References nblist_auto_update_.

Referenced by protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::apply(), protocols::rna::denovo::movers::RNA_Minimizer::apply(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::bulge_chain_minimize_legacy(), protocols::stepwise::modeler::rna::sugar::minimize_all_sampled_floating_bases(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::minimize_sugar(), protocols::symmetry::SymShakeStructureMover::minimize_with_constraints(), protocols::simple_moves::ShakeStructureMover::minimize_with_constraints(), protocols::ddg::ddGMover::minimize_with_constraints(), protocols::rna::movers::ErraserMinimizerMover::process_entire_pose(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::optimization::CartesianMinimizer::run(), and core::optimization::AtomTreeMinimizer::run().

void core::optimization::MinimizerOptions::nblist_auto_update

(

bool

setting

)

References nblist_auto_update_.

bool core::optimization::MinimizerOptions::silent

(

)

const

References silent_.

Referenced by core::optimization::Minimizer::dfpmin(), core::optimization::Minimizer::dfpmin_armijo(), core::optimization::Minimizer::lbfgs(), core::pack::RTMin::rtmin(), and core::optimization::Minimizer::run().

void core::optimization::MinimizerOptions::silent

(

bool

silent_in

)

References silent_.

bool core::optimization::MinimizerOptions::use_nblist

(

)

const

Indicate whether or not a handful of optimizations regarding the neighbor list have been enabled.

References use_nblist_.

Referenced by core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::optimization::AtomTreeMinimizer::run(), and core::optimization::CartesianMinimizer::run().

void core::optimization::MinimizerOptions::use_nblist

(

bool

use_nblist_in

)

Indicate whether or not a handful of optimizations regarding the neighbor list should be enabled.

The neighbor list is based on the move map. It includes any atoms that can be moved by the minimizer plus their neighbors. This list is not updated during minimization. All scores for atoms and atom pairs outside the neighbor list are held fixed. All scores for atoms and atom pairs within the list are not cached (usually they would be), since it assumed that they will be changing rapidly. These optimizations are effective when a large number of small moves are being made. You may prefer to enable this option when minimizing in fullatom mode, and to disable it in centroid mode.

Note

I wrote this docstring after I reading through a bunch of code to figure out what this option meant, but I don't have any expertise with the minimizer. So the above represents my understanding of this option, but there could very well be errors or misstatements.

See also

core::scoring::AtomNeighbor

References use_nblist_.

Real core::optimization::MinimizerOptions::xx_init

(

)

const

References xx_init_.

Member Data Documentation

Real core::optimization::MinimizerOptions::armijo_max_step_limit_

private

Referenced by armijo_max_step_limit().

Real core::optimization::MinimizerOptions::ax_init_

private

Referenced by ax_init().

Real core::optimization::MinimizerOptions::brent_abs_tolerance_

private

Referenced by brent_abs_tolerance().

Real core::optimization::MinimizerOptions::bx_init_

private

Referenced by bx_init().

bool core::optimization::MinimizerOptions::deriv_check_

private

Referenced by clone(), and deriv_check().

bool core::optimization::MinimizerOptions::deriv_check_to_stdout_

private

Referenced by clone(), and deriv_check_to_stdout().

bool core::optimization::MinimizerOptions::deriv_check_verbose_

private

Referenced by clone(), and deriv_check_verbose().

Real core::optimization::MinimizerOptions::ga_mutation_probability_

private

Referenced by ga_mutation_probability().

Real core::optimization::MinimizerOptions::gmax_cutoff_for_convergence_

private

Referenced by gmax_cutoff_for_convergence().

Real core::optimization::MinimizerOptions::linmin_deriv_cutoff_

private

Referenced by linmin_deriv_cutoff().

int core::optimization::MinimizerOptions::max_iter_

private

Referenced by max_iter(), and MinimizerOptions().

std::string core::optimization::MinimizerOptions::min_type_

private

Referenced by clone(), and min_type().

Real core::optimization::MinimizerOptions::minimize_tolerance_

private

Referenced by clone(), and minimize_tolerance().

bool core::optimization::MinimizerOptions::nblist_auto_update_

private

Referenced by clone(), MinimizerOptions(), and nblist_auto_update().

bool core::optimization::MinimizerOptions::silent_

private

Referenced by silent().

bool core::optimization::MinimizerOptions::use_nblist_

private

Referenced by clone(), and use_nblist().

Real core::optimization::MinimizerOptions::xx_init_

private

Referenced by xx_init().

---

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

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