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core::optimization::MinimizerOptions Class Reference

#include <MinimizerOptions.hh>

Inheritance diagram for core::optimization::MinimizerOptions:
Inheritance graph
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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
 
Realminimize_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 cmaes_rgsigma () const
 
void cmaes_rgsigma (Real s)
 
int cmaes_lambda () const
 
void cmaes_lambda (int n)
 
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 cmaes_rgsigma_
 
int cmaes_lambda_
 
Real armijo_max_step_limit_
 

Constructor & Destructor Documentation

◆ ~MinimizerOptions()

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

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

◆ MinimizerOptions()

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

◆ armijo_max_step_limit() [1/2]

Real core::optimization::MinimizerOptions::armijo_max_step_limit ( ) const

◆ armijo_max_step_limit() [2/2]

void core::optimization::MinimizerOptions::armijo_max_step_limit ( Real  lim)

◆ ax_init()

Real core::optimization::MinimizerOptions::ax_init ( ) const

References ax_init_.

◆ brent_abs_tolerance()

Real core::optimization::MinimizerOptions::brent_abs_tolerance ( ) const

References brent_abs_tolerance_.

◆ bx_init()

Real core::optimization::MinimizerOptions::bx_init ( ) const

References bx_init_.

◆ clone()

MinimizerOptionsOP core::optimization::MinimizerOptions::clone ( ) const

◆ cmaes_lambda() [1/2]

int core::optimization::MinimizerOptions::cmaes_lambda ( ) const

References cmaes_lambda_.

◆ cmaes_lambda() [2/2]

void core::optimization::MinimizerOptions::cmaes_lambda ( int  n)

References cmaes_lambda_.

◆ cmaes_rgsigma() [1/2]

Real core::optimization::MinimizerOptions::cmaes_rgsigma ( ) const

References cmaes_rgsigma_.

◆ cmaes_rgsigma() [2/2]

void core::optimization::MinimizerOptions::cmaes_rgsigma ( Real  s)

References cmaes_rgsigma_.

◆ deriv_check() [1/2]

bool core::optimization::MinimizerOptions::deriv_check ( ) const

References deriv_check_.

◆ deriv_check() [2/2]

void core::optimization::MinimizerOptions::deriv_check ( bool  deriv_check_in)

◆ deriv_check_to_stdout() [1/2]

bool core::optimization::MinimizerOptions::deriv_check_to_stdout ( ) const

◆ deriv_check_to_stdout() [2/2]

void core::optimization::MinimizerOptions::deriv_check_to_stdout ( bool  setting)

◆ deriv_check_verbose()

bool core::optimization::MinimizerOptions::deriv_check_verbose ( ) const

◆ ga_mutation_probability() [1/2]

Real core::optimization::MinimizerOptions::ga_mutation_probability ( ) const

◆ ga_mutation_probability() [2/2]

void core::optimization::MinimizerOptions::ga_mutation_probability ( Real  p)

◆ gmax_cutoff_for_convergence() [1/2]

Real core::optimization::MinimizerOptions::gmax_cutoff_for_convergence ( ) const

◆ gmax_cutoff_for_convergence() [2/2]

void core::optimization::MinimizerOptions::gmax_cutoff_for_convergence ( Real  gmax_in)

◆ linmin_deriv_cutoff() [1/2]

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().

◆ linmin_deriv_cutoff() [2/2]

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.

◆ max_iter() [1/2]

int core::optimization::MinimizerOptions::max_iter ( ) const

References max_iter_.

Referenced by protocols::electron_density::BfactorFittingMover::apply(), protocols::electron_density::VoxelSpacingRefinementMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::md::CartesianMD::apply(), protocols::rna::denovo::movers::RNA_Minimizer::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply(), protocols::simple_moves::CombinePoseMover::apply(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::relax::RangeRelaxMover::apply(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::pose_creation::MakeJunctionsMover::assign_seq(), protocols::ligand_docking::ga_ligand_dock::constraint_relax(), 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(), protocols::mpi_refinement::WorkUnit_RamaPerturber::run(), protocols::mpi_refinement::WorkUnit_bbGauss::run(), core::optimization::Minimizer::run(), core::optimization::NelderMeadSimplex::run(), protocols::rbsegment_relax::ConfChangeMover::stage1(), and protocols::rbsegment_relax::ConfChangeMover::stage2().

◆ max_iter() [2/2]

void core::optimization::MinimizerOptions::max_iter ( int  n)

References max_iter_.

◆ min_type() [1/3]

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

References min_type_.

◆ min_type() [2/3]

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

◆ min_type() [3/3]

void core::optimization::MinimizerOptions::min_type ( std::string  min_type_in)

References min_type_.

◆ minimize_tolerance() [1/3]

Real & core::optimization::MinimizerOptions::minimize_tolerance ( )

References minimize_tolerance_.

◆ minimize_tolerance() [2/3]

Real core::optimization::MinimizerOptions::minimize_tolerance ( ) const

◆ minimize_tolerance() [3/3]

void core::optimization::MinimizerOptions::minimize_tolerance ( Real  minimize_tolerance_in)

References minimize_tolerance_.

◆ nblist_auto_update() [1/2]

bool core::optimization::MinimizerOptions::nblist_auto_update ( ) const

◆ nblist_auto_update() [2/2]

void core::optimization::MinimizerOptions::nblist_auto_update ( bool  setting)

References nblist_auto_update_.

◆ silent() [1/2]

bool core::optimization::MinimizerOptions::silent ( ) const

◆ silent() [2/2]

void core::optimization::MinimizerOptions::silent ( bool  silent_in)

References silent_.

◆ use_nblist() [1/2]

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

◆ use_nblist() [2/2]

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_.

◆ xx_init()

Real core::optimization::MinimizerOptions::xx_init ( ) const

References xx_init_.

Member Data Documentation

◆ armijo_max_step_limit_

Real core::optimization::MinimizerOptions::armijo_max_step_limit_
private

Referenced by armijo_max_step_limit().

◆ ax_init_

Real core::optimization::MinimizerOptions::ax_init_
private

Referenced by ax_init().

◆ brent_abs_tolerance_

Real core::optimization::MinimizerOptions::brent_abs_tolerance_
private

Referenced by brent_abs_tolerance().

◆ bx_init_

Real core::optimization::MinimizerOptions::bx_init_
private

Referenced by bx_init().

◆ cmaes_lambda_

int core::optimization::MinimizerOptions::cmaes_lambda_
private

Referenced by cmaes_lambda().

◆ cmaes_rgsigma_

Real core::optimization::MinimizerOptions::cmaes_rgsigma_
private

Referenced by cmaes_rgsigma().

◆ deriv_check_

bool core::optimization::MinimizerOptions::deriv_check_
private

Referenced by clone(), and deriv_check().

◆ deriv_check_to_stdout_

bool core::optimization::MinimizerOptions::deriv_check_to_stdout_
private

Referenced by clone(), and deriv_check_to_stdout().

◆ deriv_check_verbose_

bool core::optimization::MinimizerOptions::deriv_check_verbose_
private

Referenced by clone(), and deriv_check_verbose().

◆ ga_mutation_probability_

Real core::optimization::MinimizerOptions::ga_mutation_probability_
private

Referenced by ga_mutation_probability().

◆ gmax_cutoff_for_convergence_

Real core::optimization::MinimizerOptions::gmax_cutoff_for_convergence_
private

◆ linmin_deriv_cutoff_

Real core::optimization::MinimizerOptions::linmin_deriv_cutoff_
private

Referenced by linmin_deriv_cutoff().

◆ max_iter_

int core::optimization::MinimizerOptions::max_iter_
private

Referenced by max_iter(), and MinimizerOptions().

◆ min_type_

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

Referenced by clone(), and min_type().

◆ minimize_tolerance_

Real core::optimization::MinimizerOptions::minimize_tolerance_
private

Referenced by clone(), and minimize_tolerance().

◆ nblist_auto_update_

bool core::optimization::MinimizerOptions::nblist_auto_update_
private

◆ silent_

bool core::optimization::MinimizerOptions::silent_
private

Referenced by silent().

◆ use_nblist_

bool core::optimization::MinimizerOptions::use_nblist_
private

Referenced by clone(), and use_nblist().

◆ xx_init_

Real core::optimization::MinimizerOptions::xx_init_
private

Referenced by xx_init().


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