Rosetta  2020.46
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Attributes | List of all members
core::optimization::MinimizerOptions Class Reference

#include <MinimizerOptions.hh>

Inheritance diagram for core::optimization::MinimizerOptions:
Inheritance graph
[legend]

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 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
void core::optimization::MinimizerOptions::armijo_max_step_limit ( Real  lim)
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
void core::optimization::MinimizerOptions::deriv_check ( bool  deriv_check_in)
bool core::optimization::MinimizerOptions::deriv_check ( ) const

References deriv_check_.

void core::optimization::MinimizerOptions::deriv_check_to_stdout ( bool  setting)
bool core::optimization::MinimizerOptions::deriv_check_to_stdout ( ) const
bool core::optimization::MinimizerOptions::deriv_check_verbose ( ) const
Real core::optimization::MinimizerOptions::ga_mutation_probability ( ) const
void core::optimization::MinimizerOptions::ga_mutation_probability ( Real  p)
Real core::optimization::MinimizerOptions::gmax_cutoff_for_convergence ( ) const
void core::optimization::MinimizerOptions::gmax_cutoff_for_convergence ( Real  gmax_in)
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
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
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
void core::optimization::MinimizerOptions::nblist_auto_update ( bool  setting)

References nblist_auto_update_.

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