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Rosetta
2021.07
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#include <MinimizerOptions.hh>
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) |
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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 , |
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bool const | deriv_check_verbose_in = false |
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References max_iter_, and nblist_auto_update_.
Referenced by clone().
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::brent_abs_tolerance | ( | ) | const |
References brent_abs_tolerance_.
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 | ) |
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 |
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 |
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 |
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.
References use_nblist_.
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Referenced by armijo_max_step_limit().
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Referenced by brent_abs_tolerance().
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Referenced by clone(), and deriv_check().
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Referenced by clone(), and deriv_check_to_stdout().
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Referenced by clone(), and deriv_check_verbose().
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Referenced by ga_mutation_probability().
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Referenced by gmax_cutoff_for_convergence().
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Referenced by linmin_deriv_cutoff().
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Referenced by max_iter(), and MinimizerOptions().
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Referenced by clone(), and min_type().
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Referenced by clone(), and minimize_tolerance().
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Referenced by clone(), MinimizerOptions(), and nblist_auto_update().
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Referenced by clone(), and use_nblist().