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Static Public Member Functions | Static Private Member Functions | List of all members
core::scoring::ScoreFunctionFactory Class Reference

A collection of functions for making a single score_function. More...

#include <ScoreFunctionFactory.hh>

Static Public Member Functions

static ScoreFunctionOP create_score_function (std::string const &weights_tag)
 Returns a ScoreFunction from the database weights file <weights_tag> More...
 
static ScoreFunctionOP create_score_function (utility::options::OptionCollection const &options, std::string const &weights_tag)
 
static ScoreFunctionOP create_score_function (std::string const &weights_tag, std::string const &patch_tag)
 Returns a ScoreFunction from the database weights file <weights_tag> with the patch <patch_tag> More...
 
static ScoreFunctionOP create_score_function (utility::options::OptionCollection const &options, std::string const &weights_tag, std::string const &patch_tag)
 
static ScoreFunctionOP create_score_function (std::string const &weights_tag, utility::vector1< std::string > const &patch_tags)
 Returns a ScoreFunction from the database weights file <weights_tag> with patches in <patch_tags> More...
 
static ScoreFunctionOP create_score_function (utility::options::OptionCollection const &options, std::string const &weights_tag, utility::vector1< std::string > const &patch_tags)
 
static void list_read_options (utility::options::OptionKeyList &opts)
 A documentation function which reports the set of options read by the create_score_function variants. More...
 
static bool validate_talaris (std::string const &weights_tag, utility::options::OptionCollection const &options)
 checks if the weights file is probably a talaris weights file and if it is consistent with the options system. static because C++ says it has to be; public because unit test spiritually const but you can't do that with static More...
 
static bool validate_beta (std::string const &weights_tag, utility::options::OptionCollection const &options)
 checks if the weights file is probably a beta_15 weights file and if it is consistent with the options system. static because C++ says it has to be; public because unit test spiritually const but you can't do that with static More...
 

Static Private Member Functions

static void apply_user_defined_reweighting_ (utility::options::OptionCollection const &options, core::scoring::ScoreFunctionOP scorefxn)
 Applies user defined re-weighting from the options system. Reweights are applied as a factor of the original, so -rg_reweight 0.5 would result in half of the previously defined rg weight. More...
 
static void load_weights_file (std::string weights_tag, ScoreFunctionOP scorefxn)
 

Detailed Description

A collection of functions for making a single score_function.

Member Function Documentation

void core::scoring::ScoreFunctionFactory::apply_user_defined_reweighting_ ( utility::options::OptionCollection const &  options,
core::scoring::ScoreFunctionOP  scorefxn 
)
staticprivate

Applies user defined re-weighting from the options system. Reweights are applied as a factor of the original, so -rg_reweight 0.5 would result in half of the previously defined rg weight.

References protocols::cluster::calibur::aa, core::scoring::apply_set_weights(), core::scoring::ref, and core::scoring::rg.

Referenced by create_score_function().

ScoreFunctionOP core::scoring::ScoreFunctionFactory::create_score_function ( std::string const &  weights_tag)
static

Returns a ScoreFunction from the database weights file <weights_tag>

example(s): scorefxn = create_score_function('standard') See also: ScoreFunction ScoreFunction.show ScoreFunction.weights ScoreType

Referenced by protocols::simple_filters::ExtraScoreEvaluatorCreator::add_evaluators(), protocols::protein_interface_design::movers::DockWithHotspotMover::apply(), protocols::legacy_sewing::LegacyAssemblyMover::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::antibody::LHSnugFitLegacy::apply(), protocols::rna::denovo::movers::RNP_HighResMover::apply(), protocols::rna::denovo::movers::RNA_Relaxer::apply(), protocols::recces::scratch::ThermalSamplingMover::apply(), protocols::simple_filters::TruncatedScoreEvaluator::apply(), protocols::relax::membrane::MPFastRelaxMover::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::enzdes::PredesignPerturbMover::apply(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::dna::argrot_dna_dis2(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover::AsymFoldandDockRbTrialMover(), protocols::rbsegment_relax::AutoRBMover::AutoRBMover(), protocols::simple_moves::StructProfileMover::calc_cenlist(), protocols::analysis::InterfaceAnalyzerMover::calc_centroid_dG(), protocols::ub_e2c::ubi_e2c_modeler::calc_interaction_energy(), protocols::relax::CentroidRelax::CentroidRelax(), protocols::rna::denovo::check_base_pair(), protocols::rna::denovo::classify_base_pairs_lores(), protocols::pose_length_moves::NearNativeLoopCloser::close_loop(), protocols::pose_length_moves::NearNativeLoopCloser::combine_chains(), protocols::protein_interface_design::filters::ClashWithTargetFilter::compute(), protocols::helical_bundle_predict::HelicalBundlePredictApplication::create_centroid_scorefunction(), create_score_function(), protocols::parser::ScoreFunctionLoader::create_scorefxn_from_tag(), protocols::ddG_main(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::default_centroid_scorefxn(), protocols::denovo_design::components::RemodelLoopMoverPoseFolder::default_score_function(), protocols::enzdes::EnzdesBaseProtocol::EnzdesBaseProtocol(), protocols::ub_e2c::ubi_e2c_modeler::evaluate_native(), protocols::hotspot_hashing::HotspotStubSet::fill(), protocols::docking::DockingEnsemblePrepackProtocol::finalize_setup(), protocols::docking::DockingPrepackProtocol::finalize_setup(), protocols::docking::membrane::QuickRelaxPartnersSeparately::finalize_setup(), protocols::membrane::MPMutateRelaxMover::finalize_setup(), protocols::docking::membrane::MPFindInterfaceMover::finalize_setup(), protocols::abinitio::AbrelaxApplication::fold(), protocols::loop_grower::FragmentExtension::FragmentExtension(), protocols::pose_length_moves::PossibleLoop::generate_output_pose(), protocols::abinitio::AbrelaxApplication::generate_scorefxn(), protocols::features::strand_assembly::SandwichFeatures::generate_scorefxn(), protocols::mainchain_potential::GenerateMainchainPotential::generate_sfxn(), protocols::antibody::design::get_ab_design_dock_high_scorefxn(), protocols::antibody::design::get_ab_design_dock_low_scorefxn(), protocols::antibody::get_Dock_ScoreFxn(), protocols::mpi_refinement::WorkUnit_Sampler::get_energy(), protocols::vip::VIP_Report::get_GOE_relaxed_report(), protocols::vip::VIP_Report::get_GOE_repack_report(), protocols::antibody::get_LoopCentral_ScoreFxn(), protocols::helix_capper::HelixNCapperMover::get_Ncap_scores(), protocols::rna::denovo::get_rna_hires_scorefxn(), core::scoring::get_score_function(), core::scoring::get_score_function_legacy(), core::pose::rna::get_scored_base_stack_list(), protocols::ligand_docking::ga_ligand_dock::GridScorer::GridScorer(), protocols::rbsegment_relax::IdealizeHelicesMover::IdealizeHelicesMover(), protocols::tcr::ind_remodel_tcr_cdr_loops(), protocols::hybridization::MRMover::init(), protocols::seeded_abinitio::SegmentHybridizer::init(), protocols::hybridization::CartesianSampler::init(), protocols::hybridization::CartesianHybridize::init(), protocols::hybridization::BackboneTorsionPerturbation::init(), protocols::hybridization::BackboneTorsionSampler::init(), protocols::hybridization::HybridizeProtocol::init(), protocols::hybridization::FoldTreeHybridize::init(), protocols::antibody::RefineBetaBarrel::init(), protocols::docking::DockingLowRes::init(), protocols::docking::DockingProtocol::init(), protocols::docking::TemperedDocking::init_from_options(), protocols::abinitio::IterativeFullatom::initialize(), protocols::dna::DnaInterfaceMultiStateDesign::initialize(), protocols::abinitio::IterativeBase::initialize(), protocols::rosetta_scripts::RosettaScriptsParser::initialize_data_map(), protocols::canonical_sampling::HamiltonianExchange::initialize_from_file(), protocols::rna::movers::ErraserMinimizerMover::initialize_from_options(), protocols::rna::denovo::RNA_FragmentMonteCarlo::initialize_score_functions(), protocols::rna::denovo::RNA_DeNovoProtocol::initialize_scorefxn(), protocols::ligand_docking::LigandBaseProtocol::LigandBaseProtocol(), protocols::loop_grower::LoopGrower::LoopGrower(), protocols::rna::denovo::movers::RNA_Relaxer::lores_monte_carlo(), protocols::forge::remodel::RemodelLigandHandler::minimize(), protocols::antibody::design::GeneralAntibodyModeler::minimize_cdrs(), protocols::vip::VIP_Mover::minimize_conformation(), protocols::ub_e2c::ubi_e2c_modeler::monoub_calc_interaction_energy(), core::pack::optimize_H_and_notify(), protocols::rbsegment_relax::OptimizeThreadingMover::OptimizeThreadingMover(), protocols::pose_reporters::EnergyReporter::parse_my_tag(), protocols::abinitio::abscript::AbscriptLoopCloserCM::parse_my_tag(), protocols::rna::movers::ErraserMinimizerMover::parse_my_tag(), protocols::relax::membrane::MPRangeRelaxMover::parse_my_tag(), protocols::docking::membrane::MPDockingMover::parse_my_tag(), protocols::RBSegmentRelaxImpl::RBSegmentRelaxImpl(), protocols::vip::VIP_Mover::relax_favorable_poses(), protocols::tcr::remodel_tcr_cdr_loops(), protocols::forge::remodel::RemodelMover::RemodelMover(), protocols::antibody_legacy::AntibodyModeler::repulsive_ramp(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::rescore_all_decoys(), protocols::abinitio::IterativeBase::rescore_nonlocal_archive(), protocols::rna::movers::RNA_DeNovoOptimizer::RNA_DeNovoOptimizer(), protocols::mpi_refinement::WorkUnit_bbGauss::run(), protocols::hybridization::DomainAssembly::run(), protocols::mpi_refinement::WorkUnit_NormalMode::run(), protocols::mpi_refinement::WorkUnit_RamaPerturber::run(), protocols::docking::SlideIntoContact::scorefunction(), protocols::simple_moves::ScoreMover::ScoreMover(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::search_rigid_body_orientation(), protocols::enzdes::SecondaryMatchProtocol::SecondaryMatchProtocol(), protocols::relax::CentroidRelax::set_cartesian(), protocols::mpi_refinement::StructAvrgMover::set_default(), protocols::ub_e2c::ubi_e2c_modeler::set_default(), protocols::simple_moves::CombinePoseMover::set_default(), protocols::antibody::LHRepulsiveRampLegacy::set_default(), protocols::abinitio::ClassicAbinitio::set_default_scores(), protocols::abinitio::MembraneAbinitio::set_default_scores(), protocols::abinitio::FragmentSampler::set_default_scores(), protocols::membrane::MPQuickRelaxMover::set_defaults(), protocols::relax::membrane::MPRangeRelaxMover::set_defaults(), protocols::mpi_refinement::MultiObjective::set_defaults(), protocols::docking::membrane::MPDockingMover::set_defaults(), protocols::antibody::snugdock::SnugDockProtocol::setup_loop_refinement_movers(), protocols::antibody::snugdock::SnugDock::setup_objects(), protocols::antibody::AntibodyModelerProtocol::setup_objects(), protocols::abinitio::abscript::setup_score(), protocols::star::setup_score(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::setup_score(), protocols::antibody_legacy::AntibodyModeler::snugfit_mcm_protocol(), protocols::vip::VIP_Mover::sort_fill_energies(), protocols::star::StarAbinitio::StarAbinitio(), protocols::symmetry::SymDockingSlideIntoContact::SymDockingSlideIntoContact(), protocols::symmetric_docking::SymFoldandDockRbTrialMover::SymFoldandDockRbTrialMover(), protocols::symmetry::SymmetrySlider::SymmetrySlider(), and protocols::vip::VIP_Mover::try_point_mutants().

ScoreFunctionOP core::scoring::ScoreFunctionFactory::create_score_function ( utility::options::OptionCollection const &  options,
std::string const &  weights_tag 
)
static
ScoreFunctionOP core::scoring::ScoreFunctionFactory::create_score_function ( std::string const &  weights_tag,
std::string const &  patch_tag 
)
static

Returns a ScoreFunction from the database weights file <weights_tag> with the patch <patch_tag>

example(s): See also: ScoreFunction ScoreFunction.show ScoreFunction.weights ScoreType

References create_score_function().

ScoreFunctionOP core::scoring::ScoreFunctionFactory::create_score_function ( utility::options::OptionCollection const &  options,
std::string const &  weights_tag,
std::string const &  patch_tag 
)
static
ScoreFunctionOP core::scoring::ScoreFunctionFactory::create_score_function ( std::string const &  weights_tag,
utility::vector1< std::string > const &  patch_tags 
)
static

Returns a ScoreFunction from the database weights file <weights_tag> with patches in <patch_tags>

References create_score_function().

ScoreFunctionOP core::scoring::ScoreFunctionFactory::create_score_function ( utility::options::OptionCollection const &  options,
std::string const &  weights_tag,
utility::vector1< std::string > const &  patch_tags 
)
static
void core::scoring::ScoreFunctionFactory::list_read_options ( utility::options::OptionKeyList &  opts)
static
void core::scoring::ScoreFunctionFactory::load_weights_file ( std::string  weights_tag,
ScoreFunctionOP  scorefxn 
)
staticprivate

Referenced by create_score_function().

bool core::scoring::ScoreFunctionFactory::validate_beta ( std::string const &  weights_tag,
utility::options::OptionCollection const &  options 
)
static

checks if the weights file is probably a beta_15 weights file and if it is consistent with the options system. static because C++ says it has to be; public because unit test spiritually const but you can't do that with static

If requested tag is beta_nov15 or beta_july15, but the user did not pass the relevant options-system option, ERROR! This is because this scorefunction family has overrides to parameters (LK solvation params, etc). Those are loaded from the command-line flag, not the weights file. Using only the weights file will give you mismatched weights/params and much sadness.

References core::scoring::BETA_GENPOT, core::scoring::BETA_JULY15, core::scoring::BETA_NOV16, and core::scoring::TR().

Referenced by create_score_function().

bool core::scoring::ScoreFunctionFactory::validate_talaris ( std::string const &  weights_tag,
utility::options::OptionCollection const &  options 
)
static

checks if the weights file is probably a talaris weights file and if it is consistent with the options system. static because C++ says it has to be; public because unit test spiritually const but you can't do that with static

If requested tag is talaris2013/talaris2014, but the user did not pass the relevant options-system option, ERROR! This is because this scorefunction family has overrides to parameters (LK solvation params, etc). Those are loaded from the command-line flag, not the weights file. Using only the weights file will give you mismatched weights/params and much sadness.

References core::scoring::TALARIS_2013, core::scoring::TALARIS_2014, and core::scoring::TR().

Referenced by create_score_function().


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