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Rosetta
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A vector for storing energy data, initially all values are 0. More...
#include <EnergyMap.hh>
Public Types | |
| using | const_iterator = MemberType::const_iterator |
| using | iterator = MemberType::iterator |
Public Member Functions | |
| EMapVector () | |
| default constructor, initializes the energies to 0 More... | |
| const_iterator | begin () const |
| const-iterator to the begining of the vector of energies More... | |
| const_iterator | end () const |
| const-iterator to the end of the vector of energies More... | |
| iterator | begin () |
| non-const-iterator to the begining of the vector of energies More... | |
| iterator | end () |
| non-const-iterator to the end of the vector of energies More... | |
| Real | get (ScoreType st) const |
| Returns the value for ScoreType <st> More... | |
| Real | set (ScoreType st, Real val) |
| Sets the value for ScoreType <st> to <val> More... | |
| Real & | operator[] (ScoreType st) |
| [] operator for getting a non-const reference to the energy for a ScoreType More... | |
| Real | operator[] (ScoreType st) const |
| [] operator for getting the value for a ScoreType More... | |
| void | zero (ScoreTypes const &l) |
| Zero a subset of the positions, as in calibrating a scale. More... | |
| void | zero () |
| Set every value to zero. More... | |
| void | clear () |
| Set every value to zero. More... | |
| Real | dot (EMapVector const &src) const |
| Returns the dot product of this object with EMapVector <src> More... | |
| Real | dot (EMapVector const &src, ScoreTypes const &l) const |
| dot product of two EMapVectors over a subset of the score types More... | |
| EMapVector & | operator+= (EMapVector const &src) |
| += operator, for summing energies More... | |
| EMapVector & | operator-= (EMapVector const &src) |
| -= operator, for subtracting energies More... | |
| EMapVector & | operator*= (Real scalar) |
| *= operator, for performing multiplication of a vector by a scalar More... | |
| EMapVector & | operator*= (EMapVector const &src) |
| *= operator, for performing element-by-element multiplication of two vectors More... | |
| EMapVector | operator* (Real scalar) const |
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| EMapVector | operator* (EMapVector const &src) const |
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| bool | operator== (EMapVector const &src) const |
| == operator for comparing two energy maps element by element More... | |
| bool | operator!= (EMapVector const &src) const |
| != operator for comparing two energy maps element by element More... | |
| void | print () const |
| print the contents of an emap vector to standard out More... | |
| void | accumulate (EMapVector const &src, ScoreTypes const &l) |
| accumulate a subset of the positions More... | |
| void | accumulate (EMapVector const &src, ScoreTypes const &l, Real const wt) |
| accumulate a subset of the positions with a common weight factor More... | |
| Real | sum () const |
| Returns the sum of this vector. More... | |
| Real | norm_squared (ScoreTypes const &l) const |
| accumulate the squared values of a subset of the positions More... | |
| bool | is_finite () const |
| Check that there aren't any non-finite (inf, NaN) entries. More... | |
| void | show_nonzero (std::ostream &out) const |
| Prints the non-zero positions of the energy map. More... | |
| std::string | show_nonzero () const |
| convert the non-zero positions of the energy map to a string More... | |
| void | show_if_nonzero_weight (std::ostream &out, EMapVector const &weights) const |
| write the energies in this energy map to the output stream for those score types that have non-zero values in the "weights" energy map. More... | |
| void | show_weighted (std::ostream &out, EMapVector const &weights) const |
| write the weighted energies in this energy map to the output stream for those score types that have non-zero values in the "weights" energy map. More... | |
| std::string | weighted_string_of (EMapVector const &weights) const |
| convert the weighted energies in this energy map to a string for those score types that have non-zero values in the "weights" energy map. More... | |
Private Types | |
| using | MemberType = std::array< Real, n_score_types > |
Private Attributes | |
| MemberType | map_ |
| Grant access to private data to the TwoBodyEMapVector. More... | |
A vector for storing energy data, initially all values are 0.
Common Methods: EMapVector.zero
| using core::scoring::EMapVector::const_iterator = MemberType::const_iterator |
| using core::scoring::EMapVector::iterator = MemberType::iterator |
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default constructor, initializes the energies to 0
References clear().
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accumulate a subset of the positions
References operator[]().
Referenced by core::optimization::activate_dof_deriv_terms_for_cart_min(), core::scoring::ScoreFunction::asym_eval_twobody_neighbor_energies(), core::scoring::eval_weighted_res_onebody_energies_for_minnode(), core::scoring::eval_weighted_res_pair_energy_for_minedge(), core::scoring::ScoreFunction::get_sub_score(), core::scoring::ScoreFunction::setup_for_minimizing_for_node(), and core::scoring::ScoreFunction::sym_eval_twobody_neighbor_energies().
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accumulate a subset of the positions with a common weight factor
References operator[]().
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non-const-iterator to the begining of the vector of energies
References map_.
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const-iterator to the begining of the vector of energies
References map_.
Referenced by protocols::moves::MCShowMover::apply(), core::scoring::ScoreFunction::check_methods(), core::io::silent::SilentStruct::energies_from_pose(), protocols::rpc::pose_energies_to_json(), and core::scoring::Energies::show().
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Set every value to zero.
example(s): emap.zero() See also: EMapVector EMapVector.get EMapVector.set ScoreFunction create_score_function
References map_.
Referenced by core::scoring::ScoreFunction::asym_eval_onebody_energies(), core::scoring::Energies::clear_energies(), protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::clear_energies(), protocols::enzdes::EnzdesBaseProtocol::disable_constraint_scoreterms(), EMapVector(), protocols::hotspot_hashing::HotspotStubSet::evaluate_stub_bumps_(), protocols::hotspot_hashing::HotspotStubSet::evaluate_stub_self_energy_(), protocols::helix_capper::HelixNCapperMover::get_Ncap_scores(), protocols::features::ResidueScoresFeatures::insert_one_body_residue_score_rows(), protocols::features::ResidueScoresFeatures::insert_two_body_residue_score_rows(), protocols::constel::NeighTeller::isneigh(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::master_go(), protocols::ligand_docking::rdf::RDFOrbitalFunction::operator()(), core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::recompute(), core::scoring::ScoreFunction::reset(), core::scoring::Energies::scoring_begin(), core::scoring::Energies::set_size(), core::scoring::ScoreFunction::sym_eval_onebody_energies(), and zero().
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Returns the dot product of this object with EMapVector <src>
example(s): we = scorefxn.weights() emap.dot(we) See also: EMapVector ScoreFunction ScoreFunction.weights create_score_function
References map_, core::scoring::n_score_types, and protocols::analysis::total.
Referenced by core::scoring::Energies::accumulate_residue_total_energy(), protocols::protein_interface_design::movers::DockWithHotspotMover::apply(), protocols::flexpack::rotamer_set::FlexbbRotamerSet::bump_check(), protocols::nmr::bump_check(), core::pack::rotamer_set::bump_check(), core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(), core::pack::rotamer_set::RotamerSet_::bump_check(), core::simple_metrics::metrics::InteractionEnergyMetric::calculate(), protocols::pack_daemon::PackDaemon::calculate_background_energies(), core::pack::compare_mingraph_and_energy_graph(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), protocols::sasa_scores::compute_avge_scores(), protocols::coupled_moves::CoupledMovesProtocol::compute_ligand_score_bonus(), core::pack::rotamer_set::RotamerSet_::compute_one_and_two_body_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energies(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), protocols::match::downstream::ScoringSecMatchRPE::eval_cd_2b_residues(), core::energy_methods::PairEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::ShortRangeTwoBodyEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_intrares_energies(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::evaluate_rotamer_intrares_energies(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_pair_energies(), core::scoring::methods::ShortRangeTwoBodyEnergy::evaluate_rotamer_pair_energies(), protocols::hotspot_hashing::HotspotStubSet::evaluate_stub_self_energy_(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::pack::rotamer_set::RotamerSets::get_bb_bbE(), protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::get_res_res_score(), core::pack::rotamer_set::RotamerSets::get_sc_bbE(), protocols::score_filters::ScoreCutoffFilter::get_score(), core::scoring::ScoreFunction::get_sub_score(), protocols::hbnet::hbnet_one_body_energies(), protocols::hbnet::hbnet_symm_one_body_energies(), core::pack::scmin::CartSCMinMultifunc::operator()(), core::pack::scmin::SCMinMultifunc::operator()(), core::optimization::SingleResidueMultifunc::operator()(), core::scoring::ScoreFunction::operator()(), core::scoring::DockingScoreFunction::operator()(), core::scoring::MinScoreScoreFunction::operator()(), core::pack::interaction_graph::LinearMemNode::project_deltaE_for_substitution(), core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::recompute(), core::energy_methods::SplitUnfoldedTwoBodyEnergy::residue_energy(), core::energy_methods::UnfoldedStateEnergy::residue_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score(), core::scoring::constraints::Constraint::score(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), core::scoring::ScoreFunction::weighted_sum(), protocols::pose_metric_calculators::EnergiesData::weighted_total(), and protocols::pose_metric_calculators::EnergiesData::weighted_total_no_master().
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dot product of two EMapVectors over a subset of the score types
References operator[](), and protocols::analysis::total.
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non-const-iterator to the end of the vector of energies
References map_.
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const-iterator to the end of the vector of energies
References map_.
Referenced by protocols::moves::MCShowMover::apply(), core::scoring::ScoreFunction::check_methods(), core::io::silent::SilentStruct::energies_from_pose(), protocols::rpc::pose_energies_to_json(), core::scoring::Energies::show(), and protocols::ddg::ddGMover::store_energies().
Returns the value for ScoreType <st>
example(s): emap.get(fa_sol) See also: EMapVector EMapVector.set ScoreFunction create_score_function
Referenced by protocols::simple_moves::DisulfideInsertionMover::apply(), core::scoring::SplitUnfoldedTwoBodyPotential::calculate_residue_emap(), protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide(), core::scoring::inline_residue_atom_pair_energy(), core::scoring::DockingScoreFunction::operator()(), core::scoring::MinScoreScoreFunction::operator()(), core::scoring::ScoreFunction::reset_energy_methods(), and protocols::hbnet::HBNet::score_network_on_pose().
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Check that there aren't any non-finite (inf, NaN) entries.
References map_, and protocols::hybridization::val.
Referenced by core::energy_methods::LoopCloseEnergy::finalize_total_energy(), core::energy_methods::RNA_FA_ElecEnergy::finalize_total_energy(), core::scoring::ScoreFunction::operator()(), core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy(), and core::energy_methods::RNA_SuiteEnergy::residue_pair_energy().
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accumulate the squared values of a subset of the positions
References protocols::analysis::total, and protocols::hybridization::val.
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!= operator for comparing two energy maps element by element
References map_.
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*= operator, for performing element-by-element multiplication of two vectors
References map_, and core::scoring::n_score_types.
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*= operator, for performing multiplication of a vector by a scalar
References map_.
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+= operator, for summing energies
References map_, and core::scoring::n_score_types.
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-= operator, for subtracting energies
References map_, and core::scoring::n_score_types.
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== operator for comparing two energy maps element by element
References map_.
[] operator for getting a non-const reference to the energy for a ScoreType
References map_, and core::scoring::n_score_types.
Referenced by accumulate(), dot(), and zero().
[] operator for getting the value for a ScoreType
References map_, and core::scoring::n_score_types.
| void core::scoring::EMapVector::print | ( | ) | const |
print the contents of an emap vector to standard out
References map_, core::scoring::n_score_types, and core::scoring::name_from_score_type().
Sets the value for ScoreType <st> to <val>
example(s): emap.set(fa_sol,13.37) See also: EMapVector EMapVector.get ScoreFunction create_score_function
References protocols::hybridization::val.
Referenced by core::scoring::SplitUnfoldedTwoBodyPotential::calculate_residue_emap(), core::scoring::ScoreFunction::extract_weights_from_stream(), and core::scoring::inline_residue_atom_pair_energy().
| void core::scoring::EMapVector::show_if_nonzero_weight | ( | std::ostream & | out, |
| EMapVector const & | weights | ||
| ) | const |
write the energies in this energy map to the output stream for those score types that have non-zero values in the "weights" energy map.
References core::chemical::element::F, core::scoring::n_score_types, core::conformation::membrane::out, and protocols::hybridization::val.
Referenced by core::pack::compare_mingraph_and_energy_graph(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), and protocols::moves::MonteCarlo::score_function().
| std::string core::scoring::EMapVector::show_nonzero | ( | ) | const |
convert the non-zero positions of the energy map to a string
| void core::scoring::EMapVector::show_nonzero | ( | std::ostream & | out | ) | const |
Prints the non-zero positions of the energy map.
Set every value to zero
example(s): emap.show_nonzero() See also: EMapVector EMapVector.get ScoreFunction create_score_function
References core::scoring::n_score_types, core::conformation::membrane::out, and protocols::hybridization::val.
Referenced by protocols::flexpack::FlexPacker::apply(), protocols::optimize_weights::IterativeOptEDriver::decide_if_sequence_recovery_improved(), core::pose::Pose::dump_scored_pdb(), core::pack::interaction_graph::LinearMemNode::project_deltaE_for_substitution(), and core::energy_methods::UnfoldedStateEnergy::UnfoldedStateEnergy().
| void core::scoring::EMapVector::show_weighted | ( | std::ostream & | out, |
| EMapVector const & | weights | ||
| ) | const |
write the weighted energies in this energy map to the output stream for those score types that have non-zero values in the "weights" energy map.
References core::chemical::element::F, core::scoring::n_score_types, core::conformation::membrane::out, and protocols::hybridization::val.
Referenced by protocols::flexpack::FlexPacker::apply(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::pack::min_pack_optimize(), and weighted_string_of().
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Returns the sum of this vector.
example(s): emap.sum() See also: EMapVector EMapVector.get EMapVector.set ScoreFunction create_score_function
References map_, and protocols::analysis::total.
Referenced by core::scoring::get_pairwise_atom_energies(), protocols::score_filters::ScoreCutoffFilter::get_score(), core::scoring::get_single_atom_energies(), protocols::protein_interface_design::hbonded(), protocols::protein_interface_design::hbonded_atom(), protocols::score_filters::ScoreCutoffFilter::report(), and protocols::simple_moves::PeriodicBoxMover::report_thermodynamics().
| std::string core::scoring::EMapVector::weighted_string_of | ( | EMapVector const & | weights | ) | const |
convert the weighted energies in this energy map to a string for those score types that have non-zero values in the "weights" energy map.
References show_weighted().
Referenced by protocols::ddg::ddGMover::apply(), protocols::unfolded_state_energy_calculator::calc_all_averages(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_five(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_four(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_one(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_three(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_two(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_zero(), core::pose::Pose::dump_scored_pdb(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), and protocols::ddg::ddGMover::relax_wildtype_structure().
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Set every value to zero.
example(s): emap.zero() See also: EMapVector EMapVector.get EMapVector.set ScoreFunction create_score_function
References clear().
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Zero a subset of the positions, as in calibrating a scale.
References operator[]().
Referenced by core::scoring::ScoreFunction::asym_eval_onebody_energies(), core::scoring::ScoreFunction::asym_eval_twobody_neighbor_energies(), core::scoring::Energies::clear(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), core::scoring::eval_weighted_res_onebody_energies_for_minnode(), core::scoring::eval_weighted_res_pair_energy_for_minedge(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::ShortRangeTwoBodyEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::ShortRangeTwoBodyEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_pair_energies(), core::scoring::methods::ShortRangeTwoBodyEnergy::evaluate_rotamer_pair_energies(), protocols::optimize_weights::IterativeOptEDriver::free_weights_and_refEs_from_vars(), protocols::protein_interface_design::hbonded(), protocols::protein_interface_design::hbonded_atom(), protocols::features::ResidueScoresFeatures::insert_two_body_long_range_residue_score_rows(), core::pack::interaction_graph::LinearMemNode::project_deltaE_for_substitution(), core::scoring::constraints::AmbiguousConstraint::score(), core::scoring::Energies::scoring_begin(), core::scoring::ScoreFunction::sym_eval_onebody_energies(), and core::scoring::ScoreFunction::sym_eval_twobody_neighbor_energies().
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Grant access to private data to the TwoBodyEMapVector.
EMapVector is an array. EMapVector[score_type] = value. Can be used for storing either energy or weight for each score_type.
Referenced by begin(), clear(), dot(), end(), is_finite(), operator!=(), operator*=(), operator+=(), operator-=(), operator==(), operator[](), print(), and sum().
1.9.1