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Rosetta 3.5
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Rosetta 3.5
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This object defines a ScoreFunction, it contains methods for calculating the various scoring components (called ScoreType's) used in Rosetta. It also contains weights that are applied to each of those components. Only scoring components with non-zero weights are calculated. More...
#include <ScoreFunction.hh>
Public Member Functions | |
| ScoreFunction () | |
| ctor More... | |
| virtual | ~ScoreFunction () |
| ScoreFunction & | operator= (ScoreFunction const &) |
| ScoreFunction (ScoreFunction const &) | |
| virtual ScoreFunctionOP | clone () const |
| void | reset () |
| Resets the ScoreFunction to default values. More... | |
| void | perturb_weights () |
| Randomly perturbs non-zero score function weights. More... | |
| std::string | serialize_weights () const |
| Serializes the non-zero score function term weights Format: { term : weight, ... }. More... | |
| void | add_weights_from_file (std::string const &filename) |
| Initializes this ScoreFunction from the given <filename> More... | |
| void | _add_weights_from_file (std::string const &filename, bool patch=false) |
| Initializes this ScoreFunction from the given <filename> no lookup in database directory. More... | |
| void | initialize_from_file (std::string const &filename) |
| Resets everything before reading the <filename> More... | |
| void | apply_patch_from_file (std::string const &filename) |
| Applies a patch from the given <filename> More... | |
| void | set_etable (std::string const &etable_name) |
| Given a <filename> (represented by a std::string), set the e_table for this ScoreFunction. More... | |
| void | set_method_weights (ScoreType const &t, utility::vector1< Real > const &wts) |
| methods::EnergyMethodOptions const & | energy_method_options () const |
| Returns the EnergyMethodOptions object contained in this ScoreFunction (const access) More... | |
| void | set_energy_method_options (methods::EnergyMethodOptions const &energy_method_options_in) |
| Returns the EnergyMethodOptions object contained in this ScoreFunction. More... | |
| void | reset_energy_methods () |
| virtual Real | operator() (pose::Pose &pose) const |
| Scores the given <pose> using this ScoreFunction. Alters the Energies object within <pose>, but does not alter this ScoreFunction. More... | |
| virtual Real | score (pose::Pose &pose) const |
| Scores the given <pose> using this ScoreFunction. Alters the Energies object within <pose>, but does not alter this ScoreFunction. More... | |
| ScoreFunctionInfoOP | info () const |
| Score the structure and store the component energies in the EnergyGraph without requiring a second evaluation of the short-ranged two body energies. Note: pose copy operations do not copy the EnergyGraph, so cloning or copying a pose that has had it's components scored will not copy over the component energies. More... | |
| Distance | max_atomic_interaction_cutoff () const |
| void | indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const |
| find which context graphs the energy methods require More... | |
| bool | are_they_neighbors (pose::Pose const &pose, Size const pos1, Size const pos2) const |
| Determine if two residues could have non-zero interaction energy after possibly changing rotamers/chi. More... | |
| Real | operator[] (ScoreType const &t) const |
| Returns the weight of the ScoreType <t> More... | |
| EnergyMap const & | weights () const |
| Returns an EnergyMap of the current set of weights. More... | |
| bool | has_zero_weight (ScoreType const &t) const |
| Returns true if the ScoreType <t> has a weight of zero,. More... | |
| bool | has_nonzero_weight (ScoreType const &t) const |
| Returns true if the ScoreType <t> has a non-zero weight. More... | |
| ScoreTypes | get_nonzero_weighted_scoretypes () const |
| Returns a list of the ScoreTypes which are non-zero with their current weights. More... | |
| void | set_weight (ScoreType const &t, Real const &setting) |
| Sets the weight for ScoreType <t> to <setting> More... | |
| Real | get_weight (ScoreType const &t) const |
| Returns the weight for ScoreType <t> More... | |
| void | add_extra_method (ScoreType const &new_type, Real const new_weight, methods::EnergyMethod const &new_method) |
| Adds a scoring method that is not necessarily included in the core library. More... | |
| void | add_extra_method (std::map< ScoreType, Real > const &new_weights, methods::EnergyMethod const &new_method) |
| Adds a scoring method that is not necessarily included in the core library. More... | |
| virtual void | setup_for_minimizing (pose::Pose &pose, kinematics::MinimizerMapBase const &min_map) const |
| Initializes a MinimizationGraph and caches it in Energies object of <pose> More... | |
| virtual void | setup_for_minimizing_for_node (MinimizationNode &min_node, conformation::Residue const &rsd, kinematics::MinimizerMapBase const &min_map, pose::Pose &pose, bool accumulate_fixed_energies, EnergyMap &fixed_energies) const |
| Initialize a single node of a MinimizationGraph with the one-body and two-body energy methods that are held within this ScoreFunction object. More... | |
| void | reinitialize_minnode_for_residue (MinimizationNode &min_node, conformation::Residue const &rsd, kinematics::MinimizerMapBase const &min_map, pose::Pose &pose) const |
| void | setup_for_minimizing_sr2b_enmeths_for_minedge (conformation::Residue const &res1, conformation::Residue const &res2, MinimizationEdge &min_edge, kinematics::MinimizerMapBase const &min_map, pose::Pose &pose, bool const res_moving_wrt_eachother, bool accumulate_fixed_energies, EnergyEdge const *energy_edge, EnergyMap &fixed_energies, Real const edge_weight=1.0) const |
| Initialize a single MinimizationEdge for a particular part of residues, storing sr2b energy method pointers on the edge for those sr2b energy methods in this ScoreFunction. More... | |
| void | setup_for_lr2benmeth_minimization_for_respair (conformation::Residue const &res1, conformation::Residue const &res2, methods::LongRangeTwoBodyEnergyCOP lr2benergy, MinimizationGraph &g, kinematics::MinimizerMapBase const &min_map, pose::Pose &p, bool const res_moving_wrt_eachother, bool accumulate_fixed_energies, ResidueNeighborConstIteratorOP rni, EnergyMap &fixed_energies, Real const edge_weight=1.0) const |
| Initialize an edge in the MinimizationGraph with a particular long-range two body. More... | |
| void | setup_for_scoring (pose::Pose &pose) const |
| For external scorers: Let the energy methods prepare for evaluating their scores on a particular structure. More... | |
| void | setup_for_packing (pose::Pose &pose, utility::vector1< bool > const &residues_repacking, utility::vector1< bool > const &residues_designing) const |
| Lets the scoring functions cache anything they need to calculate energies in a packing step (rotamer_trials or pack_rotamers) More... | |
| void | prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &set) const |
| Lets the scoring functions cache anything they need to rapidly calculate rotamer pair energies used in packing (like a trie, e.g.) More... | |
| void | update_residue_for_packing (pose::Pose &pose, Size resid) const |
| If inside packing, the pose changes conformation, inform the scoring functions that any data they have cached in the Energies object is out of date. In particular, this is to update the trie(s) during rotamer trials. More... | |
| virtual void | setup_for_derivatives (pose::Pose &pose) const |
| virtual void | finalize_after_derivatives (pose::Pose &pose) const |
| core::Real | get_sub_score (pose::Pose const &pose, utility::vector1< bool > const &residue_mask) const |
| Compute the score for subset of residues. More... | |
| void | get_sub_score (pose::Pose const &pose, utility::vector1< bool > const &residue_mask, EnergyMap &emap) const |
| Compute the score for subset of residues. More... | |
| core::Real | get_sub_score (pose::Pose &pose, utility::vector1< bool > const &residue_mask) const |
| Compute the score for subset of residues. More... | |
| void | get_sub_score (pose::Pose &pose, utility::vector1< bool > const &residue_mask, EnergyMap &emap) const |
| Compute the score for subset of residues. More... | |
| core::Real | get_sub_score_exclude_res (pose::Pose const &pose, utility::vector1< core::Size > const &exclude_list) const |
| Compute the score for subset of residues. More... | |
| void | get_sub_score_exclude_res (pose::Pose const &pose, utility::vector1< core::Size > const &exclude_list, EnergyMap &emap) const |
| Compute the score for subset of residues. More... | |
| core::Real | get_sub_score_exclude_res (pose::Pose &pose, utility::vector1< core::Size > const &exclude_list) const |
| Compute the score for subset of residues. More... | |
| void | get_sub_score_exclude_res (pose::Pose &pose, utility::vector1< core::Size > const &exclude_list, EnergyMap &emap) const |
| Compute the score for subset of residues. More... | |
| virtual void | eval_twobody_neighbor_energies (pose::Pose &pose) const |
| virtual void | eval_long_range_twobody_energies (pose::Pose &pose) const |
| AllMethodsIterator | all_energies_begin () const |
| AllMethodsIterator | all_energies_end () const |
| LR_2B_MethodIterator | long_range_energies_begin () const |
| LR_2B_MethodIterator | long_range_energies_end () const |
| TWO_B_MethodIterator | ci_2b_intrares_begin () const |
| TWO_B_MethodIterator | ci_2b_intrares_end () const |
| TWO_B_MethodIterator | cd_2b_intrares_begin () const |
| TWO_B_MethodIterator | cd_2b_intrares_end () const |
| CI_2B_Methods::const_iterator | ci_2b_begin () const |
| CI_2B_Methods::const_iterator | ci_2b_end () const |
| CD_2B_Methods::const_iterator | cd_2b_begin () const |
| CD_2B_Methods::const_iterator | cd_2b_end () const |
| CI_LR_2B_MethodIterator | ci_lr_2b_methods_begin () const |
| CI_LR_2B_MethodIterator | ci_lr_2b_methods_end () const |
| CD_LR_2B_MethodIterator | cd_lr_2b_methods_begin () const |
| CD_LR_2B_MethodIterator | cd_lr_2b_methods_end () const |
| WS_MethodIterator | ws_methods_begin () const |
| WS_MethodIterator | ws_methods_end () const |
| virtual void | eval_onebody_energies (pose::Pose &pose) const |
| void | show (std::ostream &out) const |
| void | merge (const ScoreFunction scorefxn_to_be_merged) |
| Merges in the weights of another score function. More... | |
| void | show (std::ostream &out, pose::Pose &pose) const |
| Scores <pose> and shows the raw and weighted scores for each non-zero ScoreType. More... | |
| void | show_pretty (std::ostream &out) const |
| similar output as show( ostream, pose ) but without the pose More... | |
| void | show (pose::Pose &pose) const |
| Scores <pose> and shows the raw and weighted scores for each non-zero ScoreType. More... | |
| void | show_line_headers (std::ostream &out) const |
| void | show_line (std::ostream &out, pose::Pose const &pose) const |
| void | name (std::string const &weights_tag) |
| Accumulates the unweighted one body energies of all context independent one body energies for <pose> Residue <rsd> into EnergyMap <emap> More... | |
| std::string | get_name () const |
| void | eval_ci_1b (conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const |
| virtual void | eval_cd_1b (conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const |
| Accumulates the unweighted one body energies of all context dependent one body energies for <pose> Residue <rsd> into EnergyMap <emap> More... | |
| void | eval_ci_2b (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const |
| Accumulates the unweighted context independent two body interaction energies of <pose> between Residue <rsd1> and Residue <rsd2> into EnergyMap <emap> More... | |
| void | eval_ci_2b_bb_bb (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const |
| Accumulates the unweighted context independent two body interaction energies of <pose> between the backbones of Residue <rsd1> and Residue <rsd2> into EnergyMap <emap> More... | |
| void | eval_ci_2b_bb_sc (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const |
| Accumulates the unweighted short range context independent two body interaction energies of <pose> between the backbone of Residue <rsd1> and the sidechain of Residue <rsd2> into EnergyMap <emap> More... | |
| void | eval_ci_2b_sc_sc (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const |
| Accumulates the unweighted short range context dependent two body interaction energies of <pose> between the sidechains of Residue <rsd1> and Residue <rsd2> into Energymap <emap> More... | |
| virtual void | eval_cd_2b (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const |
| Accumulate the unweighted short range context dependent two body interaction energies of <pose> between Residue <rsd1> and Residue <rsd2> into EnergyMap <emap> More... | |
| void | eval_cd_2b_bb_bb (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const |
| Accumulates the unweighted short ranged context dependent two body interaction energies of <pose> between the backbones of Residue <rsd1> and <rsd2> into EnergyMap <emap> More... | |
| void | eval_cd_2b_bb_sc (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const |
| Accumulates the unweighted short ranged context dependent two body interaction energies of <pose> between the backbone of Residue <rsd1> and the sidechain of Residue <rsd2> into EnergyMap <emap> More... | |
| void | eval_cd_2b_sc_sc (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const |
| Accumulates the unweighted short ranged context dependent two body interaction energies of <pose> between the sidechains of Residue <rsd1> and Residue <rsd2> into EnergyMap <emap> More... | |
| void | eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const |
| Accumulates for rsd the unweighted intra-residue one body energies for all context dependent and context independent two body terms that define intra-residue energies. More... | |
| void | eval_ci_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const |
| Accumulates the unweighted intra-residue one body energies for all context independent two body terms that define intra-residue energies of <pose> Residue <rsd> into EnergyMap <emap> More... | |
| virtual void | eval_cd_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const |
| Accumulates the unweighted intra-residue one body energies for all context dependent two body terms that define intra-residue energies of <pose> Residue <rsd> into EnergyMap <emap> More... | |
| void | bump_check_full (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const |
| score the sidechain from rsd1 against the entirety of rsd2 More... | |
| void | bump_check_backbone (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const |
| Scores the sidechain from <pose> Residue <rsd1> against the backbone of Residue <rsd2> More... | |
| void | evaluate_rotamer_intrares_energies (conformation::RotamerSetBase const &set, pose::Pose const &pose, utility::vector1< core::PackerEnergy > &energies) const |
| void | evaluate_rotamer_intrares_energy_maps (conformation::RotamerSetBase const &set, pose::Pose const &pose, utility::vector1< EnergyMap > &emaps) const |
| void | evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const |
| void | evaluate_rotamer_background_energies (conformation::RotamerSetBase const &set1, conformation::Residue const &residue2, pose::Pose const &pose, utility::vector1< core::PackerEnergy > &energy_vector) const |
| bool | any_lr_residue_pair_energy (pose::Pose const &pose, Size res1, Size res2) const |
| virtual void | eval_npd_atom_derivative (id::AtomID const &atom_id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, Vector &F1, Vector &F2) const |
| Real | eval_dof_derivative (id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, pose::Pose const &pose) const |
| ScoreTypes const & | score_types_by_method_type (methods::EnergyMethodType const &t) const |
| ScoreTypes const & | ci_1b_types () const |
| convenience access to all ci 1b score types More... | |
| ScoreTypes const & | cd_1b_types () const |
| convenience access to all cd 1b score types More... | |
| ScoreTypes const & | ci_2b_types () const |
| convenience access to all ci 2b score types More... | |
| ScoreTypes const & | cd_2b_types () const |
| convenience access to all cd 2b score types More... | |
| ScoreTypes const & | ci_lr_2b_types () const |
| ScoreTypes const & | cd_lr_2b_types () const |
| ScoreTypes const & | whole_structure_types () const |
| AllMethods const & | all_methods () const |
Protected Member Functions | |
| bool | any_intrares_energies () const |
Private Member Functions | |
| void | add_method (methods::EnergyMethodOP method) |
| void | remove_method (methods::EnergyMethodOP method) |
| bool | check_methods () const |
| private More... | |
| void | initialize_methods_arrays () |
| sets up the derived method vectors from the primary vectors More... | |
| void | update_intrares_energy_status () |
| check if any of the 2body methods define intra-residue energies, given our current weight set More... | |
Private Attributes | |
| std::string | name_ |
| the scorefxn name More... | |
| EnergyMap | weights_ |
| the scorefxn weights More... | |
| methods::EnergyMethodOptionsOP | energy_method_options_ |
| Options that control choice/configuration of EnergyMethods. eg etable name. More... | |
| CI_2B_Methods | ci_2b_methods_ |
| CD_2B_Methods | cd_2b_methods_ |
| CI_1B_Methods | ci_1b_methods_ |
| CD_1B_Methods | cd_1b_methods_ |
| CI_LR_2B_Methods | ci_lr_2b_methods_ |
| CD_LR_2B_Methods | cd_lr_2b_methods_ |
| LR_2B_Methods | lr_2b_methods_ |
| WS_Methods | ws_methods_ |
| AllMethods | all_methods_ |
| vector of COPs to all active methods More... | |
| AllMethods | methods_by_score_type_ |
| Map from ScoreType to the method for evaluating it. will be 0 for score_types without a method, ie ones with 0 weight. More... | |
| utility::vector1< ScoreTypes > | score_types_by_method_type_ |
| bool | score_function_info_current_ |
| ScoreFunctionInfoOP | score_function_info_ |
| bool | any_intrares_energies_ |
| TWO_B_Methods | ci_2b_intrares_ |
| TWO_B_Methods | cd_2b_intrares_ |
This object defines a ScoreFunction, it contains methods for calculating the various scoring components (called ScoreType's) used in Rosetta. It also contains weights that are applied to each of those components. Only scoring components with non-zero weights are calculated.
Definition at line 91 of file ScoreFunction.hh.
Definition at line 99 of file ScoreFunction.hh.
| typedef utility::vector1< methods::EnergyMethodCOP >::const_iterator core::scoring::ScoreFunction::AllMethodsIterator |
Definition at line 114 of file ScoreFunction.hh.
| typedef utility::vector1< methods::ContextDependentOneBodyEnergyOP > core::scoring::ScoreFunction::CD_1B_Methods |
Definition at line 104 of file ScoreFunction.hh.
| typedef utility::vector1< methods::ContextDependentTwoBodyEnergyOP > core::scoring::ScoreFunction::CD_2B_Methods |
Definition at line 102 of file ScoreFunction.hh.
| typedef utility::vector1< methods::ContextDependentLRTwoBodyEnergyOP >::const_iterator core::scoring::ScoreFunction::CD_LR_2B_MethodIterator |
Definition at line 116 of file ScoreFunction.hh.
| typedef utility::vector1< methods::ContextDependentLRTwoBodyEnergyOP > core::scoring::ScoreFunction::CD_LR_2B_Methods |
Definition at line 106 of file ScoreFunction.hh.
| typedef utility::vector1< methods::ContextIndependentOneBodyEnergyOP > core::scoring::ScoreFunction::CI_1B_Methods |
Definition at line 103 of file ScoreFunction.hh.
| typedef utility::vector1< methods::ContextIndependentTwoBodyEnergyOP > core::scoring::ScoreFunction::CI_2B_Methods |
Definition at line 101 of file ScoreFunction.hh.
| typedef utility::vector1< methods::ContextIndependentLRTwoBodyEnergyOP >::const_iterator core::scoring::ScoreFunction::CI_LR_2B_MethodIterator |
Definition at line 115 of file ScoreFunction.hh.
| typedef utility::vector1< methods::ContextIndependentLRTwoBodyEnergyOP > core::scoring::ScoreFunction::CI_LR_2B_Methods |
Definition at line 105 of file ScoreFunction.hh.
| typedef utility::vector1< methods::LongRangeTwoBodyEnergyCOP >::const_iterator core::scoring::ScoreFunction::LR_2B_MethodIterator |
Definition at line 112 of file ScoreFunction.hh.
| typedef utility::vector1< methods::LongRangeTwoBodyEnergyCOP > core::scoring::ScoreFunction::LR_2B_Methods |
Definition at line 107 of file ScoreFunction.hh.
| typedef utility::vector1< methods::TwoBodyEnergyOP >::const_iterator core::scoring::ScoreFunction::TWO_B_MethodIterator |
Definition at line 113 of file ScoreFunction.hh.
Definition at line 108 of file ScoreFunction.hh.
| typedef utility::vector1< methods::WholeStructureEnergyOP >::const_iterator core::scoring::ScoreFunction::WS_MethodIterator |
Definition at line 111 of file ScoreFunction.hh.
| typedef utility::vector1< methods::WholeStructureEnergyOP > core::scoring::ScoreFunction::WS_Methods |
Definition at line 109 of file ScoreFunction.hh.
| core::scoring::ScoreFunction::ScoreFunction | ( | ) |
ctor
Definition at line 102 of file ScoreFunction.cc.
|
virtual |
Definition at line 108 of file ScoreFunction.cc.
| core::scoring::ScoreFunction::ScoreFunction | ( | ScoreFunction const & | src) |
Definition at line 442 of file ScoreFunction.cc.
| void core::scoring::ScoreFunction::_add_weights_from_file | ( | std::string const & | filename, |
| bool | patch = false |
||
| ) |
Initializes this ScoreFunction from the given <filename> no lookup in database directory.
read weights/etc from file. Does not clear weights beforehand. no lookup in database directory
Definition at line 203 of file ScoreFunction.cc.
References tr().
| void core::scoring::ScoreFunction::add_extra_method | ( | ScoreType const & | new_type, |
| Real const | new_weight, | ||
| methods::EnergyMethod const & | new_method | ||
| ) |
Adds a scoring method that is not necessarily included in the core library.
Add a scoring method that's not necessarily included in the core library
Definition at line 2738 of file ScoreFunction.cc.
References add_method(), core::scoring::methods::EnergyMethod::clone(), core::scoring::methods::EnergyMethod::score_types(), and weights_.
| void core::scoring::ScoreFunction::add_extra_method | ( | std::map< ScoreType, Real > const & | new_weights, |
| methods::EnergyMethod const & | new_method | ||
| ) |
Adds a scoring method that is not necessarily included in the core library.
Add a scoring method that's not necessarily included in the core library
Definition at line 2758 of file ScoreFunction.cc.
References add_method(), core::scoring::methods::EnergyMethod::clone(), core::scoring::methods::EnergyMethod::score_types(), and weights_.
|
private |
private – handles setting the derived data
Definition at line 2673 of file ScoreFunction.cc.
References all_methods_, core::scoring::methods::cd_1b, cd_1b_methods_, core::scoring::methods::cd_2b, cd_2b_methods_, core::scoring::methods::cd_lr_2b, cd_lr_2b_methods_, core::scoring::methods::ci_1b, ci_1b_methods_, core::scoring::methods::ci_2b, ci_2b_methods_, core::scoring::methods::ci_lr_2b, ci_lr_2b_methods_, lr_2b_methods_, methods_by_score_type_, score_types_by_method_type_, core::scoring::methods::ws, and ws_methods_.
Referenced by add_extra_method(), and set_weight().
| void core::scoring::ScoreFunction::add_weights_from_file | ( | std::string const & | filename) |
Initializes this ScoreFunction from the given <filename>
read weights/etc from file, which may be in database directory. Does not clear weights beforehand.
Definition at line 193 of file ScoreFunction.cc.
References core::scoring::find_weights_file().
| ScoreFunction::AllMethodsIterator core::scoring::ScoreFunction::all_energies_begin | ( | ) | const |
Definition at line 1808 of file ScoreFunction.cc.
References all_methods_.
Referenced by core::optimization::SingleResidueMultifunc::operator()(), and core::scoring::symmetry::SymmetricScoreFunction::operator()().
| ScoreFunction::AllMethodsIterator core::scoring::ScoreFunction::all_energies_end | ( | ) | const |
Definition at line 1814 of file ScoreFunction.cc.
References all_methods_.
Referenced by core::optimization::SingleResidueMultifunc::operator()(), and core::scoring::symmetry::SymmetricScoreFunction::operator()().
| ScoreFunction::AllMethods const & core::scoring::ScoreFunction::all_methods | ( | ) | const |
Definition at line 2663 of file ScoreFunction.cc.
References all_methods_.
Referenced by core::pack::RTMin::rtmin(), and core::scoring::symmetry::SymmetricScoreFunction::setup_for_minimizing().
|
inlineprotected |
Definition at line 1016 of file ScoreFunction.hh.
References any_intrares_energies_.
Referenced by core::scoring::symmetry::SymmetricScoreFunction::eval_onebody_energies().
| bool core::scoring::ScoreFunction::any_lr_residue_pair_energy | ( | pose::Pose const & | pose, |
| Size | res1, | ||
| Size | res2 | ||
| ) | const |
Definition at line 1791 of file ScoreFunction.cc.
References lr_2b_methods_.
Referenced by are_they_neighbors(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::precompute_two_body_energies(), core::pack::rotamer_set::RotamerSets::precompute_two_body_energies(), and core::pack::rotamer_set::RotamerSets::prepare_otf_graph().
| void core::scoring::ScoreFunction::apply_patch_from_file | ( | std::string const & | filename) |
Applies a patch from the given <filename>
Definition at line 377 of file ScoreFunction.cc.
References core::scoring::find_weights_file().
Referenced by protocols::canonical_sampling::PatchOperation::apply().
| bool core::scoring::ScoreFunction::are_they_neighbors | ( | pose::Pose const & | pose, |
| Size const | pos1, | ||
| Size const | pos2 | ||
| ) | const |
Determine if two residues could have non-zero interaction energy after possibly changing rotamers/chi.
angles; uses any_lr_residue_pair_energy, combines with max_atomic_interaction_cutoff.
Determines whether two positions could have non-zero interaction energy
Definition at line 1773 of file ScoreFunction.cc.
References any_lr_residue_pair_energy(), max_atomic_interaction_cutoff(), and core::pose::Pose::residue().
| void core::scoring::ScoreFunction::bump_check_backbone | ( | conformation::Residue const & | rsd1, |
| conformation::Residue const & | rsd2, | ||
| pose::Pose const & | pose, | ||
| EnergyMap & | emap | ||
| ) | const |
Scores the sidechain from <pose> Residue <rsd1> against the backbone of Residue <rsd2>
low fidelity description of what it would be like to replace the sidechain of rsd1 at a particular position knowing that rsd2's sidechain might also change sychronously. only those scoring functions that specify they should be included in the bump check will be evaluated. The inaccuracy in this function is based on the change in LK solvation types and/or charges for backbone atoms when residues are mutated from one amino acid type to another (or from any other residue with backbone atoms)
Definition at line 1732 of file ScoreFunction.cc.
References cd_2b_methods_, and ci_2b_methods_.
Referenced by protocols::flexpack::rotamer_set::FlexbbRotamerSet::bump_check(), and core::pack::rotamer_set::RotamerSet_::bump_check().
| void core::scoring::ScoreFunction::bump_check_full | ( | conformation::Residue const & | rsd1, |
| conformation::Residue const & | rsd2, | ||
| pose::Pose const & | pose, | ||
| EnergyMap & | emap | ||
| ) | const |
score the sidechain from rsd1 against the entirety of rsd2
low fidelity description of what it would be like to replace the sidechain of rsd1 at a particular position – only those scoring functions that specify they should be included in the bump check will be evaluated. The inaccuracy in this function is based on the change in LK solvation types and/or charges for backbone atoms when residues are mutated from one amino acid type to another (or from any other residue with backbone atoms)
Definition at line 1704 of file ScoreFunction.cc.
References cd_2b_methods_, and ci_2b_methods_.
Referenced by protocols::flexpack::rotamer_set::FlexbbRotamerSet::bump_check(), and core::pack::rotamer_set::RotamerSet_::bump_check().
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inline |
convenience access to all cd 1b score types
Definition at line 943 of file ScoreFunction.hh.
References core::scoring::methods::cd_1b, and score_types_by_method_type_.
Referenced by core::scoring::symmetry::SymmetricScoreFunction::eval_onebody_energies(), eval_onebody_energies(), and get_sub_score().
| ScoreFunction::CD_2B_Methods::const_iterator core::scoring::ScoreFunction::cd_2b_begin | ( | ) | const |
Definition at line 1868 of file ScoreFunction.cc.
References cd_2b_methods_.
Referenced by core::scoring::eval_bbbb_sr2b_energies(), core::scoring::eval_bbsc_sr2b_energies(), and core::scoring::eval_scsc_sr2b_energies().
| ScoreFunction::CD_2B_Methods::const_iterator core::scoring::ScoreFunction::cd_2b_end | ( | ) | const |
Definition at line 1874 of file ScoreFunction.cc.
References cd_2b_methods_.
Referenced by core::scoring::eval_bbbb_sr2b_energies(), core::scoring::eval_bbsc_sr2b_energies(), and core::scoring::eval_scsc_sr2b_energies().
| ScoreFunction::TWO_B_MethodIterator core::scoring::ScoreFunction::cd_2b_intrares_begin | ( | ) | const |
Definition at line 1844 of file ScoreFunction.cc.
References cd_2b_intrares_.
| ScoreFunction::TWO_B_MethodIterator core::scoring::ScoreFunction::cd_2b_intrares_end | ( | ) | const |
Definition at line 1850 of file ScoreFunction.cc.
References cd_2b_intrares_.
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inline |
convenience access to all cd 2b score types
Definition at line 957 of file ScoreFunction.hh.
References core::scoring::methods::cd_2b, and score_types_by_method_type_.
Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy(), core::scoring::symmetry::SymmetricScoreFunction::eval_onebody_energies(), eval_onebody_energies(), core::scoring::symmetry::SymmetricScoreFunction::eval_twobody_neighbor_energies(), eval_twobody_neighbor_energies(), core::pack::interaction_graph::SimpleEdge::get_bb_E(), and get_sub_score().
| ScoreFunction::CD_LR_2B_MethodIterator core::scoring::ScoreFunction::cd_lr_2b_methods_begin | ( | ) | const |
Definition at line 1893 of file ScoreFunction.cc.
References cd_lr_2b_methods_.
Referenced by core::scoring::symmetry::SymmetricScoreFunction::eval_long_range_twobody_energies().
| ScoreFunction::CD_LR_2B_MethodIterator core::scoring::ScoreFunction::cd_lr_2b_methods_end | ( | ) | const |
Definition at line 1899 of file ScoreFunction.cc.
References cd_lr_2b_methods_.
Referenced by core::scoring::symmetry::SymmetricScoreFunction::eval_long_range_twobody_energies().
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inline |
Definition at line 970 of file ScoreFunction.hh.
References core::scoring::methods::cd_lr_2b, and score_types_by_method_type_.
Referenced by core::scoring::symmetry::SymmetricScoreFunction::eval_onebody_energies(), eval_onebody_energies(), and get_sub_score().
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private |
private
Definition at line 2016 of file ScoreFunction.cc.
References all_methods_, core::scoring::name_from_score_type(), core::scoring::hbonds::t(), and weights_.
Referenced by set_weight().
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inline |
convenience access to all ci 1b score types
Definition at line 936 of file ScoreFunction.hh.
References core::scoring::methods::ci_1b, and score_types_by_method_type_.
Referenced by get_sub_score().
| ScoreFunction::CI_2B_Methods::const_iterator core::scoring::ScoreFunction::ci_2b_begin | ( | ) | const |
Definition at line 1856 of file ScoreFunction.cc.
References ci_2b_methods_.
Referenced by core::scoring::eval_bbbb_sr2b_energies(), core::scoring::eval_bbsc_sr2b_energies(), and core::scoring::eval_scsc_sr2b_energies().
| ScoreFunction::CI_2B_Methods::const_iterator core::scoring::ScoreFunction::ci_2b_end | ( | ) | const |
Definition at line 1862 of file ScoreFunction.cc.
References ci_2b_methods_.
Referenced by core::scoring::eval_bbbb_sr2b_energies(), core::scoring::eval_bbsc_sr2b_energies(), and core::scoring::eval_scsc_sr2b_energies().
| ScoreFunction::TWO_B_MethodIterator core::scoring::ScoreFunction::ci_2b_intrares_begin | ( | ) | const |
Definition at line 1832 of file ScoreFunction.cc.
References ci_2b_intrares_.
Referenced by core::scoring::mm::mm_bond_angle_residue_type_param_set().
| ScoreFunction::TWO_B_MethodIterator core::scoring::ScoreFunction::ci_2b_intrares_end | ( | ) | const |
Definition at line 1838 of file ScoreFunction.cc.
References ci_2b_intrares_.
Referenced by core::scoring::mm::mm_bond_angle_residue_type_param_set().
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convenience access to all ci 2b score types
Definition at line 950 of file ScoreFunction.hh.
References core::scoring::methods::ci_2b, and score_types_by_method_type_.
Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy(), core::scoring::symmetry::SymmetricScoreFunction::eval_twobody_neighbor_energies(), eval_twobody_neighbor_energies(), core::pack::interaction_graph::SimpleEdge::get_bb_E(), get_sub_score(), and setup_for_minimizing_sr2b_enmeths_for_minedge().
| ScoreFunction::CI_LR_2B_MethodIterator core::scoring::ScoreFunction::ci_lr_2b_methods_begin | ( | ) | const |
Definition at line 1881 of file ScoreFunction.cc.
References ci_lr_2b_methods_.
Referenced by core::scoring::symmetry::SymmetricScoreFunction::eval_long_range_twobody_energies().
| ScoreFunction::CI_LR_2B_MethodIterator core::scoring::ScoreFunction::ci_lr_2b_methods_end | ( | ) | const |
Definition at line 1887 of file ScoreFunction.cc.
References ci_lr_2b_methods_.
Referenced by core::scoring::symmetry::SymmetricScoreFunction::eval_long_range_twobody_energies().
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Definition at line 964 of file ScoreFunction.hh.
References core::scoring::methods::ci_lr_2b, and score_types_by_method_type_.
Referenced by get_sub_score().
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Reimplemented in core::scoring::symmetry::SymmetricScoreFunction, core::scoring::MinScoreScoreFunction, and core::scoring::DockingScoreFunction.
Definition at line 112 of file ScoreFunction.cc.
Referenced by protocols::forge::components::BDR::centroid_scorefunction(), protocols::forge::remodel::RemodelMover::centroid_scorefunction(), protocols::forge::components::BDR::fullatom_scorefunction(), protocols::forge::remodel::RemodelMover::fullatom_scorefunction(), protocols::moves::MonteCarlo::MonteCarlo(), protocols::relax::FastRelax::parse_my_tag(), protocols::moves::MonteCarlo::reset_scorefxn(), protocols::simple_moves::MinMover::score_function(), protocols::moves::MonteCarlo::score_function(), protocols::fldsgn::potentials::SetSecStructEnergies::scorefunction(), protocols::fldsgn::BluePrintBDR::scorefunction(), protocols::forge::remodel::RemodelLoopMover::scorefunction(), protocols::forge::components::VarLengthBuild::scorefunction(), protocols::pack_daemon::DaemonSet::set_score_function(), core::pack::interaction_graph::OnTheFlyInteractionGraph::set_score_function(), core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::set_score_function(), and protocols::pack_daemon::DynamicAggregateFunction::set_score_function().
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Returns the EnergyMethodOptions object contained in this ScoreFunction (const access)
Definition at line 173 of file ScoreFunction.hh.
References energy_method_options_.
Referenced by core::scoring::methods::SecondaryStructureEnergy::finalize_total_energy(), core::scoring::ScoreFunctionInfo::initialize_from(), protocols::abinitio::ConstraintFragmentSampler::set_max_seq_sep(), and core::scoring::methods::PoissonBoltzmannEnergy::setup_for_scoring().
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Accumulates the unweighted one body energies of all context dependent one body energies for <pose> Residue <rsd> into EnergyMap <emap>
Reimplemented in protocols::flexpack::OtherContextScoreFunction.
Definition at line 1553 of file ScoreFunction.cc.
References cd_1b_methods_.
Referenced by core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), protocols::flexpack::OtherContextScoreFunction::eval_cd_1b(), core::scoring::symmetry::SymmetricScoreFunction::eval_onebody_energies(), eval_onebody_energies(), core::optimization::SingleResidueMultifunc::operator()(), core::pack::interaction_graph::SimpleNode::update_alternate_one_body_energy(), and core::pack::interaction_graph::SimpleNode::update_current_one_body_energy().
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virtual |
Accumulate the unweighted short range context dependent two body interaction energies of <pose> between Residue <rsd1> and Residue <rsd2> into EnergyMap <emap>
Reimplemented in protocols::flexpack::OtherContextScoreFunction.
Definition at line 1633 of file ScoreFunction.cc.
References cd_2b_methods_.
Referenced by core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), protocols::flexpack::OtherContextScoreFunction::eval_cd_2b(), core::scoring::symmetry::SymmetricScoreFunction::eval_twobody_neighbor_energies(), eval_twobody_neighbor_energies(), and core::optimization::SingleResidueMultifunc::operator()().
| void core::scoring::ScoreFunction::eval_cd_2b_bb_bb | ( | conformation::Residue const & | rsd1, |
| conformation::Residue const & | rsd2, | ||
| pose::Pose const & | pose, | ||
| EnergyMap & | emap | ||
| ) | const |
Accumulates the unweighted short ranged context dependent two body interaction energies of <pose> between the backbones of Residue <rsd1> and <rsd2> into EnergyMap <emap>
Definition at line 1648 of file ScoreFunction.cc.
References cd_2b_methods_.
Referenced by core::pack::rotamer_set::RotamerSets::get_bb_bbE(), and core::pack::interaction_graph::SimpleEdge::get_bb_E().
| void core::scoring::ScoreFunction::eval_cd_2b_bb_sc | ( | conformation::Residue const & | rsd1, |
| conformation::Residue const & | rsd2, | ||
| pose::Pose const & | pose, | ||
| EnergyMap & | emap | ||
| ) | const |
Accumulates the unweighted short ranged context dependent two body interaction energies of <pose> between the backbone of Residue <rsd1> and the sidechain of Residue <rsd2> into EnergyMap <emap>
Definition at line 1664 of file ScoreFunction.cc.
References cd_2b_methods_.
Referenced by core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), and core::pack::rotamer_set::RotamerSets::get_sc_bbE().
| void core::scoring::ScoreFunction::eval_cd_2b_sc_sc | ( | conformation::Residue const & | rsd1, |
| conformation::Residue const & | rsd2, | ||
| pose::Pose const & | pose, | ||
| EnergyMap & | emap | ||
| ) | const |
Accumulates the unweighted short ranged context dependent two body interaction energies of <pose> between the sidechains of Residue <rsd1> and Residue <rsd2> into EnergyMap <emap>
Definition at line 1679 of file ScoreFunction.cc.
References cd_2b_methods_.
Referenced by core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), and core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy().
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Accumulates the unweighted intra-residue one body energies for all context dependent two body terms that define intra-residue energies of <pose> Residue <rsd> into EnergyMap <emap>
Reimplemented in protocols::flexpack::OtherContextScoreFunction.
Definition at line 1524 of file ScoreFunction.cc.
References any_intrares_energies_, and cd_2b_intrares_.
Referenced by protocols::flexpack::OtherContextScoreFunction::eval_cd_intrares_energy(), core::scoring::symmetry::SymmetricScoreFunction::eval_onebody_energies(), eval_onebody_energies(), core::pack::interaction_graph::SimpleNode::update_alternate_one_body_energy(), and core::pack::interaction_graph::SimpleNode::update_current_one_body_energy().
| void core::scoring::ScoreFunction::eval_ci_1b | ( | conformation::Residue const & | rsd, |
| pose::Pose const & | pose, | ||
| EnergyMap & | emap | ||
| ) | const |
Definition at line 1540 of file ScoreFunction.cc.
References ci_1b_methods_.
Referenced by core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), core::scoring::symmetry::SymmetricScoreFunction::eval_onebody_energies(), eval_onebody_energies(), core::optimization::SingleResidueMultifunc::operator()(), core::pack::interaction_graph::SimpleNode::update_alternate_one_body_energy(), and core::pack::interaction_graph::SimpleNode::update_current_one_body_energy().
| void core::scoring::ScoreFunction::eval_ci_2b | ( | conformation::Residue const & | rsd1, |
| conformation::Residue const & | rsd2, | ||
| pose::Pose const & | pose, | ||
| EnergyMap & | emap | ||
| ) | const |
Accumulates the unweighted context independent two body interaction energies of <pose> between Residue <rsd1> and Residue <rsd2> into EnergyMap <emap>
Definition at line 1568 of file ScoreFunction.cc.
References ci_2b_methods_.
Referenced by core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), core::scoring::symmetry::SymmetricScoreFunction::eval_twobody_neighbor_energies(), eval_twobody_neighbor_energies(), and core::optimization::SingleResidueMultifunc::operator()().
| void core::scoring::ScoreFunction::eval_ci_2b_bb_bb | ( | conformation::Residue const & | rsd1, |
| conformation::Residue const & | rsd2, | ||
| pose::Pose const & | pose, | ||
| EnergyMap & | emap | ||
| ) | const |
Accumulates the unweighted context independent two body interaction energies of <pose> between the backbones of Residue <rsd1> and Residue <rsd2> into EnergyMap <emap>
Definition at line 1584 of file ScoreFunction.cc.
References ci_2b_methods_.
Referenced by core::pack::rotamer_set::RotamerSets::get_bb_bbE(), and core::pack::interaction_graph::SimpleEdge::get_bb_E().
| void core::scoring::ScoreFunction::eval_ci_2b_bb_sc | ( | conformation::Residue const & | rsd1, |
| conformation::Residue const & | rsd2, | ||
| pose::Pose const & | pose, | ||
| EnergyMap & | emap | ||
| ) | const |
Accumulates the unweighted short range context independent two body interaction energies of <pose> between the backbone of Residue <rsd1> and the sidechain of Residue <rsd2> into EnergyMap <emap>
Definition at line 1600 of file ScoreFunction.cc.
References ci_2b_methods_.
Referenced by core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), and core::pack::rotamer_set::RotamerSets::get_sc_bbE().
| void core::scoring::ScoreFunction::eval_ci_2b_sc_sc | ( | conformation::Residue const & | rsd1, |
| conformation::Residue const & | rsd2, | ||
| pose::Pose const & | pose, | ||
| EnergyMap & | emap | ||
| ) | const |
Accumulates the unweighted short range context dependent two body interaction energies of <pose> between the sidechains of Residue <rsd1> and Residue <rsd2> into Energymap <emap>
Definition at line 1615 of file ScoreFunction.cc.
References ci_2b_methods_.
Referenced by core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), and core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy().
| void core::scoring::ScoreFunction::eval_ci_intrares_energy | ( | conformation::Residue const & | rsd, |
| pose::Pose const & | pose, | ||
| EnergyMap & | emap | ||
| ) | const |
Accumulates the unweighted intra-residue one body energies for all context independent two body terms that define intra-residue energies of <pose> Residue <rsd> into EnergyMap <emap>
Definition at line 1510 of file ScoreFunction.cc.
References any_intrares_energies_, and ci_2b_intrares_.
Referenced by core::scoring::symmetry::SymmetricScoreFunction::eval_onebody_energies(), eval_onebody_energies(), core::pack::interaction_graph::SimpleNode::update_alternate_one_body_energy(), and core::pack::interaction_graph::SimpleNode::update_current_one_body_energy().
| Real core::scoring::ScoreFunction::eval_dof_derivative | ( | id::DOF_ID const & | dof_id, |
| id::TorsionID const & | torsion_id, | ||
| pose::Pose const & | pose | ||
| ) | const |
Definition at line 2606 of file ScoreFunction.cc.
References core::id::DOF_ID::atom_id(), core::pose::Pose::energies(), core::scoring::eval_dof_deriv_for_minnode(), core::scoring::Energies::minimization_graph(), core::pose::Pose::residue(), core::id::AtomID::rsd(), core::id::TorsionID::rsd(), core::id::TorsionID::valid(), and weights_.
Referenced by core::optimization::symmetry::atom_tree_dfunc(), core::optimization::atom_tree_dfunc(), core::optimization::cartesian_collect_torsional_deriv(), and protocols::cartesian::MolecularDynamics::getCartesianDerivatives().
| void core::scoring::ScoreFunction::eval_intrares_energy | ( | conformation::Residue const & | rsd, |
| pose::Pose const & | pose, | ||
| EnergyMap & | emap | ||
| ) | const |
Accumulates for rsd the unweighted intra-residue one body energies for all context dependent and context independent two body terms that define intra-residue energies.
Definition at line 1456 of file ScoreFunction.cc.
References any_intrares_energies_, cd_2b_intrares_, and ci_2b_intrares_.
Referenced by core::optimization::SingleResidueMultifunc::operator()().
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virtual |
Reimplemented in core::scoring::symmetry::SymmetricScoreFunction.
Definition at line 1214 of file ScoreFunction.cc.
References cd_lr_2b_methods_, ci_lr_2b_methods_, core::pose::Pose::energies(), core::scoring::Energies::nonconst_long_range_container(), core::pose::Pose::residue(), core::scoring::Energies::total_energies(), core::pose::Pose::total_residue(), and core::scoring::Energies::use_nblist().
Referenced by operator()().
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Reimplemented in core::scoring::symmetry::SymmetricScoreFunction.
Definition at line 2578 of file ScoreFunction.cc.
References core::pose::Pose::energies(), core::scoring::Energies::minimization_graph(), and weights_.
Referenced by core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::atom_tree_get_atompairE_deriv(), core::optimization::cartesian_collect_atompairE_deriv(), protocols::cartesian::MolecularDynamics::createCartesianDerivatives(), and protocols::cartesian::MolecularDynamics::getCartesianDerivatives().
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virtual |
Reimplemented in core::scoring::symmetry::SymmetricScoreFunction.
Definition at line 1401 of file ScoreFunction.cc.
References any_intrares_energies_, cd_1b_types(), cd_2b_types(), cd_lr_2b_types(), core::scoring::EMapVector::clear(), core::pose::Pose::energies(), eval_cd_1b(), eval_cd_intrares_energy(), eval_ci_1b(), eval_ci_intrares_energy(), core::scoring::eval_res_onebody_energies_for_minnode(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().
Referenced by operator()().
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virtual |
Reimplemented in core::scoring::symmetry::SymmetricScoreFunction.
Definition at line 1115 of file ScoreFunction.cc.
References cd_2b_types(), ci_2b_types(), core::pose::Pose::energies(), core::scoring::EnergyEdge::energies_not_yet_computed(), eval_cd_2b(), eval_ci_2b(), core::scoring::eval_res_pair_energy_for_minedge(), core::graph::Edge::get_node(), core::graph::Edge::get_second_node_ind(), core::scoring::EnergyEdge::mark_energies_computed(), core::pose::Pose::residue(), core::scoring::EnergyEdge::store_active_energies(), core::pose::Pose::total_residue(), core::graph::Node::upper_edge_list_end(), and core::scoring::EMapVector::zero().
Referenced by operator()().
| void core::scoring::ScoreFunction::evaluate_rotamer_background_energies | ( | conformation::RotamerSetBase const & | set1, |
| conformation::Residue const & | residue2, | ||
| pose::Pose const & | pose, | ||
| utility::vector1< core::PackerEnergy > & | energy_vector | ||
| ) | const |
Evaluate the energies between a set of rotamers and a single other (background) residue
Definition at line 1918 of file ScoreFunction.cc.
References cd_2b_methods_, ci_2b_methods_, and weights().
Referenced by core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), and core::pack::rotamer_set::RotamerSet_::compute_one_body_energies().
| void core::scoring::ScoreFunction::evaluate_rotamer_intrares_energies | ( | conformation::RotamerSetBase const & | set, |
| pose::Pose const & | pose, | ||
| utility::vector1< core::PackerEnergy > & | energies | ||
| ) | const |
Definition at line 1474 of file ScoreFunction.cc.
References any_intrares_energies_, cd_2b_intrares_, and ci_2b_intrares_.
Referenced by core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), and core::pack::rotamer_set::RotamerSet_::compute_one_body_energies().
| void core::scoring::ScoreFunction::evaluate_rotamer_intrares_energy_maps | ( | conformation::RotamerSetBase const & | set, |
| pose::Pose const & | pose, | ||
| utility::vector1< EnergyMap > & | emaps | ||
| ) | const |
Definition at line 1492 of file ScoreFunction.cc.
References any_intrares_energies_, cd_2b_intrares_, and ci_2b_intrares_.
Referenced by core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps().
| void core::scoring::ScoreFunction::evaluate_rotamer_pair_energies | ( | conformation::RotamerSetBase const & | set1, |
| conformation::RotamerSetBase const & | set2, | ||
| pose::Pose const & | pose, | ||
| ObjexxFCL::FArray2D< core::PackerEnergy > & | energy_table | ||
| ) | const |
Definition at line 1751 of file ScoreFunction.cc.
References cd_2b_methods_, ci_2b_methods_, and weights().
Referenced by core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::precompute_two_body_energies(), and core::pack::rotamer_set::RotamerSets::precompute_two_body_energies().
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Definition at line 2209 of file ScoreFunction.cc.
References all_methods_.
Referenced by core::optimization::symmetry::atom_tree_dfunc(), core::optimization::atom_tree_dfunc(), and core::optimization::cartesian_dfunc().
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inline |
Definition at line 695 of file ScoreFunction.hh.
References name_.
Referenced by core::scoring::methods::PoissonBoltzmannEnergy::setup_for_scoring().
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Returns a list of the ScoreTypes which are non-zero with their current weights.
example(s): scorefxn.get_nonzero_weighted_scoretypes() See also: ScoreFunction ScoreFunction.get_weight ScoreFunction.set_weight ScoreFunction.weights ScoreType create_score_function name_from_score_type score_type_from_name
Definition at line 342 of file ScoreFunction.hh.
References has_nonzero_weight(), and core::scoring::n_score_types.
| core::Real core::scoring::ScoreFunction::get_sub_score | ( | pose::Pose const & | pose, |
| utility::vector1< bool > const & | residue_mask | ||
| ) | const |
Compute the score for subset of residues.
Definition at line 777 of file ScoreFunction.cc.
References any_intrares_energies_, cd_1b_types(), cd_2b_types(), cd_lr_2b_methods_, cd_lr_2b_types(), ci_1b_types(), ci_2b_types(), ci_lr_2b_methods_, ci_lr_2b_types(), core::graph::Node::const_upper_edge_list_end(), core::scoring::Energies::data(), core::scoring::EnergyEdge::dot(), core::scoring::EMapVector::dot(), core::pose::Pose::energies(), core::scoring::hbonds::get_hbond_energies(), core::graph::Edge::get_node(), core::graph::Edge::get_second_node_ind(), core::scoring::hbond_lr_bb, core::scoring::EnergiesCacheableDataType::HBOND_SET, core::scoring::hbond_sr_bb, core::scoring::Energies::long_range_container(), core::pose::Pose::total_residue(), and weights_.
Referenced by get_sub_score(), and get_sub_score_exclude_res().
| void core::scoring::ScoreFunction::get_sub_score | ( | pose::Pose const & | pose, |
| utility::vector1< bool > const & | residue_mask, | ||
| EnergyMap & | emap | ||
| ) | const |
Compute the score for subset of residues.
Definition at line 905 of file ScoreFunction.cc.
References core::scoring::EMapVector::accumulate(), any_intrares_energies_, cd_1b_types(), cd_2b_types(), cd_lr_2b_methods_, cd_lr_2b_types(), ci_1b_types(), ci_2b_types(), ci_lr_2b_methods_, ci_lr_2b_types(), core::graph::Node::const_upper_edge_list_end(), core::scoring::Energies::data(), core::pose::Pose::energies(), core::scoring::EnergyEdge::fill_energy_map(), core::scoring::hbonds::get_hbond_energies(), core::graph::Edge::get_node(), core::graph::Edge::get_second_node_ind(), core::scoring::hbond_lr_bb, core::scoring::EnergiesCacheableDataType::HBOND_SET, core::scoring::hbond_sr_bb, core::scoring::Energies::long_range_container(), core::pose::Pose::total_residue(), and weights_.
| core::Real core::scoring::ScoreFunction::get_sub_score | ( | pose::Pose & | pose, |
| utility::vector1< bool > const & | residue_mask | ||
| ) | const |
Compute the score for subset of residues.
Definition at line 892 of file ScoreFunction.cc.
References core::pose::Pose::energies(), core::scoring::Energies::energies_updated(), and get_sub_score().
| void core::scoring::ScoreFunction::get_sub_score | ( | pose::Pose & | pose, |
| utility::vector1< bool > const & | residue_mask, | ||
| EnergyMap & | emap | ||
| ) | const |
Compute the score for subset of residues.
Definition at line 1024 of file ScoreFunction.cc.
References core::pose::Pose::energies(), core::scoring::Energies::energies_updated(), and get_sub_score().
| Real core::scoring::ScoreFunction::get_sub_score_exclude_res | ( | pose::Pose const & | pose, |
| utility::vector1< core::Size > const & | exclude_list | ||
| ) | const |
Compute the score for subset of residues.
Definition at line 1037 of file ScoreFunction.cc.
References get_sub_score(), and core::pose::Pose::total_residue().
Referenced by protocols::loops::addScoresForLoopParts().
| void core::scoring::ScoreFunction::get_sub_score_exclude_res | ( | pose::Pose const & | pose, |
| utility::vector1< core::Size > const & | exclude_list, | ||
| EnergyMap & | emap | ||
| ) | const |
Compute the score for subset of residues.
Definition at line 1076 of file ScoreFunction.cc.
References get_sub_score(), and core::pose::Pose::total_residue().
| Real core::scoring::ScoreFunction::get_sub_score_exclude_res | ( | pose::Pose & | pose, |
| utility::vector1< core::Size > const & | exclude_list | ||
| ) | const |
Compute the score for subset of residues.
Definition at line 1054 of file ScoreFunction.cc.
References core::pose::Pose::energies(), core::scoring::Energies::energies_updated(), get_sub_score(), and core::pose::Pose::total_residue().
| void core::scoring::ScoreFunction::get_sub_score_exclude_res | ( | pose::Pose & | pose, |
| utility::vector1< core::Size > const & | exclude_list, | ||
| EnergyMap & | emap | ||
| ) | const |
Compute the score for subset of residues.
Definition at line 1093 of file ScoreFunction.cc.
References core::pose::Pose::energies(), core::scoring::Energies::energies_updated(), get_sub_score(), and core::pose::Pose::total_residue().
Returns the weight for ScoreType <t>
examples(s): scorefxn.get_weight(fa_sol) See also: ScoreFunction ScoreFunction.set_weight ScoreType create_score_function name_from_score_type score_type_from_name
get the weight
Definition at line 2007 of file ScoreFunction.cc.
References core::scoring::hbonds::t(), and weights_.
Referenced by protocols::simple_filters::ScoreEvaluator::apply(), protocols::canonical_sampling::PatchOperation::apply(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph(), core::import_pose::atom_tree_diffs::map_of_weighted_scores(), merge(), protocols::dna::RotamerDNAHBondFilter::operator()(), protocols::pb_potential::SetupPoissonBoltzmannPotential::parse_my_tag(), protocols::simple_moves::symmetry::SymShakeStructureMover::reduce_fa_rep(), protocols::simple_moves::ShakeStructureMover::reduce_fa_rep(), and protocols::ddg::ddGMover::store_energies().
Returns true if the ScoreType <t> has a non-zero weight.
example(s): scorefxn.has_nonzero_weight(fa_sol) See also: ScoreFunction ScoreFunction.get_weight ScoreFunction.has_zero_weight ScoreFunction.set_weight ScoreFunction.weights ScoreType create_score_function name_from_score_type score_type_from_name
Definition at line 322 of file ScoreFunction.hh.
References weights_.
Referenced by core::scoring::symmetry::SymmetricScoreFunction::correct_arrays_for_symmetry(), core::scoring::symmetry::SymmetricScoreFunction::correct_finalize_score(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::finalize_total_energy(), get_nonzero_weighted_scoretypes(), core::import_pose::atom_tree_diffs::map_of_weighted_scores(), core::scoring::hbonds::nonzero_hbond_weight(), and set_weight().
Returns true if the ScoreType <t> has a weight of zero,.
example(s): scorefxn.has_zero_weight(fa_sol) See also: ScoreFunction ScoreFunction.get_weight ScoreFunction.has_nonzero_weight ScoreFunction.set_weight ScoreFunction.weights ScoreType create_score_function name_from_score_type score_type_from_name
Definition at line 302 of file ScoreFunction.hh.
References weights_.
Referenced by core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), core::scoring::methods::CustomAtomPairEnergy::eval_atom_derivative(), core::scoring::OmegaTether::eval_omega_score_all(), core::scoring::Ramachandran::eval_rama_score_all(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::scoring::ScoreFunctionInfo::initialize_from(), and core::scoring::methods::CustomAtomPairEnergy::residue_pair_energy().
| void core::scoring::ScoreFunction::indicate_required_context_graphs | ( | utility::vector1< bool > & | context_graphs_required) | const |
find which context graphs the energy methods require
scoring function fills in the context graphs that its energy methods require
input vector should be false and have num_context_graph_types slots. Each method ors its required context graphs
Definition at line 2925 of file ScoreFunction.cc.
References all_methods_.
Referenced by core::scoring::ScoreFunctionInfo::initialize_from().
| ScoreFunctionInfoOP core::scoring::ScoreFunction::info | ( | ) | const |
Score the structure and store the component energies in the EnergyGraph without requiring a second evaluation of the short-ranged two body energies. Note: pose copy operations do not copy the EnergyGraph, so cloning or copying a pose that has had it's components scored will not copy over the component energies.
return an object to describe abstractly the methods contained in this ScoreFunction so that class Energies can ensure that the ScoreFunction is properly evaluated (ie, no obsolete cashed data is used )
Definition at line 2654 of file ScoreFunction.cc.
References score_function_info_, and score_function_info_current_.
Referenced by core::pack::create_packer_graph(), core::pack::rotamer_set::RotamerSets::prepare_otf_graph(), and core::scoring::Energies::scoring_begin().
| void core::scoring::ScoreFunction::initialize_from_file | ( | std::string const & | filename) |
Resets everything before reading the <filename>
read info from file
Definition at line 137 of file ScoreFunction.cc.
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private |
sets up the derived method vectors from the primary vectors
Definition at line 2865 of file ScoreFunction.cc.
References all_methods_, cd_1b_methods_, cd_2b_methods_, cd_lr_2b_methods_, ci_1b_methods_, ci_2b_methods_, ci_lr_2b_methods_, lr_2b_methods_, methods_by_score_type_, core::scoring::methods::n_energy_method_types, core::scoring::n_score_types, score_types_by_method_type_, and ws_methods_.
| ScoreFunction::LR_2B_MethodIterator core::scoring::ScoreFunction::long_range_energies_begin | ( | ) | const |
Definition at line 1820 of file ScoreFunction.cc.
References lr_2b_methods_.
Referenced by core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energies(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_one_body_energies_for_otf_ig(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), core::pack::create_minimization_graph(), core::optimization::SingleResidueMultifunc::operator()(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::precompute_two_body_energies(), core::pack::rotamer_set::RotamerSets::precompute_two_body_energies(), core::pack::rotamer_set::RotamerSets::prepare_otf_graph(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::prepare_symm_otf_interaction_graph(), core::pack::RTMin::rtmin(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_minimizing(), and setup_for_minimizing().
| ScoreFunction::LR_2B_MethodIterator core::scoring::ScoreFunction::long_range_energies_end | ( | ) | const |
Definition at line 1826 of file ScoreFunction.cc.
References lr_2b_methods_.
Referenced by core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energies(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_one_body_energies_for_otf_ig(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), core::pack::create_minimization_graph(), core::optimization::SingleResidueMultifunc::operator()(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::precompute_two_body_energies(), core::pack::rotamer_set::RotamerSets::precompute_two_body_energies(), core::pack::rotamer_set::RotamerSets::prepare_otf_graph(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::prepare_symm_otf_interaction_graph(), core::pack::RTMin::rtmin(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_minimizing(), and setup_for_minimizing().
| Distance core::scoring::ScoreFunction::max_atomic_interaction_cutoff | ( | ) | const |
Returns the largest atomic interaction cutoff required by the EnergyMethods
determines the furthest-reach of the short-range two body energies as well as the whole-structure energies, which are allowed to require that the EnergyGraph have edges of a minimum length.
Definition at line 2895 of file ScoreFunction.cc.
References cd_2b_methods_, ci_2b_methods_, and ws_methods_.
Referenced by are_they_neighbors(), core::scoring::ScoreFunctionInfo::initialize_from(), and core::pack::interaction_graph::SymmOnTheFlyEdge::set_residues_adjacent_for_subunit_pair().
| void core::scoring::ScoreFunction::merge | ( | const ScoreFunction | scorefxn_to_be_merged) |
Merges in the weights of another score function.
example(s): scorefxn.merge(scorefxn2) See also: ScoreFunction ScoreFunction.weights Energies create_score_function
Definition at line 466 of file ScoreFunction.cc.
References get_weight(), core::scoring::n_score_types, and set_weight().
|
inline |
Accumulates the unweighted one body energies of all context independent one body energies for <pose> Residue <rsd> into EnergyMap <emap>
Definition at line 694 of file ScoreFunction.hh.
References name_.
Referenced by core::scoring::find_weights_file().
|
virtual |
Scores the given <pose> using this ScoreFunction. Alters the Energies object within <pose>, but does not alter this ScoreFunction.
Reimplemented in core::scoring::symmetry::SymmetricScoreFunction, core::scoring::MinScoreScoreFunction, and core::scoring::DockingScoreFunction.
Definition at line 581 of file ScoreFunction.cc.
References all_methods_, core::scoring::EMapVector::dot(), core::pose::Pose::energies(), eval_long_range_twobody_energies(), eval_onebody_energies(), eval_twobody_neighbor_energies(), core::scoring::Energies::finalized_energies(), core::pose::symmetry::is_symmetric(), core::scoring::Energies::minimization_graph(), core::pose::Pose::residue(), core::pose::Pose::scoring_begin(), core::pose::Pose::scoring_end(), setup_for_scoring(), core::scoring::Energies::total_energies(), core::scoring::Energies::total_energy(), core::pose::Pose::total_residue(), core::scoring::total_score, core::scoring::Energies::use_nblist(), and weights_.
Referenced by core::scoring::DockingScoreFunction::operator()(), and core::scoring::MinScoreScoreFunction::operator()().
| ScoreFunction & core::scoring::ScoreFunction::operator= | ( | ScoreFunction const & | src) |
Definition at line 412 of file ScoreFunction.cc.
References all_methods_, any_intrares_energies_, energy_method_options_, score_function_info_, score_function_info_current_, and weights_.
Referenced by core::scoring::DockingScoreFunction::operator=(), core::scoring::MinScoreScoreFunction::operator=(), and core::scoring::symmetry::SymmetricScoreFunction::operator=().
Returns the weight of the ScoreType <t>
example(s): scorefxn[fa_sol] See also: ScoreFunction ScoreFunction.get_weight ScoreFunction.set_weight ScoreFunction.weights ScoreType create_score_function name_from_score_type score_type_from_name
Definition at line 263 of file ScoreFunction.hh.
References core::scoring::hbonds::t(), and weights_.
| void core::scoring::ScoreFunction::perturb_weights | ( | ) |
Randomly perturbs non-zero score function weights.
Perturbs each non-zero weight independently by adding a Gaussian noise with u=0 and sd=weight / 8. Weights are not allowed to become negative.
Definition at line 165 of file ScoreFunction.cc.
References core::scoring::name_from_score_type(), and tr().
| void core::scoring::ScoreFunction::prepare_rotamers_for_packing | ( | pose::Pose const & | pose, |
| conformation::RotamerSetBase & | set | ||
| ) | const |
Lets the scoring functions cache anything they need to rapidly calculate rotamer pair energies used in packing (like a trie, e.g.)
Definition at line 2141 of file ScoreFunction.cc.
References all_methods_.
Referenced by core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_onebody_interactions_with_background(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::precompute_two_body_energies(), core::pack::rotamer_set::RotamerSets::prepare_sets_for_packing(), core::pack::rotamer_trials(), and core::pack::symmetric_rotamer_trials().
| void core::scoring::ScoreFunction::reinitialize_minnode_for_residue | ( | MinimizationNode & | min_node, |
| conformation::Residue const & | rsd, | ||
| kinematics::MinimizerMapBase const & | min_map, | ||
| pose::Pose & | pose | ||
| ) | const |
Definition at line 2433 of file ScoreFunction.cc.
References core::kinematics::MinimizerMapBase::domain_map(), core::conformation::Residue::seqpos(), core::scoring::MinimizationNode::setup_for_minimizing(), core::scoring::MinimizationNode::update_active_enmeths_for_residue(), and weights_.
Referenced by core::pack::reinitialize_mingraph_neighborhood_for_residue(), and core::pack::RTMin::rtmin().
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private |
Definition at line 2791 of file ScoreFunction.cc.
References all_methods_, core::scoring::methods::cd_1b, cd_1b_methods_, core::scoring::methods::cd_2b, cd_2b_methods_, core::scoring::methods::cd_lr_2b, cd_lr_2b_methods_, core::scoring::methods::ci_1b, ci_1b_methods_, core::scoring::methods::ci_2b, ci_2b_methods_, core::scoring::methods::ci_lr_2b, ci_lr_2b_methods_, lr_2b_methods_, methods_by_score_type_, score_types_by_method_type_, core::scoring::vector1_remove(), core::scoring::methods::ws, and ws_methods_.
Referenced by set_weight().
| void core::scoring::ScoreFunction::reset | ( | ) |
Resets the ScoreFunction to default values.
reset function that can be called either independently or from default ScoreFunction creation
Definition at line 122 of file ScoreFunction.cc.
Referenced by protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::jd2::parser::ScoreFunctionLoader::load_data(), protocols::protein_interface_design::movers::make_stub_scorefxn(), and protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile().
| void core::scoring::ScoreFunction::reset_energy_methods | ( | ) |
Definition at line 360 of file ScoreFunction.cc.
References core::scoring::EMapVector::get(), and core::scoring::n_score_types.
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virtual |
Scores the given <pose> using this ScoreFunction. Alters the Energies object within <pose>, but does not alter this ScoreFunction.
Definition at line 695 of file ScoreFunction.cc.
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inline |
Definition at line 929 of file ScoreFunction.hh.
References score_types_by_method_type_, and core::scoring::hbonds::t().
| std::string core::scoring::ScoreFunction::serialize_weights | ( | ) | const |
Serializes the non-zero score function term weights Format: { term : weight, ... }.
Format: { term : weight, ... }.
Definition at line 145 of file ScoreFunction.cc.
References protocols::kinmatch::str().
Referenced by protocols::pb_potential::SetupPoissonBoltzmannPotential::parse_my_tag().
| void core::scoring::ScoreFunction::set_energy_method_options | ( | methods::EnergyMethodOptions const & | energy_method_options_in) |
Returns the EnergyMethodOptions object contained in this ScoreFunction.
Sets the EnergyMethodOptions object contained in this ScoreFunction. with appropriate update of all the energy methods.
Definition at line 340 of file ScoreFunction.cc.
Referenced by protocols::flexpack::FlexPacker::apply(), and protocols::abinitio::ConstraintFragmentSampler::set_max_seq_sep().
| void core::scoring::ScoreFunction::set_etable | ( | std::string const & | etable_name) |
Given a <filename> (represented by a std::string), set the e_table for this ScoreFunction.
Given a filename (represented by a std::string), set the e_table for this ScoreFunction.
Definition at line 385 of file ScoreFunction.cc.
| void core::scoring::ScoreFunction::set_method_weights | ( | ScoreType const & | t, |
| utility::vector1< Real > const & | wts | ||
| ) |
Definition at line 399 of file ScoreFunction.cc.
Sets the weight for ScoreType <t> to <setting>
example(s): scorefxn.set_weight(fa_sol,.5) See also: ScoreFunction ScoreFunction.get_weight ScoreFunction.weights ScoreType create_score_function name_from_score_type score_type_from_name
set the weight
Definition at line 1941 of file ScoreFunction.cc.
References add_method(), check_methods(), energy_method_options_, core::scoring::ScoringManager::get_instance(), has_nonzero_weight(), methods_by_score_type_, core::scoring::python, remove_method(), score_function_info_current_, core::scoring::hbonds::t(), update_intrares_energy_status(), and weights_.
Referenced by protocols::rna::RNA_DeNovoProtocol::add_chem_shift_info(), protocols::abinitio::AbrelaxApplication::add_constraints(), core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn(), core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), protocols::abinitio::CoordinateConstraintKC::add_score_weights(), protocols::simple_moves::symmetry::SetupForSymmetryMover::apply(), protocols::topology_broker::ConstraintEvaluatorWrapper::apply(), protocols::flexpack::FlexPacker::apply(), protocols::simple_filters::ScoreEvaluator::apply(), protocols::simple_filters::TruncatedScoreEvaluator::apply(), protocols::constraints_additional::ConstraintEvaluator::apply(), protocols::abinitio::ComputeTotalDistCst::apply(), protocols::canonical_sampling::PatchOperation::apply(), core::pack::rotamer_set::build_lib_dna_rotamers(), protocols::motifs::Motif::build_rotamers(), protocols::motifs::build_rotamers_lite(), protocols::rna::classify_base_pairs(), protocols::protein_interface_design::filters::InterfaceHolesFilter::compute(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::determine_best_constraint(), protocols::relax::fix_worst_bad_ramas(), protocols::swa::rna::floating_base_chain_closure_post_process(), protocols::simple_filters::ConstraintScoreCutoffFilter::get_score(), merge(), protocols::ddg::ddGMover::minimize_with_constraints(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::abinitio::FoldConstraints::prepare_loop_in_stage3(), protocols::simple_moves::symmetry::SymShakeStructureMover::reduce_fa_rep(), protocols::simple_moves::ShakeStructureMover::reduce_fa_rep(), protocols::abinitio::ClassicAbinitio::set_current_weight(), protocols::abinitio::MembraneAbinitio::set_current_weight(), protocols::loophash::LoopHashLibrary::set_default_score_functions(), protocols::anchored_design::AnchorMoversData::set_unset_scorefunctions(), protocols::simple_moves::GreenPacker::set_weights_for_sfxn(), protocols::simple_moves::ShakeStructureMover::setup_ca_constraints(), protocols::swa::StepWisePoseSetup::setup_constraints(), and protocols::ddg::ddGMover::store_energies().
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virtual |
Reimplemented in core::scoring::symmetry::SymmetricScoreFunction.
Definition at line 2167 of file ScoreFunction.cc.
References core::pose::Pose::energies(), core::graph::Edge::get_first_node_ind(), core::graph::Edge::get_second_node_ind(), core::scoring::Energies::minimization_graph(), core::pose::Pose::residue(), core::scoring::MinimizationNode::setup_for_derivatives(), core::scoring::MinimizationEdge::setup_for_derivatives(), and core::pose::Pose::total_residue().
Referenced by core::optimization::symmetry::atom_tree_dfunc(), core::optimization::atom_tree_dfunc(), core::optimization::cartesian_dfunc(), protocols::cartesian::MolecularDynamics::createCartesianDerivatives(), and protocols::cartesian::MolecularDynamics::getCartesianDerivatives().
| void core::scoring::ScoreFunction::setup_for_lr2benmeth_minimization_for_respair | ( | conformation::Residue const & | res1, |
| conformation::Residue const & | res2, | ||
| methods::LongRangeTwoBodyEnergyCOP | lr2benergy, | ||
| MinimizationGraph & | g, | ||
| kinematics::MinimizerMapBase const & | min_map, | ||
| pose::Pose & | p, | ||
| bool const | res_moving_wrt_eachother, | ||
| bool | accumulate_fixed_energies, | ||
| ResidueNeighborConstIteratorOP | rni, | ||
| EnergyMap & | fixed_energies, | ||
| Real const | edge_weight = 1.0 |
||
| ) | const |
Initialize an edge in the MinimizationGraph with a particular long-range two body.
Definition at line 2539 of file ScoreFunction.cc.
References core::graph::Graph::add_edge(), core::scoring::MinimizationEdge::add_twobody_enmeth(), core::graph::Graph::find_edge(), core::conformation::Residue::seqpos(), and core::scoring::MinimizationEdge::weight().
Referenced by core::pack::create_minimization_graph(), core::pack::RTMin::rtmin(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_minimizing(), and setup_for_minimizing().
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virtual |
Initializes a MinimizationGraph and caches it in Energies object of <pose>
Reimplemented in core::scoring::symmetry::SymmetricScoreFunction.
Definition at line 2222 of file ScoreFunction.cc.
References all_methods_, core::scoring::MinimizationEdge::any_active_enmeths(), core::kinematics::MinimizerMapBase::domain_map(), core::graph::Graph::edge_list_begin(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::scoring::Energies::long_range_container(), long_range_energies_begin(), long_range_energies_end(), core::pose::Pose::residue(), core::scoring::Energies::set_minimization_graph(), setup_for_lr2benmeth_minimization_for_respair(), core::scoring::MinimizationEdge::setup_for_minimizing(), setup_for_minimizing_for_node(), setup_for_minimizing_sr2b_enmeths_for_minedge(), and core::pose::Pose::total_residue().
Referenced by protocols::cartesian::MolecularDynamics::MolecularDynamics(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::optimization::CartesianMinimizer::run(), and core::optimization::AtomTreeMinimizer::run().
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virtual |
Initialize a single node of a MinimizationGraph with the one-body and two-body energy methods that are held within this ScoreFunction object.
Note that energy methods should be added to the MinimizationGraph reguardless of whether or not they have been modernized to use the eval_residue_derivatives/eval_residue_pair_derivatives machinery. (Grandfathered EnergyMethods return "false" in their version of minimize_in_whole_structure_context() and have their derivatives still evaluated in the one-atom-at-a-time scheme.) The reason these grandfathered energy methods should be added to the MinimizationGraph is to ensure that their energies are still computed during minimization-score- function evaluation.
Definition at line 2377 of file ScoreFunction.cc.
References core::scoring::EMapVector::accumulate(), core::scoring::MinimizationNode::add_onebody_enmeth(), core::scoring::MinimizationNode::add_twobody_enmeth(), cd_1b_methods_, cd_2b_methods_, ci_1b_methods_, ci_2b_methods_, core::scoring::methods::ci_lr_2b, core::kinematics::MinimizerMapBase::domain_map(), core::pose::Pose::energies(), lr_2b_methods_, core::scoring::Energies::onebody_energies(), core::conformation::Residue::seqpos(), core::scoring::MinimizationNode::setup_for_minimizing(), and weights_.
Referenced by core::pack::create_minimization_graph(), core::pack::RTMin::rtmin(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_minimizing(), and setup_for_minimizing().
| void core::scoring::ScoreFunction::setup_for_minimizing_sr2b_enmeths_for_minedge | ( | conformation::Residue const & | res1, |
| conformation::Residue const & | res2, | ||
| MinimizationEdge & | min_edge, | ||
| kinematics::MinimizerMapBase const & | min_map, | ||
| pose::Pose & | pose, | ||
| bool const | res_moving_wrt_eachother, | ||
| bool | accumulate_fixed_energies, | ||
| EnergyEdge const * | energy_edge, | ||
| EnergyMap & | fixed_energies, | ||
| Real const | edge_weight = 1.0 |
||
| ) | const |
Initialize a single MinimizationEdge for a particular part of residues, storing sr2b energy method pointers on the edge for those sr2b energy methods in this ScoreFunction.
Definition at line 2503 of file ScoreFunction.cc.
References core::scoring::EnergyEdge::add_to_energy_map(), core::scoring::MinimizationEdge::add_twobody_enmeth(), cd_2b_methods_, ci_2b_methods_, and ci_2b_types().
Referenced by core::pack::create_minimization_graph(), core::pack::RTMin::rtmin(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_minimizing(), and setup_for_minimizing().
| void core::scoring::ScoreFunction::setup_for_packing | ( | pose::Pose & | pose, |
| utility::vector1< bool > const & | residues_repacking, | ||
| utility::vector1< bool > const & | residues_designing | ||
| ) | const |
Lets the scoring functions cache anything they need to calculate energies in a packing step (rotamer_trials or pack_rotamers)
Definition at line 2127 of file ScoreFunction.cc.
References all_methods_.
Referenced by protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), core::pack::min_pack(), core::pack::pack_rotamers_setup(), core::pack::rotamer_trials(), core::pack::stochastic_pack(), core::pack::symmetric_pack_rotamers_setup(), and core::pack::symmetric_rotamer_trials().
| void core::scoring::ScoreFunction::setup_for_scoring | ( | pose::Pose & | pose) | const |
For external scorers: Let the energy methods prepare for evaluating their scores on a particular structure.
Definition at line 2085 of file ScoreFunction.cc.
References all_methods_, core::pose::Pose::energies(), core::graph::Edge::get_first_node_ind(), core::graph::Edge::get_second_node_ind(), core::scoring::Energies::minimization_graph(), core::pose::Pose::residue(), core::scoring::MinimizationEdge::setup_for_scoring(), core::pose::Pose::total_residue(), and core::scoring::Energies::use_nblist().
Referenced by protocols::simple_moves::symmetry::SetupForSymmetryMover::apply(), core::scoring::symmetry::SymmetricScoreFunction::operator()(), and operator()().
| void core::scoring::ScoreFunction::show | ( | std::ostream & | out) | const |
This is now handled lazily by the Energies object itself void accumulate_residue_total_energies( pose::Pose & pose ) const;
Definition at line 451 of file ScoreFunction.cc.
References energy_method_options_, core::scoring::n_score_types, and weights_.
Referenced by protocols::abinitio::AbrelaxApplication::add_constraints(), protocols::abinitio::MembraneAbinitio::apply(), protocols::abinitio::ClassicAbinitio::apply(), protocols::idealize::basic_idealize(), protocols::abinitio::FragmentSampler::checkpointed_cycle_block(), core::pose::Pose::dump_scored_pdb(), protocols::abinitio::FoldConstraints::min_trial(), core::scoring::operator<<(), protocols::abinitio::MembraneAbinitio::print_debug(), protocols::abinitio::FragmentSampler::recover_low(), protocols::abinitio::ConstraintFragmentSampler::set_max_seq_sep(), and protocols::cartesian::MolecularDynamics::testCartesianDerivatives().
| void core::scoring::ScoreFunction::show | ( | std::ostream & | out, |
| pose::Pose & | pose | ||
| ) | const |
Scores <pose> and shows the raw and weighted scores for each non-zero ScoreType.
example(s): scorefxn.show(pose) See also: ScoreFunction ScoreFunction.weights Energies create_score_function
Definition at line 480 of file ScoreFunction.cc.
References core::pose::Pose::energies(), core::scoring::n_score_types, core::scoring::Energies::total_energies(), and weights_.
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Scores <pose> and shows the raw and weighted scores for each non-zero ScoreType.
example(s): scorefxn.show(pose) See also: ScoreFunction ScoreFunction.weights Energies create_score_function
Definition at line 678 of file ScoreFunction.hh.
References show().
Referenced by show().
| void core::scoring::ScoreFunction::show_line | ( | std::ostream & | out, |
| pose::Pose const & | pose | ||
| ) | const |
Definition at line 551 of file ScoreFunction.cc.
References core::pose::Pose::energies(), core::scoring::n_score_types, core::scoring::Energies::total_energies(), and weights_.
| void core::scoring::ScoreFunction::show_line_headers | ( | std::ostream & | out) | const |
Definition at line 539 of file ScoreFunction.cc.
References core::scoring::n_score_types, and weights_.
Referenced by core::fragment::picking_old::vall::eval::EnergyEval::pre_catalog_op().
| void core::scoring::ScoreFunction::show_pretty | ( | std::ostream & | out) | const |
similar output as show( ostream, pose ) but without the pose
Definition at line 502 of file ScoreFunction.cc.
References core::scoring::n_score_types, and weights_.
Referenced by protocols::jd2::archive::EvaluatedArchive::read_structures().
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check if any of the 2body methods define intra-residue energies, given our current weight set
Definition at line 2048 of file ScoreFunction.cc.
References any_intrares_energies_, cd_2b_intrares_, cd_2b_methods_, cd_lr_2b_methods_, ci_2b_intrares_, ci_2b_methods_, ci_lr_2b_methods_, and weights().
Referenced by set_weight().
| void core::scoring::ScoreFunction::update_residue_for_packing | ( | pose::Pose & | pose, |
| Size | resid | ||
| ) | const |
If inside packing, the pose changes conformation, inform the scoring functions that any data they have cached in the Energies object is out of date. In particular, this is to update the trie(s) during rotamer trials.
Definition at line 2154 of file ScoreFunction.cc.
References all_methods_.
Referenced by core::pack::rotamer_trials(), and core::pack::symmetric_rotamer_trials().
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Returns an EnergyMap of the current set of weights.
example(s): scorefxn.weights() See also: ScoreFunction ScoreFunction.get_weight ScoreFunction.set_weight ScoreFunction.weights ScoreType create_score_function name_from_score_type score_type_from_name
Definition at line 282 of file ScoreFunction.hh.
References weights_.
Referenced by protocols::flexpack::FlexPacker::apply(), core::pack::assign_random_rotamers(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::atom_tree_get_atompairE_deriv(), protocols::flexpack::rotamer_set::FlexbbRotamerSet::bump_check(), core::pack::rotamer_set::RotamerSet_::bump_check(), core::optimization::cartesian_collect_atompairE_deriv(), core::pack::compare_mingraph_and_energy_graph(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), core::pack::interaction_graph::SimpleEdge::compute_energy(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), core::pack::scmin::CartSCMinMultifunc::dfunc(), core::pack::scmin::SCMinMultifunc::dfunc(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::pose::Pose::dump_scored_pdb(), core::scoring::symmetry::SymmetricScoreFunction::eval_dof_derivative(), core::scoring::constraints::ConstraintSet::eval_intrares_energy(), core::scoring::constraints::ConstraintsEnergy::eval_intrares_energy_ext(), protocols::constraints_additional::MaxSeqSepConstraintSet::eval_non_residue_pair_energy(), core::scoring::constraints::ConstraintSet::eval_non_residue_pair_energy(), core::scoring::symmetry::SymmetricScoreFunction::eval_npd_atom_derivative(), core::scoring::hackelec::HackElecEnergy::evaluate_rotamer_background_energies(), evaluate_rotamer_background_energies(), core::scoring::hackelec::HackElecEnergy::evaluate_rotamer_pair_energies(), evaluate_rotamer_pair_energies(), core::pack::rotamer_set::RotamerSets::get_bb_bbE(), core::pack::interaction_graph::SimpleEdge::get_bb_E(), core::pack::rotamer_set::RotamerSets::get_sc_bbE(), core::pack::min_pack(), core::optimization::SingleResidueMultifunc::operator()(), core::scoring::DockingScoreFunction::operator()(), core::scoring::MinScoreScoreFunction::operator()(), core::scoring::symmetry::SymmetricScoreFunction::operator()(), core::pack::scmin::CartSCMinMultifunc::operator()(), core::pack::scmin::SCMinMultifunc::operator()(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::precompute_two_body_energies(), core::pack::rotamer_set::RotamerSets::precompute_two_body_energies(), core::scoring::constraints::ConstraintSet::residue_pair_energy(), core::scoring::constraints::ConstraintsEnergy::residue_pair_energy_ext(), core::scoring::Energies::scoring_begin(), protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_scorefxn(), core::scoring::NeighborList::setup(), core::scoring::methods::Fa_MbsolvEnergy::setup_for_derivatives(), core::scoring::methods::LK_hack::setup_for_derivatives(), core::scoring::methods::Fa_MbenvEnergy::setup_for_derivatives(), core::scoring::hackelec::HackElecEnergy::setup_for_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing_for_residue(), protocols::ddg::ddGMover::store_energies(), core::pack::interaction_graph::SimpleNode::update_alternate_one_body_energy(), core::pack::interaction_graph::SimpleNode::update_current_one_body_energy(), and update_intrares_energy_status().
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Definition at line 976 of file ScoreFunction.hh.
References score_types_by_method_type_, and core::scoring::methods::ws.
| ScoreFunction::WS_MethodIterator core::scoring::ScoreFunction::ws_methods_begin | ( | ) | const |
Definition at line 1905 of file ScoreFunction.cc.
References ws_methods_.
Referenced by core::scoring::symmetry::SymmetricScoreFunction::correct_finalize_score().
| ScoreFunction::WS_MethodIterator core::scoring::ScoreFunction::ws_methods_end | ( | ) | const |
Definition at line 1911 of file ScoreFunction.cc.
References ws_methods_.
Referenced by core::scoring::symmetry::SymmetricScoreFunction::correct_finalize_score().
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vector of COPs to all active methods
convenience access to the methods/alternate lookups filled by add_method along with the primary methods vectors
Definition at line 1058 of file ScoreFunction.hh.
Referenced by add_method(), all_energies_begin(), all_energies_end(), all_methods(), check_methods(), finalize_after_derivatives(), indicate_required_context_graphs(), initialize_methods_arrays(), operator()(), operator=(), prepare_rotamers_for_packing(), remove_method(), setup_for_minimizing(), setup_for_packing(), setup_for_scoring(), and update_residue_for_packing().
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Definition at line 1074 of file ScoreFunction.hh.
Referenced by any_intrares_energies(), eval_cd_intrares_energy(), eval_ci_intrares_energy(), eval_intrares_energy(), eval_onebody_energies(), evaluate_rotamer_intrares_energies(), evaluate_rotamer_intrares_energy_maps(), get_sub_score(), operator=(), and update_intrares_energy_status().
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Definition at line 1047 of file ScoreFunction.hh.
Referenced by add_method(), eval_cd_1b(), initialize_methods_arrays(), remove_method(), and setup_for_minimizing_for_node().
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Definition at line 1076 of file ScoreFunction.hh.
Referenced by cd_2b_intrares_begin(), cd_2b_intrares_end(), eval_cd_intrares_energy(), eval_intrares_energy(), evaluate_rotamer_intrares_energies(), evaluate_rotamer_intrares_energy_maps(), and update_intrares_energy_status().
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Definition at line 1045 of file ScoreFunction.hh.
Referenced by add_method(), bump_check_backbone(), bump_check_full(), cd_2b_begin(), cd_2b_end(), eval_cd_2b(), eval_cd_2b_bb_bb(), eval_cd_2b_bb_sc(), eval_cd_2b_sc_sc(), evaluate_rotamer_background_energies(), evaluate_rotamer_pair_energies(), initialize_methods_arrays(), max_atomic_interaction_cutoff(), remove_method(), setup_for_minimizing_for_node(), setup_for_minimizing_sr2b_enmeths_for_minedge(), and update_intrares_energy_status().
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Definition at line 1049 of file ScoreFunction.hh.
Referenced by add_method(), cd_lr_2b_methods_begin(), cd_lr_2b_methods_end(), eval_long_range_twobody_energies(), get_sub_score(), initialize_methods_arrays(), remove_method(), and update_intrares_energy_status().
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Definition at line 1046 of file ScoreFunction.hh.
Referenced by add_method(), eval_ci_1b(), initialize_methods_arrays(), remove_method(), and setup_for_minimizing_for_node().
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Definition at line 1075 of file ScoreFunction.hh.
Referenced by ci_2b_intrares_begin(), ci_2b_intrares_end(), eval_ci_intrares_energy(), eval_intrares_energy(), evaluate_rotamer_intrares_energies(), evaluate_rotamer_intrares_energy_maps(), and update_intrares_energy_status().
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NOTE: if you add another array here, be sure to reset it inside initialize_methods_arrays or the copy c-tor won't work these are the primary data – others can be rederived by calling update_method_vectors filled by the private member function add_method
Definition at line 1044 of file ScoreFunction.hh.
Referenced by add_method(), bump_check_backbone(), bump_check_full(), ci_2b_begin(), ci_2b_end(), eval_ci_2b(), eval_ci_2b_bb_bb(), eval_ci_2b_bb_sc(), eval_ci_2b_sc_sc(), evaluate_rotamer_background_energies(), evaluate_rotamer_pair_energies(), initialize_methods_arrays(), max_atomic_interaction_cutoff(), remove_method(), setup_for_minimizing_for_node(), setup_for_minimizing_sr2b_enmeths_for_minedge(), and update_intrares_energy_status().
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Definition at line 1048 of file ScoreFunction.hh.
Referenced by add_method(), ci_lr_2b_methods_begin(), ci_lr_2b_methods_end(), eval_long_range_twobody_energies(), get_sub_score(), initialize_methods_arrays(), remove_method(), and update_intrares_energy_status().
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Options that control choice/configuration of EnergyMethods. eg etable name.
Definition at line 1034 of file ScoreFunction.hh.
Referenced by energy_method_options(), operator=(), set_weight(), and show().
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Definition at line 1050 of file ScoreFunction.hh.
Referenced by add_method(), any_lr_residue_pair_energy(), initialize_methods_arrays(), long_range_energies_begin(), long_range_energies_end(), remove_method(), and setup_for_minimizing_for_node().
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Map from ScoreType to the method for evaluating it. will be 0 for score_types without a method, ie ones with 0 weight.
Definition at line 1062 of file ScoreFunction.hh.
Referenced by add_method(), initialize_methods_arrays(), remove_method(), and set_weight().
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the scorefxn name
Definition at line 1027 of file ScoreFunction.hh.
Referenced by get_name(), and name().
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Definition at line 1068 of file ScoreFunction.hh.
Referenced by info(), and operator=().
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Definition at line 1067 of file ScoreFunction.hh.
Referenced by info(), operator=(), and set_weight().
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Definition at line 1065 of file ScoreFunction.hh.
Referenced by add_method(), cd_1b_types(), cd_2b_types(), cd_lr_2b_types(), ci_1b_types(), ci_2b_types(), ci_lr_2b_types(), initialize_methods_arrays(), remove_method(), score_types_by_method_type(), and whole_structure_types().
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the scorefxn weights
Definition at line 1030 of file ScoreFunction.hh.
Referenced by add_extra_method(), check_methods(), eval_dof_derivative(), eval_npd_atom_derivative(), get_sub_score(), get_weight(), has_nonzero_weight(), has_zero_weight(), operator()(), operator=(), operator[](), reinitialize_minnode_for_residue(), set_weight(), setup_for_minimizing_for_node(), show(), show_line(), show_line_headers(), show_pretty(), and weights().
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Definition at line 1051 of file ScoreFunction.hh.
Referenced by add_method(), initialize_methods_arrays(), max_atomic_interaction_cutoff(), remove_method(), ws_methods_begin(), and ws_methods_end().
1.8.4