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core::scoring::symmetry::SymmetricScoreFunction Class Reference

This class is provided as a backward compatibility shim At this point it should be identical to the base ScoreFunction. More...

#include <SymmetricScoreFunction.hh>

Inheritance diagram for core::scoring::symmetry::SymmetricScoreFunction:
Inheritance graph
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Additional Inherited Members

- Public Types inherited from core::scoring::ScoreFunction
typedef utility::vector1
< methods::EnergyMethodCOP
AllMethods
 
typedef utility::vector1
< methods::ContextIndependentTwoBodyEnergyOP
CI_2B_Methods
 
typedef utility::vector1
< methods::ContextDependentTwoBodyEnergyOP
CD_2B_Methods
 
typedef utility::vector1
< methods::ContextIndependentOneBodyEnergyOP
CI_1B_Methods
 
typedef utility::vector1
< methods::ContextDependentOneBodyEnergyOP
CD_1B_Methods
 
typedef utility::vector1
< methods::ContextIndependentLRTwoBodyEnergyOP
CI_LR_2B_Methods
 
typedef utility::vector1
< methods::ContextDependentLRTwoBodyEnergyOP
CD_LR_2B_Methods
 
typedef utility::vector1
< methods::LongRangeTwoBodyEnergyCOP
LR_2B_Methods
 
typedef utility::vector1
< methods::TwoBodyEnergyOP
TWO_B_Methods
 
typedef utility::vector1
< methods::WholeStructureEnergyOP
WS_Methods
 
typedef utility::vector1
< methods::WholeStructureEnergyOP >
::const_iterator 
WS_MethodIterator
 
typedef utility::vector1
< methods::LongRangeTwoBodyEnergyCOP >
::const_iterator 
LR_2B_MethodIterator
 
typedef utility::vector1
< methods::TwoBodyEnergyOP >
::const_iterator 
TWO_B_MethodIterator
 
typedef utility::vector1
< methods::EnergyMethodCOP >
::const_iterator 
AllMethodsIterator
 
typedef utility::vector1
< methods::ContextIndependentLRTwoBodyEnergyOP >
::const_iterator 
CI_LR_2B_MethodIterator
 
typedef utility::vector1
< methods::ContextDependentLRTwoBodyEnergyOP >
::const_iterator 
CD_LR_2B_MethodIterator
 
- Public Member Functions inherited from core::scoring::ScoreFunction
 ScoreFunction ()
 default ctor that initializes its EnergyMethodOptions object from the global option collection More...
 
 ScoreFunction (utility::options::OptionCollection const &options)
 ctor that initializes its EnergyMethodOptions object from a (possibly local) option collection More...
 
 ~ScoreFunction () override
 
ScoreFunctionCOP get_self_ptr () const
 self pointers More...
 
ScoreFunctionOP get_self_ptr ()
 
virtual void assign (ScoreFunction const &src)
 NOT FOR GENERAL USE Copy the information about src into the current score function. There are deep interactions with subclasses, (the subclass information doesn't necessarily get copied) so this is primarily for advanced scorefunction manipulation. Normal usage should just use clone() and replace the OP. More...
 
virtual ScoreFunctionOP clone () const
 Create a copy of the scorefunction Virtual to keep subclass information. More...
 
ScoreFunctionOP clone_as_base_class () const
 If you want to discard subclass information, the following function is availible. More...
 
void reset ()
 Resets the ScoreFunction to default values, reading from the global options collection. More...
 
void reset (utility::options::OptionCollection const &options)
 Resets the ScoreFunction to default values, reading from a (possibly local) options collection. 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 _add_weights_from_stream (std::istream &data, bool patch=false, std::string const &filename="")
 
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)
 Sets the EnergyMethodOptions object contained in this ScoreFunction. with appropriate update of all the energy methods. 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...
 
Real score_by_scoretype (pose::Pose &pose, ScoreType const t, bool const weighted=true) const
 Returns the score of the ScoreType <t> More...
 
EnergyMap const & weights () const
 Returns an EnergyMap of the current set of weights. More...
 
Real weighted_sum (EnergyMap const &unweighted) const
 Returns the weighted sum of the given energy map, given 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 const & 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...
 
void set_weight_if_zero (ScoreType const &t, Real const &setting)
 Sets the weight for ScoreType <t> to <setting> if weight is originally zero. More...
 
void add_to_weight (ScoreType const &t, Real const &increment)
 Increments the weight for ScoreType <t> by <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 finalize_after_minimizing (pose::Pose &pose) const
 Called after minimization. More...
 
virtual void setup_for_minimizing_for_node (MinimizationNode &min_node, conformation::Residue const &rsd, basic::datacache::BasicDataCache &res_data_cache, 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, basic::datacache::BasicDataCache &res_data_cache, 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, Real const edge_dweight=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 setup_for_packing_with_rotsets (pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets) const
 Lets the scoring functions cache anything they need to calculate energies in a packing step (pack_rotamers) in the context of all available 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
 
bool check_methods_in_right_order (ScoreType const &score_type_in_first_method, ScoreType const &score_type_in_second_method) const
 check order of methods More...
 
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 show_additional (std::ostream &out, pose::Pose &pose, bool verbose=false) 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
 
bool ready_for_nonideal_scoring () const
 
AllMethods const & all_methods () const
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 
- Static Public Member Functions inherited from core::scoring::ScoreFunction
static void list_options_read (utility::options::OptionKeyList &option_list)
 
static EnergyMap extract_weights_from_file (std::string const &filename, bool patch=false)
 
static EnergyMap extract_weights_from_stream (std::istream &data, bool patch=false, std::string const &filename="")
 
- Protected Member Functions inherited from core::scoring::ScoreFunction
virtual void asym_setup_for_minimizing (pose::Pose &pose, kinematics::MinimizerMapBase const &min_map) const
 
virtual void sym_setup_for_minimizing (pose::Pose &pose, kinematics::MinimizerMapBase const &min_map) const
 
virtual void asym_setup_for_derivatives (pose::Pose &pose) const
 
virtual void sym_setup_for_derivatives (pose::Pose &pose) const
 
virtual void asym_eval_twobody_neighbor_energies (pose::Pose &pose) const
 
virtual void sym_eval_twobody_neighbor_energies (pose::Pose &pose) const
 
virtual void asym_eval_long_range_twobody_energies (pose::Pose &pose) const
 
virtual void sym_eval_long_range_twobody_energies (pose::Pose &pose) const
 
virtual void asym_eval_onebody_energies (pose::Pose &pose) const
 
virtual void sym_eval_onebody_energies (pose::Pose &pose) const
 
bool any_intrares_energies () const
 

Detailed Description

This class is provided as a backward compatibility shim At this point it should be identical to the base ScoreFunction.


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