core::scoring::ScoreFunction Class Reference

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>

Inheritance diagram for core::scoring::ScoreFunction:

Public Types
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
	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...
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...
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
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
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

Private Member Functions
	ScoreFunction (ScoreFunction const &)
	The ScoreFunction copy constructor is explicitly private as using it to make a copy is just too attractive, but discards subclass information. Use ScoreFunction::clone() instead. More...
ScoreFunction &	operator= (ScoreFunction const &)
	The ScoreFunction assignment operator is explicitly private as using it discards subclass information. Rework your algorithm to use ScoreFunctionOP's instead. More...
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...
void	intersubunit_hbond_energy (pose::Pose &pose, EnergyMap &intersubunit_energy) const
void	symmetrical_allow_hbonds (pose::Pose &pose) const
void	set_symmetric_residue_neighbors_hbonds (pose::Pose &pose) const
void	set_symmetric_cenlist (pose::Pose &pose) const
void	correct_arrays_for_symmetry (pose::Pose &pose) const
void	correct_finalize_score (pose::Pose &pose) const

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_

Detailed Description

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.

Member Typedef Documentation

typedef utility::vector1< methods::EnergyMethodCOP > core::scoring::ScoreFunction::AllMethods

typedef utility::vector1< methods::EnergyMethodCOP >::const_iterator core::scoring::ScoreFunction::AllMethodsIterator

typedef utility::vector1< methods::ContextDependentOneBodyEnergyOP > core::scoring::ScoreFunction::CD_1B_Methods

typedef utility::vector1< methods::ContextDependentTwoBodyEnergyOP > core::scoring::ScoreFunction::CD_2B_Methods

typedef utility::vector1< methods::ContextDependentLRTwoBodyEnergyOP >::const_iterator core::scoring::ScoreFunction::CD_LR_2B_MethodIterator

typedef utility::vector1< methods::ContextDependentLRTwoBodyEnergyOP > core::scoring::ScoreFunction::CD_LR_2B_Methods

typedef utility::vector1< methods::ContextIndependentOneBodyEnergyOP > core::scoring::ScoreFunction::CI_1B_Methods

typedef utility::vector1< methods::ContextIndependentTwoBodyEnergyOP > core::scoring::ScoreFunction::CI_2B_Methods

typedef utility::vector1< methods::ContextIndependentLRTwoBodyEnergyOP >::const_iterator core::scoring::ScoreFunction::CI_LR_2B_MethodIterator

typedef utility::vector1< methods::ContextIndependentLRTwoBodyEnergyOP > core::scoring::ScoreFunction::CI_LR_2B_Methods

typedef utility::vector1< methods::LongRangeTwoBodyEnergyCOP >::const_iterator core::scoring::ScoreFunction::LR_2B_MethodIterator

typedef utility::vector1< methods::LongRangeTwoBodyEnergyCOP > core::scoring::ScoreFunction::LR_2B_Methods

typedef utility::vector1< methods::TwoBodyEnergyOP >::const_iterator core::scoring::ScoreFunction::TWO_B_MethodIterator

typedef utility::vector1< methods::TwoBodyEnergyOP > core::scoring::ScoreFunction::TWO_B_Methods

typedef utility::vector1< methods::WholeStructureEnergyOP >::const_iterator core::scoring::ScoreFunction::WS_MethodIterator

typedef utility::vector1< methods::WholeStructureEnergyOP > core::scoring::ScoreFunction::WS_Methods

Constructor & Destructor Documentation

core::scoring::ScoreFunction::ScoreFunction

(

)

default ctor that initializes its EnergyMethodOptions object from the global option collection

Constructor delegation using the OptionCollection ctor, passing the global options collection in as input.

core::scoring::ScoreFunction::ScoreFunction

(

utility::options::OptionCollection const &

options

)

ctor that initializes its EnergyMethodOptions object from a (possibly local) option collection

References reset().

core::scoring::ScoreFunction::~ScoreFunction ( )

overridedefault

core::scoring::ScoreFunction::ScoreFunction ( ScoreFunction const &  )

private

The ScoreFunction copy constructor is explicitly private as using it to make a copy is just too attractive, but discards subclass information. Use ScoreFunction::clone() instead.

Member Function Documentation

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

References _add_weights_from_stream().

Referenced by add_weights_from_file(), and apply_patch_from_file().

void core::scoring::ScoreFunction::_add_weights_from_stream	(	std::istream &	data,
		bool	patch = false,
		std::string const &	filename = ""
	)

References energy_method_options_, core::chemical::num_canonical_aas, reset_energy_methods(), score_function_info_current_, set_etable(), set_weight(), core::scoring::tr(), and weights_.

Referenced by _add_weights_from_file().

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

Note

Currently only works for methods associated with a single specific score_type

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

References add_method(), core::scoring::methods::EnergyMethod::clone(), core::scoring::methods::EnergyMethod::score_types(), and weights_.

void core::scoring::ScoreFunction::add_method ( methods::EnergyMethodOP  method )

private

private – handles setting the derived data

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(), assign(), and set_weight().

void core::scoring::ScoreFunction::add_to_weight	(	ScoreType const &	t,
		Real const &	increment
	)

Increments the weight for ScoreType <t> by <setting>

example(s): scorefxn.add_to_weight(fa_sol,.5) See also: ScoreFunction ScoreFunction.get_weight ScoreFunction.set_weight ScoreType name_from_score_type score_type_from_name

adds to the current weight

References get_weight(), 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.

References _add_weights_from_file(), and core::scoring::find_weights_file().

Referenced by initialize_from_file().

ScoreFunction::AllMethodsIterator core::scoring::ScoreFunction::all_energies_begin

(

)

const

References all_methods_.

Referenced by core::optimization::SingleResidueMultifunc::operator()().

ScoreFunction::AllMethodsIterator core::scoring::ScoreFunction::all_energies_end

(

)

const

References all_methods_.

Referenced by core::optimization::SingleResidueMultifunc::operator()().

ScoreFunction::AllMethods const & core::scoring::ScoreFunction::all_methods

(

)

const

References all_methods_.

Referenced by core::pack::RTMin::rtmin(), and sym_setup_for_minimizing().

bool core::scoring::ScoreFunction::any_intrares_energies ( ) const

inlineprotected

References any_intrares_energies_.

Referenced by sym_eval_onebody_energies().

bool core::scoring::ScoreFunction::any_lr_residue_pair_energy	(	pose::Pose const &	pose,
		Size	res1,
		Size	res2
	)		const

References lr_2b_methods_.

Referenced by are_they_neighbors(), core::pack::rotamer_set::RotamerSets::prepare_otf_graph(), and core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::set_twobody_energies_multithreaded().

void core::scoring::ScoreFunction::apply_patch_from_file

(

std::string const &

filename

)

Applies a patch from the given <filename>

References _add_weights_from_file(), and 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.

Note

Includes long-range energies like constraints, gb... Returns true if the <pose> positions <pos1> and <pos2> are neighbors

Determines whether two positions could have non-zero interaction energy

References any_lr_residue_pair_energy(), max_atomic_interaction_cutoff(), and core::pose::Pose::residue().

void core::scoring::ScoreFunction::assign ( ScoreFunction const &  src )

virtual

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.

Reimplemented in core::scoring::MinScoreScoreFunction, and core::scoring::DockingScoreFunction.

References add_method(), all_methods_, any_intrares_energies_, check_methods(), energy_method_options_, initialize_methods_arrays(), score_function_info_, score_function_info_current_, update_intrares_energy_status(), and weights_.

Referenced by core::scoring::DockingScoreFunction::assign(), core::scoring::MinScoreScoreFunction::assign(), and core::scoring::MinScoreScoreFunction::MinScoreScoreFunction().

void core::scoring::ScoreFunction::asym_eval_long_range_twobody_energies ( pose::Pose &  pose ) const

protectedvirtual

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::pose::Pose::size(), core::scoring::Energies::total_energies(), and core::scoring::Energies::use_nblist().

Referenced by eval_long_range_twobody_energies(), and operator()().

void core::scoring::ScoreFunction::asym_eval_onebody_energies ( pose::Pose &  pose ) const

protectedvirtual

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::size().

Referenced by eval_onebody_energies(), and operator()().

void core::scoring::ScoreFunction::asym_eval_twobody_neighbor_energies ( pose::Pose &  pose ) const

protectedvirtual

References core::scoring::EMapVector::accumulate(), cd_2b_types(), ci_2b_types(), core::pose::Pose::energies(), eval_cd_2b(), eval_ci_2b(), core::scoring::eval_res_pair_energy_for_minedge(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::scoring::EMapVector::zero().

Referenced by eval_twobody_neighbor_energies(), and operator()().

void core::scoring::ScoreFunction::asym_setup_for_derivatives ( pose::Pose &  pose ) const

protectedvirtual

References core::pose::Pose::energies(), core::scoring::Energies::minimization_graph(), core::pose::Pose::residue(), core::pose::Pose::residue_data(), core::scoring::MinimizationNode::setup_for_derivatives(), core::scoring::MinimizationEdge::setup_for_derivatives(), and core::pose::Pose::size().

Referenced by setup_for_derivatives().

void core::scoring::ScoreFunction::asym_setup_for_minimizing ( pose::Pose &  pose, kinematics::MinimizerMapBase const &  min_map  ) const

protectedvirtual

References all_methods_, core::kinematics::MinimizerMapBase::domain_map(), 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::pose::Pose::residue_data(), core::scoring::Energies::set_minimization_graph(), setup_for_lr2benmeth_minimization_for_respair(), setup_for_minimizing_for_node(), setup_for_minimizing_sr2b_enmeths_for_minedge(), and core::pose::Pose::size().

Referenced by setup_for_minimizing().

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)

References cd_2b_methods_, and ci_2b_methods_.

Referenced by protocols::flexpack::rotamer_set::FlexbbRotamerSet::bump_check(), core::pack::rotamer_set::bump_check(), protocols::nmr::bump_check(), core::pack::rotamers::SingleResidueRotamerLibrary::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)

References cd_2b_methods_, and ci_2b_methods_.

Referenced by protocols::flexpack::rotamer_set::FlexbbRotamerSet::bump_check(), core::pack::rotamer_set::bump_check(), protocols::nmr::bump_check(), core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(), and core::pack::rotamer_set::RotamerSet_::bump_check().

ScoreTypes const& core::scoring::ScoreFunction::cd_1b_types ( ) const

inline

convenience access to all cd 1b score types

References core::scoring::methods::cd_1b, and score_types_by_method_type_.

Referenced by asym_eval_onebody_energies(), get_sub_score(), and sym_eval_onebody_energies().

ScoreFunction::CD_2B_Methods::const_iterator core::scoring::ScoreFunction::cd_2b_begin

(

)

const

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

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

References cd_2b_intrares_.

ScoreFunction::TWO_B_MethodIterator core::scoring::ScoreFunction::cd_2b_intrares_end

(

)

const

References cd_2b_intrares_.

ScoreTypes const& core::scoring::ScoreFunction::cd_2b_types ( ) const

inline

convenience access to all cd 2b score types

References core::scoring::methods::cd_2b, and score_types_by_method_type_.

Referenced by asym_eval_onebody_energies(), asym_eval_twobody_neighbor_energies(), get_sub_score(), and sym_eval_twobody_neighbor_energies().

ScoreFunction::CD_LR_2B_MethodIterator core::scoring::ScoreFunction::cd_lr_2b_methods_begin

(

)

const

References cd_lr_2b_methods_.

Referenced by protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::get_res_res_score(), and sym_eval_long_range_twobody_energies().

ScoreFunction::CD_LR_2B_MethodIterator core::scoring::ScoreFunction::cd_lr_2b_methods_end

(

)

const

References cd_lr_2b_methods_.

Referenced by protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::get_res_res_score(), and sym_eval_long_range_twobody_energies().

ScoreTypes const& core::scoring::ScoreFunction::cd_lr_2b_types ( ) const

inline

References core::scoring::methods::cd_lr_2b, and score_types_by_method_type_.

Referenced by asym_eval_onebody_energies(), and get_sub_score().

bool core::scoring::ScoreFunction::check_methods ( ) const

private

private

private

References all_methods_, core::scoring::name_from_score_type(), protocols::hybridization::t, and weights_.

Referenced by assign(), and set_weight().

bool core::scoring::ScoreFunction::check_methods_in_right_order	(	ScoreType const &	score_type_in_first_method,
		ScoreType const &	score_type_in_second_method
	)		const

check order of methods

References all_methods_.

Referenced by core::scoring::methods::FreeDOF_Energy::do_fa_stack_scorefunction_checks().

ScoreTypes const& core::scoring::ScoreFunction::ci_1b_types ( ) const

inline

convenience access to all ci 1b score types

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

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

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

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

References ci_2b_intrares_.

Referenced by core::scoring::mm::mm_bond_angle_residue_type_param_set().

ScoreTypes const& core::scoring::ScoreFunction::ci_2b_types ( ) const

inline

convenience access to all ci 2b score types

References core::scoring::methods::ci_2b, and score_types_by_method_type_.

Referenced by asym_eval_twobody_neighbor_energies(), get_sub_score(), setup_for_minimizing_sr2b_enmeths_for_minedge(), and sym_eval_twobody_neighbor_energies().

ScoreFunction::CI_LR_2B_MethodIterator core::scoring::ScoreFunction::ci_lr_2b_methods_begin

(

)

const

References ci_lr_2b_methods_.

Referenced by protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::get_res_res_score(), and sym_eval_long_range_twobody_energies().

ScoreFunction::CI_LR_2B_MethodIterator core::scoring::ScoreFunction::ci_lr_2b_methods_end

(

)

const

References ci_lr_2b_methods_.

Referenced by protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::get_res_res_score(), and sym_eval_long_range_twobody_energies().

ScoreTypes const& core::scoring::ScoreFunction::ci_lr_2b_types ( ) const

inline

References core::scoring::methods::ci_lr_2b, and score_types_by_method_type_.

Referenced by get_sub_score().

ScoreFunctionOP core::scoring::ScoreFunction::clone ( ) const

virtual

Create a copy of the scorefunction Virtual to keep subclass information.

Reimplemented in core::scoring::MinScoreScoreFunction, and core::scoring::DockingScoreFunction.

Referenced by protocols::forge::components::BDR::centroid_scorefunction(), protocols::forge::remodel::RemodelMover::centroid_scorefunction(), core::scoring::deep_copy(), protocols::moves::DualMonteCarlo::DualMonteCarlo(), core::pack::rotamer_set::RotamerSet_::filter_water_rotamers(), core::scoring::methods::OtherPoseEnergy::finalize_total_energy(), protocols::forge::components::BDR::fullatom_scorefunction(), protocols::forge::remodel::RemodelMover::fullatom_scorefunction(), core::util::getMLweight(), core::util::getMLweight_cart(), protocols::monte_carlo::MonteCarloInterface::init_interface_analyzer(), protocols::symmetry::SymShakeStructureMover::minimize_with_constraints(), protocols::simple_moves::ShakeStructureMover::minimize_with_constraints(), protocols::moves::MonteCarlo::MonteCarlo(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::parse_my_tag(), protocols::cryst::SetCrystWeightMover::parse_my_tag(), core::pack::rotamer_set::pre_bump_check(), protocols::moves::MonteCarlo::reset_scorefxn(), protocols::dna::PDBOutput::score_function(), protocols::monte_carlo::MonteCarloInterface::score_function(), core::fragment::picking_old::vall::eval::EnergyEval::score_function(), protocols::moves::MonteCarlo::score_function(), protocols::fldsgn::BluePrintBDR::scorefunction(), protocols::forge::remodel::RemodelLoopMover::scorefunction(), protocols::forge::components::VarLengthBuild::scorefunction(), protocols::loophash::LocalInserter_SimpleMin::scorefxn_cen_cst(), protocols::loophash::LocalInserter_SimpleMin::scorefxn_rama_cst(), protocols::abinitio::ConstraintFragmentSampler::set_max_seq_sep(), protocols::pack_daemon::PackDaemon::set_score_function(), protocols::pack_daemon::DaemonSet::set_score_function(), core::pack::interaction_graph::OnTheFlyInteractionGraph::set_score_function(), core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::set_score_function(), protocols::pack_daemon::DynamicAggregateFunction::set_score_function(), core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::set_score_function(), protocols::simple_moves::sidechain_moves::SidechainMCMover::set_scorefunction(), protocols::minimization_packing::GreenPacker::set_scorefunction(), core::pack::interaction_graph::SimpleInteractionGraph::set_scorefunction(), protocols::denovo_design::components::RemodelLoopMoverPoseFolder::set_scorefxn(), protocols::denovo_design::movers::BridgeChainsMover::set_scorefxn(), protocols::md::MDBase::set_scorefxn(), protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_scorefxn(), protocols::md::MDBase::set_scorefxn_obj(), sym_eval_onebody_energies(), and symmetrical_allow_hbonds().

ScoreFunctionOP core::scoring::ScoreFunction::clone_as_base_class

(

)

const

If you want to discard subclass information, the following function is availible.

void core::scoring::ScoreFunction::correct_arrays_for_symmetry ( pose::Pose &  pose ) const

private

References core::pose::datacache::CacheableDataType::CEN_LIST_INFO, core::pose::Pose::data(), has_nonzero_weight(), core::scoring::hbond_bb_sc, core::scoring::hbond_lr_bb, core::scoring::hbond_sc, core::scoring::hbond_sr_bb, set_symmetric_cenlist(), set_symmetric_residue_neighbors_hbonds(), and symmetrical_allow_hbonds().

Referenced by operator()().

void core::scoring::ScoreFunction::correct_finalize_score ( pose::Pose &  pose ) const

private

References core::pose::Pose::conformation(), core::pose::Pose::energies(), core::scoring::Energies::finalized_energies(), has_nonzero_weight(), core::scoring::hbond_lr_bb, core::scoring::hbond_sr_bb, core::scoring::interchain_contact, intersubunit_hbond_energy(), core::scoring::Energies::total_energies(), core::scoring::Energies::use_nblist(), ws_methods_begin(), and ws_methods_end().

Referenced by operator()().

methods::EnergyMethodOptions const& core::scoring::ScoreFunction::energy_method_options ( ) const

inline

Returns the EnergyMethodOptions object contained in this ScoreFunction (const access)

References energy_method_options_.

Referenced by protocols::hydrate::add_water_overcoordinated_hb_score(), core::scoring::methods::SecondaryStructureEnergy::finalize_total_energy(), core::scoring::ScoreFunctionInfo::initialize_from(), protocols::abinitio::ConstraintFragmentSampler::set_max_seq_sep(), protocols::relax::setup_for_dna(), core::scoring::methods::PoissonBoltzmannEnergy::setup_for_scoring(), and protocols::hydrate::water_specific_hbond_energy().

void core::scoring::ScoreFunction::eval_cd_1b ( conformation::Residue const &  rsd, pose::Pose const &  pose, EnergyMap &  emap  ) const

virtual

Accumulates the unweighted one body energies of all context dependent one body energies for <pose> Residue <rsd> into EnergyMap <emap>

Note

: EnergyMap is an EMapVector

Reimplemented in protocols::flexpack::OtherContextScoreFunction.

References cd_1b_methods_.

Referenced by asym_eval_onebody_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_and_two_body_energies(), 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(), protocols::hbnet::hbnet_one_body_energies(), protocols::hbnet::hbnet_symm_one_body_energies(), core::optimization::SingleResidueMultifunc::operator()(), and sym_eval_onebody_energies().

void core::scoring::ScoreFunction::eval_cd_2b ( conformation::Residue const &  rsd1, conformation::Residue const &  rsd2, pose::Pose const &  pose, EnergyMap &  emap  ) const

virtual

Accumulate the unweighted short range context dependent two body interaction energies of <pose> between Residue <rsd1> and Residue <rsd2> into EnergyMap <emap>

Note

: EnergyMap is an EMapVector

Reimplemented in protocols::flexpack::OtherContextScoreFunction.

References cd_2b_methods_.

Referenced by asym_eval_twobody_neighbor_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_and_two_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(), protocols::flexpack::OtherContextScoreFunction::eval_cd_2b(), protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::get_res_res_score(), core::optimization::SingleResidueMultifunc::operator()(), and sym_eval_twobody_neighbor_energies().

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>

Note

: EnergyMap is an EMapVector

References cd_2b_methods_.

Referenced by core::pack::rotamer_set::RotamerSets::get_bb_bbE().

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>

Note

: EnergyMap is an EMapVector

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>

Note

: EnergyMap is an EMapVector

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().

void core::scoring::ScoreFunction::eval_cd_intrares_energy ( conformation::Residue const &  rsd, pose::Pose const &  pose, EnergyMap &  emap  ) const

virtual

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>

Note

: EnergyMap is an EMapVector

Reimplemented in protocols::flexpack::OtherContextScoreFunction.

References any_intrares_energies_, and cd_2b_intrares_.

Referenced by asym_eval_onebody_energies(), protocols::flexpack::OtherContextScoreFunction::eval_cd_intrares_energy(), and sym_eval_onebody_energies().

void core::scoring::ScoreFunction::eval_ci_1b	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		EnergyMap &	emap
	)		const

References ci_1b_methods_.

Referenced by asym_eval_onebody_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_and_two_body_energies(), 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::optimization::SingleResidueMultifunc::operator()(), and sym_eval_onebody_energies().

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>

Note

: EnergyMap is an EMapVector

References ci_2b_methods_.

Referenced by asym_eval_twobody_neighbor_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_and_two_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(), protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::get_res_res_score(), core::optimization::SingleResidueMultifunc::operator()(), and sym_eval_twobody_neighbor_energies().

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>

Note

: EnergyMap is an EMapVector

References ci_2b_methods_.

Referenced by core::pack::rotamer_set::RotamerSets::get_bb_bbE().

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>

Note

: EnergyMap is an EMapVector

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>

Note

: EnergyMap is an EMapVector

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>

Note

: EnergyMap is an EMapVector

References any_intrares_energies_, and ci_2b_intrares_.

Referenced by asym_eval_onebody_energies(), and sym_eval_onebody_energies().

Real core::scoring::ScoreFunction::eval_dof_derivative	(	id::DOF_ID const &	dof_id,
		id::TorsionID const &	torsion_id,
		pose::Pose const &	pose
	)		const

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::atom_tree_dfunc(), core::optimization::symmetry::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.

Note

: EnergyMap is an EMapVector

References any_intrares_energies_, cd_2b_intrares_, and ci_2b_intrares_.

Referenced by core::optimization::SingleResidueMultifunc::operator()().

void core::scoring::ScoreFunction::eval_long_range_twobody_energies ( pose::Pose &  pose ) const

virtual

References asym_eval_long_range_twobody_energies(), core::pose::symmetry::is_symmetric(), and sym_eval_long_range_twobody_energies().

void core::scoring::ScoreFunction::eval_npd_atom_derivative ( id::AtomID const &  atom_id, pose::Pose const &  pose, kinematics::DomainMap const &  domain_map, Vector &  F1, Vector &  F2  ) const

virtual

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().

void core::scoring::ScoreFunction::eval_onebody_energies ( pose::Pose &  pose ) const

virtual

References asym_eval_onebody_energies(), core::pose::symmetry::is_symmetric(), and sym_eval_onebody_energies().

void core::scoring::ScoreFunction::eval_twobody_neighbor_energies ( pose::Pose &  pose ) const

virtual

References asym_eval_twobody_neighbor_energies(), core::pose::symmetry::is_symmetric(), and sym_eval_twobody_neighbor_energies().

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

References cd_2b_methods_, ci_2b_methods_, and weights().

Referenced by core::pack::rotamer_set::RotamerSet_::compute_one_and_two_body_energies(), 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

References any_intrares_energies_, cd_2b_intrares_, and ci_2b_intrares_.

Referenced by core::pack::rotamer_set::RotamerSet_::compute_one_and_two_body_energies(), 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

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

References cd_2b_methods_, ci_2b_methods_, and weights().

Referenced by core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), protocols::hbnet::hbnet_symm_one_body_energies(), and core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::set_twobody_energies_multithreaded().

EnergyMap core::scoring::ScoreFunction::extract_weights_from_file ( std::string const &  filename, bool  patch = false  )

static

References extract_weights_from_stream().

EnergyMap core::scoring::ScoreFunction::extract_weights_from_stream ( std::istream &  data, bool  patch = false, std::string const &  filename = ""  )

static

References core::scoring::ScoreTypeManager::is_score_type(), core::scoring::EMapVector::set(), core::scoring::tr(), and weights().

Referenced by extract_weights_from_file().

void core::scoring::ScoreFunction::finalize_after_derivatives ( pose::Pose &  pose ) const

virtual

References all_methods_.

Referenced by core::optimization::atom_tree_dfunc(), core::optimization::symmetry::atom_tree_dfunc(), and core::optimization::cartesian_dfunc().

void core::scoring::ScoreFunction::finalize_after_minimizing ( pose::Pose &  pose ) const

virtual

Called after minimization.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References all_methods_.

Referenced by core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::optimization::AtomTreeMinimizer::run(), and core::optimization::CartesianMinimizer::run().

std::string core::scoring::ScoreFunction::get_name ( ) const

inline

References name_.

Referenced by core::scoring::methods::PoissonBoltzmannEnergy::setup_for_scoring().

ScoreTypes core::scoring::ScoreFunction::get_nonzero_weighted_scoretypes ( ) const

inline

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

References has_nonzero_weight(), and core::scoring::n_score_types.

Referenced by perturb_weights(), serialize_weights(), and core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::set_score_function().

ScoreFunctionCOP core::scoring::ScoreFunction::get_self_ptr ( ) const

inline

self pointers

Referenced by protocols::topology_broker::FoldandDockClaimer::add_mover(), protocols::topology_broker::AsymFoldandDockClaimer::add_mover(), and protocols::topology_broker::FibrilModelingClaimer::add_mover().

ScoreFunctionOP core::scoring::ScoreFunction::get_self_ptr ( )

inline

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.

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::scoring::Energies::data(), core::scoring::EMapVector::dot(), core::pose::Pose::energies(), core::scoring::hbonds::get_hbond_energies(), core::scoring::hbond_lr_bb, core::scoring::EnergiesCacheableDataType::HBOND_SET, core::scoring::hbond_sr_bb, core::scoring::Energies::long_range_container(), core::pose::Pose::size(), protocols::analysis::total, 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.

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::scoring::Energies::data(), core::pose::Pose::energies(), core::scoring::hbonds::get_hbond_energies(), core::scoring::hbond_lr_bb, core::scoring::EnergiesCacheableDataType::HBOND_SET, core::scoring::hbond_sr_bb, core::scoring::Energies::long_range_container(), core::pose::Pose::size(), 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.

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.

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.

References get_sub_score(), and core::pose::Pose::size().

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.

References get_sub_score(), and core::pose::Pose::size().

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.

References core::pose::Pose::energies(), core::scoring::Energies::energies_updated(), get_sub_score(), and core::pose::Pose::size().

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.

References core::pose::Pose::energies(), core::scoring::Energies::energies_updated(), get_sub_score(), and core::pose::Pose::size().

Real core::scoring::ScoreFunction::get_weight

(

ScoreType const &

t

)

const

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

References protocols::hybridization::t, and weights_.

Referenced by add_to_weight(), protocols::canonical_sampling::PatchOperation::apply(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph(), core::scoring::rna::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges(), core::scoring::lkball::LK_BallEnergy::evaluate_rotamer_background_energies(), core::scoring::elec::FA_ElecEnergy::evaluate_rotamer_intrares_energies(), core::scoring::lkball::LK_BallEnergy::evaluate_rotamer_pair_energies(), core::scoring::cryst::XtalMLEnergy::finalize_total_energy(), core::scoring::methods::ProQ_Energy::finalize_total_energy(), core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::initialize(), core::import_pose::atom_tree_diffs::map_of_weighted_scores(), merge(), core::scoring::constraints::merge_csts_to_scorefunction(), protocols::dna::RotamerDNAHBondFilter::operator()(), perturb_weights(), protocols::symmetry::SymShakeStructureMover::reduce_fa_rep(), protocols::simple_moves::ShakeStructureMover::reduce_fa_rep(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy(), serialize_weights(), set_weight_if_zero(), core::scoring::cryst::XtalMLEnergy::setup_for_derivatives(), and protocols::ddg::ddGMover::store_energies().

bool core::scoring::ScoreFunction::has_nonzero_weight ( ScoreType const &  t ) const

inline

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

References weights_.

Referenced by correct_arrays_for_symmetry(), correct_finalize_score(), core::scoring::methods::FreeDOF_Energy::do_fa_stack_scorefunction_checks(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_atom_derivative(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_intrares_energy(), core::scoring::rna::data::RNA_ChemicalMappingEnergy::finalize_total_energy(), core::scoring::methods::FreeDOF_Energy::finalize_total_energy(), 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(), core::scoring::disulfides::FullatomDisulfideEnergy::old_eval_atom_derivative(), perturb_weights(), ready_for_nonideal_scoring(), core::scoring::rna::TNA_SuiteEnergy::residue_pair_energy(), core::scoring::rna::RNA_SuiteEnergy::residue_pair_energy(), core::scoring::elec::RNA_FA_ElecEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy(), core::scoring::methods::LK_PolarNonPolarEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy_ext(), core::scoring::methods::LK_PolarNonPolarEnergy::residue_pair_energy_ext(), core::scoring::elec::RNA_FA_ElecEnergy::score_atom_pair(), serialize_weights(), set_weight(), and core::scoring::rna::RNA_FullAtomStackingEnergy::setup_for_minimizing().

bool core::scoring::ScoreFunction::has_zero_weight ( ScoreType const &  t ) const

inline

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

References weights_.

Referenced by core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), core::scoring::methods::CustomAtomPairEnergy::eval_atom_derivative(), core::scoring::Ramachandran::eval_rama_score_all(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::scoring::ScoreFunctionInfo::initialize_from(), core::scoring::constraints::merge_csts_to_scorefunction(), ready_for_nonideal_scoring(), 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

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 )

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

References add_weights_from_file(), and reset().

void core::scoring::ScoreFunction::initialize_methods_arrays ( )

private

sets up the derived method vectors from the primary vectors

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_.

Referenced by assign(), and reset().

void core::scoring::ScoreFunction::intersubunit_hbond_energy ( pose::Pose &  pose, EnergyMap &  intersubunit_energy  ) const

private

References core::pose::Pose::conformation(), core::scoring::Energies::data(), core::pose::Pose::energies(), core::scoring::hbonds::get_hbond_weight_type(), core::scoring::hbond, core::scoring::hbond_lr_bb, core::scoring::EnergiesCacheableDataType::HBOND_SET, core::scoring::hbond_sr_bb, core::scoring::hbonds::hbw_LR_BB, core::scoring::hbonds::hbw_LR_BB_SC, core::scoring::hbonds::hbw_SC, core::scoring::hbonds::hbw_SR_BB, core::scoring::hbonds::hbw_SR_BB_SC, and core::scoring::tr().

Referenced by correct_finalize_score().

void core::scoring::ScoreFunction::list_options_read ( utility::options::OptionKeyList &  option_list )

static

References core::scoring::methods::EnergyMethodOptions::list_options_read().

Referenced by core::scoring::DockingScoreFunction::list_options_read(), core::scoring::MinScoreScoreFunction::list_options_read(), and core::scoring::ScoreFunctionFactory::list_read_options().

ScoreFunction::LR_2B_MethodIterator core::scoring::ScoreFunction::long_range_energies_begin

(

)

const

References lr_2b_methods_.

Referenced by core::pack::rotamer_set::symmetry::SymmetricRotamerSets::append_two_body_energy_computations_to_work_vector(), core::pack::rotamer_set::RotamerSets::append_two_body_energy_computations_to_work_vector(), asym_setup_for_minimizing(), core::pack::interaction_graph::SimpleEdge::compute_energy(), core::pack::rotamer_set::RotamerSet_::compute_one_and_two_body_energies(), 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::create_minimization_graph(), core::optimization::SingleResidueMultifunc::operator()(), core::pack::rotamer_set::RotamerSets::prepare_otf_graph(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::prepare_symm_otf_interaction_graph(), core::pack::RTMin::rtmin(), protocols::ncbb::SecStructMinimizeMultiFunc::setup_minimization_graph(), and sym_setup_for_minimizing().

ScoreFunction::LR_2B_MethodIterator core::scoring::ScoreFunction::long_range_energies_end

(

)

const

References lr_2b_methods_.

Referenced by core::pack::rotamer_set::symmetry::SymmetricRotamerSets::append_two_body_energy_computations_to_work_vector(), core::pack::rotamer_set::RotamerSets::append_two_body_energy_computations_to_work_vector(), asym_setup_for_minimizing(), core::pack::interaction_graph::SimpleEdge::compute_energy(), core::pack::rotamer_set::RotamerSet_::compute_one_and_two_body_energies(), 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::create_minimization_graph(), core::optimization::SingleResidueMultifunc::operator()(), core::pack::rotamer_set::RotamerSets::prepare_otf_graph(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::prepare_symm_otf_interaction_graph(), core::pack::RTMin::rtmin(), protocols::ncbb::SecStructMinimizeMultiFunc::setup_minimization_graph(), and sym_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.

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

References get_weight(), core::scoring::n_score_types, and set_weight().

void core::scoring::ScoreFunction::name ( std::string const &  weights_tag )

inline

Accumulates the unweighted one body energies of all context independent one body energies for <pose> Residue <rsd> into EnergyMap <emap>

Note

: EnergyMap is an EMapVector

References name_.

Referenced by core::scoring::find_weights_file().

Real core::scoring::ScoreFunction::operator() ( pose::Pose &  pose ) const

virtual

Scores the given <pose> using this ScoreFunction. Alters the Energies object within <pose>, but does not alter this ScoreFunction.

Reimplemented in core::scoring::MinScoreScoreFunction, and core::scoring::DockingScoreFunction.

References all_methods_, asym_eval_long_range_twobody_energies(), asym_eval_onebody_energies(), asym_eval_twobody_neighbor_energies(), correct_arrays_for_symmetry(), correct_finalize_score(), core::scoring::EMapVector::dot(), core::pose::Pose::energies(), core::scoring::Energies::finalized_energies(), core::scoring::EMapVector::is_finite(), 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::pose::Pose::size(), sym_eval_long_range_twobody_energies(), sym_eval_onebody_energies(), sym_eval_twobody_neighbor_energies(), core::scoring::Energies::total_energies(), core::scoring::Energies::total_energy(), 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 &  )

private

The ScoreFunction assignment operator is explicitly private as using it discards subclass information. Rework your algorithm to use ScoreFunctionOP's instead.

Real core::scoring::ScoreFunction::operator[] ( ScoreType const &  t ) const

inline

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

References protocols::hybridization::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.

• 68% of the time, percent change [0, 12.5)
• 26% of the time, percent change [12.5, 25)
• 4% of the time, percent change [25...

References get_nonzero_weighted_scoretypes(), get_weight(), has_nonzero_weight(), protocols::mean_field::max(), core::scoring::name_from_score_type(), core::conformation::membrane::normal, set_weight(), and core::scoring::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.)

References all_methods_.

Referenced by core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::add_longrange_twobody_energies_multithreaded(), 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(), protocols::hbnet::hbnet_symm_one_body_energies(), core::pack::rotamer_set::RotamerSets::prepare_sets_for_packing(), core::pack::rotamer_trials(), core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::set_twobody_energies_multithreaded(), and core::pack::symmetric_rotamer_trials().

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > core::scoring::ScoreFunction::provide_authorship_info_for_unpublished ( ) const

virtual

Provide a list of authors and their e-mail addresses, as strings.

Returns

A list of pairs of (author, e-mail address). Empty list if not unpublished.

The default implementation of this provides a vector of unpublished author info from all energy methods that this scorefunction has that have nonzero weights.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

References all_methods_.

utility::vector1< basic::citation_manager::CitationCollectionCOP > core::scoring::ScoreFunction::provide_citation_info ( ) const

virtual

Provide the citation.

Returns

A vector of citation collections. This allows the scorefunction to provide citations for itself and for any modules that it invokes (particularl energy methods).

The default implementation of this provides a vector of citations from all energy methods that this scorefunction has that have nonzero weights.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

References all_methods_.

bool core::scoring::ScoreFunction::ready_for_nonideal_scoring

(

)

const

References core::scoring::bond_geometry, core::scoring::cart_bonded, core::scoring::cart_bonded_angle, core::scoring::cart_bonded_improper, core::scoring::cart_bonded_length, core::scoring::cart_bonded_proper, core::scoring::cart_bonded_torsion, has_nonzero_weight(), has_zero_weight(), core::scoring::mm_bend, core::scoring::mm_lj_inter_atr, core::scoring::mm_lj_inter_rep, core::scoring::mm_lj_intra_atr, core::scoring::mm_lj_intra_rep, core::scoring::mm_stretch, core::scoring::mm_twist, core::scoring::pro_close, and core::scoring::rna_bond_geometry.

Referenced by core::optimization::AtomTreeMinimizer::check_setup(), core::pack::min_pack_setup(), core::pack::RTMin::rtmin(), and core::optimization::CartesianMinimizer::run().

void core::scoring::ScoreFunction::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

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().

void core::scoring::ScoreFunction::remove_method ( methods::EnergyMethodOP  method )

private

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, reading from the global options collection.

reset function that can be called either independently or from default ScoreFunction creation

Referenced by initialize_from_file(), and ScoreFunction().

void core::scoring::ScoreFunction::reset

(

utility::options::OptionCollection const &

options

)

Resets the ScoreFunction to default values, reading from a (possibly local) options collection.

References any_intrares_energies_, core::scoring::EMapVector::clear(), energy_method_options_, initialize_methods_arrays(), score_function_info_, score_function_info_current_, and weights_.

void core::scoring::ScoreFunction::reset_energy_methods

(

)

References core::scoring::EMapVector::get(), core::scoring::n_score_types, set_weight(), and weights_.

Referenced by _add_weights_from_stream(), set_energy_method_options(), set_etable(), and set_method_weights().

Real core::scoring::ScoreFunction::score ( pose::Pose &  pose ) const

virtual

Scores the given <pose> using this ScoreFunction. Alters the Energies object within <pose>, but does not alter this ScoreFunction.

Note

: Synonym for () operator. Makes code look a little nicer. Doesn't do anything but call () operator.

Referenced by protocols::monte_carlo::MonteCarloInterface::calculate_score(), and score_by_scoretype().

Real core::scoring::ScoreFunction::score_by_scoretype	(	pose::Pose &	pose,
		ScoreType const	t,
		bool const	weighted = true
	)		const

Returns the score of the ScoreType <t>

References core::pose::Pose::energies(), score(), protocols::hybridization::t, core::scoring::Energies::total_energies(), and weights_.

ScoreTypes const& core::scoring::ScoreFunction::score_types_by_method_type ( methods::EnergyMethodType const &  t ) const

inline

References score_types_by_method_type_, and protocols::hybridization::t.

std::string core::scoring::ScoreFunction::serialize_weights

(

)

const

Serializes the non-zero score function term weights Format: { term : weight, ... }.

Format: { term : weight, ... }.

References get_nonzero_weighted_scoretypes(), get_weight(), has_nonzero_weight(), and protocols::kinmatch::str().

void core::scoring::ScoreFunction::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.

References energy_method_options_, reset_energy_methods(), and score_function_info_current_.

Referenced by protocols::hydrate::add_water_overcoordinated_hb_score(), protocols::flexpack::FlexPacker::apply(), protocols::relax::setup_for_dna(), and protocols::hydrate::water_specific_hbond_energy().

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.

References energy_method_options_, reset_energy_methods(), and score_function_info_current_.

Referenced by _add_weights_from_stream().

void core::scoring::ScoreFunction::set_method_weights	(	ScoreType const &	t,
		utility::vector1< Real > const &	wts
	)

References energy_method_options_, reset_energy_methods(), and score_function_info_current_.

void core::scoring::ScoreFunction::set_symmetric_cenlist ( pose::Pose &  pose ) const

private

References core::pose::datacache::CacheableDataType::CEN_LIST_INFO, core::pose::Pose::conformation(), core::pose::Pose::data(), and core::pose::Pose::size().

Referenced by correct_arrays_for_symmetry().

void core::scoring::ScoreFunction::set_symmetric_residue_neighbors_hbonds ( pose::Pose &  pose ) const

private

private

References core::pose::Pose::conformation(), core::scoring::Energies::data(), core::pose::Pose::energies(), core::scoring::EnergiesCacheableDataType::HBOND_SET, and core::pose::Pose::size().

Referenced by correct_arrays_for_symmetry().

void core::scoring::ScoreFunction::set_weight	(	ScoreType const &	t,
		Real const &	setting
	)

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

References add_method(), check_methods(), energy_method_options_, has_nonzero_weight(), methods_by_score_type_, core::scoring::python, remove_method(), score_function_info_current_, protocols::hybridization::t, update_intrares_energy_status(), and weights_.

Referenced by _add_weights_from_stream(), 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(), add_to_weight(), protocols::topology_broker::ConstraintEvaluatorWrapper::apply(), protocols::flexpack::FlexPacker::apply(), protocols::simple_filters::ScoreEvaluator::apply(), protocols::symmetry::SetupForSymmetryMover::apply(), protocols::simple_filters::TruncatedScoreEvaluator::apply(), protocols::hybridization::HybridizeProtocol::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::toolbox::match_enzdes_util::EnzConstraintParameters::determine_best_constraint(), protocols::symmetric_docking::SymDockProtocol::docking_lowres_filter(), protocols::relax::fix_worst_bad_ramas(), core::pose::symmetry::get_buildingblock_and_neighbor_subs(), protocols::constraint_filters::ConstraintScoreCutoffFilter::get_score(), merge(), core::scoring::constraints::merge_csts_to_scorefunction(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), perturb_weights(), protocols::abinitio::FoldConstraints::prepare_loop_in_stage3(), protocols::symmetry::SymShakeStructureMover::reduce_fa_rep(), protocols::simple_moves::ShakeStructureMover::reduce_fa_rep(), reset_energy_methods(), set_weight_if_zero(), protocols::minimization_packing::GreenPacker::set_weights_for_sfxn(), protocols::simple_moves::ShakeStructureMover::setup_ca_constraints(), and protocols::ddg::ddGMover::store_energies().

void core::scoring::ScoreFunction::set_weight_if_zero	(	ScoreType const &	t,
		Real const &	setting
	)

Sets the weight for ScoreType <t> to <setting> if weight is originally zero.

example(s): scorefxn.set_weight_if_zero(fa_sol,.5) See also: ScoreFunction ScoreFunction.get_weight ScoreFunction.set_weight ScoreType create_score_function name_from_score_type score_type_from_name

set the weight if zero

References get_weight(), and set_weight().

void core::scoring::ScoreFunction::setup_for_derivatives ( pose::Pose &  pose ) const

virtual

References asym_setup_for_derivatives(), core::pose::symmetry::is_symmetric(), and sym_setup_for_derivatives().

Referenced by core::optimization::atom_tree_dfunc(), core::optimization::symmetry::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,
		Real const	edge_dweight = 1.0
	)		const

Initialize an edge in the MinimizationGraph with a particular long-range two body.

References core::scoring::MinimizationEdge::add_twobody_enmeth(), and core::conformation::Residue::seqpos().

Referenced by asym_setup_for_minimizing(), core::pack::create_minimization_graph(), core::pack::RTMin::rtmin(), protocols::ncbb::SecStructMinimizeMultiFunc::setup_minimization_graph(), and sym_setup_for_minimizing().

void core::scoring::ScoreFunction::setup_for_minimizing ( pose::Pose &  pose, kinematics::MinimizerMapBase const &  min_map  ) const

virtual

Initializes a MinimizationGraph and caches it in Energies object of <pose>

Note

: for use during minimization

References asym_setup_for_minimizing(), core::pose::symmetry::is_symmetric(), and sym_setup_for_minimizing().

Referenced by protocols::cartesian::MolecularDynamics::MolecularDynamics(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::optimization::AtomTreeMinimizer::run(), and core::optimization::CartesianMinimizer::run().

void core::scoring::ScoreFunction::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

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.

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 asym_setup_for_minimizing(), core::pack::create_minimization_graph(), core::pack::RTMin::rtmin(), protocols::ncbb::SecStructMinimizeMultiFunc::setup_minimization_graph(), and sym_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.

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 asym_setup_for_minimizing(), core::pack::create_minimization_graph(), core::pack::RTMin::rtmin(), protocols::ncbb::SecStructMinimizeMultiFunc::setup_minimization_graph(), and sym_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)

Note

: the Etable caches tries for each of the residues, the hydrogen bond function caches backbone/backbone hydrogen bonds

References all_methods_.

Referenced by core::pack::task::residue_selector::find_clashing_shell(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), core::pack::min_pack_setup(), core::pack::off_rotamer_pack_setup(), core::pack::pack_rotamers_setup(), core::pack::rotamer_trials(), and core::pack::symmetric_rotamer_trials().

void core::scoring::ScoreFunction::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.

The exact order of events when setting up for packing are as follows:

1. setup_for_packing() is called for all energy methods
2. rotamers are built
3. setup_for_packing_with_rotsets() is called for all energy methods
4. prepare_rotamers_for_packing() is called for all energy methods
5. The energy methods are asked to score all rotamers and rotamer pairs
6. Annealing begins

   Remarks

   The pose is specifically non-const here so that energy methods can store data in it

   Note

   : Used in ApproximateBuriedUnsatPenalty to pre-compute compatible rotamers

   The exact order of events when setting up for packing are as follows:

1. setup_for_packing() is called for all energy methods
2. rotamers are built
3. setup_for_packing_with_rotsets() is called for all energy methods
4. prepare_rotamers_for_packing() is called for all energy methods
5. The energy methods are asked to score all rotamers and rotamer pairs
6. Annealing

   Remarks

   The pose is specifically non-const here so that energy methods can store data in it

   Note

   : Used in ApproximateBuriedUnsatPenalty to pre-compute compatible rotamers

References all_methods_.

Referenced by core::pack::pack_rotamers_setup().

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.

Note

: invoked during scoring.

References all_methods_, core::pose::Pose::energies(), core::scoring::Energies::minimization_graph(), core::pose::Pose::residue(), core::pose::Pose::residue_data(), core::scoring::MinimizationEdge::setup_for_scoring(), core::pose::Pose::size(), core::pose::Pose::total_residue(), and core::scoring::Energies::use_nblist().

Referenced by protocols::symmetry::SetupForSymmetryMover::apply(), 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;

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(), show(), 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

References core::pose::Pose::energies(), core::chemical::element::F, core::scoring::sasa::LJ, core::scoring::n_score_types, core::scoring::Energies::total_energies(), and weights_.

void core::scoring::ScoreFunction::show

(

pose::Pose &

pose

)

const

Scores <pose> and shows the raw and weighted scores for each non-zero ScoreType.

Note

: this function is mostly for convenience in PyRosetta

example(s): scorefxn.show(pose) See also: ScoreFunction ScoreFunction.weights Energies create_score_function

References show(), and core::scoring::tr().

void core::scoring::ScoreFunction::show_additional	(	std::ostream &	out,
		pose::Pose &	pose,
		bool	verbose = false
	)		const

References all_methods_.

Referenced by protocols::abinitio::FragmentSampler::checkpointed_cycle_block().

void core::scoring::ScoreFunction::show_line	(	std::ostream &	out,
		pose::Pose const &	pose
	)		const

References core::pose::Pose::energies(), core::chemical::element::F, core::scoring::n_score_types, core::scoring::Energies::total_energies(), and weights_.

void core::scoring::ScoreFunction::show_line_headers

(

std::ostream &

out

)

const

References core::scoring::sasa::LJ, core::scoring::n_score_types, and weights_.

void core::scoring::ScoreFunction::show_pretty

(

std::ostream &

out

)

const

similar output as show( ostream, pose ) but without the pose

References core::chemical::element::F, core::scoring::sasa::LJ, core::scoring::n_score_types, and weights_.

Referenced by protocols::jd2::archive::EvaluatedArchive::read_structures().

void core::scoring::ScoreFunction::sym_eval_long_range_twobody_energies ( pose::Pose &  pose ) const

protectedvirtual

References cd_lr_2b_methods_begin(), cd_lr_2b_methods_end(), ci_lr_2b_methods_begin(), ci_lr_2b_methods_end(), core::pose::Pose::conformation(), core::pose::Pose::energies(), core::scoring::Energies::nonconst_long_range_container(), core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::Energies::total_energies(), and core::scoring::Energies::use_nblist().

Referenced by eval_long_range_twobody_energies(), and operator()().

void core::scoring::ScoreFunction::sym_eval_onebody_energies ( pose::Pose &  pose ) const

protectedvirtual

References any_intrares_energies(), cd_1b_types(), core::scoring::EMapVector::clear(), clone(), core::pose::Pose::conformation(), core::pose::Pose::energies(), eval_cd_1b(), eval_cd_intrares_energy(), eval_ci_1b(), eval_ci_intrares_energy(), core::scoring::eval_weighted_res_onebody_energies_for_minnode(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by eval_onebody_energies(), and operator()().

void core::scoring::ScoreFunction::sym_eval_twobody_neighbor_energies ( pose::Pose &  pose ) const

protectedvirtual

References core::scoring::EMapVector::accumulate(), cd_2b_types(), ci_2b_types(), core::pose::Pose::conformation(), core::pose::Pose::energies(), eval_cd_2b(), eval_ci_2b(), core::scoring::eval_weighted_res_pair_energy_for_minedge(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::scoring::EMapVector::zero().

Referenced by eval_twobody_neighbor_energies(), and operator()().

void core::scoring::ScoreFunction::sym_setup_for_derivatives ( pose::Pose &  pose ) const

protectedvirtual

References core::pose::Pose::conformation(), core::pose::Pose::energies(), core::pose::Pose::residue(), core::pose::Pose::residue_data(), and core::scoring::MinimizationEdge::setup_for_derivatives().

Referenced by setup_for_derivatives().

void core::scoring::ScoreFunction::sym_setup_for_minimizing ( pose::Pose &  pose, kinematics::MinimizerMapBase const &  min_map  ) const

protectedvirtual

References all_methods(), core::pose::Pose::conformation(), core::kinematics::MinimizerMapBase::domain_map(), 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::pose::Pose::residue_data(), setup_for_lr2benmeth_minimization_for_respair(), setup_for_minimizing_for_node(), setup_for_minimizing_sr2b_enmeths_for_minedge(), and core::pose::Pose::size().

Referenced by setup_for_minimizing().

void core::scoring::ScoreFunction::symmetrical_allow_hbonds ( pose::Pose &  pose ) const

private

References clone(), core::pose::Pose::conformation(), core::scoring::Energies::data(), core::pose::Pose::energies(), core::scoring::hbond, and core::scoring::EnergiesCacheableDataType::HBOND_SET.

Referenced by correct_arrays_for_symmetry().

void core::scoring::ScoreFunction::update_intrares_energy_status ( )

private

check if any of the 2body methods define intra-residue energies, given our current weight set

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 assign(), and 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.

References all_methods_.

Referenced by core::pack::rotamer_trials(), and core::pack::symmetric_rotamer_trials().

EnergyMap const& core::scoring::ScoreFunction::weights ( ) const

inline

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

References weights_.

Referenced by core::scoring::methods::FreeDOF_Energy::accumulate_stack_energy(), core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::add_longrange_twobody_energies_multithreaded(), 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::bump_check(), protocols::nmr::bump_check(), core::pack::rotamers::SingleResidueRotamerLibrary::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::rotamer_set::RotamerSet_::compute_one_and_two_body_energies(), 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(), protocols::relax::RelaxScriptManager::determine_closest_scorefunction(), core::pack::scmin::SCMinMultifunc::dfunc(), core::pack::scmin::CartSCMinMultifunc::dfunc(), core::scoring::methods::FreeDOF_Energy::do_fa_stack_scorefunction_checks(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::pose::Pose::dump_scored_pdb(), 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::elec::FA_ElecEnergy::evaluate_rotamer_background_energies(), evaluate_rotamer_background_energies(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::evaluate_rotamer_intrares_energies(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::evaluate_rotamer_pair_energies(), core::scoring::elec::FA_ElecEnergy::evaluate_rotamer_pair_energies(), evaluate_rotamer_pair_energies(), extract_weights_from_stream(), core::pack::rotamer_set::RotamerSets::get_bb_bbE(), core::scoring::methods::FreeDOF_Energy::get_hbond_energy(), protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::get_res_res_score(), core::pack::rotamer_set::RotamerSets::get_sc_bbE(), protocols::hbnet::hbnet_one_body_energies(), protocols::hbnet::hbnet_symm_one_body_energies(), core::pack::min_pack_optimize(), core::pack::off_rotamer_pack_setup(), core::optimization::SingleResidueMultifunc::operator()(), core::pack::scmin::SCMinMultifunc::operator()(), core::pack::scmin::CartSCMinMultifunc::operator()(), core::scoring::DockingScoreFunction::operator()(), core::scoring::MinScoreScoreFunction::operator()(), core::scoring::constraints::ConstraintSet::residue_pair_energy(), core::scoring::constraints::ConstraintsEnergy::residue_pair_energy_ext(), core::scoring::Energies::scoring_begin(), core::pack::interaction_graph::NPDHBSimpleInteractionGraph::set_scorefunction(), 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::membrane::FaMPSolvEnergy::setup_for_derivatives(), protocols::membrane::scoring::FaWaterToBilayerEnergy::setup_for_derivatives(), core::scoring::membrane::FaMPEnvEnergy::setup_for_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing_for_residue(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::setup_for_packing_with_rotsets(), core::scoring::hbonds::NPDHBondEnergy::setup_for_scoring(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::setup_for_scoring(), protocols::ddg::ddGMover::store_energies(), update_intrares_energy_status(), and protocols::hydrate::water_specific_hbond_energy().

ScoreTypes const& core::scoring::ScoreFunction::whole_structure_types ( ) const

inline

References score_types_by_method_type_, and core::scoring::methods::ws.

ScoreFunction::WS_MethodIterator core::scoring::ScoreFunction::ws_methods_begin

(

)

const

References ws_methods_.

Referenced by correct_finalize_score(), and core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::initialize().

ScoreFunction::WS_MethodIterator core::scoring::ScoreFunction::ws_methods_end

(

)

const

References ws_methods_.

Referenced by correct_finalize_score(), and core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::initialize().

Member Data Documentation

AllMethods core::scoring::ScoreFunction::all_methods_

private

vector of COPs to all active methods

convenience access to the methods/alternate lookups filled by add_method along with the primary methods vectors

Referenced by add_method(), all_energies_begin(), all_energies_end(), all_methods(), assign(), asym_setup_for_minimizing(), check_methods(), check_methods_in_right_order(), finalize_after_derivatives(), finalize_after_minimizing(), indicate_required_context_graphs(), initialize_methods_arrays(), operator()(), prepare_rotamers_for_packing(), provide_authorship_info_for_unpublished(), provide_citation_info(), remove_method(), setup_for_packing(), setup_for_packing_with_rotsets(), setup_for_scoring(), show_additional(), and update_residue_for_packing().

bool core::scoring::ScoreFunction::any_intrares_energies_

private

Referenced by any_intrares_energies(), assign(), asym_eval_onebody_energies(), eval_cd_intrares_energy(), eval_ci_intrares_energy(), eval_intrares_energy(), evaluate_rotamer_intrares_energies(), evaluate_rotamer_intrares_energy_maps(), get_sub_score(), reset(), and update_intrares_energy_status().

CD_1B_Methods core::scoring::ScoreFunction::cd_1b_methods_

private

Referenced by add_method(), eval_cd_1b(), initialize_methods_arrays(), remove_method(), and setup_for_minimizing_for_node().

TWO_B_Methods core::scoring::ScoreFunction::cd_2b_intrares_

private

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().

CD_2B_Methods core::scoring::ScoreFunction::cd_2b_methods_

private

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().

CD_LR_2B_Methods core::scoring::ScoreFunction::cd_lr_2b_methods_

private

Referenced by add_method(), asym_eval_long_range_twobody_energies(), cd_lr_2b_methods_begin(), cd_lr_2b_methods_end(), get_sub_score(), initialize_methods_arrays(), remove_method(), and update_intrares_energy_status().

CI_1B_Methods core::scoring::ScoreFunction::ci_1b_methods_

private

Referenced by add_method(), eval_ci_1b(), initialize_methods_arrays(), remove_method(), and setup_for_minimizing_for_node().

TWO_B_Methods core::scoring::ScoreFunction::ci_2b_intrares_

private

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().

CI_2B_Methods core::scoring::ScoreFunction::ci_2b_methods_

private

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

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().

CI_LR_2B_Methods core::scoring::ScoreFunction::ci_lr_2b_methods_

private

Referenced by add_method(), asym_eval_long_range_twobody_energies(), ci_lr_2b_methods_begin(), ci_lr_2b_methods_end(), get_sub_score(), initialize_methods_arrays(), remove_method(), and update_intrares_energy_status().

methods::EnergyMethodOptionsOP core::scoring::ScoreFunction::energy_method_options_

private

Options that control choice/configuration of EnergyMethods. eg etable name.

Referenced by _add_weights_from_stream(), assign(), energy_method_options(), reset(), set_energy_method_options(), set_etable(), set_method_weights(), set_weight(), and show().

LR_2B_Methods core::scoring::ScoreFunction::lr_2b_methods_

private

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().

AllMethods core::scoring::ScoreFunction::methods_by_score_type_

private

Map from ScoreType to the method for evaluating it. will be 0 for score_types without a method, ie ones with 0 weight.

Referenced by add_method(), initialize_methods_arrays(), remove_method(), and set_weight().

std::string core::scoring::ScoreFunction::name_

private

the scorefxn name

Referenced by get_name(), and name().

ScoreFunctionInfoOP core::scoring::ScoreFunction::score_function_info_

mutableprivate

Referenced by assign(), info(), and reset().

bool core::scoring::ScoreFunction::score_function_info_current_

mutableprivate

Referenced by _add_weights_from_stream(), assign(), info(), reset(), set_energy_method_options(), set_etable(), set_method_weights(), and set_weight().

utility::vector1< ScoreTypes > core::scoring::ScoreFunction::score_types_by_method_type_

private

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().

EnergyMap core::scoring::ScoreFunction::weights_

private

the scorefxn weights

Referenced by _add_weights_from_stream(), add_extra_method(), assign(), check_methods(), eval_dof_derivative(), eval_npd_atom_derivative(), get_sub_score(), get_weight(), has_nonzero_weight(), has_zero_weight(), operator()(), operator[](), reinitialize_minnode_for_residue(), reset(), reset_energy_methods(), score_by_scoretype(), set_weight(), setup_for_minimizing_for_node(), show(), show_line(), show_line_headers(), show_pretty(), and weights().

WS_Methods core::scoring::ScoreFunction::ws_methods_

private

Referenced by add_method(), initialize_methods_arrays(), max_atomic_interaction_cutoff(), remove_method(), ws_methods_begin(), and ws_methods_end().

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

• src/core/scoring/ScoreFunction.hh
• src/core/scoring/ScoreFunction.cc