Rosetta  2018.48
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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:
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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
 

Static Public Member Functions

static void list_options_read (utility::options::OptionKeyList &option_list)
 

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...
 
ScoreFunctionoperator= (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< ScoreTypesscore_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

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 = "" 
)
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
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
ScoreFunction::AllMethodsIterator core::scoring::ScoreFunction::all_energies_end ( ) const
ScoreFunction::AllMethods const & core::scoring::ScoreFunction::all_methods ( ) const
bool core::scoring::ScoreFunction::any_intrares_energies ( ) const
inlineprotected
bool core::scoring::ScoreFunction::any_lr_residue_pair_energy ( pose::Pose const &  pose,
Size  res1,
Size  res2 
) const
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
void core::scoring::ScoreFunction::asym_eval_onebody_energies ( pose::Pose pose) const
protectedvirtual
void core::scoring::ScoreFunction::asym_eval_twobody_neighbor_energies ( pose::Pose pose) const
protectedvirtual
void core::scoring::ScoreFunction::asym_setup_for_derivatives ( pose::Pose pose) const
protectedvirtual
void core::scoring::ScoreFunction::asym_setup_for_minimizing ( pose::Pose pose,
kinematics::MinimizerMapBase const &  min_map 
) const
protectedvirtual
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(), 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(), 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
ScoreFunction::CD_2B_Methods::const_iterator core::scoring::ScoreFunction::cd_2b_end ( ) const
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
ScoreFunction::CD_LR_2B_MethodIterator core::scoring::ScoreFunction::cd_lr_2b_methods_begin ( ) const
ScoreFunction::CD_LR_2B_MethodIterator core::scoring::ScoreFunction::cd_lr_2b_methods_end ( ) const
ScoreTypes const& core::scoring::ScoreFunction::cd_lr_2b_types ( ) const
inline
bool core::scoring::ScoreFunction::check_methods ( ) const
private
bool core::scoring::ScoreFunction::check_methods_in_right_order ( ScoreType const &  score_type_in_first_method,
ScoreType const &  score_type_in_second_method 
) const
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
ScoreFunction::CI_2B_Methods::const_iterator core::scoring::ScoreFunction::ci_2b_end ( ) const
ScoreFunction::TWO_B_MethodIterator core::scoring::ScoreFunction::ci_2b_intrares_begin ( ) const
ScoreFunction::TWO_B_MethodIterator core::scoring::ScoreFunction::ci_2b_intrares_end ( ) const
ScoreTypes const& core::scoring::ScoreFunction::ci_2b_types ( ) const
inline
ScoreFunction::CI_LR_2B_MethodIterator core::scoring::ScoreFunction::ci_lr_2b_methods_begin ( ) const
ScoreFunction::CI_LR_2B_MethodIterator core::scoring::ScoreFunction::ci_lr_2b_methods_end ( ) const
ScoreTypes const& core::scoring::ScoreFunction::ci_lr_2b_types ( ) const
inline
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(), 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
void core::scoring::ScoreFunction::correct_finalize_score ( pose::Pose pose) const
private
methods::EnergyMethodOptions const& core::scoring::ScoreFunction::energy_method_options ( ) const
inline
void core::scoring::ScoreFunction::eval_cd_1b ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
EnergyMap emap 
) const
virtual
void core::scoring::ScoreFunction::eval_cd_2b ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
EnergyMap emap 
) const
virtual
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
void core::scoring::ScoreFunction::eval_ci_2b ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
EnergyMap emap 
) const
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
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
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
void core::scoring::ScoreFunction::eval_onebody_energies ( pose::Pose pose) const
virtual
void core::scoring::ScoreFunction::eval_twobody_neighbor_energies ( pose::Pose pose) const
virtual
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
void core::scoring::ScoreFunction::evaluate_rotamer_intrares_energies ( conformation::RotamerSetBase const &  set,
pose::Pose const &  pose,
utility::vector1< core::PackerEnergy > &  energies 
) const
void core::scoring::ScoreFunction::evaluate_rotamer_intrares_energy_maps ( conformation::RotamerSetBase const &  set,
pose::Pose const &  pose,
utility::vector1< EnergyMap > &  emaps 
) const
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
void core::scoring::ScoreFunction::finalize_after_derivatives ( pose::Pose pose) const
virtual
void core::scoring::ScoreFunction::finalize_after_minimizing ( pose::Pose pose) const
virtual
std::string core::scoring::ScoreFunction::get_name ( ) const
inline
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
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
void core::scoring::ScoreFunction::get_sub_score ( pose::Pose const &  pose,
utility::vector1< bool > const &  residue_mask,
EnergyMap emap 
) const
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
void core::scoring::ScoreFunction::get_sub_score_exclude_res ( pose::Pose pose,
utility::vector1< core::Size > const &  exclude_list,
EnergyMap emap 
) const
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::RNA_SuiteEnergy::residue_pair_energy(), core::scoring::rna::TNA_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
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
void core::scoring::ScoreFunction::intersubunit_hbond_energy ( pose::Pose pose,
EnergyMap intersubunit_energy 
) const
private
void core::scoring::ScoreFunction::list_options_read ( utility::options::OptionKeyList &  option_list)
static
ScoreFunction::LR_2B_MethodIterator core::scoring::ScoreFunction::long_range_energies_begin ( ) const
ScoreFunction::LR_2B_MethodIterator core::scoring::ScoreFunction::long_range_energies_end ( ) const
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
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
bool core::scoring::ScoreFunction::ready_for_nonideal_scoring ( ) const
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
void core::scoring::ScoreFunction::remove_method ( methods::EnergyMethodOP  method)
private
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)
void core::scoring::ScoreFunction::reset_energy_methods ( )
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
ScoreTypes const& core::scoring::ScoreFunction::score_types_by_method_type ( methods::EnergyMethodType const &  t) const
inline
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)
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 
)
void core::scoring::ScoreFunction::set_symmetric_cenlist ( pose::Pose pose) const
private
void core::scoring::ScoreFunction::set_symmetric_residue_neighbors_hbonds ( pose::Pose pose) const
private
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
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
void core::scoring::ScoreFunction::setup_for_minimizing ( pose::Pose pose,
kinematics::MinimizerMapBase const &  min_map 
) const
virtual
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
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
void core::scoring::ScoreFunction::show ( std::ostream &  out) const
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
void core::scoring::ScoreFunction::show_line ( std::ostream &  out,
pose::Pose const &  pose 
) const
void core::scoring::ScoreFunction::show_line_headers ( std::ostream &  out) const
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
void core::scoring::ScoreFunction::sym_eval_onebody_energies ( pose::Pose pose) const
protectedvirtual
void core::scoring::ScoreFunction::sym_eval_twobody_neighbor_energies ( pose::Pose pose) const
protectedvirtual
void core::scoring::ScoreFunction::sym_setup_for_derivatives ( pose::Pose pose) const
protectedvirtual
void core::scoring::ScoreFunction::sym_setup_for_minimizing ( pose::Pose pose,
kinematics::MinimizerMapBase const &  min_map 
) const
protectedvirtual
void core::scoring::ScoreFunction::symmetrical_allow_hbonds ( pose::Pose pose) const
private
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(), 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(), 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(), core::pack::scmin::SCMinMultifunc::dfunc(), core::pack::scmin::CartSCMinMultifunc::dfunc(), core::scoring::methods::FreeDOF_Energy::do_fa_stack_scorefunction_checks(), core::optimization::CartesianMultifunc::dump(), core::optimization::AtomTreeMultifunc::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(), 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::pack::rotamer_set::symmetry::SymmetricRotamerSets::precompute_two_body_energies(), core::pack::rotamer_set::RotamerSets::precompute_two_body_energies(), core::scoring::constraints::ConstraintSet::residue_pair_energy(), core::scoring::constraints::ConstraintsEnergy::residue_pair_energy_ext(), core::scoring::Energies::scoring_begin(), 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(), core::scoring::membrane::FaMPEnvEnergy::setup_for_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing_for_residue(), core::scoring::hbonds::NPDHBondEnergy::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
ScoreFunction::WS_MethodIterator core::scoring::ScoreFunction::ws_methods_begin ( ) const
ScoreFunction::WS_MethodIterator core::scoring::ScoreFunction::ws_methods_end ( ) const

Member Data Documentation

AllMethods core::scoring::ScoreFunction::all_methods_
private
bool core::scoring::ScoreFunction::any_intrares_energies_
private
CD_1B_Methods core::scoring::ScoreFunction::cd_1b_methods_
private
TWO_B_Methods core::scoring::ScoreFunction::cd_2b_intrares_
private
CD_2B_Methods core::scoring::ScoreFunction::cd_2b_methods_
private
CD_LR_2B_Methods core::scoring::ScoreFunction::cd_lr_2b_methods_
private
CI_1B_Methods core::scoring::ScoreFunction::ci_1b_methods_
private
TWO_B_Methods core::scoring::ScoreFunction::ci_2b_intrares_
private
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
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
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
utility::vector1< ScoreTypes > core::scoring::ScoreFunction::score_types_by_method_type_
private
EnergyMap core::scoring::ScoreFunction::weights_
private
WS_Methods core::scoring::ScoreFunction::ws_methods_
private

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