Rosetta 3.4
Public Types | Public Member Functions | Protected Member Functions
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>

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List of all members.

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 ()
 ctor
 ~ScoreFunction ()
ScoreFunctionoperator= (ScoreFunction const &)
 ScoreFunction (ScoreFunction const &)
virtual ScoreFunctionOP clone () const
void reset ()
 Resets the ScoreFunction to default values.
void perturb_weights ()
 Randomly perturbs non-zero score function weights.
std::string serialize_weights () const
 Serializes the non-zero score function term weights Format: { term : weight, ... }.
void add_weights_from_file (std::string const &filename)
 Initializes this ScoreFunction from the given <filename>
void _add_weights_from_file (std::string const &filename, bool patch=false)
 Initializes this ScoreFunction from the given <filename> no lookup in database directory.
void initialize_from_file (std::string const &filename)
 Resets everything before reading the <filename>
void apply_patch_from_file (std::string const &filename)
 Applies a patch from the given <filename>
void set_etable (std::string const &etable_name)
 Given a <filename> (represented by a std::string), set the e_table for this ScoreFunction.
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)
void set_energy_method_options (methods::EnergyMethodOptions const &energy_method_options_in)
 Returns the EnergyMethodOptions object contained in this ScoreFunction.
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.
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.
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.
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
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.
Real operator[] (ScoreType const &t) const
 Returns the weight of the ScoreType <t>
EnergyMap const & weights () const
 Returns an EnergyMap of the current set of weights.
bool has_zero_weight (ScoreType const &t) const
 Returns true if the ScoreType <t> has a weight of zero,.
bool has_nonzero_weight (ScoreType const &t) const
 Returns true if the ScoreType <t> has a non-zero weight.
ScoreTypes get_nonzero_weighted_scoretypes () const
 Returns a list of the ScoreTypes which are non-zero with their current weights.
void set_weight (ScoreType const &t, Real const &setting)
 Sets the weight for ScoreType <t> to <setting>
Real get_weight (ScoreType const &t) const
 Returns the weight for ScoreType <t>
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.
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.
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>
virtual void setup_for_minimizing_for_node (MinimizationNode &min_node, conformation::Residue const &rsd, kinematics::MinimizerMapBase const &min_map, pose::Pose &pose, bool accumulate_fixed_energies, EnergyMap &fixed_energies) const
 Initialize a single node of a MinimizationGraph with the one-body and two-body energy methods that are held within this ScoreFunction object.
void reinitialize_minnode_for_residue (MinimizationNode &min_node, conformation::Residue const &rsd, kinematics::MinimizerMapBase const &min_map, pose::Pose &pose) const
void setup_for_minimizing_sr2b_enmeths_for_minedge (conformation::Residue const &res1, conformation::Residue const &res2, MinimizationEdge &min_edge, kinematics::MinimizerMapBase const &min_map, pose::Pose &pose, bool const res_moving_wrt_eachother, bool accumulate_fixed_energies, EnergyEdge const *energy_edge, EnergyMap &fixed_energies, Real const edge_weight=1.0) const
 Initialize a single MinimizationEdge for a particular part of residues, storing sr2b energy method pointers on the edge for those sr2b energy methods in this ScoreFunction.
void setup_for_lr2benmeth_minimization_for_respair (conformation::Residue const &res1, conformation::Residue const &res2, methods::LongRangeTwoBodyEnergyCOP lr2benergy, MinimizationGraph &g, kinematics::MinimizerMapBase const &min_map, pose::Pose &p, bool const res_moving_wrt_eachother, bool accumulate_fixed_energies, ResidueNeighborConstIteratorOP rni, EnergyMap &fixed_energies, Real const edge_weight=1.0) const
 Initialize an edge in the MinimizationGraph with a particular long-range two body.
void setup_for_scoring (pose::Pose &pose) const
 For external scorers: Let the energy methods prepare for evaluating their scores on a particular structure.
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)
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.)
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.
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.
void get_sub_score (pose::Pose const &pose, utility::vector1< bool > const &residue_mask, EnergyMap &emap) const
 Compute the score for subset of residues.
core::Real get_sub_score (pose::Pose &pose, utility::vector1< bool > const &residue_mask) const
 Compute the score for subset of residues.
void get_sub_score (pose::Pose &pose, utility::vector1< bool > const &residue_mask, EnergyMap &emap) const
 Compute the score for subset of residues.
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.
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.
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.
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.
virtual void eval_twobody_neighbor_energies (pose::Pose &pose) const
virtual void eval_long_range_twobody_energies (pose::Pose &pose) const
AllMethodsIterator all_energies_begin () const
AllMethodsIterator all_energies_end () const
LR_2B_MethodIterator long_range_energies_begin () const
LR_2B_MethodIterator long_range_energies_end () const
TWO_B_MethodIterator ci_2b_intrares_begin () const
TWO_B_MethodIterator ci_2b_intrares_end () const
TWO_B_MethodIterator cd_2b_intrares_begin () const
TWO_B_MethodIterator cd_2b_intrares_end () const
CI_2B_Methods::const_iterator ci_2b_begin () const
CI_2B_Methods::const_iterator ci_2b_end () const
CD_2B_Methods::const_iterator cd_2b_begin () const
CD_2B_Methods::const_iterator cd_2b_end () const
CI_LR_2B_MethodIterator ci_lr_2b_methods_begin () const
CI_LR_2B_MethodIterator ci_lr_2b_methods_end () const
CD_LR_2B_MethodIterator cd_lr_2b_methods_begin () const
CD_LR_2B_MethodIterator cd_lr_2b_methods_end () const
WS_MethodIterator ws_methods_begin () const
WS_MethodIterator ws_methods_end () const
virtual void eval_onebody_energies (pose::Pose &pose) const
void show (std::ostream &out) const
void merge (const ScoreFunction scorefxn_to_be_merged)
 Merges in the weights of another score function.
void show (std::ostream &out, pose::Pose &pose) const
 Scores <pose> and shows the raw and weighted scores for each non-zero ScoreType.
void show_pretty (std::ostream &out) const
 similar output as show( ostream, pose ) but without the pose
void show (pose::Pose &pose) const
 Scores <pose> and shows the raw and weighted scores for each non-zero ScoreType.
void show_line_headers (std::ostream &out) const
void show_line (std::ostream &out, pose::Pose const &pose) const
void eval_ci_1b (conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const
 Accumulates the unweighted one body energies of all context independent one body energies for <pose> Residue <rsd> into EnergyMap <emap>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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.
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>
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>
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
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>
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
ScoreTypes const & cd_1b_types () const
 convenience access to all cd 1b score types
ScoreTypes const & ci_2b_types () const
 convenience access to all ci 2b score types
ScoreTypes const & cd_2b_types () const
 convenience access to all cd 2b score types
ScoreTypes const & ci_lr_2b_types () const
ScoreTypes const & cd_lr_2b_types () const
ScoreTypes const & whole_structure_types () const
AllMethods const & all_methods () const

Protected Member Functions

bool any_intrares_energies () const

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 ( )

ctor

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

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 tr().

void core::scoring::ScoreFunction::add_extra_method ( ScoreType const &  new_type,
Real const  new_weight,
methods::EnergyMethod const &  new_method 
)

Adds a scoring method that is not necessarily included in the core library.

Add a scoring method that's not necessarily included in the core library

Note:
Currently only works for methods associated with a single specific score_type

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

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

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 core::scoring::find_weights_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 [inline, protected]
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 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::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)

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

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

score the sidechain from rsd1 against the entirety of rsd2

low fidelity description of what it would be like to replace the sidechain of rsd1 at a particular position -- only those scoring functions that specify they should be included in the bump check will be evaluated. The inaccuracy in this function is based on the change in LK solvation types and/or charges for backbone atoms when residues are mutated from one amino acid type to another (or from any other residue with backbone atoms)

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

ScoreTypes const& core::scoring::ScoreFunction::cd_1b_types ( ) const [inline]
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
ScoreFunction::TWO_B_MethodIterator core::scoring::ScoreFunction::cd_2b_intrares_end ( ) const
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]
ScoreTypes const& core::scoring::ScoreFunction::ci_1b_types ( ) const [inline]

convenience access to all ci 1b score types

References core::scoring::methods::ci_1b.

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]
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

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

Referenced by core::pack::interaction_graph::OnTheFlyNode::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

Referenced by core::pack::interaction_graph::OnTheFlyNode::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.

Referenced by protocols::flexpack::OtherContextScoreFunction::eval_cd_intrares_energy(), core::scoring::symmetry::SymmetricScoreFunction::eval_onebody_energies(), and 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

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

Referenced by core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::scoring::symmetry::SymmetricScoreFunction::eval_twobody_neighbor_energies(), and 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

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

Referenced by core::pack::interaction_graph::OnTheFlyNode::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

Referenced by core::pack::interaction_graph::OnTheFlyNode::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

Referenced by core::scoring::symmetry::SymmetricScoreFunction::eval_onebody_energies(), and 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
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

Evaluate the energies between a set of rotamers and a single other (background) residue

References weights().

Referenced by core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), and core::pack::rotamer_set::RotamerSet_::compute_one_body_energies().

void core::scoring::ScoreFunction::evaluate_rotamer_intrares_energies ( conformation::RotamerSetBase const &  set,
pose::Pose const &  pose,
utility::vector1< core::PackerEnergy > &  energies 
) const
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]
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.

void core::scoring::ScoreFunction::get_sub_score ( pose::Pose const &  pose,
utility::vector1< bool > const &  residue_mask,
EnergyMap emap 
) const
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().

core::Real core::scoring::ScoreFunction::get_sub_score ( pose::Pose const &  pose,
utility::vector1< bool > const &  residue_mask 
) 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().

core::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::total_residue().

Referenced by protocols::loops::addScoresForLoopParts().

void core::scoring::ScoreFunction::get_sub_score_exclude_res ( pose::Pose pose,
utility::vector1< core::Size > const &  exclude_list,
EnergyMap emap 
) const
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::total_residue().

core::Real core::scoring::ScoreFunction::get_sub_score_exclude_res ( pose::Pose pose,
utility::vector1< core::Size > const &  exclude_list 
) const
Real core::scoring::ScoreFunction::get_weight ( ScoreType const &  t) const
bool core::scoring::ScoreFunction::has_nonzero_weight ( ScoreType const &  t) const [inline]
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

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 )

Referenced by core::pack::create_packer_graph(), core::pack::pack_scorefxn_pose_handshake(), 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

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.

Referenced by are_they_neighbors(), and core::scoring::ScoreFunctionInfo::initialize_from().

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().

Real core::scoring::ScoreFunction::operator() ( pose::Pose pose) const [virtual]
ScoreFunction & core::scoring::ScoreFunction::operator= ( ScoreFunction const &  src)
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 core::scoring::hbonds::t().

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 core::scoring::name_from_score_type(), and tr().

void core::scoring::ScoreFunction::prepare_rotamers_for_packing ( pose::Pose const &  pose,
conformation::RotamerSetBase set 
) const
void core::scoring::ScoreFunction::reinitialize_minnode_for_residue ( MinimizationNode min_node,
conformation::Residue const &  rsd,
kinematics::MinimizerMapBase const &  min_map,
pose::Pose pose 
) const
void core::scoring::ScoreFunction::reset ( )
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.
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 protocols::kinmatch::str().

void core::scoring::ScoreFunction::set_energy_method_options ( methods::EnergyMethodOptions const &  energy_method_options_in)

Returns the EnergyMethodOptions object contained in this ScoreFunction.

Sets the EnergyMethodOptions object contained in this ScoreFunction. with appropriate update of all the energy methods.

Referenced by protocols::flexpack::FlexPacker::apply(), and protocols::abinitio::ConstraintFragmentSampler::set_max_seq_sep().

void core::scoring::ScoreFunction::set_etable ( std::string const &  etable_name)

Given a <filename> (represented by a std::string), set the e_table for this ScoreFunction.

Given a filename (represented by a std::string), set the e_table for this ScoreFunction.

void core::scoring::ScoreFunction::set_method_weights ( ScoreType const &  t,
utility::vector1< Real > const &  wts 
)
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 core::scoring::ScoringManager::get_instance(), has_nonzero_weight(), core::scoring::python, and core::scoring::hbonds::t().

Referenced by protocols::abinitio::AbrelaxApplication::add_constraints(), core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn(), core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), protocols::abinitio::CoordinateConstraintKC::add_score_weights(), protocols::simple_moves::symmetry::SetupForSymmetryMover::apply(), protocols::simple_filters::TruncatedScoreEvaluator::apply(), protocols::simple_filters::ScoreEvaluator::apply(), protocols::simple_filters::SelectRDC_Evaluator::apply(), protocols::flexpack::FlexPacker::apply(), protocols::constraints_additional::ConstraintEvaluator::apply(), protocols::canonical_sampling::PatchOperation::apply(), protocols::abinitio::ComputeTotalDistCst::apply(), JDtestmover::apply(), core::pack::rotamer_set::build_lib_dna_rotamers(), protocols::motifs::Motif::build_rotamers(), protocols::motifs::build_rotamers_lite(), protocols::protein_interface_design::filters::InterfaceHolesFilter::compute(), protocols::relax::fix_worst_bad_ramas(), protocols::swa::rna::floating_base_chain_closure_post_process(), protocols::toolbox::pose_manipulation::insert_pose_into_pose(), protocols::abinitio::IterativeBase::IterativeBase(), merge(), protocols::abinitio::FoldConstraints::prepare_loop_in_stage3(), protocols::simple_moves::symmetry::SymShakeStructureMover::reduce_fa_rep(), protocols::simple_moves::ShakeStructureMover::reduce_fa_rep(), protocols::abinitio::MembraneAbinitio::set_current_weight(), protocols::abinitio::ClassicAbinitio::set_current_weight(), protocols::swa::RigidBodySampler::set_o2star_trials(), and protocols::simple_moves::ShakeStructureMover::setup_ca_constraints().

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 
) 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,
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(), core::scoring::methods::ci_lr_2b, core::kinematics::MinimizerMapBase::domain_map(), core::pose::Pose::energies(), core::scoring::Energies::onebody_energies(), core::conformation::Residue::seqpos(), and core::scoring::MinimizationNode::setup_for_minimizing().

Referenced by core::pack::create_minimization_graph(), core::pack::RTMin::rtmin(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_minimizing(), and setup_for_minimizing().

void core::scoring::ScoreFunction::setup_for_minimizing_sr2b_enmeths_for_minedge ( conformation::Residue const &  res1,
conformation::Residue const &  res2,
MinimizationEdge min_edge,
kinematics::MinimizerMapBase const &  min_map,
pose::Pose pose,
bool const  res_moving_wrt_eachother,
bool  accumulate_fixed_energies,
EnergyEdge const *  energy_edge,
EnergyMap fixed_energies,
Real const  edge_weight = 1.0 
) const
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

Referenced by core::pack::min_pack(), core::pack::pack_rotamers_setup(), core::pack::rotamer_trials(), core::pack::stochastic_pack(), core::pack::symmetric_pack_rotamers_setup(), and core::pack::symmetric_rotamer_trials().

void core::scoring::ScoreFunction::setup_for_scoring ( pose::Pose pose) const
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::scoring::n_score_types, and core::scoring::Energies::total_energies().

void core::scoring::ScoreFunction::show ( std::ostream &  out) const
void core::scoring::ScoreFunction::show ( pose::Pose pose) const [inline]

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().

Referenced by show().

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::scoring::n_score_types.

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.

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

Referenced by protocols::flexpack::FlexPacker::apply(), core::pack::assign_random_rotamers(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::atom_tree_get_atompairE_deriv(), protocols::flexpack::rotamer_set::FlexbbRotamerSet::bump_check(), core::pack::rotamer_set::RotamerSet_::bump_check(), core::optimization::cartesian_collect_atompairE_deriv(), core::pack::compare_mingraph_and_energy_graph(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), core::pack::interaction_graph::SimpleEdge::compute_energy(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), core::optimization::AtomTreeMultifunc::dump(), core::pose::Pose::dump_scored_pdb(), core::scoring::symmetry::SymmetricScoreFunction::eval_dof_derivative(), core::scoring::constraints::ConstraintSet::eval_intrares_energy(), core::scoring::constraints::ConstraintsEnergy::eval_intrares_energy_ext(), protocols::constraints_additional::MaxSeqSepConstraintSet::eval_non_residue_pair_energy(), core::scoring::constraints::ConstraintSet::eval_non_residue_pair_energy(), core::scoring::symmetry::SymmetricScoreFunction::eval_npd_atom_derivative(), evaluate_rotamer_background_energies(), core::scoring::hackelec::HackElecEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_intrares_energies(), core::scoring::etable::BaseEtableEnergy< EtableEnergy >::evaluate_rotamer_pair_energies(), core::scoring::hackelec::HackElecEnergy::evaluate_rotamer_pair_energies(), core::pack::rotamer_set::RotamerSets::get_bb_bbE(), core::pack::rotamer_set::RotamerSets::get_sc_bbE(), core::pack::min_pack(), core::scoring::symmetry::SymmetricScoreFunction::operator()(), core::scoring::DockingScoreFunction::operator()(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::precompute_two_body_energies(), core::pack::rotamer_set::RotamerSets::precompute_two_body_energies(), core::scoring::constraints::ConstraintSet::residue_pair_energy(), core::scoring::constraints::ConstraintsEnergy::residue_pair_energy_ext(), core::scoring::Energies::scoring_begin(), protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_scorefxn(), core::scoring::NeighborList::setup(), core::scoring::methods::LK_hack::setup_for_derivatives(), core::scoring::methods::Fa_MbsolvEnergy::setup_for_derivatives(), core::scoring::methods::Fa_MbenvEnergy::setup_for_derivatives(), core::scoring::hackelec::HackElecEnergy::setup_for_derivatives(), and core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing_for_residue().

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

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