#include <SASAEnergy.hh>

Inheritance diagram for core::scoring::methods::SASAEnergy:

Public Types
typedef ContextIndependentLRTwoBodyEnergy	parent

Public Types inherited from core::scoring::methods::ContextIndependentLRTwoBodyEnergy
typedef LongRangeTwoBodyEnergy	parent

Public Types inherited from core::scoring::methods::LongRangeTwoBodyEnergy
typedef TwoBodyEnergy	parent

Public Types inherited from core::scoring::methods::TwoBodyEnergy
typedef EnergyMethod	parent

Public Types inherited from core::scoring::methods::EnergyMethod
typedef utility::pointer::ReferenceCount	parent

Public Member Functions
	SASAEnergy (EnergyMethodOptions const &options)
	for use by ScoringManager More...

	SASAEnergy (SASAEnergy const &src)

LongRangeEnergyType	long_range_type () const override

bool	defines_residue_pair_energy (pose::Pose const &pose, Size res1, Size res2) const override

EnergyMethodOP	clone () const override
	clone More...

void	setup_for_packing (pose::Pose &pose, utility::vector1< bool > const &residues_repacking, utility::vector1< bool > const &) const override
	if an energy method needs to cache data in the Energies object, before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More...

void	setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const override
	if an energy method needs to cache something in the pose (e.g. in pose.energies()), before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing. More...

void	setup_for_derivatives (pose::Pose &pose, ScoreFunction const &) const override
	Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. More...

bool	requires_a_setup_for_scoring_for_residue_opportunity_during_minimization (pose::Pose const &) const override
	Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. More...

void	setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &, ScoreFunction const &sfxn, ResSingleMinimizationData &resdata) const override
	Do any setup work should the coordinates of this residue (who is still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called) have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. This function is used for both intra-residue setup and pre-inter-residue setup. More...

bool	requires_a_setup_for_derivatives_for_residue_opportunity (pose::Pose const &) const override
	Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More...

void	setup_for_derivatives_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data, basic::datacache::BasicDataCache &) const override
	Do any setup work necessary before evaluating the derivatives for this residue. More...

void	setup_for_minimizing_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &scorefxn, kinematics::MinimizerMapBase const &min_map, basic::datacache::BasicDataCache &, ResSingleMinimizationData &resdata) const override
	Called at the beginning of minimization, allowing this energy method to cache data pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. More...

void	setup_for_minimizing_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &, ScoreFunction const &scorefxn, kinematics::MinimizerMapBase const &min_map, ResSingleMinimizationData const &res1data, ResSingleMinimizationData const &res2data, ResPairMinimizationData &pairdata) const override
	Called at the beginning of minimization, allowing this energy method to cache data pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. More...

bool	use_extended_residue_pair_energy_interface () const override
	Rely on the extended version of the residue_pair_energy function during score-function evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which the derived base class has (or should have) cached a piece of data that will make residue-pair energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should return 'true' from this function to use the extended interface. The default method implemented in this class returns 'false'. More...

void	residue_pair_energy_ext (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResPairMinimizationData const &pairdata, pose::Pose const &, ScoreFunction const &, EnergyMap &emap) const override
	Evaluate the two-body energies for a particular residue, in the context of a given Pose, and with the help of a piece of cached data for minimization, increment those two body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is invoked. This function should not be called unless the use_extended_residue_pair_energy_interface() method returns "true". Default implementation provided by this base class calls utility::exit(). More...

bool	use_extended_intrares_energy_interface () const override
	Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy during minimization routines should return "true" when this function is invoked on them. This class provides a default "return false" implementation so that classes not desiring to take advantage of this alternate interface need to do nothing. More...

void	eval_intrares_energy_ext (conformation::Residue const &rsd, ResSingleMinimizationData const &data_cache, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override
	Evaluate the intra-residue energy for a given residue using the data held within the ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return "true" in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies. More...

void	eval_intrares_derivatives (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs) const override
	Evaluate the derivative for the intra-residue component of this energy method for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd. More...

void	eval_residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &, ResSingleMinimizationData const &, ResPairMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const override
	Evaluate the derivative for an atom in rsd1 with respect to rsd2 in the context of a particular pose, and increment the F1 and F2 vectors. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. DEPRECATED. Too slow. Too much overhead for each atom; slowed fast-relax runs by ~40%. More...

void	prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &set) const override
	If an energy method needs to cache data in a packing::RotamerSet object before rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More...

void	update_residue_for_packing (pose::Pose &, Size resid) const override
	If the pose changes in the middle of a packing (as happens in rotamer trials) and if an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing. More...

void	residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const override
	Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap. More...

void	evaluate_rotamer_intrares_energies (conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< core::PackerEnergy > &energies) const override
	Batch computation of rotamer intrares energies. Need not be overriden in derived class – by default, iterates over all rotamers, and calls derived class's intrares _energy method. More...

void	evaluate_rotamer_intrares_energy_maps (conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< EnergyMap > &emaps) const override
	Batch computation of rotamer intrares energy map. Need not be overriden in derived class – by default, iterates over all rotamers, and calls derived class's intrares _energy method. More...

void	evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const override
	Batch computation of rotamer pair energies. Need not be overriden in derived class – by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...

void	evaluate_rotamer_background_energies (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const override
	Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...

void	evaluate_rotamer_background_energy_maps (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< EnergyMap > &emaps) const override
	Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...

void	indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const override
	SASAEnergy distance cutoff set to the same cutoff used by EtableEnergy, for now. More...

bool	defines_intrares_energy (EnergyMap const &) const override
	SASAEnergy does define intraresidue interactions. More...

void	eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override
	Evaluate the intra-residue energy for a given residue. More...

Real	packing_interaction_cutoff () const
	this is our own special function More...

Public Member Functions inherited from core::scoring::methods::ContextIndependentLRTwoBodyEnergy
	ContextIndependentLRTwoBodyEnergy (EnergyMethodCreatorOP)

	~ContextIndependentLRTwoBodyEnergy () override

EnergyMethodType	method_type () const override
	Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure. More...

Public Member Functions inherited from core::scoring::methods::LongRangeTwoBodyEnergy
	LongRangeTwoBodyEnergy (EnergyMethodCreatorOP creator)
	Constructor with an EnergyMethodCreator to inform the grandparent EnergyMethod class which ScoreTypes this EnergyMethod computes. More...

	~LongRangeTwoBodyEnergy () override

Public Member Functions inherited from core::scoring::methods::TwoBodyEnergy
	TwoBodyEnergy (EnergyMethodCreatorOP)
	Constructor, requiring an EnergyMethodCreator. No default constructor provided to force EnergyMethod writers to provide an energy-method-creator at construction time. More...

	~TwoBodyEnergy () override

virtual bool	defines_score_for_residue_pair (conformation::Residue const &res1, conformation::Residue const &res2, bool res_moving_wrt_eachother) const
	During minimization, energy methods are allowed to decide that they say nothing about a particular residue pair (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default implementation returns "true" for all residue pairs. Context-dependent two-body energies have the option of behaving as if they are context-independent by returning "false" for residue pairs that do no move wrt each other. More...

virtual bool	requires_a_setup_for_scoring_for_residue_pair_opportunity (pose::Pose const &pose) const
	Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More...

virtual void	setup_for_scoring_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &minsingle_data1, ResSingleMinimizationData const &minsingle_data2, pose::Pose const &pose, ScoreFunction const &sfxn, ResPairMinimizationData &data_cache) const
	Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. More...

virtual bool	requires_a_setup_for_derivatives_for_residue_pair_opportunity (pose::Pose const &pose) const
	Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More...

virtual void	setup_for_derivatives_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &minsingle_data1, ResSingleMinimizationData const &minsingle_data2, pose::Pose const &pose, ScoreFunction const &sfxn, ResPairMinimizationData &data_cache) const
	Do any setup work necessary before evaluating the derivatives for this residue pair. More...

virtual void	backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluate the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the weighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy. More...

virtual void	backbone_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluate the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy. More...

virtual void	sidechain_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluate the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy. More...

virtual bool	defines_intrares_energy_for_residue (conformation::Residue const &res) const
	If a score function defines no intra-residue scores for a particular residue, then it may opt-out of being asked during minimization to evaluate the score for this residue. More...

virtual bool	defines_intrares_dof_derivatives (pose::Pose const &p) const
	Use the dof_derivative interface for this energy method when calculating derivatives? It is possible to define both dof_derivatives and atom-derivatives; they are not mutually exclusive. More...

virtual Real	eval_intraresidue_dof_derivative (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights) const
	Evaluate the DOF derivative for a particular residue. The Pose merely serves as context, and the input residue is not required to be a member of the Pose. More...

virtual void	bump_energy_full (conformation::Residue const &, conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const

virtual void	bump_energy_backbone (conformation::Residue const &, conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const

Public Member Functions inherited from core::scoring::methods::EnergyMethod
	EnergyMethod (EnergyMethodCreatorOP creator)
	Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for. More...

virtual void	setup_for_packing_with_rotsets (pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets, ScoreFunction const &sfxn) const
	if an energy method needs to cache data in the Energies object, before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing. More...

virtual bool	requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring (pose::Pose const &pose) const
	Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false. More...

virtual void	setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, basic::datacache::BasicDataCache &residue_data_cache) const
	Do any setup work before scoring, caching any slow-to-compute data that will be used during energy evaluation inside of the input Residue object's data cache. (The Residue on the whole is given as a constant reference, but non-constant access to its data cache is granted.) More...

virtual void	setup_for_minimizing (pose::Pose &, ScoreFunction const &, kinematics::MinimizerMapBase const &) const
	Called at the beginning of atom tree minimization, this method allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose's Energies object's "use_nblist()" method returns true. More...

virtual void	finalize_after_minimizing (pose::Pose &pose) const
	Called after minimization, allowing a derived class to do some teardown steps. More...

virtual void	finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const
	called at the end of derivatives evaluation More...

virtual bool	minimize_in_whole_structure_context (pose::Pose const &) const
	Should this EnergyMethod have score and derivative evaluation evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that's serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return "true" will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction's traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return "true" cannot be included in RTMin. More...

virtual bool	defines_high_order_terms (pose::Pose const &) const
	Should this EnergyMethod have score and derivative evaluation evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta's get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns "false". More...

virtual void	eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &sfxn, EnergyMap const &emap, Vector &F1, Vector &F2) const
	Evaluate the XYZ derivative for an atom in the pose. Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom's XYZ derivative. More...

virtual void	finalize_total_energy (pose::Pose &pose, ScoreFunction const &sfxn, EnergyMap &total_energy) const
	called by the ScoreFunction at the end of energy evaluation. The derived class has the opportunity to accumulate a score into the pose's total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call. More...

ScoreTypes const &	score_types () const
	Returns the score types that this energy method computes. More...

virtual void	show_additional_info (std::ostream &, pose::Pose &, bool) const
	show additional information of the energy method More...

virtual bool	energy_method_provides_citation_info () const
	Does this energy method provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	energy_method_is_unpublished () const
	Does this energy method indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. More...

Private Member Functions
core::Size	version () const override
	Return the version of the energy method. More...

Private Attributes
SASAPotential const &	potential_

bool const	exclude_DNA_DNA_

Additional Inherited Members
Protected Member Functions inherited from core::scoring::methods::EnergyMethod
void	set_score_types (EnergyMethodCreatorOP creator)
	Override the entirety of the score types list if they were initialized incorrectly in a parent's constructor. More...

Member Typedef Documentation

typedef ContextIndependentLRTwoBodyEnergy core::scoring::methods::SASAEnergy::parent

Constructor & Destructor Documentation

core::scoring::methods::SASAEnergy::SASAEnergy ( EnergyMethodOptions const & options )

for use by ScoringManager

core::scoring::methods::SASAEnergy::SASAEnergy ( SASAEnergy const & src )

default

Member Function Documentation

EnergyMethodOP core::scoring::methods::SASAEnergy::clone ( ) const

overridevirtual

clone

Implements core::scoring::methods::EnergyMethod.

bool core::scoring::methods::SASAEnergy::defines_intrares_energy ( EnergyMap const & ) const

overridevirtual

SASAEnergy does define intraresidue interactions.

Implements core::scoring::methods::TwoBodyEnergy.

bool core::scoring::methods::SASAEnergy::defines_residue_pair_energy	(	pose::Pose const &	pose,
		Size	res1,
		Size	res2
	)		const

overridevirtual

Implements core::scoring::methods::LongRangeTwoBodyEnergy.

void core::scoring::methods::SASAEnergy::eval_intrares_derivatives	(	conformation::Residue const &	rsd,
		ResSingleMinimizationData const &	min_data,
		pose::Pose const &	pose,
		EnergyMap const &	weights,
		utility::vector1< DerivVectorPair > &	atom_derivs
	)		const

overridevirtual

Evaluate the derivative for the intra-residue component of this energy method for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References core::scoring::SASAPotential::eval_residue_pair_derivatives(), core::scoring::fa_sasa, and potential_.

void core::scoring::methods::SASAEnergy::eval_intrares_energy	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)		const

overridevirtual

Evaluate the intra-residue energy for a given residue.

Implements core::scoring::methods::TwoBodyEnergy.

References core::scoring::fa_sasa, core::scoring::SASAPotential::get_res_res_sasa(), and potential_.

void core::scoring::methods::SASAEnergy::eval_intrares_energy_ext	(	conformation::Residue const &	rsd,
		ResSingleMinimizationData const &	data_cache,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)		const

overridevirtual

Evaluate the intra-residue energy for a given residue using the data held within the ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return "true" in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References exclude_DNA_DNA_, core::scoring::fa_sasa, core::scoring::SASAPotential::get_res_res_sasa(), core::conformation::Residue::is_DNA(), and potential_.

void core::scoring::methods::SASAEnergy::eval_residue_pair_derivatives	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		ResSingleMinimizationData const &	,
		ResSingleMinimizationData const &	,
		ResPairMinimizationData const &	min_data,
		pose::Pose const &	pose,
		EnergyMap const &	weights,
		utility::vector1< DerivVectorPair > &	r1_atom_derivs,
		utility::vector1< DerivVectorPair > &	r2_atom_derivs
	)		const

overridevirtual

Evaluate the derivative for an atom in rsd1 with respect to rsd2 in the context of a particular pose, and increment the F1 and F2 vectors. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. DEPRECATED. Too slow. Too much overhead for each atom; slowed fast-relax runs by ~40%.

Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect to each other and increment the derivatives in atom-derivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References core::scoring::SASAPotential::eval_residue_pair_derivatives(), core::scoring::fa_sasa, and potential_.

void core::scoring::methods::SASAEnergy::evaluate_rotamer_background_energies	(	conformation::RotamerSetBase const &	set,
		conformation::Residue const &	residue,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights,
		utility::vector1< core::PackerEnergy > &	energy_vector
	)		const

overridevirtual

Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

void core::scoring::methods::SASAEnergy::evaluate_rotamer_background_energy_maps	(	conformation::RotamerSetBase const &	set,
		conformation::Residue const &	residue,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights,
		utility::vector1< EnergyMap > &	emaps
	)		const

overridevirtual

Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

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

overridevirtual

Batch computation of rotamer intrares energies. Need not be overriden in derived class – by default, iterates over all rotamers, and calls derived class's intrares _energy method.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

void core::scoring::methods::SASAEnergy::evaluate_rotamer_intrares_energy_maps	(	conformation::RotamerSetBase const &	set,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		utility::vector1< EnergyMap > &	emaps
	)		const

overridevirtual

Batch computation of rotamer intrares energy map. Need not be overriden in derived class – by default, iterates over all rotamers, and calls derived class's intrares _energy method.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

void core::scoring::methods::SASAEnergy::evaluate_rotamer_pair_energies	(	conformation::RotamerSetBase const &	set1,
		conformation::RotamerSetBase const &	set2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights,
		ObjexxFCL::FArray2D< core::PackerEnergy > &	energy_table
	)		const

overridevirtual

Batch computation of rotamer pair energies. Need not be overriden in derived class – by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

void core::scoring::methods::SASAEnergy::indicate_required_context_graphs ( utility::vector1< bool > & context_graphs_required ) const

overridevirtual

SASAEnergy distance cutoff set to the same cutoff used by EtableEnergy, for now.

SASAEnergy requires no context graphs

Implements core::scoring::methods::EnergyMethod.

LongRangeEnergyType core::scoring::methods::SASAEnergy::long_range_type ( ) const

inlineoverridevirtual

Implements core::scoring::methods::LongRangeTwoBodyEnergy.

References core::scoring::methods::sasa_lr.

Referenced by setup_for_derivatives(), and setup_for_scoring().

Real core::scoring::methods::SASAEnergy::packing_interaction_cutoff ( ) const

inline

this is our own special function

void core::scoring::methods::SASAEnergy::prepare_rotamers_for_packing	(	pose::Pose const &	,
		conformation::RotamerSetBase &
	)		const

overridevirtual

If an energy method needs to cache data in a packing::RotamerSet object before rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

default implementation noop

Reimplemented from core::scoring::methods::EnergyMethod.

References core::scoring::methods::TR().

bool core::scoring::methods::SASAEnergy::requires_a_setup_for_derivatives_for_residue_opportunity ( pose::Pose const & pose ) const

overridevirtual

Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

bool core::scoring::methods::SASAEnergy::requires_a_setup_for_scoring_for_residue_opportunity_during_minimization ( pose::Pose const & pose ) const

overridevirtual

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

Default return-false implementation.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

void core::scoring::methods::SASAEnergy::residue_pair_energy	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)		const

overridevirtual

Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.

Implements core::scoring::methods::TwoBodyEnergy.

References exclude_DNA_DNA_, core::scoring::fa_sasa, core::scoring::SASAPotential::get_res_res_sasa(), core::conformation::Residue::is_DNA(), and potential_.

void core::scoring::methods::SASAEnergy::residue_pair_energy_ext	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		ResPairMinimizationData const &	min_data,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)		const

overridevirtual

Evaluate the two-body energies for a particular residue, in the context of a given Pose, and with the help of a piece of cached data for minimization, increment those two body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is invoked. This function should not be called unless the use_extended_residue_pair_energy_interface() method returns "true". Default implementation provided by this base class calls utility::exit().

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References exclude_DNA_DNA_, core::scoring::fa_sasa, core::scoring::SASAPotential::get_res_res_sasa(), core::conformation::Residue::is_DNA(), and potential_.

void core::scoring::methods::SASAEnergy::setup_for_derivatives	(	pose::Pose &	pose,
		ScoreFunction const &	sfxn
	)		const

overridevirtual

Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.

default implementation noop

Reimplemented from core::scoring::methods::EnergyMethod.

References core::pose::Pose::energies(), core::scoring::fa_sasa, long_range_type(), potential_, core::scoring::SASAPotential::setup_for_scoring(), and core::pose::Pose::size().

void core::scoring::methods::SASAEnergy::setup_for_derivatives_for_residue	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		ResSingleMinimizationData &	min_data,
		basic::datacache::BasicDataCache &	res_data_cache
	)		const

overridevirtual

Do any setup work necessary before evaluating the derivatives for this residue.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

void core::scoring::methods::SASAEnergy::setup_for_minimizing_for_residue	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		kinematics::MinimizerMapBase const &	minmap,
		basic::datacache::BasicDataCache &	residue_data_cache,
		ResSingleMinimizationData &	res_data_cache
	)		const

overridevirtual

Called at the beginning of minimization, allowing this energy method to cache data pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

void core::scoring::methods::SASAEnergy::setup_for_minimizing_for_residue_pair	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		kinematics::MinimizerMapBase const &	minmap,
		ResSingleMinimizationData const &	res1_data_cache,
		ResSingleMinimizationData const &	res2_data_cache,
		ResPairMinimizationData &	data_cache
	)		const

overridevirtual

Called at the beginning of minimization, allowing this energy method to cache data pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

void core::scoring::methods::SASAEnergy::setup_for_packing	(	pose::Pose &	,
		utility::vector1< bool > const &	,
		utility::vector1< bool > const &
	)		const

overridevirtual

if an energy method needs to cache data in the Energies object, before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

default implementation noop

Reimplemented from core::scoring::methods::EnergyMethod.

References core::scoring::methods::TR().

void core::scoring::methods::SASAEnergy::setup_for_scoring	(	pose::Pose &	,
		ScoreFunction const &
	)		const

overridevirtual

if an energy method needs to cache something in the pose (e.g. in pose.energies()), before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

Reimplemented from core::scoring::methods::EnergyMethod.

References core::pose::Pose::energies(), core::scoring::fa_sasa, long_range_type(), potential_, core::scoring::SASAPotential::setup_for_scoring(), and core::pose::Pose::size().

void core::scoring::methods::SASAEnergy::setup_for_scoring_for_residue	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		ResSingleMinimizationData &	min_data
	)		const

overridevirtual

Do any setup work should the coordinates of this residue (who is still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called) have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. This function is used for both intra-residue setup and pre-inter-residue setup.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

void core::scoring::methods::SASAEnergy::update_residue_for_packing	(	pose::Pose &	,
		Size	resid
	)		const

overridevirtual

If the pose changes in the middle of a packing (as happens in rotamer trials) and if an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

default implementation noop

Reimplemented from core::scoring::methods::EnergyMethod.

bool core::scoring::methods::SASAEnergy::use_extended_intrares_energy_interface ( ) const

overridevirtual

Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy during minimization routines should return "true" when this function is invoked on them. This class provides a default "return false" implementation so that classes not desiring to take advantage of this alternate interface need to do nothing.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

bool core::scoring::methods::SASAEnergy::use_extended_residue_pair_energy_interface ( ) const

overridevirtual

Rely on the extended version of the residue_pair_energy function during score-function evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which the derived base class has (or should have) cached a piece of data that will make residue-pair energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should return 'true' from this function to use the extended interface. The default method implemented in this class returns 'false'.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

core::Size core::scoring::methods::SASAEnergy::version ( ) const

overrideprivatevirtual

Return the version of the energy method.

Implements core::scoring::methods::EnergyMethod.