#include <FA_ElecEnergy.hh>

Public Member Functions
	FA_ElecEnergy (methods::EnergyMethodOptions const &options)

	FA_ElecEnergy (FA_ElecEnergy const &src)

void	initialize ()
	Initilize constants. More...

virtual methods::EnergyMethodOP	clone () const
	clone More...

virtual void	setup_for_minimizing (pose::Pose &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map) const
	stashes nblist if use_nblist is true More...

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

virtual void	setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const

virtual void	setup_for_packing (pose::Pose &pose, utility::vector1< bool > const &, utility::vector1< bool > const &) const

virtual void	prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &set) const

virtual void	update_residue_for_packing (pose::Pose &pose, Size resid) const
	ensure this function gets called. The default behavior is to do nothing. More...

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

virtual bool	minimize_in_whole_structure_context (pose::Pose const &pose) const
	Returns true if we're using neighborlist-autoupdate. More...

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	use_extended_residue_pair_energy_interface () const
	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...

virtual void	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
	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...

void	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
	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...

virtual 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
	Evaluate the atom derivative f1/f2 vectors for all atoms on rsd1 in response to the atoms on rsd2, and all the atoms on rsd2 as they in response to the atoms on rsd1. This method is used with the MinimizationGraph and when nblist_autoupdate is not in use. More...

virtual void	eval_atom_derivative (id::AtomID const &atom_id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &, EnergyMap const &weights, Vector &F1, Vector &F2) const
	Evaluate the derivative vectors for a particular atom in a given (asymmetric) pose when nblist_autoupdate is being used. nblist_autoupdate cannot be used with symmetric poses, in rtmin, or in minpack. 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...

void	finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) 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...

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

virtual 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
	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...

virtual 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
	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...

virtual bool	defines_intrares_energy (EnergyMap const &) const
	Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not. More...

etable::count_pair::CountPairFunctionCOP	get_intrares_countpair (conformation::Residue const &, pose::Pose const &, ScoreFunction const &) const
	Interface function for class NeighborList. More...

etable::count_pair::CountPairFunctionCOP	get_count_pair_function (Size const, Size const, pose::Pose const &, ScoreFunction const &) const
	Interface function for class NeighborList. More...

etable::count_pair::CountPairFunctionCOP	get_count_pair_function (conformation::Residue const &rsd1, conformation::Residue const &rsd2) const

virtual Distance	atomic_interaction_cutoff () const
	FA_ElecEnergy distance cutoff. More...

virtual bool	divides_backbone_and_sidechain_energetics () const
	A derived class should return true for this function if it implements its own versions of the backbone_backbone_energy, backbone_sidechain_energy and sidechain_sidechain_energy functions. The default sidechain_sidechain_energy implemented by the TwoBodyEnergy base class calls residue_pair_energy. If the derived class implements its own versions of these functions, then calling code may avoid calling it on pairs of residues that are "provably distant" based on a pair of bounding spheres for a sidechains and backbones and this method's atomic_interaction_cutoff energy method. More...

virtual void	indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const
	FA_ElecEnergy. More...

Real	hydrogen_interaction_cutoff2 () const
	How close two heavy atoms have to be such that their hydrogen atoms might interact, squared. More...

Real	hydrogen_interaction_cutoff () const
	How close two heavy atoms have to be such that their hydrogen atoms might interact. More...

Energy	heavyatom_heavyatom_energy (ElecAtom const &at1, ElecAtom const &at2, DistanceSquared &d2, Size &) const

Energy	heavyatom_hydrogenatom_energy (ElecAtom const &at1, ElecAtom const &at2, Size &) const

Energy	hydrogenatom_heavyatom_energy (ElecAtom const &at1, ElecAtom const &at2, Size &) const

Energy	hydrogenatom_hydrogenatom_energy (ElecAtom const &at1, ElecAtom const &at2, Size &) const

Real	elec_weight (bool at1isbb, bool at2isbb) const
	This has to go. More...

Real	elec_weight (bool at1isbb, bool at2isbb, weight_triple const &wts) const

Public Member Functions inherited from core::scoring::methods::ContextIndependentTwoBodyEnergy
	ContextIndependentTwoBodyEnergy (EnergyMethodCreatorOP)
	Constructor with an EnergyMethodCreator to inform the ancestor EnergyMethod class which ScoreTypes this EnergyMethod is responsible for computing. More...

virtual	~ContextIndependentTwoBodyEnergy ()

EnergyMethodType	method_type () const
	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::ShortRangeTwoBodyEnergy
	ShortRangeTwoBodyEnergy (EnergyMethodCreatorOP)
	Constructor with EnergyMethodCreator to provide to the EnergyMethod grandparent the list of the ScoreTypes this EnergyMethod is responsible for computing. More...

virtual	~ShortRangeTwoBodyEnergy ()

virtual 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
	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...

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...

virtual	~TwoBodyEnergy ()

virtual void	setup_for_minimizing_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, ResSingleMinimizationData &res_data_cache) const
	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...

virtual bool	requires_a_setup_for_scoring_for_residue_opportunity (pose::Pose const &pose) const
	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...

virtual void	setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const
	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...

virtual bool	requires_a_setup_for_derivatives_for_residue_opportunity (pose::Pose const &pose) const
	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...

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

virtual void	eval_intrares_energy_ext (conformation::Residue const &rsd, ResSingleMinimizationData const &data_cache, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	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...

virtual 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
	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...

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

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

virtual void	evaluate_rotamer_intrares_energy_maps (conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< EnergyMap > &emaps) const
	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...

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...

	EnergyMethod (EnergyMethod const &src)
	Copy constructor copies over the score types of the source. More...

virtual	~EnergyMethod ()

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

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

Public Attributes
	__pad0__:ContextIndependentTwoBodyEnergy parent

Protected Member Functions
etable::coulomb::Coulomb const &	coulomb () const

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...

Private Member Functions
void	setup_weight_triple (EnergyMap const &weights, weight_triple &wttrip) const
	Private methods. More...

trie::RotamerTrieBaseOP	create_rotamer_trie (conformation::RotamerSetBase const &rotset, pose::Pose const &pose) const
	create a rotamer trie for a particular set, deciding upon the kind of count pair data that needs to be contained by the trie. More...

trie::RotamerTrieBaseOP	create_rotamer_trie (conformation::Residue const &res, pose::Pose const &) const

trie::TrieCountPairBaseOP	get_count_pair_function_trie (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn) const
	figure out the trie count pair function to use Need to refactor this so that the decision "what kind of count pair behavior should I use" can be decoupled from class instantiation, and therefore shared between the creation of the trie count pair classes and the regular count pair classes More...

trie::TrieCountPairBaseOP	get_count_pair_function_trie (conformation::Residue const &res1, conformation::Residue const &res2, trie::RotamerTrieBaseCOP trie1, trie::RotamerTrieBaseCOP trie2, pose::Pose const &pose, ScoreFunction const &sfxn) const

Real	score_atom_pair (conformation::Residue const &res1, conformation::Residue const &res2, Size const at1, Size const at2, EnergyMap &emap, Real const cpweight, Real &d2) const

void	set_nres_mono (core::pose::Pose const &pose) const

bool	monomer_test (Size irsd, Size jrsd) const

virtual core::Size	version () const
	Return the version of the energy method. More...

Private Attributes
etable::coulomb::Coulomb	coulomb_

bool	exclude_protein_protein_

bool	exclude_monomer_

bool	exclude_DNA_DNA_

Real	wbb_bb_

Real	wbb_sc_

Real	wsc_sc_

Size	nres_monomer_

Additional Inherited Members
Public Types inherited from core::scoring::methods::ContextIndependentTwoBodyEnergy
typedef ShortRangeTwoBodyEnergy	parent

Public Types inherited from core::scoring::methods::ShortRangeTwoBodyEnergy
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

Constructor & Destructor Documentation

core::scoring::elec::FA_ElecEnergy::FA_ElecEnergy ( methods::EnergyMethodOptions const & options )

References coulomb_, and core::scoring::etable::coulomb::Coulomb::initialize().

Referenced by clone().

core::scoring::elec::FA_ElecEnergy::FA_ElecEnergy ( FA_ElecEnergy const & src )

References coulomb_, and core::scoring::etable::coulomb::Coulomb::initialize().

Member Function Documentation

Distance core::scoring::elec::FA_ElecEnergy::atomic_interaction_cutoff ( ) const

virtual

FA_ElecEnergy distance cutoff.

Reports the maximum heavy atom/heavy atom distance at which two residues have a non-zero fa_elec interaction energy.

Implements core::scoring::methods::ShortRangeTwoBodyEnergy.

References hydrogen_interaction_cutoff().

Referenced by create_rotamer_trie().

void core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)		const

virtual

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.

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

Reimplemented in core::scoring::elec::RNA_FA_ElecEnergy.

References core::chemical::ResidueType::all_bb_atoms(), core::conformation::Residue::atomic_charge(), chemical, coulomb(), core::scoring::etable::count_pair::CP_CROSSOVER_4, defines_score_for_residue_pair(), core::scoring::etable::coulomb::Coulomb::eval_atom_atom_fa_elecE(), core::scoring::fa_elec, core::scoring::fa_elec_bb_bb, core::conformation::Residue::is_bonded(), core::conformation::Residue::is_pseudo_bonded(), score, core::conformation::Residue::type(), weight, and core::conformation::Residue::xyz().

void core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)		const

virtual

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.

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

References core::chemical::ResidueType::all_bb_atoms(), core::chemical::ResidueType::all_sc_atoms(), core::conformation::Residue::atomic_charge(), chemical, coulomb(), core::scoring::etable::count_pair::CP_CROSSOVER_4, defines_score_for_residue_pair(), core::scoring::etable::coulomb::Coulomb::eval_atom_atom_fa_elecE(), core::scoring::fa_elec, core::scoring::fa_elec_bb_sc, core::conformation::Residue::is_bonded(), core::conformation::Residue::is_pseudo_bonded(), score, core::conformation::Residue::type(), weight, and core::conformation::Residue::xyz().

methods::EnergyMethodOP core::scoring::elec::FA_ElecEnergy::clone ( ) const

virtual

clone

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

Reimplemented in core::scoring::elec::RNA_FA_ElecEnergy, core::scoring::elec::FA_ElecEnergyAroAll, and core::scoring::elec::FA_ElecEnergyAroAro.

References FA_ElecEnergy().

etable::coulomb::Coulomb const& core::scoring::elec::FA_ElecEnergy::coulomb ( ) const

inlineprotected

References coulomb_.

Referenced by backbone_backbone_energy(), backbone_sidechain_energy(), eval_atom_derivative(), core::scoring::elec::FA_ElecEnergyAroAll::eval_atom_derivative_aro_aro(), core::scoring::elec::FA_ElecEnergyAroAro::eval_atom_derivative_aro_aro(), core::scoring::elec::RNA_FA_ElecEnergy::eval_atom_derivative_RNA(), eval_residue_pair_derivatives(), finalize_total_energy(), heavyatom_heavyatom_energy(), heavyatom_hydrogenatom_energy(), hydrogen_interaction_cutoff(), hydrogenatom_heavyatom_energy(), hydrogenatom_hydrogenatom_energy(), core::scoring::elec::FA_ElecEnergyAroAll::residue_pair_energy_aro_aro(), core::scoring::elec::FA_ElecEnergyAroAro::residue_pair_energy_aro_aro(), core::scoring::elec::RNA_FA_ElecEnergy::rna_fa_elec_one_way(), score_atom_pair(), setup_for_minimizing(), setup_for_minimizing_for_residue_pair(), and sidechain_sidechain_energy().

trie::RotamerTrieBaseOP core::scoring::elec::FA_ElecEnergy::create_rotamer_trie	(	conformation::RotamerSetBase const &	rotset,
		pose::Pose const &	pose
	)		const

private

create a rotamer trie for a particular set, deciding upon the kind of count pair data that needs to be contained by the trie.

References core::io::serialization::at(), atomic_interaction_cutoff(), core::scoring::trie::create_cpdata_correspondence_for_rotamerset(), core::scoring::trie::create_trie(), hydrogen_interaction_cutoff(), and utility_exit.

Referenced by prepare_rotamers_for_packing(), setup_for_packing(), and update_residue_for_packing().

trie::RotamerTrieBaseOP core::scoring::elec::FA_ElecEnergy::create_rotamer_trie	(	conformation::Residue const &	res,
		pose::Pose const &
	)		const

private

Create a one-residue rotamer trie

References core::io::serialization::at(), atomic_interaction_cutoff(), core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::scoring::trie::create_trie(), hydrogen_interaction_cutoff(), and utility_exit.

virtual bool core::scoring::elec::FA_ElecEnergy::defines_intrares_energy ( EnergyMap const & weights ) const

inlinevirtual

Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not.

For example, the Etable method defines intra-residue energies only when one or more of the fa_intra_{atr,rep,sol} weights are non-zero.

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

Reimplemented in core::scoring::elec::RNA_FA_ElecEnergy, core::scoring::elec::FA_ElecEnergyAroAll, and core::scoring::elec::FA_ElecEnergyAroAro.

bool core::scoring::elec::FA_ElecEnergy::defines_score_for_residue_pair	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		bool	res_moving_wrt_eachother
	)		const

virtual

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.

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

References exclude_DNA_DNA_, exclude_monomer_, exclude_protein_protein_, core::conformation::Residue::is_DNA(), core::conformation::Residue::is_protein(), monomer_test(), and core::conformation::Residue::seqpos().

Referenced by backbone_backbone_energy(), backbone_sidechain_energy(), evaluate_rotamer_background_energies(), evaluate_rotamer_pair_energies(), get_count_pair_function(), get_count_pair_function_trie(), residue_pair_energy(), and sidechain_sidechain_energy().

virtual bool core::scoring::elec::FA_ElecEnergy::divides_backbone_and_sidechain_energetics ( ) const

inlinevirtual

A derived class should return true for this function if it implements its own versions of the backbone_backbone_energy, backbone_sidechain_energy and sidechain_sidechain_energy functions. The default sidechain_sidechain_energy implemented by the TwoBodyEnergy base class calls residue_pair_energy. If the derived class implements its own versions of these functions, then calling code may avoid calling it on pairs of residues that are "provably distant" based on a pair of bounding spheres for a sidechains and backbones and this method's atomic_interaction_cutoff energy method.

Reimplemented from core::scoring::methods::ShortRangeTwoBodyEnergy.

Real core::scoring::elec::FA_ElecEnergy::elec_weight	(	bool	at1isbb,
		bool	at2isbb
	)		const

inline

This has to go.

References wbb_bb_, wbb_sc_, and wsc_sc_.

Referenced by eval_atom_derivative(), eval_residue_pair_derivatives(), heavyatom_heavyatom_energy(), heavyatom_hydrogenatom_energy(), hydrogenatom_heavyatom_energy(), and hydrogenatom_hydrogenatom_energy().

Real core::scoring::elec::FA_ElecEnergy::elec_weight	(	bool	at1isbb,
		bool	at2isbb,
		weight_triple const &	wts
	)		const

inline

References core::scoring::elec::weight_triple::wbb_bb_, core::scoring::elec::weight_triple::wbb_sc_, and core::scoring::elec::weight_triple::wsc_sc_.

void core::scoring::elec::FA_ElecEnergy::eval_atom_derivative	(	id::AtomID const &	atom_id,
		pose::Pose const &	pose,
		kinematics::DomainMap const &	domain_map,
		ScoreFunction const &	,
		EnergyMap const &	weights,
		Vector &	F1,
		Vector &	F2
	)		const

virtual

Evaluate the derivative vectors for a particular atom in a given (asymmetric) pose when nblist_autoupdate is being used. nblist_autoupdate cannot be used with symmetric poses, in rtmin, or in minpack.

for use only with the nblist auto-update algorithm

Reimplemented in core::scoring::elec::RNA_FA_ElecEnergy, core::scoring::elec::FA_ElecEnergyAroAll, and core::scoring::elec::FA_ElecEnergyAroAro.

References core::id::AtomID::atomno(), core::scoring::AtomNeighbor::atomno(), coulomb(), numeric::xyzVector< class >::cross(), core::scoring::EnergiesCacheableDataType::ELEC_NBLIST, elec_weight(), core::pose::Pose::energies(), core::scoring::etable::coulomb::Coulomb::eval_dfa_elecE_dr_over_r(), core::scoring::Energies::nblist(), core::pose::Pose::residue(), core::id::AtomID::rsd(), core::scoring::AtomNeighbor::rsd(), setup_weight_triple(), core::scoring::Energies::use_nblist(), core::scoring::Energies::use_nblist_auto_update(), and core::scoring::AtomNeighbor::weight().

virtual void core::scoring::elec::FA_ElecEnergy::eval_intrares_energy	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)		const

inlinevirtual

Evaluate the intra-residue energy for a given residue.

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

Reimplemented in core::scoring::elec::RNA_FA_ElecEnergy, core::scoring::elec::FA_ElecEnergyAroAll, and core::scoring::elec::FA_ElecEnergyAroAro.

void core::scoring::elec::FA_ElecEnergy::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

virtual

Evaluate the atom derivative f1/f2 vectors for all atoms on rsd1 in response to the atoms on rsd2, and all the atoms on rsd2 as they in response to the atoms on rsd1. This method is used with the MinimizationGraph and when nblist_autoupdate is not in use.

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

References core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atomic_charge(), coulomb(), numeric::xyzVector< class >::cross(), core::scoring::elec_pair_nblist, elec_weight(), core::pose::Pose::energies(), core::scoring::etable::coulomb::Coulomb::eval_dfa_elecE_dr_over_r(), core::scoring::ResPairMinimizationData::get_data(), core::scoring::ResPairMinimizationData::get_data_ref(), numeric::xyzVector< class >::length_squared(), core::conformation::Residue::seqpos(), setup_weight_triple(), core::scoring::Energies::use_nblist_auto_update(), and core::conformation::Residue::xyz().

void core::scoring::elec::FA_ElecEnergy::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

virtual

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::ShortRangeTwoBodyEnergy.

Reimplemented in core::scoring::elec::RNA_FA_ElecEnergy, core::scoring::elec::FA_ElecEnergyAroAll, and core::scoring::elec::FA_ElecEnergyAroAro.

References cp, core::scoring::Energies::data(), defines_score_for_residue_pair(), core::scoring::methods::elec_method, core::scoring::EnergiesCacheableDataType::ELEC_TRIE_COLLECTION, core::pose::Pose::energies(), core::scoring::fa_elec, core::scoring::fa_elec_bb_bb, core::scoring::fa_elec_bb_sc, core::scoring::fa_elec_sc_sc, basic::datacache::BasicDataCache::get(), get_count_pair_function_trie(), core::conformation::RotamerSetBase::get_trie(), core::conformation::RotamerSetBase::num_rotamers(), core::conformation::RotamerSetBase::resid(), core::pose::Pose::residue(), core::conformation::Residue::seqpos(), wbb_bb_, wbb_sc_, core::scoring::ScoreFunction::weights(), and wsc_sc_.

void core::scoring::elec::FA_ElecEnergy::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

virtual

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::ShortRangeTwoBodyEnergy.

Reimplemented in core::scoring::elec::RNA_FA_ElecEnergy, core::scoring::elec::FA_ElecEnergyAroAll, and core::scoring::elec::FA_ElecEnergyAroAro.

References cp, defines_score_for_residue_pair(), core::scoring::methods::elec_method, core::scoring::fa_elec, core::scoring::fa_elec_bb_bb, core::scoring::fa_elec_bb_sc, core::scoring::fa_elec_sc_sc, get_count_pair_function_trie(), core::conformation::RotamerSetBase::get_trie(), core::conformation::RotamerSetBase::resid(), core::pose::Pose::residue(), wbb_bb_, wbb_sc_, core::scoring::ScoreFunction::weights(), and wsc_sc_.

void core::scoring::elec::FA_ElecEnergy::finalize_total_energy	(	pose::Pose &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	total_energy
	)		const

virtual

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.

called at the end of energy evaluation

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

References core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atomic_charge(), core::scoring::AtomNeighbor::atomno(), core::scoring::NeighborList::check_domain_map(), coulomb(), core::scoring::Energies::domain_map(), core::scoring::EnergiesCacheableDataType::ELEC_NBLIST, core::pose::Pose::energies(), core::scoring::etable::coulomb::Coulomb::eval_atom_atom_fa_elecE(), core::scoring::fa_elec, core::scoring::fa_elec_bb_bb, core::scoring::fa_elec_bb_sc, core::scoring::fa_elec_sc_sc, core::conformation::Residue::natoms(), core::scoring::Energies::nblist(), core::pose::Pose::residue(), core::scoring::AtomNeighbor::rsd(), score, core::pose::Pose::total_residue(), core::scoring::total_score, core::scoring::Energies::use_nblist(), core::scoring::Energies::use_nblist_auto_update(), core::scoring::AtomNeighbor::weight(), and core::conformation::Residue::xyz().

etable::count_pair::CountPairFunctionCOP core::scoring::elec::FA_ElecEnergy::get_count_pair_function	(	Size const	res1,
		Size const	res2,
		pose::Pose const &	pose,
		ScoreFunction const &
	)		const

Interface function for class NeighborList.

References core::pose::Pose::residue().

Referenced by setup_for_minimizing_for_residue_pair().

etable::count_pair::CountPairFunctionCOP core::scoring::elec::FA_ElecEnergy::get_count_pair_function	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2
	)		const

References core::scoring::etable::count_pair::CP_CROSSOVER_4, defines_score_for_residue_pair(), core::conformation::Residue::is_bonded(), and core::conformation::Residue::is_pseudo_bonded().

trie::TrieCountPairBaseOP core::scoring::elec::FA_ElecEnergy::get_count_pair_function_trie	(	conformation::RotamerSetBase const &	set1,
		conformation::RotamerSetBase const &	set2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn
	)		const

private

figure out the trie count pair function to use Need to refactor this so that the decision "what kind of count pair behavior should I use" can be decoupled from class instantiation, and therefore shared between the creation of the trie count pair classes and the regular count pair classes

References core::scoring::methods::elec_method, core::conformation::RotamerSetBase::get_trie(), core::conformation::RotamerSetBase::resid(), and core::pose::Pose::residue().

Referenced by evaluate_rotamer_background_energies(), and evaluate_rotamer_pair_energies().

trie::TrieCountPairBaseOP core::scoring::elec::FA_ElecEnergy::get_count_pair_function_trie	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		trie::RotamerTrieBaseCOP	trie1,
		trie::RotamerTrieBaseCOP	trie2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn
	)		const

private

References core::scoring::etable::count_pair::CP_NO_BONDS, core::scoring::etable::count_pair::CP_ONE_BOND, defines_score_for_residue_pair(), and core::conformation::Residue::seqpos().

etable::count_pair::CountPairFunctionCOP core::scoring::elec::FA_ElecEnergy::get_intrares_countpair	(	conformation::Residue const &	,
		pose::Pose const &	,
		ScoreFunction const &
	)		const

Interface function for class NeighborList.

References utility_exit_with_message.

Energy core::scoring::elec::FA_ElecEnergy::heavyatom_heavyatom_energy	(	ElecAtom const &	at1,
		ElecAtom const &	at2,
		DistanceSquared &	d2,
		Size &
	)		const

inline

References core::scoring::elec::ElecAtom::charge(), coulomb(), elec_weight(), core::scoring::etable::coulomb::Coulomb::eval_atom_atom_fa_elecE(), core::scoring::elec::ElecAtom::isbb(), and core::conformation::Atom::xyz().

Energy core::scoring::elec::FA_ElecEnergy::heavyatom_hydrogenatom_energy	(	ElecAtom const &	at1,
		ElecAtom const &	at2,
		Size &
	)		const

inline

References core::scoring::elec::ElecAtom::charge(), coulomb(), elec_weight(), core::scoring::etable::coulomb::Coulomb::eval_atom_atom_fa_elecE(), core::scoring::elec::ElecAtom::isbb(), and core::conformation::Atom::xyz().

Real core::scoring::elec::FA_ElecEnergy::hydrogen_interaction_cutoff ( ) const

inline

How close two heavy atoms have to be such that their hydrogen atoms might interact.

References coulomb(), and core::chemical::MAX_CHEMICAL_BOND_TO_HYDROGEN_LENGTH.

Referenced by atomic_interaction_cutoff(), create_rotamer_trie(), and hydrogen_interaction_cutoff2().

Real core::scoring::elec::FA_ElecEnergy::hydrogen_interaction_cutoff2 ( ) const

inline

How close two heavy atoms have to be such that their hydrogen atoms might interact, squared.

References hydrogen_interaction_cutoff().

Referenced by residue_pair_energy().

Energy core::scoring::elec::FA_ElecEnergy::hydrogenatom_heavyatom_energy	(	ElecAtom const &	at1,
		ElecAtom const &	at2,
		Size &
	)		const

inline

References core::scoring::elec::ElecAtom::charge(), coulomb(), elec_weight(), core::scoring::etable::coulomb::Coulomb::eval_atom_atom_fa_elecE(), core::scoring::elec::ElecAtom::isbb(), and core::conformation::Atom::xyz().

Energy core::scoring::elec::FA_ElecEnergy::hydrogenatom_hydrogenatom_energy	(	ElecAtom const &	at1,
		ElecAtom const &	at2,
		Size &
	)		const

inline

References core::scoring::elec::ElecAtom::charge(), coulomb(), elec_weight(), core::scoring::etable::coulomb::Coulomb::eval_atom_atom_fa_elecE(), core::scoring::elec::ElecAtom::isbb(), and core::conformation::Atom::xyz().

void core::scoring::elec::FA_ElecEnergy::indicate_required_context_graphs ( utility::vector1< bool > & context_graphs_required ) const

virtual

FA_ElecEnergy.

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

Reimplemented in core::scoring::elec::RNA_FA_ElecEnergy, core::scoring::elec::FA_ElecEnergyAroAll, and core::scoring::elec::FA_ElecEnergyAroAro.

void core::scoring::elec::FA_ElecEnergy::initialize ( )

Initilize constants.

References coulomb_, and core::scoring::etable::coulomb::Coulomb::initialize().

bool core::scoring::elec::FA_ElecEnergy::minimize_in_whole_structure_context ( pose::Pose const & pose ) const

virtual

Returns true if we're using neighborlist-autoupdate.

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

Reimplemented in core::scoring::elec::RNA_FA_ElecEnergy, core::scoring::elec::FA_ElecEnergyAroAll, and core::scoring::elec::FA_ElecEnergyAroAro.

References core::pose::Pose::energies(), and core::scoring::Energies::use_nblist_auto_update().

bool core::scoring::elec::FA_ElecEnergy::monomer_test	(	Size	irsd,
		Size	jrsd
	)		const

private

References nres_monomer_.

Referenced by defines_score_for_residue_pair().

void core::scoring::elec::FA_ElecEnergy::prepare_rotamers_for_packing	(	pose::Pose const &	,
		conformation::RotamerSetBase &
	)		const

virtual

default implementation noop

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

Reimplemented in core::scoring::elec::RNA_FA_ElecEnergy, core::scoring::elec::FA_ElecEnergyAroAll, and core::scoring::elec::FA_ElecEnergyAroAro.

References create_rotamer_trie(), core::scoring::methods::elec_method, and core::conformation::RotamerSetBase::store_trie().

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

virtual

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

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

Reimplemented in core::scoring::elec::RNA_FA_ElecEnergy, core::scoring::elec::FA_ElecEnergyAroAll, and core::scoring::elec::FA_ElecEnergyAroAro.

References core::conformation::Residue::attached_H_begin(), core::conformation::Residue::attached_H_end(), core::scoring::etable::count_pair::CP_CROSSOVER_4, defines_score_for_residue_pair(), numeric::xyzVector< class >::distance_squared(), core::pose::Pose::energies(), core::scoring::fa_elec, hydrogen_interaction_cutoff2(), core::conformation::Residue::is_bonded(), core::conformation::Residue::is_pseudo_bonded(), core::conformation::Residue::nheavyatoms(), score, score_atom_pair(), core::scoring::Energies::use_nblist(), weight, and core::conformation::Residue::xyz().

void core::scoring::elec::FA_ElecEnergy::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

virtual

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 core::scoring::elec_pair_nblist, core::pose::Pose::energies(), core::scoring::fa_elec, core::scoring::ResPairMinimizationData::get_data(), core::scoring::ResPairMinimizationData::get_data_ref(), score, score_atom_pair(), core::conformation::Residue::seqpos(), core::scoring::Energies::use_nblist_auto_update(), and weight.

Real core::scoring::elec::FA_ElecEnergy::score_atom_pair	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		Size const	at1,
		Size const	at2,
		EnergyMap &	emap,
		Real const	cpweight,
		Real &	d2
	)		const

inlineprivate

References core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atomic_charge(), coulomb(), core::scoring::etable::coulomb::Coulomb::eval_atom_atom_fa_elecE(), core::scoring::fa_elec_bb_bb, core::scoring::fa_elec_bb_sc, core::scoring::fa_elec_sc_sc, and core::conformation::Residue::xyz().

Referenced by residue_pair_energy(), and residue_pair_energy_ext().

void core::scoring::elec::FA_ElecEnergy::set_nres_mono ( core::pose::Pose const & pose ) const

private

References core::conformation::Residue::is_upper_terminus(), core::pose::Pose::n_residue(), nres_monomer_, and core::pose::Pose::residue().

Referenced by setup_for_derivatives(), setup_for_minimizing(), setup_for_packing(), and setup_for_scoring().

void core::scoring::elec::FA_ElecEnergy::setup_for_derivatives	(	pose::Pose &	pose,
		ScoreFunction const &	sfxn
	)		const

virtual

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.

Reimplemented in core::scoring::elec::RNA_FA_ElecEnergy, core::scoring::elec::FA_ElecEnergyAroAll, and core::scoring::elec::FA_ElecEnergyAroAro.

References core::scoring::fa_elec, core::scoring::fa_elec_bb_bb, core::scoring::fa_elec_bb_sc, core::scoring::fa_elec_sc_sc, set_nres_mono(), core::pose::Pose::update_residue_neighbors(), wbb_bb_, wbb_sc_, core::scoring::ScoreFunction::weights(), and wsc_sc_.

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

virtual

stashes nblist if use_nblist is true

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

References coulomb(), core::kinematics::MinimizerMapBase::domain_map(), core::scoring::EnergiesCacheableDataType::ELEC_NBLIST, core::pose::Pose::energies(), core::scoring::etable::coulomb::Coulomb::max_dis(), run::nblist_autoupdate_narrow, option, core::scoring::NeighborList::set_auto_update(), set_nres_mono(), core::scoring::Energies::use_nblist(), core::scoring::Energies::use_nblist_auto_update(), and XX.

void core::scoring::elec::FA_ElecEnergy::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

virtual

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.

References coulomb(), core::scoring::elec_pair_nblist, core::pose::Pose::energies(), get_count_pair_function(), core::scoring::ResPairMinimizationData::get_data(), core::conformation::Residue::seqpos(), core::scoring::ResPairMinimizationData::set_data(), and core::scoring::Energies::use_nblist_auto_update().

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

virtual

default implementation noop

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

Reimplemented in core::scoring::elec::RNA_FA_ElecEnergy, core::scoring::elec::FA_ElecEnergyAroAll, and core::scoring::elec::FA_ElecEnergyAroAro.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, create_rotamer_trie(), core::scoring::Energies::data(), core::scoring::EnergiesCacheableDataType::ELEC_TRIE_COLLECTION, core::pose::Pose::energies(), core::pose::Pose::residue(), basic::datacache::BasicDataCache::set(), set_nres_mono(), and core::pose::Pose::total_residue().

void core::scoring::elec::FA_ElecEnergy::setup_for_scoring	(	pose::Pose &	pose,
		ScoreFunction const &	scfxn
	)		const

virtual

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

Reimplemented in core::scoring::elec::RNA_FA_ElecEnergy, core::scoring::elec::FA_ElecEnergyAroAll, and core::scoring::elec::FA_ElecEnergyAroAro.

References core::scoring::EnergiesCacheableDataType::ELEC_NBLIST, core::pose::Pose::energies(), core::scoring::Energies::nblist(), core::scoring::NeighborList::prepare_for_scoring(), set_nres_mono(), core::pose::Pose::update_residue_neighbors(), and core::scoring::Energies::use_nblist().

void core::scoring::elec::FA_ElecEnergy::setup_weight_triple	(	EnergyMap const &	weights,
		weight_triple &	wttrip
	)		const

private

Private methods.

References core::scoring::fa_elec, core::scoring::fa_elec_bb_bb, core::scoring::fa_elec_bb_sc, core::scoring::fa_elec_sc_sc, core::scoring::elec::weight_triple::wbb_bb_, core::scoring::elec::weight_triple::wbb_sc_, and core::scoring::elec::weight_triple::wsc_sc_.

Referenced by eval_atom_derivative(), and eval_residue_pair_derivatives().

void core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)		const

virtual

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.

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

References core::chemical::ResidueType::all_sc_atoms(), core::conformation::Residue::atomic_charge(), chemical, coulomb(), core::scoring::etable::count_pair::CP_CROSSOVER_4, defines_score_for_residue_pair(), core::scoring::etable::coulomb::Coulomb::eval_atom_atom_fa_elecE(), core::scoring::fa_elec, core::scoring::fa_elec_sc_sc, core::conformation::Residue::is_bonded(), core::conformation::Residue::is_pseudo_bonded(), score, core::conformation::Residue::type(), weight, and core::conformation::Residue::xyz().

void core::scoring::elec::FA_ElecEnergy::update_residue_for_packing	(	pose::Pose &	,
		Size	resid
	)		const

virtual

ensure this function gets called. The default behavior is to do nothing.

default implementation noop

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

Reimplemented in core::scoring::elec::RNA_FA_ElecEnergy, core::scoring::elec::FA_ElecEnergyAroAll, and core::scoring::elec::FA_ElecEnergyAroAro.

References create_rotamer_trie(), core::scoring::Energies::data(), core::scoring::EnergiesCacheableDataType::ELEC_TRIE_COLLECTION, core::pose::Pose::energies(), basic::datacache::BasicDataCache::get(), and core::pose::Pose::residue().

bool core::scoring::elec::FA_ElecEnergy::use_extended_residue_pair_energy_interface ( ) const

virtual

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.

Reimplemented in core::scoring::elec::RNA_FA_ElecEnergy.

core::Size core::scoring::elec::FA_ElecEnergy::version ( ) const

privatevirtual

Return the version of the energy method.

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

Reimplemented in core::scoring::elec::RNA_FA_ElecEnergy, core::scoring::elec::FA_ElecEnergyAroAll, and core::scoring::elec::FA_ElecEnergyAroAro.