#include <LK_BallEnergy.hh>

Public Types
typedef ContextIndependentTwoBodyEnergy	parent

typedef chemical::ResidueType	ResidueType
	convenience typedefs More...

typedef utility::vector1< Size >	Sizes

typedef utility::vector1< Vector >	Vectors

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

Public Member Functions
	LK_BallEnergy (EnergyMethodOptions const &options)
	HACKING //////////////////////////. More...

virtual EnergyMethodOP	clone () const
	clone More...

	LK_BallEnergy (LK_BallEnergy const &src)

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

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

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

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

virtual void	setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const
	I AM HAVING A SLEEPOVER. More...

Real	calculate_lk_desolvation_of_single_atom_by_residue (Size const atom1, conformation::Residue const &rsd1, conformation::Residue const &rsd2)
	helper function for outside use More...

Real	calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair (Size const atom1, conformation::Residue const &rsd1, conformation::Residue const &rsd2)

void	calculate_lk_ball_atom_energies (Size const atom1, conformation::Residue const &rsd1, Vectors const &atom1_waters, Size const atom2, conformation::Residue const &rsd2, Real &lk_desolvation_of_atom1_by_atom2, Real &lk_ball_desolvation_of_atom1_by_atom2) const
	get the lk-ball desolvation of atom1 by atom2, and the unoriented lk desolvation of atom1 by atom2 More...

void	calculate_lk_ball_atom_energies_cp (Size const atom1, conformation::Residue const &rsd1, Vectors const &atom1_waters, Size const atom2, conformation::Residue const &rsd2, etable::count_pair::CPCrossoverBehavior const &cp_crossover, Real &lk_desolvation_of_atom1_by_atom2, Real &lk_ball_desolvation_of_atom1_by_atom2) const

Real	get_lk_fractional_contribution_for_single_water (Vector const &atom2_xyz, Size const atom2_type, Vector const &atom1_water) const

void	eval_desolvation_derivs_no_count_pair (Real const d2, Size const atom1, conformation::Residue const &rsd1, Size const atom2, conformation::Residue const &rsd2, Real &atom1_lk_desolvation_by_atom2_deriv, Real &atom2_lk_desolvation_by_atom1_deriv)

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

virtual void	residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const
	This guy is used during scoring if we are not minimizing. More...

void	residue_pair_energy (conformation::Residue const &rsd1, LKB_ResidueInfo const &rsd1_info, conformation::Residue const &rsd2, LKB_ResidueInfo const &rsd2_info, EnergyMap &emap) const

void	accumulate_single_atom_contributions (Size const atom1, Size const atom1_type_index, Vectors const &atom1_waters, utility::vector1< Real > const &atom1_wts, conformation::Residue const &rsd1, Size const atom2_type_index, Vector const &atom2_xyz, Real const lk_desolvation_of_atom1_by_atom2, EnergyMap &emap) const

void	setup_for_minimizing_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &scorefxn, kinematics::MinimizerMapBase const &min_map, ResSingleMinimizationData &resdata) 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...

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
	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
	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
	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	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...

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

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

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

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	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...

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 Distance	atomic_interaction_cutoff () const
	how far apart must two heavy atoms be to have a zero interaction energy? More...

void	indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const
	Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed. More...

Real	eval_lk_fraction (Real const d2_delta) const

Real	eval_d_lk_fraction_dr_over_r (Real const d2_delta) const

Real	get_lk_fractional_contribution (Vector const &atom2_xyz, Size const atom2_type_index, Vectors const &atom1_waters, Size &closest_water, Real &closest_water_dis2) const

Real	get_lk_fractional_contribution (Vector const &atom2_xyz, Size const atom2_type_index, Vectors const &atom1_waters) const

Real	eval_lk_ball_fraction_deriv (Vector const &atom2_xyz, Size const atom2_type_index, Vectors const &atom1_waters, bool const evaluate_deriv, Vector &f1, Vector &f2) const
	for external use 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...

void	sum_deriv_contributions_for_atom_pair_one_way (Size const atom1, conformation::Residue const &rsd1, Vectors const &atom1_waters, utility::vector1< Real > const &atom1_wts, Size const atom2, conformation::Residue const &rsd2, scoring::EnergyMap const &weights, Real const weight_factor, Real const d2, Vector &F1, Vector &F2) const

void	sum_deriv_contributions_for_atom_pair (Size const atom1, conformation::Residue const &rsd1, LKB_ResidueInfo const &rsd1_info, Size const atom2, conformation::Residue const &rsd2, LKB_ResidueInfo const &rsd2_info, pose::Pose const &pose, scoring::EnergyMap const &weights, Real const cp_weight, Vector &F1, Vector &F2) const

void	setup_d2_bounds ()

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 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	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 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	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	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_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...

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...

Private Member Functions
virtual core::Size	version () const
	HACK. More...

Private Attributes
etable::Etable const &	etable_

ObjexxFCL::FArray3D< Real > const &	solv1_
	these guys are taken from the etable More...

ObjexxFCL::FArray3D< Real > const &	solv2_

ObjexxFCL::FArray3D< Real > const &	dsolv1_

Real const	safe_max_dis2_

Real const	etable_bins_per_A2_

bool const	use_intra_dna_cp_crossover_4_

utility::vector1< Real >	d2_low_

utility::vector1< bool >	atom_type_is_charged_

utility::vector1< Real >	lk_ball_prefactor_

Static Private Attributes
static Real const	ramp_width_A2_

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 ContextIndependentTwoBodyEnergy core::scoring::methods::LK_BallEnergy::parent

typedef chemical::ResidueType core::scoring::methods::LK_BallEnergy::ResidueType

convenience typedefs

typedef utility::vector1< Size > core::scoring::methods::LK_BallEnergy::Sizes

typedef utility::vector1< Vector > core::scoring::methods::LK_BallEnergy::Vectors

Constructor & Destructor Documentation

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

HACKING //////////////////////////.

References setup_d2_bounds().

Referenced by clone().

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

References setup_d2_bounds().

Member Function Documentation

void core::scoring::methods::LK_BallEnergy::accumulate_single_atom_contributions	(	Size const	atom1,
		Size const	atom1_type_index,
		Vectors const &	atom1_waters,
		utility::vector1< Real > const &	atom1_wts,
		conformation::Residue const &	rsd1,
		Size const	atom2_type_index,
		Vector const &	atom2_xyz,
		Real const	lk_desolvation_of_atom1_by_atom2,
		EnergyMap &	emap
	)		const

References get_lk_fractional_contribution(), core::scoring::lk_ball, core::scoring::lk_ball_iso, and core::scoring::lk_ball_wtd.

Referenced by residue_pair_energy().

Distance core::scoring::methods::LK_BallEnergy::atomic_interaction_cutoff ( ) const

virtual

how far apart must two heavy atoms be to have a zero interaction energy?

If hydrogen atoms interact at the same range as heavy atoms, then this distance should build-in a 2 * max-bound-h-distance-cutoff buffer. There is an improper mixing here between run-time aquired chemical knowledge (max-bound-h-distance-cutoff) and compile time aquired scoring knowledge (max atom cutoff); this could be resolved by adding a boolean uses_hydrogen_interaction_distance() to the SRTBEnergy class along with a method of the ChemicalManager max_bound_h_distance_cutoff().

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

References etable_, and core::scoring::etable::Etable::max_dis().

void core::scoring::methods::LK_BallEnergy::calculate_lk_ball_atom_energies	(	Size const	atom1,
		conformation::Residue const &	rsd1,
		Vectors const &	atom1_waters,
		Size const	atom2,
		conformation::Residue const &	rsd2,
		Real &	lk_desolvation_of_atom1_by_atom2,
		Real &	lk_ball_desolvation_of_atom1_by_atom2
	)		const

get the lk-ball desolvation of atom1 by atom2, and the unoriented lk desolvation of atom1 by atom2

References core::conformation::Residue::atom(), core::scoring::etable::count_pair::CP_CROSSOVER_4, etable_bins_per_A2_, get_lk_fractional_contribution(), safe_max_dis2_, solv1_, core::conformation::Atom::type(), and core::conformation::Residue::xyz().

void core::scoring::methods::LK_BallEnergy::calculate_lk_ball_atom_energies_cp	(	Size const	atom1,
		conformation::Residue const &	rsd1,
		Vectors const &	atom1_waters,
		Size const	atom2,
		conformation::Residue const &	rsd2,
		etable::count_pair::CPCrossoverBehavior const &	cp_crossover,
		Real &	lk_desolvation_of_atom1_by_atom2,
		Real &	lk_ball_desolvation_of_atom1_by_atom2
	)		const

References core::conformation::Residue::atom(), etable_bins_per_A2_, get_lk_fractional_contribution(), safe_max_dis2_, core::conformation::Residue::seqpos(), solv1_, core::conformation::Atom::type(), and core::conformation::Residue::xyz().

Real core::scoring::methods::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue	(	Size const	atom1,
		conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2
	)

helper function for outside use

helper function for outsiders

References core::conformation::Residue::atom(), core::scoring::etable::count_pair::CP_CROSSOVER_4, etable_bins_per_A2_, core::conformation::Residue::nheavyatoms(), safe_max_dis2_, solv1_, core::conformation::Atom::type(), and core::conformation::Residue::xyz().

Real core::scoring::methods::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair	(	Size const	atom1,
		conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2
	)

References core::conformation::Residue::atom(), etable_bins_per_A2_, core::conformation::Residue::nheavyatoms(), safe_max_dis2_, solv1_, core::conformation::Atom::type(), and core::conformation::Residue::xyz().

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

virtual

clone

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

References LK_BallEnergy().

virtual bool core::scoring::methods::LK_BallEnergy::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.

Real core::scoring::methods::LK_BallEnergy::eval_d_lk_fraction_dr_over_r ( Real const d2_delta ) const

References ramp_width_A2_.

Referenced by eval_lk_ball_fraction_deriv(), and sum_deriv_contributions_for_atom_pair_one_way().

void core::scoring::methods::LK_BallEnergy::eval_desolvation_derivs_no_count_pair	(	Real const	d2,
		Size const	atom1,
		conformation::Residue const &	rsd1,
		Size const	atom2,
		conformation::Residue const &	rsd2,
		Real &	atom1_lk_desolvation_by_atom2_deriv,
		Real &	atom2_lk_desolvation_by_atom1_deriv
	)

References core::conformation::Residue::atom(), dsolv1_, etable_bins_per_A2_, safe_max_dis2_, and core::conformation::Atom::type().

virtual void core::scoring::methods::LK_BallEnergy::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.

Real core::scoring::methods::LK_BallEnergy::eval_lk_ball_fraction_deriv	(	Vector const &	atom2_xyz,
		Size const	atom2_type,
		Vectors const &	atom1_waters,
		bool const	evaluate_deriv,
		Vector &	f1,
		Vector &	f2
	)		const

for external use

Note that we calculate the lk_ball_iso derivative as well as the lk_ball derivative...

Derivatives are only included for heavyatoms.

For a non-polar heavyatom, the derivs are for all polar atoms that it desolvates

For a polar heavyatom, derivs are for all polar atoms that it desolvates as well as all atoms it's being desolvated by.

Given an atom desolvating a polar atom: the lk_ball_iso deriv is the standard lk deriv, but make sure we use the correct array! (see LK_hack code)

the lk_ball score = wt * lk_polar, so the derivs have two components. One looks like wt * lk_polar deriv contribution. The other looks like the lk_polar term * the derivative of the wt. The derivative of the wt is found by getting the closest water, taking the derivative of the wt term wrt distance and using f1/f2 contributions for the desolvating atom xyz and the water xyz.

Compute the f1 and f2 vectors for the derivative of the lk_fraction term for atom2 desolvating atom1

Note: f1 and f2 are zeroed and filled within this function, rather than being accumulated into; We pretend that atom1 is the "moving" atom Should eliminate code duplication with next routine... currently this is for outside use.

References numeric::xyzVector< class >::clear(), numeric::xyzVector< class >::cross(), eval_d_lk_fraction_dr_over_r(), and get_lk_fractional_contribution().

Referenced by core::scoring::methods::apply_lk_ball_fraction_weight_for_hbonds().

Real core::scoring::methods::LK_BallEnergy::eval_lk_fraction ( Real const d2_delta ) const

Stolen from LK_SigmoidalFunc in lk_hack d2_delta = d2 - d2_low

References ramp_width_A2_.

Referenced by get_lk_fractional_contribution(), and get_lk_fractional_contribution_for_single_water().

void core::scoring::methods::LK_BallEnergy::eval_residue_pair_derivatives	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		ResSingleMinimizationData const &	res1data,
		ResSingleMinimizationData const &	res2data,
		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

F1 and F2 are not zeroed – contributions from this atom are just summed in

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

References core::conformation::Residue::atom_is_hydrogen(), core::scoring::etab_pair_nblist, core::scoring::ResPairMinimizationData::get_data(), core::scoring::ResPairMinimizationData::get_data_ref(), core::conformation::Residue::natoms(), core::scoring::methods::retrieve_lkb_resdata(), sum_deriv_contributions_for_atom_pair(), and weight.

void core::scoring::methods::LK_BallEnergy::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.

References core::scoring::EMapVector::dot(), core::conformation::RotamerSetBase::get_n_residue_types(), core::conformation::RotamerSetBase::get_n_rotamers_for_residue_type(), core::conformation::RotamerSetBase::get_residue_type_begin(), core::scoring::methods::LKB_ResidueInfo::has_waters(), residue_pair_energy(), core::scoring::methods::retrieve_lkb_residue_info(), core::scoring::methods::retrieve_lkb_rotamer_set_info(), core::conformation::RotamerSetBase::rotamer(), and core::conformation::Residue::seqpos().

void core::scoring::methods::LK_BallEnergy::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.

References core::scoring::EMapVector::dot(), core::conformation::RotamerSetBase::get_n_residue_types(), core::conformation::RotamerSetBase::get_n_rotamers_for_residue_type(), core::conformation::RotamerSetBase::get_residue_type_begin(), residue_pair_energy(), core::scoring::methods::retrieve_lkb_rotamer_set_info(), and core::conformation::RotamerSetBase::rotamer().

Real core::scoring::methods::LK_BallEnergy::get_lk_fractional_contribution	(	Vector const &	atom2_xyz,
		Size const	atom2_type,
		Vectors const &	atom1_waters,
		Size &	closest_water,
		Real &	closest_water_d2_delta
	)		const

Note: closest_water may be set to 0 upon return if none of the waters are within ramp_width_A2_

References d2_low_, numeric::xyzVector< class >::distance_squared(), eval_lk_fraction(), ramp_width_A2_, and water.

Referenced by accumulate_single_atom_contributions(), calculate_lk_ball_atom_energies(), calculate_lk_ball_atom_energies_cp(), eval_lk_ball_fraction_deriv(), get_lk_fractional_contribution(), and sum_deriv_contributions_for_atom_pair_one_way().

Real core::scoring::methods::LK_BallEnergy::get_lk_fractional_contribution	(	Vector const &	atom2_xyz,
		Size const	atom2_type_index,
		Vectors const &	atom1_waters
	)		const

References get_lk_fractional_contribution().

Real core::scoring::methods::LK_BallEnergy::get_lk_fractional_contribution_for_single_water	(	Vector const &	atom2_xyz,
		Size const	atom2_type,
		Vector const &	atom1_water
	)		const

References d2_low_, numeric::xyzVector< class >::distance_squared(), eval_lk_fraction(), and ramp_width_A2_.

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

virtual

Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.

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

bool core::scoring::methods::LK_BallEnergy::minimize_in_whole_structure_context ( pose::Pose const & ) const

virtual

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.

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

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

virtual

default implementation noop

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

References core::conformation::RotamerSetBase::data(), core::conformation::RotamerSetCacheableDataType::LK_BALL_ROTAMER_SET_INFO, core::conformation::RotamerSetBase::num_rotamers(), core::conformation::RotamerSetBase::rotamer(), and basic::datacache::BasicDataCache::set().

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

virtual

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::LK_BallEnergy::requires_a_setup_for_scoring_for_residue_opportunity ( pose::Pose const & pose ) const

virtual

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::LK_BallEnergy::residue_pair_energy	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		pose::Pose const &	pose,
		ScoreFunction const &	,
		EnergyMap &	emap
	)		const

virtual

This guy is used during scoring if we are not minimizing.

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

References core::scoring::methods::retrieve_lkb_residue_info(), and core::conformation::Residue::seqpos().

Referenced by evaluate_rotamer_background_energies(), evaluate_rotamer_pair_energies(), and residue_pair_energy_ext().

void core::scoring::methods::LK_BallEnergy::residue_pair_energy	(	conformation::Residue const &	rsd1,
		LKB_ResidueInfo const &	rsd1_info,
		conformation::Residue const &	rsd2,
		LKB_ResidueInfo const &	rsd2_info,
		EnergyMap &	emap
	)		const

References accumulate_single_atom_contributions(), core::conformation::Residue::atom(), core::scoring::methods::LKB_ResidueInfo::atom_weights(), core::scoring::methods::determine_crossover_behavior(), etable_bins_per_A2_, core::conformation::Residue::nheavyatoms(), safe_max_dis2_, solv1_, solv2_, core::conformation::Atom::type(), use_intra_dna_cp_crossover_4_, core::scoring::methods::LKB_ResidueInfo::waters(), and core::conformation::Residue::xyz().

void core::scoring::methods::LK_BallEnergy::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::methods::LKB_ResPairMinData::res1_data(), core::scoring::methods::LKB_ResPairMinData::res2_data(), residue_pair_energy(), and core::scoring::methods::retrieve_lkb_pairdata().

void core::scoring::methods::LK_BallEnergy::setup_d2_bounds ( )

References core::scoring::etable::Etable::atom_set(), atom_type_is_charged_, d2_low_, etable_, core::chemical::AtomType::lj_radius(), lk_ball_prefactor_, core::chemical::AtomType::name(), ramp_width_A2_, numeric::square(), and core::scoring::methods::TR.

Referenced by LK_BallEnergy().

void core::scoring::methods::LK_BallEnergy::setup_for_derivatives	(	pose::Pose &	pose,
		ScoreFunction const &	scfxn
	)		const

virtual

I AM HAVING A SLEEPOVER.

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

References core::scoring::methods::compute_and_store_pose_waters(), and core::pose::Pose::update_residue_neighbors().

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

virtual

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

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

References setup_for_scoring_for_residue().

void core::scoring::methods::LK_BallEnergy::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

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 core::scoring::methods::LKB_ResidueInfo::build_waters(), core::scoring::methods::LKB_ResidueInfo::initialize(), core::scoring::methods::retrieve_nonconst_lkb_resdata(), and core::conformation::Residue::type().

void core::scoring::methods::LK_BallEnergy::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 core::scoring::methods::LKB_ResPairMinData::initialize(), core::scoring::methods::retrieve_lkb_resdata_ptr(), and core::scoring::methods::retrieve_nonconst_lkb_pairdata().

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

virtual

default implementation noop

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

References core::scoring::methods::compute_and_store_pose_waters(), and core::pose::Pose::update_residue_neighbors().

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

virtual

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

References core::scoring::methods::compute_and_store_pose_waters(), and core::pose::Pose::update_residue_neighbors().

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

virtual

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.

References core::scoring::methods::LKB_ResidueInfo::build_waters(), and core::scoring::methods::retrieve_nonconst_lkb_resdata().

Referenced by setup_for_derivatives_for_residue().

void core::scoring::methods::LK_BallEnergy::sum_deriv_contributions_for_atom_pair	(	Size const	atom1,
		conformation::Residue const &	rsd1,
		LKB_ResidueInfo const &	rsd1_info,
		Size const	atom2,
		conformation::Residue const &	rsd2,
		LKB_ResidueInfo const &	rsd2_info,
		pose::Pose const &	pose,
		scoring::EnergyMap const &	weights,
		Real const	cp_weight,
		Vector &	F1,
		Vector &	F2
	)		const

Note: Assumes that atom1 is the "moving" atom, ie the atom for which eval_atom_derivative was called; Calculates the water positions for atom2 if d2 < safe_max_dis2

References core::scoring::methods::LKB_ResidueInfo::atom_weights(), numeric::xyzVector< class >::distance_squared(), safe_max_dis2_, sum_deriv_contributions_for_atom_pair_one_way(), core::scoring::methods::LKB_ResidueInfo::waters(), and core::conformation::Residue::xyz().

Referenced by eval_residue_pair_derivatives().

void core::scoring::methods::LK_BallEnergy::sum_deriv_contributions_for_atom_pair_one_way	(	Size const	atom1,
		conformation::Residue const &	rsd1,
		Vectors const &	atom1_waters,
		utility::vector1< Real > const &	atom1_wts,
		Size const	atom2,
		conformation::Residue const &	rsd2,
		scoring::EnergyMap const &	weights,
		Real const	weight_factor,
		Real const	d2,
		Vector &	F1,
		Vector &	F2
	)		const

Note: atom2 is desolvating atom1. atom1_waters is non-empty; Pretend that atom1 is the atom whose derivs are being calculated. weight_factor may include -1 term to switch the order...

References core::conformation::Residue::atom(), core::conformation::Residue::atom_name(), numeric::xyzVector< class >::cross(), dsolv1_, etable_bins_per_A2_, eval_d_lk_fraction_dr_over_r(), get_lk_fractional_contribution(), core::scoring::lk_ball, core::scoring::lk_ball_iso, core::scoring::lk_ball_wtd, core::conformation::Residue::name(), solv1_, core::conformation::Atom::type(), utility_exit_with_message, and core::conformation::Residue::xyz().

Referenced by sum_deriv_contributions_for_atom_pair().

void core::scoring::methods::LK_BallEnergy::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.

References core::scoring::methods::LKB_ResidueInfo::build_waters(), core::pose::Pose::residue(), and core::scoring::methods::retrieve_nonconst_lkb_residue_info().

bool core::scoring::methods::LK_BallEnergy::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.

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

privatevirtual

HACK.

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