#include <LK_BallEnergy.hh>

Inheritance diagram for core::scoring::lkball::LK_BallEnergy:

Public Types
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::VirtualBase	parent

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

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

	LK_BallEnergy (LK_BallEnergy const &src)

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

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

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

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

void	setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const override
	Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. 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, Size atom1_n_attached_waters, Size atom1_water_offset, WaterCoords const &rsd1_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, Size atom1_n_attached_waters, Size atom1_water_offset, WaterCoords 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)

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

void	residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override
	This guy is used during scoring if we are not minimizing, or inside linmem_ig packing and things like that... More...

bool	divides_backbone_and_sidechain_energetics () const override
	Let the energy-method consumers (e.g. the packer) use bounding-sphere logic for deciding whether bb/bb, bb/sc, and sc/sc energies should be evaluated. More...

void	backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override
	The sum bbE(r1,r2) + bs(r1,r2) + bs(r2,r1) + ss(r1,r2) must equal rpe(r1,r2). This function evaluates only the energies of bb/bb interactions. More...

void	backbone_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override
	The sum bbE(r1,r2) + bs(r1,r2) + bs(r2,r1) + ss(r1,r2) must equal rpe(r1,r2). This function evaluates only the energies of bb/sc interactions; that is, the backbone from residue 1 with the sidechain of residue 2. More...

void	sidechain_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override
	The sum bbE(r1,r2) + bs(r1,r2) + bs(r2,r1) + ss(r1,r2) must equal rpe(r1,r2). This function evaluates only the energies of sc/sc interactions. More...

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

void	accumulate_single_atom_contributions (Size atom1_n_attached_waters, Size atom1_water_offset, WaterCoords const &rsd1_waters, AtomWeights 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, basic::datacache::BasicDataCache &res_data_cache, ResSingleMinimizationData &resdata) const override
	Called at the beginning of minimization, allowing this energy method to cache data pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. More...

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

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

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

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

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

bool	defines_intrares_energy (EnergyMap const &) const override
	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...

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

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

void	eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const override
	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...

Distance	atomic_interaction_cutoff () const override
	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 override
	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, Real const width) const

Real	eval_d_lk_fraction_dr_over_r (Real const d2_delta, Real const width) const

Real	get_lk_fractional_contribution (Vector const &atom2_xyz, Size const atom2_type_index, Size atom1_n_attached_waters, Size atom1_water_offset, WaterCoords const &rsd1_waters, WaterDerivContributions &d_weighted_d2_d_di, Real &weighted_water_dis2) const

Real	get_lk_fractional_contribution (Vector const &atom2_xyz, Size const atom2_type_index, Size const atom1_n_attached_waters, Size const atom1_water_offset, WaterCoords const &rsd1_waters) const

Real	get_lkbr_fractional_contribution (Vector const &atom1_base, Vector const &atom2_base, Size atom1_n_attached_waters, Size atom2_n_attached_waters, Size atom1_water_offset, Size atom2_water_offset, WaterCoords const &rsd1_waters, WaterCoords const &rsd2_waters) const

Real	get_lkbr_fractional_contribution_noangle (Size atom1_n_attached_waters, Size atom2_n_attached_waters, Size atom1_water_offset, Size atom2_water_offset, WaterCoords const &rsd1_waters, WaterCoords const &rsd2_waters) const

Real	get_lkbr_fractional_contribution (Vector const &atom1_base, Vector const &atom2_base, Size atom1_n_attached_waters, Size atom2_n_attached_waters, Size atom1_water_offset, Size atom2_water_offset, WaterCoords const &rsd1_waters, WaterCoords const &rsd2_waters, WaterDerivVectors &d_weighted_d2_d_di1, Real &weighted_d2_water_delta, Real &pointterm_lkbr, Real &angleterm_lkbr, Real &d_angleterm_lkbr_dr, bool compute_derivs=true) const

void	evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const override
	Batch computation of rotamer pair energies. Need not be overriden in derived class – by default, iterates over all pairs of rotamers, and calls the derived class's residue_pair_energy method. More...

void	evaluate_rotamer_background_energies (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const override
	Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamr. More...

void	sum_deriv_contributions_for_heavyatom_pair_one_way (Size const heavyatom1, conformation::Residue const &rsd1, LKB_ResidueInfo const &rsd1_info, Size const heavyatom2, conformation::Residue const &rsd2, LKB_ResidueInfo const &rsd2_info, EnergyMap const &weights, Real const weight_factor, Real const d2, utility::vector1< DerivVectorPair > &r1_at_derivs, utility::vector1< DerivVectorPair > &r2_at_derivs) const

void	sum_deriv_contributions_for_heavyatom_pair (Real const d2, Size const heavyatom1, conformation::Residue const &rsd1, LKB_ResidueInfo const &rsd1_info, Size const heavyatom2, conformation::Residue const &rsd2, LKB_ResidueInfo const &rsd2_info, pose::Pose const &, EnergyMap const &weights, Real const cp_weight, utility::vector1< DerivVectorPair > &r1_at_derivs, utility::vector1< DerivVectorPair > &r2_at_derivs) const

void	setup_d2_bounds ()

etable::Etable const &	etable () const

ObjexxFCL::FArray3D< Real > const &	solv1 () const

ObjexxFCL::FArray3D< Real > const &	solv2 () const

Real	etable_bins_per_A2 () const

Real	lkb_max_dis () const

Real	lkb_max_dis2 () const

Real	fasol_max_dis2 () const

bool	slim_etable () const

core::Real	get_ramp_width_A2 () const

core::Real	get_overlap_width_A2 () const

core::Real	get_multi_water_fade () const

core::Real	get_lkbridge_angle_widthscale () const

core::Real	get_overlap_target_len2 () const

core::Real	get_overlap_gap2 () const

core::Real	get_d2_low (core::Size idx) const

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

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...

	~ContextIndependentTwoBodyEnergy () override

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

Public Member Functions inherited from core::scoring::methods::ShortRangeTwoBodyEnergy
	ShortRangeTwoBodyEnergy (EnergyMethodCreatorOP)
	Constructor with EnergyMethodCreator to provide to the EnergyMethod grandparent the list of the ScoreTypes this EnergyMethod is responsible for computing. More...

	~ShortRangeTwoBodyEnergy () override

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

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

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

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

	~TwoBodyEnergy () override

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

virtual bool	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...

virtual bool	requires_a_setup_for_scoring_for_residue_opportunity_during_minimization (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_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 utility::vector1 < id::PartialAtomID >	atoms_with_dof_derivatives (conformation::Residue const &res, pose::Pose const &p) const
	For a particular residue, list which atoms go into defining the DOF derivatives, including any atoms on adjacent residues. The Pose is provided for context, but there is no requirement that res be a member of that Pose. 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...

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

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

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

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

virtual bool	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...

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

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

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Public Attributes
	__pad0__:ContextIndependentTwoBodyEnergy parent

Private Member Functions
lkbtrie::LKBRotamerTrieOP	create_rotamer_trie (conformation::RotamerSetBase const &rotset) const

lkbtrie::LKBRotamerTrieOP	create_rotamer_trie (conformation::Residue const &res) 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

Private Attributes
etable::EtableCOP	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	etable_bins_per_A2_

Real	lkb_max_dis_

Real	lkb_max_dis2_

Real	fasol_max_dis2_

bool const	slim_etable_

Real	ramp_width_A2_

Real	overlap_width_A2_

Real	multi_water_fade_

Real	lkbridge_angle_widthscale_

Real	overlap_target_len2_

Real	overlap_gap2_

utility::vector1< Real >	d2_low_

utility::vector1< bool >	atom_type_is_charged_

utility::vector1< Real >	lk_ball_prefactor_

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 chemical::ResidueType core::scoring::lkball::LK_BallEnergy::ResidueType

convenience typedefs

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

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

Constructor & Destructor Documentation

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

References etable_, fasol_max_dis2_, lkb_max_dis2_, lkb_max_dis_, protocols::mean_field::max(), overlap_gap2_, overlap_target_len2_, overlap_width_A2_, setup_d2_bounds(), slim_etable_, and solv1_.

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

References setup_d2_bounds().

Member Function Documentation

void core::scoring::lkball::LK_BallEnergy::accumulate_single_atom_contributions	(	Size	atom1_n_attached_waters,
		Size	atom1_water_offset,
		WaterCoords const &	rsd1_waters,
		AtomWeights 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 core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges().

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

overridevirtual

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 lkb_max_dis_.

Referenced by create_rotamer_trie(), core::scoring::lkball::lkbtrie::LKBTrieEvaluator::hydrogen_interaction_cutoff2(), and setup_for_minimizing_for_residue_pair().

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

overridevirtual

The sum bbE(r1,r2) + bs(r1,r2) + bs(r2,r1) + ss(r1,r2) must equal rpe(r1,r2). This function evaluates only the energies of bb/bb interactions.

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

References core::scoring::etable::count_pair::CP_CROSSOVER_3, core::scoring::etable::count_pair::CP_CROSSOVER_4, protocols::ligand_docking::ga_ligand_dock::crossover(), core::conformation::Residue::data(), core::conformation::Residue::data_ptr(), core::conformation::Residue::is_polymer_bonded(), and core::conformation::residue_datacache::LK_BALL_INFO.

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

overridevirtual

The sum bbE(r1,r2) + bs(r1,r2) + bs(r2,r1) + ss(r1,r2) must equal rpe(r1,r2). This function evaluates only the energies of bb/sc interactions; that is, the backbone from residue 1 with the sidechain of residue 2.

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

References core::scoring::etable::count_pair::CP_CROSSOVER_3, core::scoring::etable::count_pair::CP_CROSSOVER_4, protocols::ligand_docking::ga_ligand_dock::crossover(), core::conformation::Residue::data(), core::conformation::Residue::data_ptr(), core::conformation::Residue::is_polymer_bonded(), and core::conformation::residue_datacache::LK_BALL_INFO.

void core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies	(	Size const	atom1,
		conformation::Residue const &	rsd1,
		Size	atom1_n_attached_waters,
		Size	atom1_water_offset,
		WaterCoords const &	rsd1_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_3, core::scoring::etable::count_pair::CP_CROSSOVER_4, protocols::ligand_docking::ga_ligand_dock::crossover(), etable_, etable_bins_per_A2_, fasol_max_dis2_, get_lk_fractional_contribution(), core::conformation::Residue::is_polymer_bonded(), protocols::antibody::l1, slim_etable_, solv1_, core::conformation::Atom::type(), and core::conformation::Residue::xyz().

void core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies_cp	(	Size const	atom1,
		conformation::Residue const &	rsd1,
		Size	atom1_n_attached_waters,
		Size	atom1_water_offset,
		WaterCoords 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_, etable_bins_per_A2_, fasol_max_dis2_, get_lk_fractional_contribution(), protocols::antibody::l1, core::conformation::Residue::seqpos(), slim_etable_, solv1_, core::conformation::Atom::type(), and core::conformation::Residue::xyz().

Real core::scoring::lkball::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_3, core::scoring::etable::count_pair::CP_CROSSOVER_4, protocols::ligand_docking::ga_ligand_dock::crossover(), etable_, etable_bins_per_A2_, fasol_max_dis2_, core::conformation::Residue::is_polymer_bonded(), protocols::antibody::l1, core::conformation::Residue::nheavyatoms(), slim_etable_, solv1_, core::conformation::Atom::type(), and core::conformation::Residue::xyz().

Real core::scoring::lkball::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_, etable_bins_per_A2_, fasol_max_dis2_, protocols::antibody::l1, core::conformation::Residue::nheavyatoms(), slim_etable_, solv1_, core::conformation::Atom::type(), and core::conformation::Residue::xyz().

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

overridevirtual

clone

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

lkbtrie::LKBRotamerTrieOP core::scoring::lkball::LK_BallEnergy::create_rotamer_trie ( conformation::RotamerSetBase const & rotset ) const

private

References atomic_interaction_cutoff(), core::scoring::trie::create_cpdata_correspondence_for_rotamerset(), core::scoring::lkball::create_rotamer_descriptor(), core::conformation::RotamerSetBase::num_rotamers(), core::scoring::lkball::retrieve_lkb_rotamer_set_info(), and core::conformation::RotamerSetBase::rotamer().

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

lkbtrie::LKBRotamerTrieOP core::scoring::lkball::LK_BallEnergy::create_rotamer_trie ( conformation::Residue const & res ) const

private

References atomic_interaction_cutoff(), core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::scoring::lkball::create_rotamer_descriptor(), and core::scoring::lkball::retrieve_lkb_resdata().

bool core::scoring::lkball::LK_BallEnergy::defines_intrares_energy ( EnergyMap const & weights ) const

inlineoverridevirtual

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.

bool core::scoring::lkball::LK_BallEnergy::divides_backbone_and_sidechain_energetics ( ) const

overridevirtual

Let the energy-method consumers (e.g. the packer) use bounding-sphere logic for deciding whether bb/bb, bb/sc, and sc/sc energies should be evaluated.

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

etable::Etable const & core::scoring::lkball::LK_BallEnergy::etable ( ) const

References etable_.

Referenced by core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges().

Real core::scoring::lkball::LK_BallEnergy::etable_bins_per_A2 ( ) const

inline

References etable_bins_per_A2_.

Referenced by core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges().

void core::scoring::lkball::LK_BallEnergy::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

overridevirtual

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.

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) "Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations" Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

default implementation does not alter either the F1 or F2 vectors.

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

Real core::scoring::lkball::LK_BallEnergy::eval_d_lk_fraction_dr_over_r	(	Real const	d2_delta,
		Real const	width
	)		const

Referenced by get_lkbr_fractional_contribution(), and sum_deriv_contributions_for_heavyatom_pair_one_way().

void core::scoring::lkball::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_, etable_bins_per_A2_, fasol_max_dis2_, slim_etable_, and core::conformation::Atom::type().

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

inlineoverridevirtual

Evaluate the intra-residue energy for a given residue.

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

Real core::scoring::lkball::LK_BallEnergy::eval_lk_fraction	(	Real const	d2_delta,
		Real const	width
	)		const

Stolen from LK_SigmoidalFunc in lk_hack d2_delta = d2 - d2_low

Referenced by get_lk_fractional_contribution(), get_lk_fractional_contribution_for_single_water(), get_lkbr_fractional_contribution(), and get_lkbr_fractional_contribution_noangle().

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

overridevirtual

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

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

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

References core::conformation::Residue::atom_is_hydrogen(), fasol_max_dis2_, core::scoring::ResPairMinimizationData::get_data_ref(), core::scoring::lk_ball_bridge_uncpl, core::scoring::lkball_nblist, core::conformation::Residue::natoms(), core::scoring::lkball::retrieve_lkb_resdata(), sum_deriv_contributions_for_heavyatom_pair(), and core::conformation::Residue::xyz().

void core::scoring::lkball::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

overridevirtual

Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamr.

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

References core::scoring::Energies::data(), core::pose::Pose::energies(), etable_, get_count_pair_function_trie(), core::conformation::RotamerSetBase::get_trie(), core::scoring::ScoreFunction::get_weight(), core::scoring::lk_ball, core::scoring::lk_ball_bridge, core::scoring::lk_ball_bridge_uncpl, core::scoring::lk_ball_iso, core::scoring::lk_ball_wtd, core::scoring::EnergiesCacheableDataType::LKB_TRIE_COLLECTION, core::scoring::methods::lkball_method, core::conformation::RotamerSetBase::num_rotamers(), core::conformation::RotamerSetBase::resid(), core::pose::Pose::residue(), and core::conformation::Residue::seqpos().

void core::scoring::lkball::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

overridevirtual

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

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

References etable_, get_count_pair_function_trie(), core::conformation::RotamerSetBase::get_trie(), core::scoring::ScoreFunction::get_weight(), core::scoring::lk_ball, core::scoring::lk_ball_bridge, core::scoring::lk_ball_bridge_uncpl, core::scoring::lk_ball_iso, core::scoring::lk_ball_wtd, core::scoring::methods::lkball_method, and core::conformation::RotamerSetBase::resid().

Real core::scoring::lkball::LK_BallEnergy::fasol_max_dis2 ( ) const

inline

References fasol_max_dis2_.

Referenced by core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges().

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

overridevirtual

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.

trie::TrieCountPairBaseOP core::scoring::lkball::LK_BallEnergy::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::conformation::RotamerSetBase::get_trie(), core::scoring::methods::lkball_method, core::conformation::RotamerSetBase::resid(), and core::pose::Pose::residue().

Referenced by evaluate_rotamer_background_energies(), and evaluate_rotamer_pair_energies().

trie::TrieCountPairBaseOP core::scoring::lkball::LK_BallEnergy::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_CROSSOVER_3, core::scoring::etable::count_pair::CP_CROSSOVER_4, core::scoring::etable::count_pair::CP_MULTIPLE_BONDS_OR_PSEUDOBONDS, core::scoring::etable::count_pair::CP_ONE_BOND, protocols::ligand_docking::ga_ligand_dock::crossover(), core::conformation::Residue::is_polymer_bonded(), and core::conformation::Residue::seqpos().

core::Real core::scoring::lkball::LK_BallEnergy::get_d2_low ( core::Size idx ) const

inline

References d2_low_.

Real core::scoring::lkball::LK_BallEnergy::get_lk_fractional_contribution	(	Vector const &	atom2_xyz,
		Size const	atom2_type,
		Size	atom1_n_attached_waters,
		Size	atom1_water_offset,
		WaterCoords const &	rsd1_waters,
		WaterDerivContributions &	d_weighted_d2_d_di,
		Real &	weighted_d2_water_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_, eval_lk_fraction(), multi_water_fade_, and ramp_width_A2_.

Referenced by accumulate_single_atom_contributions(), calculate_lk_ball_atom_energies(), calculate_lk_ball_atom_energies_cp(), core::scoring::lkball::lkbtrie::LKBTrieEvaluator::heavyatom_heavyatom_energy(), and sum_deriv_contributions_for_heavyatom_pair_one_way().

Real core::scoring::lkball::LK_BallEnergy::get_lk_fractional_contribution	(	Vector const &	atom2_xyz,
		Size const	atom2_type_index,
		Size const	atom1_n_attached_waters,
		Size const	atom1_water_offset,
		WaterCoords const &	rsd1_waters
	)		const

References d2_low_, eval_lk_fraction(), multi_water_fade_, and ramp_width_A2_.

Real core::scoring::lkball::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_, eval_lk_fraction(), and ramp_width_A2_.

Real core::scoring::lkball::LK_BallEnergy::get_lkbr_fractional_contribution	(	Vector const &	atom1_base,
		Vector const &	atom2_base,
		Size	atom1_n_attached_waters,
		Size	atom2_n_attached_waters,
		Size	atom1_water_offset,
		Size	atom2_water_offset,
		WaterCoords const &	rsd1_waters,
		WaterCoords const &	rsd2_waters
	)		const

Referenced by core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges(), core::scoring::lkball::lkbtrie::LKBTrieEvaluator::heavyatom_heavyatom_energy(), and sum_deriv_contributions_for_heavyatom_pair_one_way().

Real core::scoring::lkball::LK_BallEnergy::get_lkbr_fractional_contribution	(	Vector const &	atom1_base,
		Vector const &	atom2_base,
		Size	atom1_n_attached_waters,
		Size	atom2_n_attached_waters,
		Size	atom1_water_offset,
		Size	atom2_water_offset,
		WaterCoords const &	rsd1_waters,
		WaterCoords const &	rsd2_waters,
		WaterDerivVectors &	d_weighted_d2_d_di1,
		Real &	weighted_d2_water_delta,
		Real &	pointterm_lkbr,
		Real &	angleterm_lkbr,
		Real &	d_angleterm_lkbr_dr,
		bool	compute_derivs = `true`
	)		const

References eval_d_lk_fraction_dr_over_r(), eval_lk_fraction(), lkbridge_angle_widthscale_, multi_water_fade_, overlap_gap2_, overlap_target_len2_, and overlap_width_A2_.

Real core::scoring::lkball::LK_BallEnergy::get_lkbr_fractional_contribution_noangle	(	Size	atom1_n_attached_waters,
		Size	atom2_n_attached_waters,
		Size	atom1_water_offset,
		Size	atom2_water_offset,
		WaterCoords const &	rsd1_waters,
		WaterCoords const &	rsd2_waters
	)		const

References eval_lk_fraction(), multi_water_fade_, overlap_gap2_, and overlap_width_A2_.

core::Real core::scoring::lkball::LK_BallEnergy::get_lkbridge_angle_widthscale ( ) const

inline

References lkbridge_angle_widthscale_.

core::Real core::scoring::lkball::LK_BallEnergy::get_multi_water_fade ( ) const

inline

References multi_water_fade_.

core::Real core::scoring::lkball::LK_BallEnergy::get_overlap_gap2 ( ) const

inline

References overlap_gap2_.

core::Real core::scoring::lkball::LK_BallEnergy::get_overlap_target_len2 ( ) const

inline

References overlap_target_len2_.

core::Real core::scoring::lkball::LK_BallEnergy::get_overlap_width_A2 ( ) const

inline

References overlap_width_A2_.

core::Real core::scoring::lkball::LK_BallEnergy::get_ramp_width_A2 ( ) const

inline

References ramp_width_A2_.

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

overridevirtual

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.

Real core::scoring::lkball::LK_BallEnergy::lkb_max_dis ( ) const

inline

References lkb_max_dis_.

Real core::scoring::lkball::LK_BallEnergy::lkb_max_dis2 ( ) const

inline

References lkb_max_dis2_.

Referenced by core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges().

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

overridevirtual

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::lkball::LK_BallEnergy::prepare_rotamers_for_packing	(	pose::Pose const &	,
		conformation::RotamerSetBase &
	)		const

overridevirtual

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

default implementation noop

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

References create_rotamer_trie(), core::conformation::RotamerSetBase::data(), core::conformation::residue_datacache::LK_BALL_INFO, core::conformation::RotamerSetCacheableDataType::LK_BALL_ROTAMER_SET_INFO, core::scoring::methods::lkball_method, core::conformation::RotamerSetBase::nonconst_rotamer(), core::conformation::RotamerSetBase::num_rotamers(), rot(), and core::conformation::RotamerSetBase::store_trie().

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

overridevirtual

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

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

bool core::scoring::lkball::LK_BallEnergy::requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring ( pose::Pose const & pose ) const

overridevirtual

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

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

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

overridevirtual

This guy is used during scoring if we are not minimizing, or inside linmem_ig packing and things like that...

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

References core::conformation::Residue::data(), and core::conformation::residue_datacache::LK_BALL_INFO.

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

References core::scoring::etable::count_pair::CP_CROSSOVER_3, core::scoring::etable::count_pair::CP_CROSSOVER_4, protocols::ligand_docking::ga_ligand_dock::crossover(), and core::conformation::Residue::is_polymer_bonded().

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

References core::chemical::AtomTypeSet::atom_type_index(), atom_type_is_charged_, d2_low_, etable_, core::chemical::AtomType::lj_radius(), lk_ball_prefactor_, protocols::mean_field::max(), core::chemical::AtomTypeSet::n_atomtypes(), core::chemical::AtomType::name(), ramp_width_A2_, and core::scoring::electron_density::square().

Referenced by LK_BallEnergy().

void core::scoring::lkball::LK_BallEnergy::setup_for_derivatives	(	pose::Pose &	pose,
		ScoreFunction const &	sfxn
	)		const

overridevirtual

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

default implementation noop

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

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

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

overridevirtual

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

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

References core::scoring::lkball::update_cached_lkb_resinfo().

Referenced by setup_for_minimizing_for_residue().

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

overridevirtual

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

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

References setup_for_derivatives_for_residue().

void core::scoring::lkball::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

overridevirtual

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

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

References atomic_interaction_cutoff(), core::scoring::etable::count_pair::CP_CROSSOVER_3, core::scoring::etable::count_pair::CP_CROSSOVER_4, protocols::ligand_docking::ga_ligand_dock::crossover(), core::scoring::ResPairMinimizationData::get_data(), core::conformation::Residue::is_polymer_bonded(), core::scoring::lkb_respair_data, core::scoring::lkball_nblist, and core::scoring::ResPairMinimizationData::set_data().

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

overridevirtual

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

default implementation noop

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

References core::conformation::Residue::aa(), core::chemical::aa_vrt, create_rotamer_trie(), core::scoring::Energies::data(), core::pose::Pose::energies(), core::scoring::EnergiesCacheableDataType::LKB_TRIE_COLLECTION, core::pose::Pose::residue(), core::pose::Pose::residue_data(), core::pose::Pose::size(), and core::scoring::lkball::update_cached_lkb_resinfo().

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

overridevirtual

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

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

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

Referenced by protocols::cryst::ReportGradientsMover::compute().

void core::scoring::lkball::LK_BallEnergy::setup_for_scoring_for_residue	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		basic::datacache::BasicDataCache &	residue_data_cache
	)		const

overridevirtual

Do any setup work before scoring, caching any slow-to-compute data that will be used during energy evaluation inside of the input Residue object's data cache. (The Residue on the whole is given as a constant reference, but non-constant access to its data cache is granted.)

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

References core::scoring::lkball::update_cached_lkb_resinfo().

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

overridevirtual

The sum bbE(r1,r2) + bs(r1,r2) + bs(r2,r1) + ss(r1,r2) must equal rpe(r1,r2). This function evaluates only the energies of sc/sc interactions.

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

References core::scoring::etable::count_pair::CP_CROSSOVER_3, core::scoring::etable::count_pair::CP_CROSSOVER_4, protocols::ligand_docking::ga_ligand_dock::crossover(), core::conformation::Residue::data(), core::conformation::Residue::data_ptr(), core::conformation::Residue::is_polymer_bonded(), and core::conformation::residue_datacache::LK_BALL_INFO.

bool core::scoring::lkball::LK_BallEnergy::slim_etable ( ) const

inline

References slim_etable_.

Referenced by core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges().

ObjexxFCL::FArray3D< Real > const& core::scoring::lkball::LK_BallEnergy::solv1 ( ) const

inline

References solv1_.

Referenced by core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges().

ObjexxFCL::FArray3D< Real > const& core::scoring::lkball::LK_BallEnergy::solv2 ( ) const

inline

References solv2_.

Referenced by core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges().

void core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair	(	Real const	d2,
		Size const	heavyatom1,
		conformation::Residue const &	rsd1,
		LKB_ResidueInfo const &	rsd1_info,
		Size const	heavyatom2,
		conformation::Residue const &	rsd2,
		LKB_ResidueInfo const &	rsd2_info,
		pose::Pose const &	,
		EnergyMap const &	weights,
		Real const	cp_weight,
		utility::vector1< DerivVectorPair > &	r1_at_derivs,
		utility::vector1< DerivVectorPair > &	r2_at_derivs
	)		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 sum_deriv_contributions_for_heavyatom_pair_one_way().

Referenced by eval_residue_pair_derivatives().

void core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way	(	Size const	heavyatom1,
		conformation::Residue const &	rsd1,
		LKB_ResidueInfo const &	rsd1_info,
		Size const	heavyatom2,
		conformation::Residue const &	rsd2,
		LKB_ResidueInfo const &	rsd2_info,
		EnergyMap const &	weights,
		Real const	weight_factor,
		Real const	d2,
		utility::vector1< DerivVectorPair > &	r1_at_derivs,
		utility::vector1< DerivVectorPair > &	r2_at_derivs
	)		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::scoring::lkball::LKB_ResidueInfo::atom1_derivs(), core::scoring::lkball::LKB_ResidueInfo::atom2_derivs(), core::scoring::lkball::LKB_ResidueInfo::atom3_derivs(), core::scoring::lkball::LKB_ResidueInfo::atom_weights(), dsolv1_, etable_, etable_bins_per_A2_, eval_d_lk_fraction_dr_over_r(), fasol_max_dis2_, get_lk_fractional_contribution(), get_lkbr_fractional_contribution(), core::scoring::lkball::LKB_ResidueInfo::get_water_builder(), core::scoring::lk_ball, core::scoring::lk_ball_bridge, core::scoring::lk_ball_bridge_uncpl, core::scoring::lk_ball_iso, core::scoring::lk_ball_wtd, lkbridge_angle_widthscale_, core::scoring::lkball::LKB_ResidueInfo::n_attached_waters(), overlap_width_A2_, ramp_width_A2_, slim_etable_, solv1_, solv2_, core::conformation::Atom::type(), core::scoring::lkball::LKB_ResidueInfo::water_offset_for_atom(), core::scoring::lkball::LKB_ResidueInfo::waters(), and core::conformation::Residue::xyz().

Referenced by sum_deriv_contributions_for_heavyatom_pair().

void core::scoring::lkball::LK_BallEnergy::update_residue_for_packing	(	pose::Pose &	,
		Size	resid
	)		const

overridevirtual

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

default implementation noop

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

References core::conformation::Residue::aa(), core::chemical::aa_vrt, create_rotamer_trie(), core::scoring::Energies::data(), core::pose::Pose::energies(), core::scoring::EnergiesCacheableDataType::LKB_TRIE_COLLECTION, core::pose::Pose::residue(), core::pose::Pose::residue_data(), and core::scoring::lkball::update_cached_lkb_resinfo().