#include <LK_PolarNonPolarEnergy.hh>

Inheritance diagram for core::scoring::methods::LK_PolarNonPolarEnergy:

Public Types
typedef ContextIndependentTwoBodyEnergy	parent

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_PolarNonPolarEnergy (etable::Etable const &etable_in, bool const analytic_etable_evaluation)

virtual EnergyMethodOP	clone () const
	clone More...

	LK_PolarNonPolarEnergy (LK_PolarNonPolarEnergy const &src)

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

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

virtual void	setup_for_minimizing (pose::Pose &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map) 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 bool	defines_score_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, 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 etable::count_pair::CountPairFunctionCOP	get_count_pair_function (Size const res1, Size const res2, pose::Pose const &pose, ScoreFunction const &) const

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

virtual etable::count_pair::CountPairFunctionCOP	get_intrares_countpair (conformation::Residue const &rsd1, pose::Pose const &, ScoreFunction const &) const

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

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

void	eval_atom_derivative_intra_RNA (id::AtomID const &atom_id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, EnergyMap const &weights, Vector &F1, Vector &F2) const

virtual void	eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const
	called during gradient-based minimization inside dfunc More...

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

virtual bool	defines_intrares_energy (EnergyMap const &weights) 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 &rsd, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) 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...

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

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

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

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

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

virtual	~TwoBodyEnergy ()

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

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

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

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

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

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

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

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

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

virtual void	eval_residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &, ResSingleMinimizationData const &, ResPairMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const
	Evaluate the 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...

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_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const
	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...

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

virtual void	update_residue_for_packing (pose::Pose &, Size resid) const
	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...

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

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

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

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

Private Member Functions
Vector	get_base_vector (conformation::Residue const &rsd1, Size const i, pose::Pose const &pose) const

void	get_residue_energy_RNA_intra (conformation::Residue const &rsd, pose::Pose const &pose, Real &lk_polar_intra_RNA_score, Real &lk_nonpolar_intra_RNA_score, Real &lk_costheta_intra_RNA_score, bool const compute_polar, bool const compute_nonpolar) const

void	get_residue_pair_energy_one_way (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, Real &lk_polar_score, Real &lk_nonpolar_score, Real &lk_costheta_score, bool const compute_polar, bool const compute_nonpolar) const

Real	eval_lk (conformation::Atom const &atom1, conformation::Atom const &atom2, Real &deriv, bool const &eval_deriv) const

std::pair< Real, Real >	eval_lk_efficient (conformation::Atom const &atom1, conformation::Atom const &atom2, Real &deriv, bool const &eval_deriv) const

void	distribute_pseudo_base_atom_derivatives (pose::Pose const &pose) const

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

Private Attributes
etable::EtableEvaluatorOP	etable_evaluator_

Real const	safe_max_dis2_

Real const	max_dis_

bool const	verbose_

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_PolarNonPolarEnergy::parent

Constructor & Destructor Documentation

core::scoring::methods::LK_PolarNonPolarEnergy::LK_PolarNonPolarEnergy	(	etable::Etable const &	etable_in,
		bool const	analytic_etable_evaluation
	)

References etable_evaluator_.

Referenced by clone().

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

Member Function Documentation

Distance core::scoring::methods::LK_PolarNonPolarEnergy::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 max_dis_.

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

virtual

clone

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

References LK_PolarNonPolarEnergy().

bool core::scoring::methods::LK_PolarNonPolarEnergy::defines_intrares_energy ( EnergyMap const & weights ) const

virtual

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.

References core::scoring::lk_nonpolar_intra_RNA, and core::scoring::lk_polar_intra_RNA.

Referenced by eval_atom_derivative().

bool core::scoring::methods::LK_PolarNonPolarEnergy::defines_score_for_residue_pair	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		bool	res_moving_wrt_eachother
	)		const

virtual

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

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

References core::conformation::Residue::seqpos().

Referenced by get_count_pair_function().

void core::scoring::methods::LK_PolarNonPolarEnergy::distribute_pseudo_base_atom_derivatives ( pose::Pose const & pose ) const

private

void core::scoring::methods::LK_PolarNonPolarEnergy::eval_atom_derivative	(	id::AtomID const &	id,
		pose::Pose const &	pose,
		kinematics::DomainMap const &	domain_map,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights,
		Vector &	F1,
		Vector &	F2
	)		const

virtual

called during gradient-based minimization inside dfunc

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

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

References core::id::AtomID::atomno(), core::scoring::AtomNeighbor::atomno(), core::scoring::etable::count_pair::CP_CROSSOVER_4, defines_intrares_energy(), core::pose::Pose::energies(), eval_atom_derivative_intra_RNA(), eval_lk(), get_base_vector(), core::scoring::ScoreFunction::has_nonzero_weight(), core::scoring::lk_costheta, core::scoring::lk_nonpolar, core::scoring::lk_polar, core::scoring::EnergiesCacheableDataType::LK_POLARNONPOLAR_NBLIST, core::scoring::Energies::nblist(), protocols::sic_dock::scores::nbr, core::pose::Pose::residue(), core::id::AtomID::rsd(), core::scoring::AtomNeighbor::rsd(), and core::scoring::Energies::use_nblist_auto_update().

void core::scoring::methods::LK_PolarNonPolarEnergy::eval_atom_derivative_intra_RNA	(	id::AtomID const &	atom_id,
		pose::Pose const &	pose,
		kinematics::DomainMap const &	domain_map,
		EnergyMap const &	weights,
		Vector &	F1,
		Vector &	F2
	)		const

References core::conformation::Residue::atom_name(), core::id::AtomID::atomno(), core::scoring::etable::count_pair::CP_CROSSOVER_4, eval_lk(), core::chemical::element::F, get_base_vector(), core::chemical::rna::is_base_phosphate_atom_pair(), core::scoring::lk_nonpolar_intra_RNA, core::scoring::lk_polar_intra_RNA, core::pose::Pose::residue(), core::id::AtomID::rsd(), safe_max_dis2_, and verbose_.

Referenced by eval_atom_derivative().

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

virtual

Evaluate the intra-residue energy for a given residue.

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

References get_residue_energy_RNA_intra(), core::scoring::ScoreFunction::has_nonzero_weight(), core::conformation::Residue::is_RNA(), core::scoring::lk_costheta, core::scoring::lk_nonpolar, core::scoring::lk_nonpolar_intra_RNA, core::scoring::lk_polar, and core::scoring::lk_polar_intra_RNA.

Real core::scoring::methods::LK_PolarNonPolarEnergy::eval_lk	(	conformation::Atom const &	atom1,
		conformation::Atom const &	atom2,
		Real &	deriv,
		bool const &	eval_deriv
	)		const

private

References etable_evaluator_.

Referenced by eval_atom_derivative(), eval_atom_derivative_intra_RNA(), get_residue_energy_RNA_intra(), and get_residue_pair_energy_one_way().

std::pair< Real, Real > core::scoring::methods::LK_PolarNonPolarEnergy::eval_lk_efficient	(	conformation::Atom const &	atom1,
		conformation::Atom const &	atom2,
		Real &	deriv,
		bool const &	eval_deriv
	)		const

private

References etable_evaluator_.

Referenced by residue_pair_energy_ext().

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

virtual

called by the ScoreFunction at the end of energy evaluation. The derived class has the opportunity to accumulate a score into the pose's total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

called at the end of energy evaluation

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

Vector core::scoring::methods::LK_PolarNonPolarEnergy::get_base_vector	(	conformation::Residue const &	rsd1,
		Size const	i,
		pose::Pose const &	pose
	)		const

private

References core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::bonded_neighbor(), core::conformation::Residue::connect_map(), core::chemical::ResConnID::connid(), core::chemical::ResidueType::n_residue_connections_for_atom(), core::chemical::ResConnID::resid(), core::pose::Pose::residue(), core::chemical::ResidueType::residue_connections_for_atom(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by eval_atom_derivative(), eval_atom_derivative_intra_RNA(), get_residue_energy_RNA_intra(), get_residue_pair_energy_one_way(), and residue_pair_energy_ext().

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

virtual

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

Referenced by setup_for_minimizing_for_residue_pair().

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

virtual

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

etable::count_pair::CountPairFunctionCOP core::scoring::methods::LK_PolarNonPolarEnergy::get_intrares_countpair	(	conformation::Residue const &	rsd1,
		pose::Pose const &	,
		ScoreFunction const &
	)		const

virtual

References core::scoring::etable::count_pair::CP_CROSSOVER_4.

void core::scoring::methods::LK_PolarNonPolarEnergy::get_residue_energy_RNA_intra	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		Real &	lk_polar_intra_RNA_score,
		Real &	lk_nonpolar_intra_RNA_score,
		Real &	lk_costheta_intra_RNA_score,
		bool const	compute_polar,
		bool const	compute_nonpolar
	)		const

private

References core::scoring::etable::count_pair::CP_CROSSOVER_4, eval_lk(), core::chemical::element::F, get_base_vector(), core::chemical::rna::is_base_phosphate_atom_pair(), safe_max_dis2_, core::scoring::methods::TR(), and verbose_.

Referenced by eval_intrares_energy().

void core::scoring::methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		pose::Pose const &	pose,
		Real &	lk_polar_score,
		Real &	lk_nonpolar_score,
		Real &	lk_costheta_score,
		bool const	compute_polar,
		bool const	compute_nonpolar
	)		const

private

References core::conformation::Residue::atom(), core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::scoring::etable::count_pair::CP_CROSSOVER_4, eval_lk(), core::chemical::element::F, get_base_vector(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), core::conformation::Residue::name1(), core::conformation::Residue::nheavyatoms(), safe_max_dis2_, core::conformation::Residue::seqpos(), core::scoring::methods::TR(), verbose_, and core::conformation::Residue::xyz().

Referenced by residue_pair_energy().

void core::scoring::methods::LK_PolarNonPolarEnergy::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.

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

virtual

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

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

References get_residue_pair_energy_one_way(), core::scoring::ScoreFunction::has_nonzero_weight(), core::scoring::lk_costheta, core::scoring::lk_nonpolar, and core::scoring::lk_polar.

void core::scoring::methods::LK_PolarNonPolarEnergy::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::conformation::Residue::atom(), core::scoring::ResiduePairNeighborList::atom_neighbors(), core::conformation::Residue::atom_type(), core::scoring::etable::count_pair::CP_CROSSOVER_4, eval_lk_efficient(), get_base_vector(), core::scoring::ResPairMinimizationData::get_data_ref(), core::scoring::ScoreFunction::has_nonzero_weight(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), core::scoring::lk_costheta, core::scoring::lk_nonpolar, core::scoring::lk_polar, core::scoring::lk_PolarNonPolar_pair_nblist, core::conformation::Residue::nheavyatoms(), and core::conformation::Residue::xyz().

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

virtual

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

default implementation noop

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

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

void core::scoring::methods::LK_PolarNonPolarEnergy::setup_for_minimizing	(	pose::Pose &	,
		ScoreFunction const &	,
		kinematics::MinimizerMapBase const &
	)		const

virtual

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.

default implementation noop

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

References core::kinematics::MinimizerMapBase::domain_map(), core::pose::Pose::energies(), core::scoring::EnergiesCacheableDataType::LK_POLARNONPOLAR_NBLIST, max_dis_, core::scoring::Energies::use_nblist(), core::scoring::Energies::use_nblist_auto_update(), and XX.

void core::scoring::methods::LK_PolarNonPolarEnergy::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 get_count_pair_function(), core::scoring::ResPairMinimizationData::get_data(), core::scoring::lk_PolarNonPolar_pair_nblist, max_dis_, and core::scoring::ResPairMinimizationData::set_data().

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

virtual

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

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

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

bool core::scoring::methods::LK_PolarNonPolarEnergy::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_PolarNonPolarEnergy::version ( ) const

privatevirtual

Return the version of the energy method.

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