#include <ConstraintsEnergy.hh>

Public Member Functions
	ConstraintsEnergy ()

virtual	~ConstraintsEnergy ()

virtual EnergyMethodOP	clone () const

virtual methods::LongRangeEnergyType	long_range_type () const
	Identification for this LR2B energy that links it with the long-range energy container that it stores in the Energies object. More...

virtual bool	defines_residue_pair_energy (pose::Pose const &pose, Size res1, Size res2) const
	Interface from the LongRangeTwoBodyEnery base class; returns "true" if there's any non-zero or potentially non-zero interaction between a pair of residues in a pose. More...

virtual void	residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluate constraint residue_pair_energy. Defers entirely to cst_set. 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	use_extended_residue_pair_energy_interface () const
	Returns true as the ConstraintsEnergy caches its residue pair constraints in the ResPairMinimicationData objects stored on edges in the MinimizationGraph. 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
	The ConstraintsEnergy caches all residue-pair constraints operating between a particular pair of residues in the min_data object so that it does not need to search for those constraints when scoring during minimization. More...

virtual bool	defines_score_for_residue_pair (conformation::Residue const &res1, conformation::Residue const &res2, bool res_moving_wrt_eachother) const
	Returns false if residue1 and residue2 have no inter-residue pair constraints or if the two residues are not moving wrt each other. More...

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
	Cache the intra-residue constraints in the ResSingleMinimizationData object for rapid retrieval during minimization and allow the constraints to store data in the res_data_cache if they need to. More...

virtual void	setup_for_minimizing_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, ResSingleMinimizationData const &res1_data_cache, ResSingleMinimizationData const &res2_data_cache, ResPairMinimizationData &respair_data_cache) const
	Cache the residue-pair constraints in the ResPairMinimizationData object for rapid retrieval during minimization and allow constraints to cache useful data in the respair_data_cache if they need to. More...

virtual bool	requires_a_setup_for_scoring_for_residue_pair_opportunity (pose::Pose const &pose) const
	Request the opportunity to setup for scoring. 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
	Ask for the opportunity to setup for derivative evaluation. 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. More...

void	prepare_constraints_energy_container (pose::Pose &pose) const

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

virtual void	setup_for_packing (pose::Pose &pose, utility::vector1< bool > const &residues_repacking, utility::vector1< bool > const &residues_designing) const
	Make sure that the ConstraintsEnergyContainer is ready for packing. More...

virtual void	setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const
	Setup constraint-set specific derivatives. More...

bool	defines_high_order_terms (pose::Pose const &) const
	Returns true if there are three-body or higher-body constraints that the user has defined. High-order terms will not be correctly evaluated in RTMin or other extra-pose techniques for minimization (but will work correctly when minimizing an entire Pose). More...

virtual bool	defines_intrares_energy (EnergyMap const &weights) const
	Intraresidue constraints can exist; the ConstraintsEnergy class cannot tell whether or not any intraresidue constraints exist when only given the weight set, so for safety it says "yes, I define intraresidue energies" and guarantees they will be evaluated properly if they do exist. More...

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

virtual bool	use_extended_intrares_energy_interface () const
	request of minimization routines that they use the extended intraresidue energy interface 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 energies using ConstraintCOPs cached in the data_cache object. More...

virtual bool	requires_a_setup_for_scoring_for_residue_opportunity (pose::Pose const &pose) const
	Ask for the opportunity to setup for scoring for evaluating 1-body constraints. More...

virtual void	setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const
	Allow the component constraints to setup for scoring for a particular residue. 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...

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
	The DunbrackConstraint, which adds a "constant term" to the energy for a particular rotamer so that the particular rotamer matches the score of the best rotamer at a particular phi/psi, defines derivatives for phi and psi. or rather – it doesn't, but it should. 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	finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const
	called at the end of energy evaluation More...

virtual 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
	called during gradient-based minimization inside dfunc More...

Real	eval_dof_derivative (id::DOF_ID const &id, id::TorsionID const &tor, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap const &weights) const
	Evaluate dof derivatives when DOF_constraints are in use. More...

virtual void	indicate_required_context_graphs (utility::vector1< bool > &) const
	constraints are context independent More...

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

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

virtual	~ContextIndependentLRTwoBodyEnergy ()

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::LongRangeTwoBodyEnergy
	LongRangeTwoBodyEnergy (EnergyMethodCreatorOP creator)
	Constructor with an EnergyMethodCreator to inform the grandparent EnergyMethod class which ScoreTypes this EnergyMethod computes. More...

virtual	~LongRangeTwoBodyEnergy ()

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	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 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...

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 the derived class's residue_pair_energy method. 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 rotamr. 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 rotamr. 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	prepare_rotamers_for_packing (pose::Pose const &, conformation::RotamerSetBase &) const

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

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

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

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

Public Attributes
	__pad0__:ContextIndependentLRTwoBodyEnergy parent

	__pad1__:EnergyMethodOP EnergyMethodOP

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

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

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

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

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...

Constructor & Destructor Documentation

core::scoring::constraints::ConstraintsEnergy::ConstraintsEnergy ( )

Referenced by clone().

core::scoring::constraints::ConstraintsEnergy::~ConstraintsEnergy ( )

virtual

Member Function Documentation

methods::EnergyMethodOP core::scoring::constraints::ConstraintsEnergy::clone ( ) const

virtual

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

References ConstraintsEnergy().

bool core::scoring::constraints::ConstraintsEnergy::defines_high_order_terms ( pose::Pose const & pose ) const

virtual

Returns true if there are three-body or higher-body constraints that the user has defined. High-order terms will not be correctly evaluated in RTMin or other extra-pose techniques for minimization (but will work correctly when minimizing an entire Pose).

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

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

bool core::scoring::constraints::ConstraintsEnergy::defines_intrares_dof_derivatives ( pose::Pose const & p ) const

virtual

The DunbrackConstraint, which adds a "constant term" to the energy for a particular rotamer so that the particular rotamer matches the score of the best rotamer at a particular phi/psi, defines derivatives for phi and psi. or rather – it doesn't, but it should.

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

bool core::scoring::constraints::ConstraintsEnergy::defines_intrares_energy ( EnergyMap const & weights ) const

virtual

Intraresidue constraints can exist; the ConstraintsEnergy class cannot tell whether or not any intraresidue constraints exist when only given the weight set, so for safety it says "yes, I define intraresidue energies" and guarantees they will be evaluated properly if they do exist.

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

bool core::scoring::constraints::ConstraintsEnergy::defines_residue_pair_energy	(	pose::Pose const &	pose,
		Size	res1,
		Size	res2
	)		const

virtual

Interface from the LongRangeTwoBodyEnery base class; returns "true" if there's any non-zero or potentially non-zero interaction between a pair of residues in a pose.

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

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

bool core::scoring::constraints::ConstraintsEnergy::defines_score_for_residue_pair	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		bool	res_moving_wrt_eachother
	)		const

virtual

Returns false if residue1 and residue2 have no inter-residue pair constraints or if the two residues are not moving wrt each other.

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

void core::scoring::constraints::ConstraintsEnergy::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

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::pose::Pose::constraint_set().

Real core::scoring::constraints::ConstraintsEnergy::eval_dof_derivative	(	id::DOF_ID const &	id,
		id::TorsionID const &	tor,
		pose::Pose const &	pose,
		ScoreFunction const &	scorefxn,
		EnergyMap const &	weights
	)		const

Evaluate dof derivatives when DOF_constraints are in use.

uses the dof constraints – depricated interface

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

virtual

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

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

References core::scoring::cst_res_data, core::scoring::ResSingleMinimizationData::get_data(), core::conformation::Residue::natoms(), and core::conformation::Residue::seqpos().

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

virtual

Evaluate the intra-residue constraint energy for a given residue.

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

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

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

virtual

Evaluate the intra-residue energies using ConstraintCOPs cached in the data_cache object.

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

References core::scoring::cst_res_data, core::scoring::ResSingleMinimizationData::get_data(), and core::scoring::ScoreFunction::weights().

Real core::scoring::constraints::ConstraintsEnergy::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

virtual

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.

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

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

virtual

Evaluate the derivative for an atom in rsd1 with respect to rsd2 in the context of a particular pose, and increment the F1 and F2 vectors.

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

References core::scoring::cst_respair_data, core::scoring::ResPairMinimizationData::get_data(), core::conformation::Residue::natoms(), and core::conformation::Residue::seqpos().

void core::scoring::constraints::ConstraintsEnergy::finalize_total_energy	(	pose::Pose &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	totals
	)		const

virtual

called at the end of energy evaluation

called at the end of energy evaluation; allows for the evaluation of constraints that cannot be decomposed into residue pairs. Defers entirely to cst_set.

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

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

void core::scoring::constraints::ConstraintsEnergy::indicate_required_context_graphs ( utility::vector1< bool > & ) const

virtual

constraints are context independent

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

methods::LongRangeEnergyType core::scoring::constraints::ConstraintsEnergy::long_range_type ( ) const

virtual

Identification for this LR2B energy that links it with the long-range energy container that it stores in the Energies object.

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

References core::scoring::methods::constraints_lr.

bool core::scoring::constraints::ConstraintsEnergy::minimize_in_whole_structure_context ( pose::Pose const & ) const

virtual

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

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

void core::scoring::constraints::ConstraintsEnergy::prepare_constraints_energy_container ( pose::Pose & pose ) const

References core::pose::Pose::constraint_set(), core::scoring::methods::constraints_lr, core::pose::Pose::energies(), and utility::pointer::owning_ptr< T >::get().

Referenced by setup_for_packing(), and setup_for_scoring().

bool core::scoring::constraints::ConstraintsEnergy::requires_a_setup_for_derivatives_for_residue_opportunity ( pose::Pose const & pose ) const

virtual

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

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

bool core::scoring::constraints::ConstraintsEnergy::requires_a_setup_for_derivatives_for_residue_pair_opportunity ( pose::Pose const & pose ) const

virtual

Ask for the opportunity to setup for derivative evaluation.

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

bool core::scoring::constraints::ConstraintsEnergy::requires_a_setup_for_scoring_for_residue_opportunity ( pose::Pose const & pose ) const

virtual

Ask for the opportunity to setup for scoring for evaluating 1-body constraints.

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

bool core::scoring::constraints::ConstraintsEnergy::requires_a_setup_for_scoring_for_residue_pair_opportunity ( pose::Pose const & pose ) const

virtual

Request the opportunity to setup for scoring.

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

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

virtual

Evaluate constraint residue_pair_energy. Defers entirely to cst_set.

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

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

void core::scoring::constraints::ConstraintsEnergy::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

The ConstraintsEnergy caches all residue-pair constraints operating between a particular pair of residues in the min_data object so that it does not need to search for those constraints when scoring during minimization.

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

References core::scoring::cst_respair_data, core::scoring::ResPairMinimizationData::get_data(), and core::scoring::ScoreFunction::weights().

void core::scoring::constraints::ConstraintsEnergy::setup_for_derivatives	(	pose::Pose &	pose,
		ScoreFunction const &	scfxn
	)		const

virtual

Setup constraint-set specific derivatives.

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

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

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

virtual

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

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

References core::scoring::cst_res_data, and core::scoring::ResSingleMinimizationData::get_data().

void core::scoring::constraints::ConstraintsEnergy::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

virtual

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

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

References core::scoring::cst_respair_data, and core::scoring::ResPairMinimizationData::get_data().

void core::scoring::constraints::ConstraintsEnergy::setup_for_minimizing_for_residue	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		kinematics::MinimizerMapBase const &	minmap,
		ResSingleMinimizationData &	res_data_cache
	)		const

virtual

Cache the intra-residue constraints in the ResSingleMinimizationData object for rapid retrieval during minimization and allow the constraints to store data in the res_data_cache if they need to.

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

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

void core::scoring::constraints::ConstraintsEnergy::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 &	respair_data_cache
	)		const

virtual

Cache the residue-pair constraints in the ResPairMinimizationData object for rapid retrieval during minimization and allow constraints to cache useful data in the respair_data_cache if they need to.

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

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

void core::scoring::constraints::ConstraintsEnergy::setup_for_packing	(	pose::Pose &	pose,
		utility::vector1< bool > const &	residues_repacking,
		utility::vector1< bool > const &	residues_designing
	)		const

virtual

Make sure that the ConstraintsEnergyContainer is ready for packing.

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

References prepare_constraints_energy_container().

void core::scoring::constraints::ConstraintsEnergy::setup_for_scoring	(	pose::Pose &	pose,
		ScoreFunction const &	scfxn
	)		const

virtual

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

References core::pose::Pose::constraint_set(), and prepare_constraints_energy_container().

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

virtual

Allow the component constraints to setup for scoring for a particular residue.

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

References core::scoring::cst_res_data, and core::scoring::ResSingleMinimizationData::get_data().

void core::scoring::constraints::ConstraintsEnergy::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

virtual

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.

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

References core::scoring::cst_respair_data, and core::scoring::ResPairMinimizationData::get_data().

bool core::scoring::constraints::ConstraintsEnergy::use_extended_intrares_energy_interface ( ) const

virtual

request of minimization routines that they use the extended intraresidue energy interface

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

bool core::scoring::constraints::ConstraintsEnergy::use_extended_residue_pair_energy_interface ( ) const

virtual

Returns true as the ConstraintsEnergy caches its residue pair constraints in the ResPairMinimicationData objects stored on edges in the MinimizationGraph.

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

core::Size core::scoring::constraints::ConstraintsEnergy::version ( ) const

virtual

Return the version of the energy method.

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

Member Data Documentation

core::scoring::constraints::ConstraintsEnergy::__pad0__

core::scoring::constraints::ConstraintsEnergy::__pad1__

The documentation for this class was generated from the following files:

symlinks/rosetta/src/core/scoring/constraints/ConstraintsEnergy.hh
symlinks/rosetta/src/core/scoring/constraints/ConstraintsEnergy.cc

Public Member Functions

Public Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation