#include <DEEREnergy.hh>

Inheritance diagram for core::energy_methods::DEEREnergy:

[legend]

Public Member Functions
	DEEREnergy (scoring::methods::EnergyMethodCreatorOP energymethodcreator)
	Constructor. More...

	DEEREnergy (scoring::methods::EnergyMethodOptions const &)
	Constructor for obtaining command-line options. More...

	DEEREnergy ()
	Default Constructor. More...

	DEEREnergy (DEEREnergy const &other)
	Copy constructor. More...

core::scoring::methods::EnergyMethodOP	clone () const override
	Copy function. More...

	~DEEREnergy () override
	Destructor. More...

scoring::methods::LongRangeEnergyType	long_range_type () const override
	INHERITED FUNCTIONS. More...

void	setup_for_scoring (pose::Pose &pose, scoring::ScoreFunction const &) const override
	Set up scoring process. More...

void	residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, scoring::ScoreFunction const &, scoring::EnergyMap &emap) const override
	Add energy/score for a given pair of residues to map. More...

void	setup_for_minimizing (pose::Pose &, scoring::ScoreFunction const &, kinematics::MinimizerMapBase const &) const override
	A declared but unused function. More...

bool	defines_intrares_energy (scoring::EnergyMap const &) const override
	Returns "false" by default. More...

bool	defines_residue_pair_energy (pose::Pose const &pose, Size rsd1, Size rsd2) const override
	Fetches if two residues are "connected" (i.e. there is a score) More...

void	setup_for_derivatives (pose::Pose &pose, scoring::ScoreFunction const &) const override
	Calculates the derivatives for minimization. Done numerically. More...

void	eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, scoring::ScoreFunction const &, scoring::EnergyMap &emap) const override
	A declared but unused function. More...

void	finalize_total_energy (pose::Pose &, scoring::ScoreFunction const &, scoring::EnergyMap &) const override
	A declared but unused function. More...

void	eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &, scoring::ScoreFunction const &, scoring::EnergyMap const &emap, numeric::xyzVector< Real > &F1, numeric::xyzVector< Real > &F2) const override
	Apply atom derivative to atom. More...

void	indicate_required_context_graphs (utility::vector1< bool > &) const override
	A declared but unused function. More...

Size	version () const override
	Version 1 (as of 3 January 2021) More...

scoring::epr_deer::DEERDataCacheCOP const	get_const_deer_data (pose::Pose const &pose) const
	NON-VIRTUAL FUNCTIONS. More...

scoring::epr_deer::DEERDataCacheOP	get_deer_data (pose::Pose &pose) const
	Returns the DEERDataCache in the pose (non-const) More...

std::map< Size, Real >	iter_over_labels (pose::Pose &pose, int const &mod=0) const
	This checks if multiple sets of spin labels is being used. More...

Real	get_score (pose::Pose &pose, scoring::epr_deer::EPRSpinLabel &sl, Size const &edge_id, int const &mod=0) const
	Calculates the score for a specific data set. More...

void	initialize_energy_method (pose::Pose &pose) const
	Initializes energy method. More...

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

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

	~LongRangeTwoBodyEnergy () override

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 void	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
	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	setup_for_minimizing_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, ResSingleMinimizationData const &res1_data_cache, ResSingleMinimizationData const &res2_data_cache, ResPairMinimizationData &data_cache) const
	Called at the beginning of minimization, allowing this energy method to cache data pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. More...

virtual 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_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, basic::datacache::BasicDataCache &res_data_cache) 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 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...

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...

virtual void	setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, basic::datacache::BasicDataCache &residue_data_cache) const
	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...

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

virtual void	setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, basic::datacache::BasicDataCache &residue_data_cache) const
	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...

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	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...

virtual bool	has_atomistic_energies () const
	Does this EnergyMethod have a non-trivial implementation of the (one body) atomistic energy method? Note that this may return false even if the score term theoretically could support atomistic energies. And even if this function returns true, it's not necessarily the case that all atoms will get assigned an energy, or that the sum over all atoms (or atom pairs) will result in the same energy as the residue-level approach. The atomistic functions are intended for supplemental informational purposes only. The residue-level energies are the main interface for EnergyMethods. More...

virtual bool	has_atomistic_pairwise_energies () const
	Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method? NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. More...

virtual void	atomistic_energy (core::Size atmno, conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) const
	Evaluate the (one body) energy associated with a particular atom This may be a "self" energy, or it may be the single atom contribution from a whole structure term. NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_energies() More...

virtual void	atomistic_pair_energy (core::Size atmno1, conformation::Residue const &rsd1, core::Size atomno2, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) const
	Evaluate the energy for a particular pair of atoms This function may be fed the same residue with different atom numbers NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_pairwise_energies() More...

virtual void	eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &sfxn, EnergyMap const &emap, Vector &F1, Vector &F2) const
	Evaluate the XYZ derivative for an atom in the pose. Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom's XYZ derivative. More...

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

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...

Additional Inherited Members
Public Types inherited from core::scoring::methods::ContextDependentLRTwoBodyEnergy
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::VirtualBase	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

◆ DEEREnergy() [1/4]

core::energy_methods::DEEREnergy::DEEREnergy ( scoring::methods::EnergyMethodCreatorOP energymethodcreator )

Constructor.

Parameters

energymethodcreator Creator object

◆ DEEREnergy() [2/4]

core::energy_methods::DEEREnergy::DEEREnergy ( scoring::methods::EnergyMethodOptions const & )

Constructor for obtaining command-line options.

◆ DEEREnergy() [3/4]

core::energy_methods::DEEREnergy::DEEREnergy ( )

Default Constructor.

Referenced by clone().

◆ DEEREnergy() [4/4]

core::energy_methods::DEEREnergy::DEEREnergy ( DEEREnergy const & other )

Copy constructor.

◆ ~DEEREnergy()

core::energy_methods::DEEREnergy::~DEEREnergy ( )

override

Destructor.

Member Function Documentation

◆ clone()

core::scoring::methods::EnergyMethodOP core::energy_methods::DEEREnergy::clone ( ) const

overridevirtual

Copy function.

Returns: Pointer to new object that is a copy of this object

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

References DEEREnergy().

◆ defines_intrares_energy()

bool core::energy_methods::DEEREnergy::defines_intrares_energy ( scoring::EnergyMap const & ) const

overridevirtual

Returns "false" by default.

Returns: Returns false (DEER cannot evaluate anything intra-residue)

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

◆ defines_residue_pair_energy()

bool core::energy_methods::DEEREnergy::defines_residue_pair_energy	(	pose::Pose const &	pose,
		Size	rsd1,
		Size	rsd2
	)		const

overridevirtual

Fetches if two residues are "connected" (i.e. there is a score)

Parameters

pose	Pose being scored
rsd1	First residue
rsd2	Second residue

Returns: Whether the pair of residues are linked by data

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

References get_const_deer_data().

◆ eval_atom_derivative()

void core::energy_methods::DEEREnergy::eval_atom_derivative	(	id::AtomID const &	id,
		pose::Pose const &	pose,
		kinematics::DomainMap const &	,
		scoring::ScoreFunction const &	,
		scoring::EnergyMap const &	emap,
		numeric::xyzVector< Real > &	F1,
		numeric::xyzVector< Real > &	F2
	)		const

override

Apply atom derivative to atom.

Parameters

id	Atom ID in pose
pose	Pose being modified
emap	Energy map with scores used by derivatives
F1	vector to modify for atom
F2	vector to modify for atom

References core::scoring::epr_deer_score, and get_const_deer_data().

◆ eval_intrares_energy()

void core::energy_methods::DEEREnergy::eval_intrares_energy	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		scoring::ScoreFunction const &	,
		scoring::EnergyMap &	emap
	)		const

overridevirtual

A declared but unused function.

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

◆ finalize_total_energy()

void core::energy_methods::DEEREnergy::finalize_total_energy	(	pose::Pose &	,
		scoring::ScoreFunction const &	,
		scoring::EnergyMap &
	)		const

overridevirtual

A declared but unused function.

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

◆ get_const_deer_data()

scoring::epr_deer::DEERDataCacheCOP const core::energy_methods::DEEREnergy::get_const_deer_data ( pose::Pose const & pose ) const

NON-VIRTUAL FUNCTIONS.

Returns the DEERDataCache in the pose (const)

Parameters

pose	Pose with DEERDataCache stashed in it

Returns: Pointer to const DEERDataCache object @detail This will crash if the DEERDataCache object is absent!

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::EPR_DEER_DATA.

Referenced by defines_residue_pair_energy(), eval_atom_derivative(), iter_over_labels(), residue_pair_energy(), and setup_for_derivatives().

◆ get_deer_data()

scoring::epr_deer::DEERDataCacheOP core::energy_methods::DEEREnergy::get_deer_data ( pose::Pose & pose ) const

Returns the DEERDataCache in the pose (non-const)

Parameters

pose	Pose with DEERDataCache stashed in it

Returns: Pointer to non-const DEERDataCache object @detail This will crash if the DEERDataCache object is absent!

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::EPR_DEER_DATA.

Referenced by get_score(), iter_over_labels(), and setup_for_derivatives().

◆ get_score()

Real core::energy_methods::DEEREnergy::get_score	(	pose::Pose &	pose,
		scoring::epr_deer::EPRSpinLabel &	sl,
		Size const &	edge_id,
		int const &	mod = `0`
	)		const

Calculates the score for a specific data set.

Parameters

pose	Pose being scored
sl	Spin label being used to obtain score
edge_id	Index of data being scored (in DEERDataCache)
mod	Modifier to X-axis (zero when scored)

Returns: Score corresponding to the data

References get_deer_data(), core::scoring::epr_deer::EPRSpinLabel::histogram(), core::scoring::epr_deer::EPRSpinLabel::label_everything(), and core::pose::Pose::pdb_info().

Referenced by iter_over_labels().

◆ indicate_required_context_graphs()

void core::energy_methods::DEEREnergy::indicate_required_context_graphs ( utility::vector1< bool > & ) const

overridevirtual

A declared but unused function.

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

◆ initialize_energy_method()

void core::energy_methods::DEEREnergy::initialize_energy_method ( pose::Pose & pose ) const

Initializes energy method.

Parameters

pose	Pose being evaluated/used for scoring

References core::pose::Pose::data(), core::pose::Pose::energies(), core::pose::datacache::CacheableDataType::EPR_DEER_DATA, core::scoring::epr_deer_score, core::scoring::Energies::long_range_container(), long_range_type(), core::scoring::Energies::nonconst_long_range_container(), core::scoring::Energies::set_long_range_container(), and core::pose::Pose::size().

Referenced by setup_for_scoring().

◆ iter_over_labels()

std::map< Size, Real > core::energy_methods::DEEREnergy::iter_over_labels	(	pose::Pose &	pose,
		int const &	mod = `0`
	)		const

This checks if multiple sets of spin labels is being used.

Parameters

pose	Pose being scored
mod	Modifier to X-axis (for calculating derivatives)

Returns: Map of edges/data indices to scores for those edges/indices @detail This is used when spin labels are obtained for specific @detail proteins a priori, e.g., by triangulation/multilateration, @detail and the solution is underdetermined, so multiple solutions @detail are required.

References core::scoring::epr_deer::add_to_map(), get_const_deer_data(), get_deer_data(), and get_score().

Referenced by setup_for_derivatives(), and setup_for_scoring().

◆ long_range_type()

scoring::methods::LongRangeEnergyType core::energy_methods::DEEREnergy::long_range_type ( ) const

overridevirtual

INHERITED FUNCTIONS.

Inherited function specifying where the data is getting stored

Returns: Descriptor of this energy method

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

References core::scoring::methods::epr_deer_lr.

Referenced by initialize_energy_method().

◆ residue_pair_energy()

void core::energy_methods::DEEREnergy::residue_pair_energy	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		pose::Pose const &	pose,
		scoring::ScoreFunction const &	,
		scoring::EnergyMap &	emap
	)		const

overridevirtual

Add energy/score for a given pair of residues to map.

Parameters

rsd1	First residue
rsd2	Second residue
pose	Pose being scored
emap	Where we are adding the score @detail Because some sets of data may be between more than two @detail residues, this function looks at a map kept in @detail DEERDataCache specifically maintained for this purpose

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

References core::scoring::epr_deer_score, get_const_deer_data(), and core::conformation::Residue::seqpos().

◆ setup_for_derivatives()

void core::energy_methods::DEEREnergy::setup_for_derivatives	(	pose::Pose &	pose,
		scoring::ScoreFunction const &
	)		const

overridevirtual

Calculates the derivatives for minimization. Done numerically.

Parameters

pose	Pose being scored/modified

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

References core::scoring::epr_deer::add_to_map(), get_const_deer_data(), get_deer_data(), iter_over_labels(), core::pose::Pose::residue(), core::pose::Pose::update_residue_neighbors(), and core::conformation::Residue::xyz().

◆ setup_for_minimizing()

void core::energy_methods::DEEREnergy::setup_for_minimizing	(	pose::Pose &	,
		scoring::ScoreFunction const &	,
		kinematics::MinimizerMapBase const &
	)		const

overridevirtual

A declared but unused function.

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

◆ setup_for_scoring()

void core::energy_methods::DEEREnergy::setup_for_scoring	(	pose::Pose &	pose,
		scoring::ScoreFunction const &
	)		const

overridevirtual

Set up scoring process.

Parameters

pose	Pose being scored

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

References initialize_energy_method(), iter_over_labels(), and core::pose::Pose::update_residue_neighbors().

◆ version()

Size core::energy_methods::DEEREnergy::version ( ) const

overridevirtual

Version 1 (as of 3 January 2021)

Returns: Version 1

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

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

src/core/energy_methods/DEEREnergy.hh
src/core/energy_methods/DEEREnergy.cc

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

◆ DEEREnergy() [1/4]

◆ DEEREnergy() [2/4]

◆ DEEREnergy() [3/4]

◆ DEEREnergy() [4/4]

◆ ~DEEREnergy()

Member Function Documentation

◆ clone()

◆ defines_intrares_energy()

◆ defines_residue_pair_energy()

◆ eval_atom_derivative()

◆ eval_intrares_energy()

◆ finalize_total_energy()

◆ get_const_deer_data()

◆ get_deer_data()

◆ get_score()

◆ indicate_required_context_graphs()

◆ initialize_energy_method()

◆ iter_over_labels()

◆ long_range_type()

◆ residue_pair_energy()

◆ setup_for_derivatives()

◆ setup_for_minimizing()

◆ setup_for_scoring()

◆ version()