#include <HBondEnergy.hh>

Public Member Functions
	HBondEnergy (HBondOptions const &opts)
	ctor More...

	HBondEnergy (HBondEnergy const &src)
	copy ctor More...

virtual	~HBondEnergy ()

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

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

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

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

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

virtual void	residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const
	note that this only evaluates sc-sc and sc-bb energies 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 two residues are not moving wrt each other; the two parts of the HBondEnergy function which are non-pairwise-decomposable are held fixed during minimization – the neighbor counts, and the bb/bb hbond availability status. This means that the hbond-energy function can be efficiently evaluated during minimization. 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
	Use the extended residue pair energy interface to distinguish between score function evaluation during minimization from score function evaluation during regular scoring. 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 energy between a pair of residues during minimization; during minimization, the bb/bb hbond status is held fixed, so it is possible to evaluate the bb/bb, bb/sc and sc/sc hydrogen bonds in this function call. 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
	Setup the bb/bb hbond presence data for a particular residue – this data is taken out of the HbondSet in the Pose. 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
	Link the bb/bb hbond information in the ResidueSingleMinimizationData to the ResiduePairMinimizationData. More...

virtual bool	requires_a_setup_for_derivatives_for_residue_pair_opportunity (pose::Pose const &pose) const
	Construct the set of all hydrogen bonds between two residues before. 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
	Do any setup work necessary before evaluating the derivatives for this residue. 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
	WORKING\| MODELED AFTER THE VERSION IN OccludedHbondSolEnergy...Need to make sure that this is correct!: Parin Sripakdeevong/////. More...

void	hbond_derivs_1way (EnergyMap const &weights, HBondSet const &hbond_set, HBondDatabaseCOP database, conformation::Residue const &don_rsd, conformation::Residue const &acc_rsd, Size const don_nb, Size const acc_nb, bool const exclude_bsc, bool const exclude_scb, Real const ssdep_weight_factor, utility::vector1< DerivVectorPair > &don_atom_derivs, utility::vector1< DerivVectorPair > &acc_atom_derivs) const

virtual void	backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluates the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulates the unweighted 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
	Evaluates the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulates the unweighted 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
	Evaluates the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy. 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	finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) 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...

virtual Distance	atomic_interaction_cutoff () const
	f1 and f2 are zeroed More...

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...

Real	hydrogen_interaction_cutoff2 () const
	the atomic interaction cutoff and the hydrogen interaction cutoff are the same. More...

virtual void	indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const
	HBondEnergy is context sensitive. 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 &sfxn, EnergyMap &emap) const
	Evaluate the intra-residue energy for a given residue. More...

Energy	heavyatom_heavyatom_energy (hbtrie::HBAtom const &at1, hbtrie::HBAtom const &at2, DistanceSquared &d2, Size &) const

Energy	heavyatom_hydrogenatom_energy (hbtrie::HBAtom const &at1, hbtrie::HBAtom const &at2, bool flipped=false) const

Energy	drawn_out_heavyatom_hydrogenatom_energy (hbtrie::HBAtom const &at1, hbtrie::HBAtom const &at2, bool flipped) const
	code to evaluate a hydrogen bond energy for the trie that didn't belong in the header itself – it certainly does enough work such that inlining it would not likely produce a speedup. More...

Energy	hydrogenatom_heavyatom_energy (hbtrie::HBAtom const &at1, hbtrie::HBAtom const &at2, Size &) const

Energy	hydrogenatom_hydrogenatom_energy (hbtrie::HBAtom const &, hbtrie::HBAtom const &, Size &) const

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

virtual	~ContextDependentTwoBodyEnergy ()

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

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

virtual	~TwoBodyEnergy ()

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

virtual bool	defines_intrares_energy_for_residue (conformation::Residue const &res) const
	If a score function defines no intra-residue scores for a particular residue, then it may opt-out of being asked during minimization to evaluate the score for this residue. More...

virtual bool	use_extended_intrares_energy_interface () const
	Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy during minimization routines should return "true" when this function is invoked on them. This class provides a default "return false" implementation so that classes not desiring to take advantage of this alternate interface need to do nothing. More...

virtual void	eval_intrares_energy_ext (conformation::Residue const &rsd, ResSingleMinimizationData const &data_cache, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
	Evaluate the intra-residue energy for a given residue using the data held within the ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return "true" in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies. More...

virtual bool	defines_intrares_dof_derivatives (pose::Pose const &p) const
	Use the dof_derivative interface for this energy method when calculating derivatives? It is possible to define both dof_derivatives and atom-derivatives; they are not mutually exclusive. More...

virtual Real	eval_intraresidue_dof_derivative (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights) const
	Evaluate the DOF derivative for a particular residue. The Pose merely serves as context, and the input residue is not required to be a member of the Pose. More...

virtual void	bump_energy_full (conformation::Residue const &, conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const

virtual void	bump_energy_backbone (conformation::Residue const &, conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const

virtual void	evaluate_rotamer_intrares_energies (conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< core::PackerEnergy > &energies) const
	Batch computation of rotamer intrares energies. Need not be overriden in derived class – by default, iterates over all rotamers, and calls derived class's intrares _energy method. More...

virtual void	evaluate_rotamer_intrares_energy_maps (conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< EnergyMap > &emaps) const
	Batch computation of rotamer intrares energy map. Need not be overriden in derived class – by default, iterates over all rotamers, and calls derived class's intrares _energy method. More...

Public Member Functions inherited from core::scoring::methods::EnergyMethod
	EnergyMethod (EnergyMethodCreatorOP creator)
	Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for. More...

	EnergyMethod (EnergyMethod const &src)
	Copy constructor copies over the score types of the source. More...

virtual	~EnergyMethod ()

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

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

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

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

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

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

Public Attributes
	__pad0__:ContextDependentTwoBodyEnergy parent

Private Member Functions
hbtrie::HBondRotamerTrieOP	create_rotamer_trie (conformation::RotamerSetBase const &rotset, pose::Pose const &pose) const

hbtrie::HBondRotamerTrieOP	create_rotamer_trie (conformation::Residue const &res, pose::Pose const &pose) const

virtual core::Size	version () const

Private Attributes
HBondOptionsCOP	options_

HBondDatabaseCOP	database_

Vector	normal_

Vector	center_

Real	thickness_

Real	steepness_

EnergyMap	weights_

int	rotamer_seq_sep_

int	res1_

int	res2_

int	res1_nb_

int	res2_nb_

boost::unordered_map < core::Size, core::Size >	num_hbonds_

Additional Inherited Members
Public Types inherited from core::scoring::methods::ContextDependentTwoBodyEnergy
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

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::hbonds::HBondEnergy::HBondEnergy ( HBondOptions const & opts )

ctor

Referenced by clone().

core::scoring::hbonds::HBondEnergy::HBondEnergy ( HBondEnergy const & src )

copy ctor

core::scoring::hbonds::HBondEnergy::~HBondEnergy ( )

virtual

Member Function Documentation

Distance core::scoring::hbonds::HBondEnergy::atomic_interaction_cutoff ( ) const

virtual

f1 and f2 are zeroed

HACK! MAX_R defines the maximum donorH to acceptor distance.

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

References core::scoring::hbonds::MAX_R.

Referenced by create_rotamer_trie(), eval_residue_pair_derivatives(), and residue_pair_energy_ext().

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

virtual

Evaluates the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulates the unweighted energy.

The hydrogen bonds must have already been found and added to the minpair_data container in a call to setup_for_derivatives_for_residue_pair() where the input residues are guaranteed to not have changed since that call.

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

References core::scoring::Energies::data(), database_, core::pose::Pose::energies(), basic::datacache::BasicDataCache::get(), core::scoring::EnergiesCacheableDataType::HBOND_SET, core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::conformation::Residue::is_DNA(), core::scoring::hbonds::HBondSet::nbrs(), options_, and core::conformation::Residue::seqpos().

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

virtual

Evaluates the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy.

Note: this function enforces the bb/sc hbond exclusion rule

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

References core::scoring::hbonds::HBondSet::acc_bbg_in_bb_bb_hbond(), core::scoring::Energies::data(), database_, core::scoring::hbonds::HBondSet::don_bbg_in_bb_bb_hbond(), core::pose::Pose::energies(), basic::datacache::BasicDataCache::get(), core::scoring::EnergiesCacheableDataType::HBOND_SET, core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::conformation::Residue::is_DNA(), core::conformation::Residue::is_protein(), core::scoring::hbonds::HBondSet::nbrs(), options_, and core::conformation::Residue::seqpos().

methods::EnergyMethodOP core::scoring::hbonds::HBondEnergy::clone ( ) const

virtual

clone

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

References HBondEnergy().

hbtrie::HBondRotamerTrieOP core::scoring::hbonds::HBondEnergy::create_rotamer_trie	(	conformation::RotamerSetBase const &	rotset,
		pose::Pose const &	pose
	)		const

private

References atomic_interaction_cutoff(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::Energies::data(), core::pose::Pose::energies(), basic::datacache::BasicDataCache::get(), core::scoring::EnergiesCacheableDataType::HBOND_SET, core::conformation::RotamerSetBase::num_rotamers(), options_, and core::conformation::RotamerSetBase::rotamer().

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

hbtrie::HBondRotamerTrieOP core::scoring::hbonds::HBondEnergy::create_rotamer_trie	(	conformation::Residue const &	res,
		pose::Pose const &	pose
	)		const

private

References atomic_interaction_cutoff(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::Energies::data(), core::pose::Pose::energies(), basic::datacache::BasicDataCache::get(), core::scoring::EnergiesCacheableDataType::HBOND_SET, and options_.

bool core::scoring::hbonds::HBondEnergy::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::hbond_intra, and options_.

bool core::scoring::hbonds::HBondEnergy::defines_score_for_residue_pair	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		bool	res_moving_wrt_eachother
	)		const

virtual

Returns false if two residues are not moving wrt each other; the two parts of the HBondEnergy function which are non-pairwise-decomposable are held fixed during minimization – the neighbor counts, and the bb/bb hbond availability status. This means that the hbond-energy function can be efficiently evaluated during minimization.

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

virtual bool core::scoring::hbonds::HBondEnergy::divides_backbone_and_sidechain_energetics ( ) const

inlinevirtual

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.

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

Energy core::scoring::hbonds::HBondEnergy::drawn_out_heavyatom_hydrogenatom_energy	(	hbtrie::HBAtom const &	at1,
		hbtrie::HBAtom const &	at2,
		bool	flipped
	)		const

code to evaluate a hydrogen bond energy for the trie that didn't belong in the header itself – it certainly does enough work such that inlining it would not likely produce a speedup.

Referenced by heavyatom_hydrogenatom_energy().

void core::scoring::hbonds::HBondEnergy::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

WORKING| MODELED AFTER THE VERSION IN OccludedHbondSolEnergy...Need to make sure that this is correct!: Parin Sripakdeevong/////.

Store all the hbonds formed between these two residues in the data_cache object so that they are available for derivative evaluation.

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

References core::scoring::Energies::data(), database_, core::pose::Pose::energies(), basic::datacache::BasicDataCache::get(), hbond_derivs_1way(), core::scoring::EnergiesCacheableDataType::HBOND_SET, core::conformation::Residue::is_RNA(), and options_.

void core::scoring::hbonds::HBondEnergy::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 database_, core::scoring::hbonds::identify_intra_res_hbonds(), core::conformation::Residue::is_RNA(), and options_.

void core::scoring::hbonds::HBondEnergy::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

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

WORKING| MODELED AFTER THE VERSION IN OccludedHbondSolEnergy...Need to make sure that this is correct!: Parin Sripakdeevong/////.

Retrieves the cached hbond data from the minpair_data object and calculates the derivative for an atom on rsd1 wrt rsd2. This method requires that setup_for_derivatives_for_residue_pair have been called on this residue pair beforehand, and that the two residues have not changed since that call.

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

References atomic_interaction_cutoff(), core::scoring::Energies::data(), database_, distance_squared(), core::pose::Pose::energies(), basic::datacache::BasicDataCache::get(), core::scoring::ResPairMinimizationData::get_data(), core::scoring::ResPairMinimizationData::get_data_ref(), core::scoring::hbonds::get_ssdep_weight(), hbond_derivs_1way(), core::scoring::hbond_respair_data, core::scoring::EnergiesCacheableDataType::HBOND_SET, core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), options_, core::scoring::hbonds::SSWeightParameters::ssdep_, and core::conformation::Residue::xyz().

void core::scoring::hbonds::HBondEnergy::evaluate_rotamer_background_energies	(	conformation::RotamerSetBase const &	set,
		conformation::Residue const &	residue,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights,
		utility::vector1< core::PackerEnergy > &	energy_vector
	)		const

virtual

Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.

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

References cp, core::scoring::Energies::data(), core::pose::Pose::energies(), basic::datacache::BasicDataCache::get(), core::graph::Graph::get_node(), core::conformation::RotamerSetBase::get_trie(), core::scoring::methods::hbond_method, core::scoring::EnergiesCacheableDataType::HBOND_SET, core::scoring::EnergiesCacheableDataType::HBOND_TRIE_COLLECTION, core::conformation::Residue::is_DNA(), core::scoring::hbonds::HBondSet::nbrs(), core::conformation::RotamerSetBase::num_rotamers(), options_, res1_, res1_nb_, res2_, res2_nb_, core::conformation::RotamerSetBase::resid(), core::pose::Pose::residue(), rotamer_seq_sep_, core::conformation::Residue::seqpos(), core::scoring::Energies::tenA_neighbor_graph(), and weights_.

void core::scoring::hbonds::HBondEnergy::evaluate_rotamer_pair_energies	(	conformation::RotamerSetBase const &	set1,
		conformation::RotamerSetBase const &	set2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap const &	weights,
		ObjexxFCL::FArray2D< core::PackerEnergy > &	energy_table
	)		const

virtual

Batch computation of rotamer pair energies. Need not be overriden in derived class – by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.

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

References cp, core::scoring::Energies::data(), core::pose::Pose::energies(), basic::datacache::BasicDataCache::get(), core::graph::Graph::get_node(), core::conformation::RotamerSetBase::get_trie(), core::scoring::methods::hbond_method, core::scoring::EnergiesCacheableDataType::HBOND_SET, core::scoring::hbonds::HBondSet::nbrs(), options_, res1_, res1_nb_, res2_, res2_nb_, core::conformation::RotamerSetBase::resid(), core::pose::Pose::residue(), rotamer_seq_sep_, core::scoring::Energies::tenA_neighbor_graph(), and weights_.

void core::scoring::hbonds::HBondEnergy::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.

References core::scoring::Energies::data(), core::pose::Pose::energies(), basic::datacache::BasicDataCache::get(), core::scoring::hbonds::get_hbond_energies(), core::scoring::hbond_bb_sc, core::scoring::hbond_intra, core::scoring::hbond_lr_bb_sc, core::scoring::hbond_sc, core::scoring::EnergiesCacheableDataType::HBOND_SET, core::scoring::hbond_sr_bb_sc, core::scoring::num_hbonds, num_hbonds_, options_, and core::scoring::Energies::use_nblist().

void core::scoring::hbonds::HBondEnergy::hbond_derivs_1way	(	EnergyMap const &	weights,
		HBondSet const &	hbond_set,
		HBondDatabaseCOP	database,
		conformation::Residue const &	don_rsd,
		conformation::Residue const &	acc_rsd,
		Size const	don_nb,
		Size const	acc_nb,
		bool const	exclude_bsc,
		bool const	exclude_scb,
		Real const	ssdep_weight_factor,
		utility::vector1< DerivVectorPair > &	don_atom_derivs,
		utility::vector1< DerivVectorPair > &	acc_atom_derivs
	)		const

Triplication of the loops that iterate across hbond donors and acceptors Find all hbonds for a pair of residues and add those found hbonds to the hb_pair_dat object; these hbonds will be used for derivative evaluation, so evaluate the F1/F2 derivative vectors now. This function respects the exclude bsc and scb variables to avoid hbonds. Called by setup_for_derivatives_for_residue_pair pba modified

Referenced by eval_intrares_derivatives(), and eval_residue_pair_derivatives().

Energy core::scoring::hbonds::HBondEnergy::heavyatom_heavyatom_energy	(	hbtrie::HBAtom const &	at1,
		hbtrie::HBAtom const &	at2,
		DistanceSquared &	d2,
		Size &
	)		const

inline

References numeric::xyzVector< class >::distance_squared(), and core::scoring::hbonds::hbtrie::HBAtom::xyz().

Energy core::scoring::hbonds::HBondEnergy::heavyatom_hydrogenatom_energy	(	hbtrie::HBAtom const &	at1,
		hbtrie::HBAtom const &	at2,
		bool	flipped = `false`
	)		const

inline

References numeric::xyzVector< class >::distance_squared(), drawn_out_heavyatom_hydrogenatom_energy(), core::scoring::hbonds::MAX_R2, core::scoring::hbonds::MIN_R2, core::scoring::hbonds::hbtrie::HBAtom::non_hbonding_atom(), and core::scoring::hbonds::hbtrie::HBAtom::xyz().

Referenced by hydrogenatom_heavyatom_energy().

Real core::scoring::hbonds::HBondEnergy::hydrogen_interaction_cutoff2 ( ) const

the atomic interaction cutoff and the hydrogen interaction cutoff are the same.

References core::scoring::hbonds::MAX_R.

Energy core::scoring::hbonds::HBondEnergy::hydrogenatom_heavyatom_energy	(	hbtrie::HBAtom const &	at1,
		hbtrie::HBAtom const &	at2,
		Size &
	)		const

inline

References heavyatom_hydrogenatom_energy().

Energy core::scoring::hbonds::HBondEnergy::hydrogenatom_hydrogenatom_energy	(	hbtrie::HBAtom const &	,
		hbtrie::HBAtom const &	,
		Size &
	)		const

inline

void core::scoring::hbonds::HBondEnergy::indicate_required_context_graphs ( utility::vector1< bool > & context_graphs_required ) const

virtual

HBondEnergy is context sensitive.

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

References core::scoring::ten_A_neighbor_graph.

bool core::scoring::hbonds::HBondEnergy::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::hbonds::HBondEnergy::prepare_rotamers_for_packing	(	pose::Pose const &	,
		conformation::RotamerSetBase &
	)		const

virtual

default implementation noop

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

References create_rotamer_trie(), core::scoring::methods::hbond_method, and core::conformation::RotamerSetBase::store_trie().

bool core::scoring::hbonds::HBondEnergy::requires_a_setup_for_derivatives_for_residue_pair_opportunity ( pose::Pose const & pose ) const

virtual

Construct the set of all hydrogen bonds between two residues before.

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

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

virtual

note that this only evaluates sc-sc and sc-bb energies

Note that this only evaluates sc-sc and sc-bb energies unless options_->decompose_bb_hb_into_pair_energies is set to true, in which case, this function also evaluates bb-bb energies. Note also that this function enforces the bb/sc hbond exclusion rule.

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

void core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		ResPairMinimizationData const &	pairdata,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)		const

virtual

Evaluate the energy between a pair of residues during minimization; during minimization, the bb/bb hbond status is held fixed, so it is possible to evaluate the bb/bb, bb/sc and sc/sc hydrogen bonds in this function call.

computes the residue pair energy during minimization; this includes bb/bb energies as opposed to the standard residue_pair_energy interface, which does not include bb/bb energies. On the other hand, this interface presumes that no new bb/bb hydrogen bonds are formed during the course of minimization, and no existing bb/bb hydrogen bonds are lost. Note: this function does not directly enforce the bb/sc exclusion rule logic, but rather, takes the boolean "bb_don_avail" and "bb_acc_avail" data stored in the pairdata object

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

void core::scoring::hbonds::HBondEnergy::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

Setup the bb/bb hbond presence data for a particular residue – this data is taken out of the HbondSet in the Pose.

Note that this function helps enforce the bb/sc exclusion rule by setting the donor and acceptor availability for backbone donors and acceptors. If the backbone-sidechain-exclusion rule is not being enforced, then this function marks all donors and acceptors as being available. If it is being enforced, then is uses the hbondset functions don_bbg_in_bb_bb_hbond and acc_bbg_in_bb_bb_hbond. The decisions made in this function impact the evaluation of energies in the above residue_pair_energy_ext method.

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

References core::scoring::hbonds::HBondSet::acc_bbg_in_bb_bb_hbond(), core::scoring::Energies::data(), core::scoring::hbonds::HBondSet::don_bbg_in_bb_bb_hbond(), core::pose::Pose::energies(), basic::datacache::BasicDataCache::get(), core::scoring::ResSingleMinimizationData::get_data(), core::scoring::hbond_res_data, core::scoring::EnergiesCacheableDataType::HBOND_SET, core::conformation::Residue::is_protein(), core::conformation::Residue::natoms(), core::scoring::hbonds::HBondSet::nbrs(), options_, core::conformation::Residue::seqpos(), and core::scoring::ResSingleMinimizationData::set_data().

void core::scoring::hbonds::HBondEnergy::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

Link the bb/bb hbond information in the ResidueSingleMinimizationData to the ResiduePairMinimizationData.

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

References core::scoring::ResSingleMinimizationData::get_data(), core::scoring::ResPairMinimizationData::get_data(), core::scoring::hbond_res_data, core::scoring::hbond_respair_data, core::scoring::ResPairMinimizationData::set_data(), and core::scoring::hbonds::HBondResPairMinData::set_res1_data().

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

virtual

default implementation noop

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

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::scoring::MembraneEmbed::center(), center_, core::scoring::Membrane_FAPotential::compute_fa_projection(), core::pose::Pose::conformation(), create_rotamer_trie(), core::scoring::Energies::data(), core::pose::Pose::energies(), core::scoring::ScoringManager::get_instance(), core::scoring::ScoringManager::get_Membrane_FAPotential(), core::scoring::EnergiesCacheableDataType::HBOND_SET, core::scoring::EnergiesCacheableDataType::HBOND_TRIE_COLLECTION, core::conformation::membrane::MembraneInfo::membrane_center(), core::scoring::Membrane_FAEmbed_from_pose(), core::conformation::Conformation::membrane_info(), core::conformation::membrane::MembraneInfo::membrane_normal(), core::conformation::membrane::MembraneInfo::membrane_steepness(), core::conformation::membrane::MembraneInfo::membrane_thickness(), core::scoring::MembraneEmbed_from_pose(), core::scoring::MembraneEmbed::normal(), normal_, options_, core::pose::Pose::residue(), basic::datacache::BasicDataCache::set(), core::scoring::Membrane_FAEmbed::steepness(), steepness_, core::scoring::Membrane_FAEmbed::thickness(), thickness_, core::pose::Pose::total_residue(), and core::pose::Pose::update_residue_neighbors().

void core::scoring::hbonds::HBondEnergy::setup_for_scoring	(	pose::Pose &	pose,
		ScoreFunction const &
	)		const

virtual

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

References core::scoring::MembraneEmbed::center(), center_, core::scoring::Membrane_FAPotential::compute_fa_projection(), core::pose::Pose::conformation(), core::scoring::Energies::data(), dssp, core::pose::Pose::energies(), basic::datacache::BasicDataCache::get(), core::scoring::ScoringManager::get_instance(), core::scoring::ScoringManager::get_Membrane_FAPotential(), basic::datacache::BasicDataCache::has(), core::scoring::EnergiesCacheableDataType::HBOND_SET, core::scoring::dssp::Dssp::insert_ss_into_pose(), core::conformation::membrane::MembraneInfo::membrane_center(), core::scoring::Membrane_FAEmbed_from_pose(), core::conformation::Conformation::membrane_info(), core::conformation::membrane::MembraneInfo::membrane_normal(), core::conformation::membrane::MembraneInfo::membrane_steepness(), core::conformation::membrane::MembraneInfo::membrane_thickness(), core::scoring::MembraneEmbed_from_pose(), core::scoring::MembraneEmbed::normal(), normal_, num_hbonds_, options_, basic::datacache::BasicDataCache::set(), core::scoring::Membrane_FAEmbed::steepness(), steepness_, core::scoring::Membrane_FAEmbed::thickness(), thickness_, core::pose::Pose::total_residue(), core::pose::Pose::update_residue_neighbors(), and core::scoring::Energies::use_nblist().

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

virtual

Evaluates the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulates the unweighted energy.

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

References database_, core::pose::Pose::energies(), core::graph::Graph::get_node(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_membrane(), options_, core::conformation::Residue::seqpos(), and core::scoring::Energies::tenA_neighbor_graph().

void core::scoring::hbonds::HBondEnergy::update_residue_for_packing	(	pose::Pose &	,
		Size	resid
	)		const

virtual

ensure this function gets called. The default behavior is to do nothing.

default implementation noop

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

References create_rotamer_trie(), core::scoring::Energies::data(), core::pose::Pose::energies(), basic::datacache::BasicDataCache::get(), core::scoring::EnergiesCacheableDataType::HBOND_TRIE_COLLECTION, and core::pose::Pose::residue().

bool core::scoring::hbonds::HBondEnergy::use_extended_residue_pair_energy_interface ( ) const

virtual

Use the extended residue pair energy interface to distinguish between score function evaluation during minimization from score function evaluation during regular scoring.

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

core::Size core::scoring::hbonds::HBondEnergy::version ( ) const

privatevirtual

Version 2: 2011-06-27 Fixing chi2 SER/THR and chi3 TYR derivatives when they act as acceptors.

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