#include <NeighborList.hh>

Inheritance diagram for core::scoring::NeighborList:

Public Member Functions
	NeighborList (kinematics::DomainMap const &domain_map, Real const XX_cutoff, Real const XH_cutoff, Real const HH_cutoff)

	~NeighborList () override

NeighborListOP	clone () const

AtomNeighbors const &	atom_neighbors (int const pos, int const atomno) const

AtomNeighbors const &	atom_neighbors (id::AtomID const &id) const

AtomNeighbors const &	upper_atom_neighbors (int const pos, int const atomno) const

AtomNeighbors const &	upper_atom_neighbors (id::AtomID const &id) const

AtomNeighbors const &	intrares_upper_atom_neighbors (int const pos, int const atomno) const

AtomNeighbors const &	intrares_upper_atom_neighbors (id::AtomID const &id) const

template<class T_Etable >
void	setup (pose::Pose const &pose, ScoreFunction const &sfxn, T_Etable const &etable_method) const
	Initialize the nblist so that it reflects the current coordinates in the pose. More...

void	check_domain_map (kinematics::DomainMap const &domain_map_in) const

void	clear ()

kinematics::DomainMap const &	domain_map () const

template<class T_Etable >
void	prepare_for_scoring (pose::Pose const &pose, ScoreFunction const &sfxn, T_Etable const &etable_method) const
	If auto_update_, ensure that no atom in the pose has not moved too much since the last time the neighborlist was updated. The neighborlist tracks the starting coords for all atoms, and then updates. More...

void	set_auto_update (Distance move_tolerance)

void	disable_auto_update ()

Protected Member Functions
void	declare_atoms_neighbors (id::AtomID at1, id::AtomID at2, Size path_dist, Real weight, Real weight_func=1.0) const

void	declare_atom_neighbor_1sided (id::AtomID at1, id::AtomID at2, Size path_dist, Real weight, Real weight_func=1.0) const

Private Member Functions
void	update_from_wide_nblist (pose::Pose const &pose) const

DistanceSquared	atom_pair_cutoff (bool atom1_is_hydrogen, bool atom2_is_hydrogen) const

Private Attributes
bool	auto_update_

DistanceSquared	move_tolerance_sqr_

Distance const	wide_nblist_extension_

DistanceSquared	wide_move_tolerance_sqr_

utility::vector1< utility::vector1< AtomNeighbors > >	nblist_

utility::vector1< utility::vector1< AtomNeighbors > >	upper_nblist_

utility::vector1< utility::vector1< AtomNeighbors > >	intrares_upper_nblist_

utility::vector1< utility::vector1< AtomNeighbors > >	wide_nblist_

utility::vector1< utility::vector1< Vector > >	reference_coords_

utility::vector1< utility::vector1< Vector > >	wide_reference_coords_

kinematics::DomainMap const	domain_map_

DistanceSquared const	XX_cutoff_

DistanceSquared const	XH_cutoff_

DistanceSquared const	HH_cutoff_

Distance const	sqrt_XX_cutoff_

Distance const	sqrt_XH_cutoff_

Distance const	sqrt_HH_cutoff_

DistanceSquared const	XX_cutoff_wide_
	Separation square distance for atom pairs in kept in the wide neighbor list. More...

DistanceSquared const	XH_cutoff_wide_

DistanceSquared const	HH_cutoff_wide_

utility::vector1< utility::vector1< Size > >	atom_needs_update_from_wide_

utility::vector1< id::AtomID >	atoms_to_update_

Size	n_prepare_for_scorings_

Size	n_update_from_wide_

Size	n_full_updates_

Constructor & Destructor Documentation

◆ NeighborList()

core::scoring::NeighborList::NeighborList	(	kinematics::DomainMap const &	domain_map,
		Real const	XX_cutoff,
		Real const	XH_cutoff,
		Real const	HH_cutoff
	)

◆ ~NeighborList()

core::scoring::NeighborList::~NeighborList ( )

override

References auto_update_, n_full_updates_, n_prepare_for_scorings_, n_update_from_wide_, and core::scoring::tr().

Member Function Documentation

◆ atom_neighbors() [1/2]

AtomNeighbors const& core::scoring::NeighborList::atom_neighbors ( id::AtomID const & id ) const

inline

References nblist_.

◆ atom_neighbors() [2/2]

AtomNeighbors const& core::scoring::NeighborList::atom_neighbors	(	int const	pos,
		int const	atomno
	)		const

inline

References nblist_.

Referenced by core::energy_methods::RNA_FA_ElecEnergy::eval_atom_derivative(), core::energy_methods::StackElecEnergy::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergy::eval_atom_derivative(), core::scoring::methods::MMLJEnergyInter::eval_atom_derivative(), and core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative().

◆ atom_pair_cutoff()

DistanceSquared core::scoring::NeighborList::atom_pair_cutoff	(	bool	atom1_is_hydrogen,
		bool	atom2_is_hydrogen
	)		const

inlineprivate

References HH_cutoff_, XH_cutoff_, and XX_cutoff_.

Referenced by setup(), and update_from_wide_nblist().

◆ check_domain_map()

void core::scoring::NeighborList::check_domain_map ( kinematics::DomainMap const & domain_map_in ) const

References domain_map_, and nblist_.

Referenced by core::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy >::eval_residue_pair_derivatives(), core::energy_methods::StackElecEnergy::finalize_total_energy(), core::energy_methods::RNA_FA_ElecEnergy::finalize_total_energy(), core::energy_methods::RNA_CoarseDistEnergy::finalize_total_energy(), and core::scoring::elec::FA_ElecEnergy::finalize_total_energy().

◆ clear()

void core::scoring::NeighborList::clear ( )

inline

References nblist_.

◆ clone()

NeighborListOP core::scoring::NeighborList::clone ( ) const

inline

◆ declare_atom_neighbor_1sided()

void core::scoring::NeighborList::declare_atom_neighbor_1sided	(	id::AtomID	at1,
		id::AtomID	at2,
		Size	path_dist,
		Real	weight,
		Real	weight_func = `1.0`
	)		const

protected

Add at2 to atom 1's neighbor lists, but don't touch at2's neighbor lists.

References core::id::AtomID::atomno(), intrares_upper_nblist_, nblist_, core::id::AtomID::rsd(), upper_nblist_, and core::scoring::packstat::weight_func().

Referenced by update_from_wide_nblist().

◆ declare_atoms_neighbors()

void core::scoring::NeighborList::declare_atoms_neighbors	(	id::AtomID	at1,
		id::AtomID	at2,
		Size	path_dist,
		Real	weight,
		Real	weight_func = `1.0`
	)		const

protected

References core::id::AtomID::atomno(), intrares_upper_nblist_, nblist_, core::id::AtomID::rsd(), upper_nblist_, and core::scoring::packstat::weight_func().

Referenced by setup().

◆ disable_auto_update()

void core::scoring::NeighborList::disable_auto_update ( )

References auto_update_.

◆ domain_map()

kinematics::DomainMap const& core::scoring::NeighborList::domain_map ( ) const

inline

References domain_map_.

◆ intrares_upper_atom_neighbors() [1/2]

AtomNeighbors const& core::scoring::NeighborList::intrares_upper_atom_neighbors ( id::AtomID const & id ) const

inline

References intrares_upper_nblist_.

◆ intrares_upper_atom_neighbors() [2/2]

AtomNeighbors const& core::scoring::NeighborList::intrares_upper_atom_neighbors	(	int const	pos,
		int const	atomno
	)		const

inline

References intrares_upper_nblist_.

◆ prepare_for_scoring()

template<class T_Etable >

void core::scoring::NeighborList::prepare_for_scoring	(	pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		T_Etable const &	etable_method
	)		const

If auto_update_, ensure that no atom in the pose has not moved too much since the last time the neighborlist was updated. The neighborlist tracks the starting coords for all atoms, and then updates.

References atom_needs_update_from_wide_, core::id::AtomID::atomno(), atoms_to_update_, auto_update_, core::scoring::methods::etable_method, move_tolerance_sqr_, n_full_updates_, n_prepare_for_scorings_, n_update_from_wide_, core::conformation::Residue::natoms(), reference_coords_, core::pose::Pose::residue(), core::id::AtomID::rsd(), setup(), core::pose::Pose::size(), update_from_wide_nblist(), wide_move_tolerance_sqr_, wide_reference_coords_, and core::conformation::Residue::xyz().

Referenced by core::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy >::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::setup_for_scoring(), core::energy_methods::RNA_FA_ElecEnergy::setup_for_scoring(), core::energy_methods::StackElecEnergy::setup_for_scoring(), core::energy_methods::FA_GrpElecEnergy::setup_for_scoring(), core::energy_methods::RNA_FullAtomStackingEnergy::setup_for_scoring(), and core::scoring::elec::FA_ElecEnergy::setup_for_scoring().

◆ set_auto_update()

void core::scoring::NeighborList::set_auto_update ( Distance move_tolerance )

References auto_update_, move_tolerance_sqr_, wide_move_tolerance_sqr_, and wide_nblist_extension_.

◆ setup()

template<class T_Etable >

void core::scoring::NeighborList::setup	(	pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		T_Etable const &	etable_method
	)		const

Initialize the nblist so that it reflects the current coordinates in the pose.

const so that it may be called within setup_for_scoring T_Etable class must implement the following functions: bool defines_intrares_energy( EnergyMap const & ) const; CountPairFunctionCOP get_intrares_countpair( conformation::Residue const &, pose::Pose const &, ScoreFunction const & ) const; CountPairFunctionCOP get_count_pair_function( Size &, Size &, pose::Pose const &, ScoreFunction const & ) const;

References core::conformation::Residue::atom(), core::conformation::Residue::atom_is_hydrogen(), atom_needs_update_from_wide_, atom_pair_cutoff(), auto_update_, core::pose::Pose::conformation(), declare_atoms_neighbors(), domain_map_, core::scoring::methods::etable_method, core::conformation::Conformation::get_residue_mask(), core::conformation::Conformation::get_residue_weight(), HH_cutoff_wide_, intrares_upper_nblist_, core::conformation::Residue::natoms(), nblist_, core::conformation::Residue::nbr_radius(), core::pose::pose_max_nbr_radius(), reference_coords_, core::pose::Pose::residue(), core::conformation::residue_point_graph_from_conformation(), core::pose::Pose::size(), sqrt_XX_cutoff_, upper_nblist_, core::scoring::packstat::weight_func(), core::scoring::ScoreFunction::weights(), wide_nblist_, wide_nblist_extension_, wide_reference_coords_, XH_cutoff_wide_, XX_cutoff_, XX_cutoff_wide_, core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().