#include <SurfaceEnergies.hh>

Inheritance diagram for core::scoring::solid_surface::SurfaceEnergies:

Public Types
typedef Energies	parent

Public Types inherited from core::scoring::Energies
typedef scoring::EnergyGraph	EnergyGraph

typedef scoring::NeighborList	NeighborList

typedef scoring::ScoreType	ScoreType

typedef scoring::ScoreFunctionInfo	ScoreFunctionInfo

typedef basic::datacache::BasicDataCache	BasicDataCache

typedef id::AtomID	AtomID

typedef id::AtomID_Mask	AtomID_Mask

typedef kinematics::DomainMap	DomainMap

typedef utility::graph::Graph	Graph

typedef scoring::EnergyMap	EnergyMap

Public Member Functions
	SurfaceEnergies ()
	ctor – ensure correct initial state More...

	SurfaceEnergies (SurfaceEnergies const &src)
	copy ctor – deep copy More...

Energies &	operator= (Energies const &rhs) override
	assignment operator – deep copy More...

bool	same_type_as_me (Energies const &other, bool recurse=true) const override

	~SurfaceEnergies () override
	dtor More...

EnergiesOP	clone () const override

void	set_total_residue (Size total_residue)
	The SurfaceEnergies object needs to know how many residues are in its pose; it also has to be told which residues are considered part of the surface and which residues are not part of the surface. More...

void	reset_surface_residue_information ()
	Wipe away all the information in the SurfacEnergies object describing which residues are considered part of the surface and which residues are not part of the surface. (Afterwards, all residues are going to be considered part of the surface). More...

void	set_residue_range_not_surface (Size seqpos_begin, Size seqpos_end)
	Tell the SurfacEnergies that the following residues are considered not part of the surface. More...

bool	residue_is_surface (Size seqpos) const
	Does the SurfaceEnergies object consider a particular residue to be part of the surface? More...

Public Member Functions inherited from core::scoring::Energies
	Energies ()
	ctor – ensure correct initial state More...

	Energies (Energies const &src)
	copy ctor – deep copy More...

	~Energies () override
	dtor More...

void	set_owner (pose::Pose *owner)
	Pose must claim its Energies object; this should happen once, at the time the Pose is allocated. Future copying of the Energies object will not change ownership. The purpose of ownership is to allow lazy context-graph creation. When context graphs are requested that have not been created, they must be created and their edges must be updated to represent the current conformation of the pose. More...

Real	total_energy () const
	energy access More...

Real &	total_energy ()

EnergyMap const &	total_energies () const
	Returns the total_energies EnergyMap after first computing the component energies if they are not up-to-date. More...

EnergyMap	total_energies_weighted () const
	Returns the weighted total energies. More...

EnergyMap &	total_energies ()
	Returns a non-const reference to the total_energies EnergyMap so that external sources may append additional information to the Energies object. This is primarily useful for outputting score data with structures when those terms are not part of the energy function. This function will update the component energies if they are not up-to-date. More...

EnergyMap const &	onebody_energies (int const seqpos) const
	Read access to the components of the one-body energies. More...

EnergyMap &	onebody_energies (int const seqpos)
	Write access to the components of the one-body energies. This access is intended only for the ScoreFunction. More...

EnergyMap const &	finalized_energies () const
	Read access to the components of the "finalized" energies; These will include any score component calculated in the finalize phase of score function evaluation. These energies are copied between Energies objects, and are not evaluated during the component- energy update. More...

EnergyMap &	finalized_energies ()
	Write access to the components of the "finalized" energies. This access is intended only for the ScoreFunction. More...

EnergyMap const &	residue_total_energies (int const seqpos) const
	Returns the unweighted total_energies EnergyMap for Residue <seqpos> More...

Real	residue_total_energy (int const seqpos) const
	Returns the weighted total energy of residue <seqpos> More...

EnergyGraph const &	energy_graph () const
	Read access to the EnergyGraph. More...

EnergyGraph &	energy_graph ()
	Write access to the EnergyGraph. More...

TenANeighborGraph const &	tenA_neighbor_graph () const
	get the graph encoding # neighbors within 10 Angstroms If the graph has not been requested up until this point, then it will be instantiated and filled. If the pose has changed size since the last score function evaluation (or if the pose has never been scored) this function will exit. More...

TenANeighborGraph &	tenA_neighbor_graph ()
	Write access to the graph encoding # neighbors within 10 Angstroms If the graph has not been requested up until this point, then it will be instantiated and filled. If the pose has changed size since the last score function evaluation (or if the pose has never been scored) this function will exit. More...

scoring::TwelveANeighborGraph const &	twelveA_neighbor_graph () const
	get the graph encoding # neighbors within 12 Angstroms More...

scoring::TwelveANeighborGraph &	twelveA_neighbor_graph ()
	get the graph encoding # CB (or Gly CA) neighbors within 12 Angstroms of the side-chain "centroid" atom for each residue. More...

scoring::ContextGraphCOP	context_graph (scoring::ContextGraphType type) const
	const access to a particular context graph More...

scoring::ContextGraphOP	context_graph (scoring::ContextGraphType type)
	non-const access to a particular context graph More...

void	require_context_graph (scoring::ContextGraphType) const
	Allows non-scorefunction components of Rosetta to impose requirements on the context graphs that this object maintains. More...

EnergyMap	weights () const
	Returns an EnergyMap of the ScoreFunction weights from the last scoring. More...

void	weights (EnergyMap new_weights)
	Setter for the weights in this Energies object. More...

void	update_residue_neighbors (DomainMap const &domain_map_in, pose::Pose const &pose)
	update the residue neighbors More...

bool	residue_neighbors_updated () const

bool	energies_updated () const
	Returns true if the score is up-to-date. More...

bool	res_moved (int const seqpos) const
	check if rsd has changed internal conformation, necessitating, recomputation of 1d energies like dun,intra,prob,etc More...

void	reset_res_moved (int const seqpos)

void	clear_energies ()
	for debugging – forget all stored energies, does not change size More...

Size	size () const
	Returns the number of held residue energies. More...

bool	scoring () const
	are we in the midst of a scoring calculation? More...

void	show (std::ostream &out) const

void	show (std::ostream &out, Size res) const

void	show () const

void	show (Size res) const
	Shows the energy information of residue <seqpos> More...

void	show_totals (std::ostream &out) const

void	show_total_headers (std::ostream &out) const

void	structure_has_moved (Size const nres) const
	called (eg by pose) to notify us of a change to the structure More...

void	scoring_begin (scoring::ScoreFunction const &sfxn, pose::Pose const &pose)
	Notification of the start of a scoring calculation. More...

void	scoring_end (scoring::ScoreFunction const &scorefxn)
	signal from the scorefxn that scoring is over More...

scoring::ScoreFunctionInfo const &	get_scorefxn_info () const
	get scorefxn info More...

void	clear ()
	kill everything (that nobody forgot about) More...

bool	use_nblist_of_type (EnergiesCacheableDataType::Enum const &type) const

bool	use_nblist () const

bool	use_nblist_auto_update () const

MinimizationGraphOP	minimization_graph ()

MinimizationGraphCOP	minimization_graph () const

void	set_minimization_graph (MinimizationGraphOP)

scoring::NeighborList const &	nblist (EnergiesCacheableDataType::Enum const &type) const

void	set_nblist (EnergiesCacheableDataType::Enum const &type, scoring::NeighborListOP nblist_in)

void	set_use_nblist (pose::Pose const &pose, DomainMap const &domain_map_in, bool const use_nblist_auto_update)

void	reset_nblist ()

BasicDataCache const &	data () const
	BasicDataCache indexed by enum in core/scoring/EnergiesCacheableDataType.hh. More...

BasicDataCache &	data ()
	BasicDataCache indexed by enum in core/scoring/EnergiesCacheableDataType.hh. More...

bool	discard_conformation_domain_map () const
	instructs Pose whether the domain map info in the Conformation object should be discarded More...

int	domain_map (int const pos) const
	Return the color assigned to a particular residue (index = pos) as held in the domain map describing how this residue has moved with respect to the other residues in the pose. More...

DomainMap const &	domain_map () const
	Read access for the domain map. More...

void	set_long_range_container (methods::LongRangeEnergyType, LREnergyContainerOP)

LREnergyContainerOP	nonconst_long_range_container (methods::LongRangeEnergyType)

LREnergyContainerCOP	long_range_container (methods::LongRangeEnergyType) const

Private Member Functions
void	fill_point_graph (pose::Pose const &pose, conformation::PointGraphOP pg) const override
	Create a point graph representing the xyz coordinates of the "neighbor atoms." (Each residue_type indicates one of its atoms to be used for neighbor detection – e.g. CB for most amino acids, CA for GLY.) The point graph will then be used in a call to find_neighbors to add upper-edges to neighboring residues. More...

Private Attributes
Size	total_residue_
	Create a new surface grid, bounding box and dimension for the surface residues. This might get called if the range on the score function changes or if the surface moves. (NOTE: currently not prepared to handle the case where the surface moves!) More...

utility::vector1< std::pair< Size, Size > >	non_surface_ranges_

utility::vector1< bool >	is_surface_

Real	neighbor_cutoff_

Additional Inherited Members
Protected Member Functions inherited from core::scoring::Energies
conformation::PointGraphOP	point_graph ()
	get access to the point graph. For derived classes More...

EnergyGraph &	energy_graph_no_state_check ()
	Write access to the EnergyGraph. More...

utility::vector1< ContextGraphOP > &	context_graphs () const

utility::vector1< bool > &	required_context_graphs () const

Real	max_context_neighbor_cutoff () const

void	set_max_context_neighbor_cutoff (Real val) const

pose::Pose *	owner () const

int	domain_map_during_minimization (int const pos) const
	Read access for the domain map. There is only one difference to the public interface to the domain_map_: we don't reequire that scoring is performed. This function is used during minimization by derived classes of the minimizer. More...

Detailed Description

A derived class from class Energies for efficiently representing the interactions between a protein and a fixed surface

Member Typedef Documentation

◆ parent

typedef Energies core::scoring::solid_surface::SurfaceEnergies::parent

Constructor & Destructor Documentation

◆ SurfaceEnergies() [1/2]

core::scoring::solid_surface::SurfaceEnergies::SurfaceEnergies ( )

ctor – ensure correct initial state

◆ SurfaceEnergies() [2/2]

core::scoring::solid_surface::SurfaceEnergies::SurfaceEnergies ( SurfaceEnergies const & src )

default

copy ctor – deep copy

◆ ~SurfaceEnergies()

core::scoring::solid_surface::SurfaceEnergies::~SurfaceEnergies ( )

overridedefault

dtor

Member Function Documentation

◆ clone()

EnergiesOP core::scoring::solid_surface::SurfaceEnergies::clone ( ) const

overridevirtual

make a copy of this Energies( allocate actual memory for it )

Reimplemented from core::scoring::Energies.

◆ fill_point_graph()

void core::scoring::solid_surface::SurfaceEnergies::fill_point_graph	(	pose::Pose const &	pose,
		conformation::PointGraphOP	pg
	)		const

overrideprivatevirtual

Create a point graph representing the xyz coordinates of the "neighbor atoms." (Each residue_type indicates one of its atoms to be used for neighbor detection – e.g. CB for most amino acids, CA for GLY.) The point graph will then be used in a call to find_neighbors to add upper-edges to neighboring residues.

determine distance cutoff threshold based on scorefxn_info_ and then add edges to the PointGraph class

Reimplemented from core::scoring::Energies.

References core::pose::Pose::conformation(), core::scoring::Energies::get_scorefxn_info(), is_surface_, protocols::mean_field::max(), core::scoring::ScoreFunctionInfo::max_atomic_interaction_distance(), core::scoring::Energies::max_context_neighbor_cutoff(), non_surface_ranges_, core::pose::pose_max_nbr_radius(), and core::conformation::residue_point_graph_from_conformation().

◆ operator=()

Energies & core::scoring::solid_surface::SurfaceEnergies::operator= ( Energies const & rhs )

overridevirtual

assignment operator – deep copy

Reimplemented from core::scoring::Energies.

References is_surface_, neighbor_cutoff_, non_surface_ranges_, core::scoring::Energies::operator=(), and total_residue_.

◆ reset_surface_residue_information()

void core::scoring::solid_surface::SurfaceEnergies::reset_surface_residue_information ( )

Wipe away all the information in the SurfacEnergies object describing which residues are considered part of the surface and which residues are not part of the surface. (Afterwards, all residues are going to be considered part of the surface).

References is_surface_, non_surface_ranges_, and total_residue_.

Referenced by set_total_residue().

◆ residue_is_surface()

bool core::scoring::solid_surface::SurfaceEnergies::residue_is_surface ( Size seqpos ) const

Does the SurfaceEnergies object consider a particular residue to be part of the surface?

References is_surface_.

◆ same_type_as_me()

bool core::scoring::solid_surface::SurfaceEnergies::same_type_as_me	(	Energies const &	other,
		bool	recurse = `true`
	)		const

overridevirtual

determine whether my type is the same as another Conformation's

If recurse is true, then this is the first call to same_type_as_me;

Reimplemented from core::scoring::Energies.

References core::scoring::Energies::same_type_as_me().

◆ set_residue_range_not_surface()

void core::scoring::solid_surface::SurfaceEnergies::set_residue_range_not_surface	(	Size	seqpos_begin,
		Size	seqpos_end
	)

Tell the SurfacEnergies that the following residues are considered not part of the surface.

References is_surface_, non_surface_ranges_, and total_residue_.

◆ set_total_residue()

void core::scoring::solid_surface::SurfaceEnergies::set_total_residue ( Size total_residue )

The SurfaceEnergies object needs to know how many residues are in its pose; it also has to be told which residues are considered part of the surface and which residues are not part of the surface.

References reset_surface_residue_information(), and total_residue_.

Member Data Documentation

◆ is_surface_

utility::vector1< bool > core::scoring::solid_surface::SurfaceEnergies::is_surface_

private

Referenced by fill_point_graph(), operator=(), reset_surface_residue_information(), residue_is_surface(), and set_residue_range_not_surface().

◆ neighbor_cutoff_

Real core::scoring::solid_surface::SurfaceEnergies::neighbor_cutoff_

mutableprivate

Referenced by operator=().

◆ non_surface_ranges_

utility::vector1< std::pair< Size, Size > > core::scoring::solid_surface::SurfaceEnergies::non_surface_ranges_

private

Referenced by fill_point_graph(), operator=(), reset_surface_residue_information(), and set_residue_range_not_surface().

◆ total_residue_

Size core::scoring::solid_surface::SurfaceEnergies::total_residue_

private

Create a new surface grid, bounding box and dimension for the surface residues. This might get called if the range on the score function changes or if the surface moves. (NOTE: currently not prepared to handle the case where the surface moves!)

Wipe everything held in the surface grid, ensuring that in the next score function evaluation, a new grid will be computed.

Referenced by operator=(), reset_surface_residue_information(), set_residue_range_not_surface(), and set_total_residue().

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

src/core/scoring/solid_surface/SurfaceEnergies.hh
src/core/scoring/solid_surface/SurfaceEnergies.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ parent

Constructor & Destructor Documentation

◆ SurfaceEnergies() [1/2]

◆ SurfaceEnergies() [2/2]

◆ ~SurfaceEnergies()

Member Function Documentation

◆ clone()

◆ fill_point_graph()

◆ operator=()

◆ reset_surface_residue_information()

◆ residue_is_surface()

◆ same_type_as_me()

◆ set_residue_range_not_surface()

◆ set_total_residue()

Member Data Documentation

◆ is_surface_

◆ neighbor_cutoff_

◆ non_surface_ranges_

◆ total_residue_