A cached energies object. More...

#include <Energies.hh>

Inheritance diagram for core::scoring::Energies:

[legend]

Public Types
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
	Energies ()
	ctor – ensure correct initial state More...

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

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

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

	~Energies () override
	dtor More...

virtual EnergiesOP	clone () const

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

Protected Member Functions
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...

Private Types
enum	EnergyState { BAD , MOD , GOOD }
	should push this into energygraph once it stabilizes More...

Private Member Functions
void	set_size (Size const size_in)
	Internal method to resize data that is dependent on the number of residues in the Pose. More...

void	require_scoring () const
	will die if not in the middle of an energy evaluation More...

void	update_component_energies () const
	Lazy component evaluation for residue pair energies;. More...

void	accumulate_residue_total_energies () const
	Lazy update of residue total component energies; only compute them when they are requested. Forces an update of the energy_graph_. More...

void	accumulate_residue_total_energy () const
	Lazy update of the per-residue total weighted energy. Only computed when requested. Does not force an update of the energy_graph_. More...

void	accumulate_residue_energies (ScoreType const &type) const
	sum the residue energies to this type to get a total energy More...

void	set_scorefxn_info (scoring::ScoreFunctionInfoOP info)
	update the context graphs and the energy graph according to a new score function type More...

void	internalize_new_domain_map ()
	Save state information from the domain map and wipe dirty energies. More...

void	prepare_neighbor_graphs ()
	Delete edges from energy_graph and tenA_neighbor_graph according to the movement history described by the domain map. More...

void	delete_graph_edges_using_domain_map (utility::graph::Graph &g)
	removes all edges in the graph that represent connections that have changed; More...

void	update_domainmap_for_lr_energy_container (LREnergyContainerOP lrec)
	Reset the "already computed" status for pairs of residues represented in a particular long-range energy container using the domain map. More...

virtual void	update_neighbor_links (pose::Pose const &pose)
	Detect the new set of neighbors given the structure of the Pose (find_neighbors()) and add new edges to the neighbor graphs so that the status of the neighbor graphs is current wrt the current conformation. More...

virtual void	fill_point_graph (pose::Pose const &pose, conformation::PointGraphOP pg) const
	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...

void	copy_nblists (Energies const &other)
	During Energies copy-ctor and assignment operator, copy over the neighbor lists objects (clone them). More...

void	copy_context_graphs (Energies const &other)
	During Energies copy-ctor and assignment operator, copy over the context graphs and the historical information about who required them (a score term, e.g. the HBondEnergy, or some other function, e.g. pack_rotamers) More...

void	copy_lr_energy_containers (Energies const &other)
	During Energies copy-ctor and assignment operator, copy over the long-range energy containers from the source Energies object. More...

virtual void	require_context_graph_ (scoring::ContextGraphType type, bool external) const
	Internal method that handles the bookkeeping for intializing a new context graph, either requested by a scoring term (external = false) or some other function (external = true ). More...

Private Attributes
Size	size_
	our internal nres More...

pose::Pose *	owner_

EnergyGraphOP	energy_graph_

utility::vector1< ContextGraphOP >	context_graphs_
	The collection of context graphs used by the context-dependent energy components which the Energies object is responsible for maintaining. Context graphs are allocated as requested, (e.g. in a call to tenA_neighbor_graph() ), if they have not yet been allocated. If a portion of the code requires a context graph (e.g the packer), it may call require_context_graph( int cgtype ), which will create the context graph immediately. More...

utility::vector1< bool >	externally_required_context_graphs_
	those required by non-score function entities (e.g. the packer). More...

utility::vector1< bool >	required_context_graphs_
	OR of the sfxn required context graphs and the externally required ones. More...

Real	max_context_neighbor_cutoff_
	The maximum neighbor cutoff for all required context graphs;. More...

utility::vector1< LREnergyContainerOP >	long_range_energy_containers_

std::map< EnergiesCacheableDataType::Enum, scoring::NeighborListOP >	nblist_
	atom-atom neighborlists More...

bool	use_nblist_

bool	use_nblist_auto_update_

MinimizationGraphOP	minimization_graph_

utility::vector1< EnergyMap >	onebody_energies_

bool	residue_total_energies_uptodate_
	cached energy component totals – summed twobody and one body interactions for each residue More...

utility::vector1< EnergyMap >	residue_total_energies_

bool	residue_total_energy_uptodate_
	cached energy totals – only the weighted sum, no components. More...

utility::vector1< Real >	residue_total_energy_

EnergyMap	total_energies_
	cached total energies More...

Real	total_energy_

EnergyMap	finalized_energies_
	Energies computed during the finalize() stage of scoring. More...

scoring::ScoreFunctionInfoOP	scorefxn_info_
	info about last score evaluation More...

EnergyMap	scorefxn_weights_
	ScoreFunction weights from the last scoring call. More...

DomainMap	domain_map_

bool	scoring_
	are we within a scoring evaluation? More...

EnergyState	energy_state_

EnergyState	graph_state_

BasicDataCache	data_cache_
	BasicDataCache indexed by enum in core/scoring/EnergiesCacheableDataType.hh. More...

conformation::PointGraphOP	point_graph_

Friends
std::ostream &	operator<< (std::ostream &out, const Energies &e)

Detailed Description

A cached energies object.

Stores total, residue, and residue-pair energies, as well as residue neighbor information.

Meant to replace fullatom_energies:: namespace.

Stores residue neighbor information as well as cached residue pair energies in O(N) space using a graph.

Also stores a DomainMap object which is used during scoring to know which rsd pairs have changed relative orientation and which residues have changed internally

Note: We distinguish between two kinds of per-residue (1D) energy: onebody residue energies and twobody residue energies. Onebody residue energies are things like dunbrack, intrares, Paa, which depend only on the state of the residue in question. Twobody residue energies (like the residue atr energy) are summations of twobody interactions involving a single residue. The onebody energies can be reused at positions whose internal phi/psi/chi conformation hasn't changed. Twobody residue energies, on the other hand must be invalidated if the structure has changed at all.

Member Typedef Documentation

◆ AtomID

typedef id::AtomID core::scoring::Energies::AtomID

◆ AtomID_Mask

typedef id::AtomID_Mask core::scoring::Energies::AtomID_Mask

◆ BasicDataCache

typedef basic::datacache::BasicDataCache core::scoring::Energies::BasicDataCache

◆ DomainMap

typedef kinematics::DomainMap core::scoring::Energies::DomainMap

◆ EnergyGraph

typedef scoring::EnergyGraph core::scoring::Energies::EnergyGraph

◆ EnergyMap

typedef scoring::EnergyMap core::scoring::Energies::EnergyMap

◆ Graph

typedef utility::graph::Graph core::scoring::Energies::Graph

◆ NeighborList

typedef scoring::NeighborList core::scoring::Energies::NeighborList

◆ ScoreFunctionInfo

typedef scoring::ScoreFunctionInfo core::scoring::Energies::ScoreFunctionInfo

◆ ScoreType

typedef scoring::ScoreType core::scoring::Energies::ScoreType

Member Enumeration Documentation

◆ EnergyState

enum core::scoring::Energies::EnergyState

private

should push this into energygraph once it stabilizes

Enumerator
BAD
MOD
GOOD

Constructor & Destructor Documentation

◆ Energies() [1/2]

core::scoring::Energies::Energies ( )

ctor – ensure correct initial state

◆ Energies() [2/2]

core::scoring::Energies::Energies ( Energies const & src )

copy ctor – deep copy

References copy_context_graphs(), copy_lr_energy_containers(), and copy_nblists().

◆ ~Energies()

core::scoring::Energies::~Energies ( )

override

dtor

Member Function Documentation

◆ accumulate_residue_energies()

void core::scoring::Energies::accumulate_residue_energies ( ScoreType const & type ) const

private

sum the residue energies to this type to get a total energy

◆ accumulate_residue_total_energies()

void core::scoring::Energies::accumulate_residue_total_energies ( ) const

private

Lazy update of residue total component energies; only compute them when they are requested. Forces an update of the energy_graph_.

References energies_updated(), energy_graph_, energy_state_, GOOD, long_range_energy_containers_, core::scoring::n_score_types, core::scoring::n_shortranged_2b_score_types, onebody_energies_, residue_total_energies_, residue_total_energies_uptodate_, scorefxn_weights_, size_, core::scoring::total_score, and use_nblist().

Referenced by residue_total_energies(), and show().

◆ accumulate_residue_total_energy()

void core::scoring::Energies::accumulate_residue_total_energy ( ) const

private

Lazy update of the per-residue total weighted energy. Only computed when requested. Does not force an update of the energy_graph_.

References core::scoring::EMapVector::dot(), energy_graph_, long_range_energy_containers_, core::scoring::n_shortranged_2b_score_types, onebody_energies_, residue_total_energy_, residue_total_energy_uptodate_, scorefxn_weights_, and size_.

Referenced by residue_total_energy().

◆ clear()

void core::scoring::Energies::clear ( )

kill everything (that nobody forgot about)

The Energies object does a lot of bookkeeping to figure out when things are out of date and when they are not out of date. If you change the conformation of the Pose, then when the Pose is next scored, only the energies that were invalidated by the move are recalculated. Similarly, if you change which score function you're using (e.g. adding a new term, but notably, not when simply reweighting an existing term), then the Energies object will reset itself into an empty state. The Energies object goes to great lengths to make sure that you do not ever need to call its clear function.

There are truly only a handful of reasons to call clear() on an Energies object:

You are getting ready to serialize the Pose and want to cut down on its memory footprint,
You are using a term where you've told the energy function it's pairwise decomposable, but it really isn't (i.e. it's a whole structure energy masquerading as a 2body energy) and you suspect you have accumulated enough "error" in your approximation of the structure that rescoring it completely from scratch will help. (I don't know of any terms that fit this bill), or
You are trying to measure runtime performance of a particular term and need the term to be re-evaluated across the whole Pose.

References clear_energies(), domain_map_, scorefxn_weights_, set_scorefxn_info(), size_, and core::scoring::EMapVector::zero().

◆ clear_energies()

void core::scoring::Energies::clear_energies ( )

for debugging – forget all stored energies, does not change size

References BAD, core::scoring::EMapVector::clear(), context_graphs_, domain_map_, energy_graph_, energy_state_, graph_state_, long_range_energy_containers_, onebody_energies_, residue_total_energies_, residue_total_energies_uptodate_, residue_total_energy_, residue_total_energy_uptodate_, size_, and total_energies_.

Referenced by clear().

◆ clone()

EnergiesOP core::scoring::Energies::clone ( ) const

virtual

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

Reimplemented in core::scoring::symmetry::SymmetricEnergies, and core::scoring::solid_surface::SurfaceEnergies.

Referenced by core::pose::Pose::set_new_energies_object().

◆ context_graph() [1/2]

scoring::ContextGraphOP core::scoring::Energies::context_graph ( scoring::ContextGraphType type )

non-const access to a particular context graph

References context_graphs_, GOOD, graph_state_, and require_context_graph_().

◆ context_graph() [2/2]

scoring::ContextGraphCOP core::scoring::Energies::context_graph ( scoring::ContextGraphType type ) const

const access to a particular context graph

References context_graphs_, GOOD, graph_state_, and require_context_graph_().

◆ context_graphs()

utility::vector1< ContextGraphOP > & core::scoring::Energies::context_graphs ( ) const

protected

References context_graphs_.

Referenced by core::scoring::symmetry::SymmetricEnergies::require_context_graph_(), and core::scoring::symmetry::SymmetricEnergies::update_neighbor_links().

◆ copy_context_graphs()

void core::scoring::Energies::copy_context_graphs ( Energies const & other )

private

During Energies copy-ctor and assignment operator, copy over the context graphs and the historical information about who required them (a score term, e.g. the HBondEnergy, or some other function, e.g. pack_rotamers)

References context_graphs_, externally_required_context_graphs_, max_context_neighbor_cutoff_, and required_context_graphs_.

Referenced by Energies(), and operator=().

◆ copy_lr_energy_containers()

void core::scoring::Energies::copy_lr_energy_containers ( Energies const & other )

private

During Energies copy-ctor and assignment operator, copy over the long-range energy containers from the source Energies object.

References long_range_energy_containers_.

Referenced by Energies(), and operator=().

◆ copy_nblists()

void core::scoring::Energies::copy_nblists ( Energies const & other )

private

During Energies copy-ctor and assignment operator, copy over the neighbor lists objects (clone them).

References nblist_.

Referenced by Energies(), and operator=().

◆ data() [1/2]

BasicDataCache& core::scoring::Energies::data ( )

inline

BasicDataCache indexed by enum in core/scoring/EnergiesCacheableDataType.hh.

References data_cache_.

◆ data() [2/2]

BasicDataCache const& core::scoring::Energies::data ( ) const

inline

BasicDataCache indexed by enum in core/scoring/EnergiesCacheableDataType.hh.

References data_cache_.

◆ delete_graph_edges_using_domain_map()

void core::scoring::Energies::delete_graph_edges_using_domain_map ( utility::graph::Graph & g )

private

removes all edges in the graph that represent connections that have changed;

O(N) as it iterates across the edges that already exist, instead over over all pairs that moved with respect to each other (which would be O(N^2)) and deleting any obsolete edges

References domain_map_.

Referenced by prepare_neighbor_graphs().

◆ discard_conformation_domain_map()

bool core::scoring::Energies::discard_conformation_domain_map ( ) const

instructs Pose whether the domain map info in the Conformation object should be discarded

because the Energies object does not update the EnergyGraph during minimization, the Pose should not direct the conformation object to discard its movement data. Movement data should be discarded immediately after a call to update_neighbors where use_nblist_ has been false.

References use_nblist_.

◆ domain_map() [1/2]

DomainMap const& core::scoring::Energies::domain_map ( ) const

inline

Read access for the domain map.

References domain_map_, and require_scoring().

◆ domain_map() [2/2]

int core::scoring::Energies::domain_map ( int const pos ) const

inline

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.

CAUTION new behavior: domain_map may not return 0 for residues that have undergone internal degree of freedom changes since the last scoring. Ask the res_moved() method for that information

References domain_map_, and require_scoring().

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().

◆ domain_map_during_minimization()

int core::scoring::Energies::domain_map_during_minimization ( int const pos ) const

inlineprotected

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.

References domain_map_.

Referenced by core::scoring::symmetry::SymmetricEnergies::update_neighbor_links().

◆ energies_updated()

bool core::scoring::Energies::energies_updated ( ) const

inline

Returns true if the score is up-to-date.

example(s): pose.energies().energies_updated() See also: Energies Energies.residue_total_energy Energies.residue_total_energies Pose ScoreFunction ScoreFunction.show create_score_function

References energy_state_, and GOOD.

Referenced by accumulate_residue_total_energies(), core::simple_metrics::metrics::InteractionEnergyMetric::calculate(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::calculate(), protocols::simple_filters::InterfaceHbondsFilter::compute(), protocols::multistate_design::SingleStateFitnessFunction::evaluate(), protocols::jd3::job_summaries::EnergyJobSummary::extract_energy(), protocols::jd3::job_summaries::StandardPoseJobSummary::extract_energy(), protocols::moves::get_energies(), protocols::hbnet::get_hbond_atom_pairs(), protocols::helix_capper::HelixNCapperMover::get_Ncap_scores(), core::scoring::ScoreFunction::get_sub_score(), core::scoring::ScoreFunction::get_sub_score_exclude_res(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_pose_energies_table(), protocols::features::ResidueScoresFeatures::insert_two_body_residue_score_rows(), protocols::mean_field::EnergiesByTaskCalculator::recompute(), protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::recompute(), residue_total_energies(), residue_total_energy(), protocols::hbnet::HBNet::select_best_networks(), protocols::moves::PyMOLMover::send_energy(), protocols::moves::PyMOLMover::send_hbonds(), and protocols::features::ProteinSilentReport::write_full_report().

◆ energy_graph() [1/2]

Energies::EnergyGraph & core::scoring::Energies::energy_graph ( )

Write access to the EnergyGraph.

get the energy graph - see comments for const version of this method

References energy_graph_, GOOD, and graph_state_.

◆ energy_graph() [2/2]

Energies::EnergyGraph const & core::scoring::Energies::energy_graph ( ) const

Read access to the EnergyGraph.

get the energy graph (const)

assert that the graph state reflects the current set of neighbors; if the structure has moved, the neighbors may have changed. update_residue_neighbors should have been called first. If nb_list_ is true then update_residue_neighbors will set the graph state to GOOD without updating the neighbors.

References energy_graph_, GOOD, and graph_state_.

◆ energy_graph_no_state_check()

Energies::EnergyGraph & core::scoring::Energies::energy_graph_no_state_check ( )

protected

Write access to the EnergyGraph.

IA: Note derived classes may need access to graph before it has been initalized! In particular a derived class might overload update_residue_neighbors.

References energy_graph_.

Referenced by core::scoring::symmetry::SymmetricEnergies::update_neighbor_links().

◆ fill_point_graph()

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

privatevirtual

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 in core::scoring::symmetry::SymmetricEnergies, and core::scoring::solid_surface::SurfaceEnergies.

References core::pose::Pose::conformation(), protocols::mean_field::max(), max_context_neighbor_cutoff_, core::pose::pose_max_nbr_radius(), core::conformation::residue_point_graph_from_conformation(), and scorefxn_info_.

Referenced by require_context_graph_(), and update_neighbor_links().

◆ finalized_energies() [1/2]

EnergyMap& core::scoring::Energies::finalized_energies ( )

inline

Write access to the components of the "finalized" energies. This access is intended only for the ScoreFunction.

References finalized_energies_.

◆ finalized_energies() [2/2]

EnergyMap const& core::scoring::Energies::finalized_energies ( ) const

inline

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.

References finalized_energies_.

Referenced by core::scoring::ScoreFunction::correct_finalize_score(), and core::scoring::ScoreFunction::operator()().

◆ get_scorefxn_info()

scoring::ScoreFunctionInfo const& core::scoring::Energies::get_scorefxn_info ( ) const

inline

get scorefxn info

References scorefxn_info_.

Referenced by core::scoring::solid_surface::SurfaceEnergies::fill_point_graph(), core::scoring::symmetry::SymmetricEnergies::fill_point_graph(), show_total_headers(), show_totals(), and core::scoring::symmetry::SymmetricEnergies::update_neighbor_links().

◆ internalize_new_domain_map()

void core::scoring::Energies::internalize_new_domain_map ( )

private

Save state information from the domain map and wipe dirty energies.

References domain_map_, energy_graph_, onebody_energies_, and size_.

Referenced by scoring_begin(), set_use_nblist(), and update_residue_neighbors().

◆ long_range_container()

LREnergyContainerCOP core::scoring::Energies::long_range_container ( methods::LongRangeEnergyType lrtype ) const

References long_range_energy_containers_.

◆ max_context_neighbor_cutoff()

Real core::scoring::Energies::max_context_neighbor_cutoff ( ) const

protected

References max_context_neighbor_cutoff_.

Referenced by core::scoring::solid_surface::SurfaceEnergies::fill_point_graph(), core::scoring::symmetry::SymmetricEnergies::fill_point_graph(), and core::scoring::symmetry::SymmetricEnergies::require_context_graph_().

◆ minimization_graph() [1/2]

MinimizationGraphOP core::scoring::Energies::minimization_graph ( )

References minimization_graph_.

◆ minimization_graph() [2/2]

MinimizationGraphCOP core::scoring::Energies::minimization_graph ( ) const

References minimization_graph_.

◆ nblist()

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

References nblist_, and use_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(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< AnalyticEtableEnergy >::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative(), 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(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), 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().

◆ nonconst_long_range_container()

LREnergyContainerOP core::scoring::Energies::nonconst_long_range_container ( methods::LongRangeEnergyType lrtype )

References long_range_energy_containers_.

◆ onebody_energies() [1/2]

EnergyMap& core::scoring::Energies::onebody_energies ( int const seqpos )

inline

Write access to the components of the one-body energies. This access is intended only for the ScoreFunction.

References onebody_energies_.

◆ onebody_energies() [2/2]

EnergyMap const& core::scoring::Energies::onebody_energies ( int const seqpos ) const

inline

Read access to the components of the one-body energies.

References onebody_energies_.

Referenced by core::optimization::activate_dof_deriv_terms_for_cart_min(), core::scoring::ScoreFunction::asym_eval_onebody_energies(), protocols::pack_daemon::PackDaemon::calculate_background_energies(), core::pack::compare_mingraph_and_energy_graph(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), core::scoring::Ramachandran::eval_rama_score_all(), core::scoring::Ramachandran2B::eval_rama_score_all(), protocols::relax::fix_worst_bad_ramas(), protocols::residue_optimization::MetapatchEnumeration::generate_derived_types(), core::scoring::ScoreFunction::get_sub_score(), protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::recompute(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), core::scoring::ScoreFunction::setup_for_minimizing_for_node(), and core::scoring::ScoreFunction::sym_eval_onebody_energies().

◆ operator=()

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

virtual

◆ owner()

pose::Pose * core::scoring::Energies::owner ( ) const

protected

References owner_.

Referenced by core::scoring::symmetry::SymmetricEnergies::require_context_graph_(), and set_owner().

◆ point_graph()

conformation::PointGraphOP core::scoring::Energies::point_graph ( )

protected

get access to the point graph. For derived classes

References point_graph_.

Referenced by require_context_graph_(), core::scoring::symmetry::SymmetricEnergies::require_context_graph_(), and core::scoring::symmetry::SymmetricEnergies::update_neighbor_links().

◆ prepare_neighbor_graphs()

void core::scoring::Energies::prepare_neighbor_graphs ( )

private

Delete edges from energy_graph and tenA_neighbor_graph according to the movement history described by the domain map.

References BAD, context_graphs_, delete_graph_edges_using_domain_map(), energy_graph_, graph_state_, long_range_energy_containers_, and update_domainmap_for_lr_energy_container().

Referenced by scoring_begin(), and update_residue_neighbors().

◆ require_context_graph()

void core::scoring::Energies::require_context_graph ( scoring::ContextGraphType type ) const

Allows non-scorefunction components of Rosetta to impose requirements on the context graphs that this object maintains.

References require_context_graph_().

◆ require_context_graph_()

void core::scoring::Energies::require_context_graph_	(	scoring::ContextGraphType	type,
		bool	external
	)		const

privatevirtual

Internal method that handles the bookkeeping for intializing a new context graph, either requested by a scoring term (external = false) or some other function (external = true ).

Create a context graph. If the requirement is external, someone other than a ScoreFunction has declared that the context graph is needed (possibly by asking for it right now) so the graph must also be made up-to-date.

Reimplemented in core::scoring::symmetry::SymmetricEnergies.

References context_graphs_, core::scoring::ContextGraphFactory::create_context_graph(), externally_required_context_graphs_, fill_point_graph(), max_context_neighbor_cutoff_, core::chemical::ResidueType::nbr_radius(), owner_, point_graph(), required_context_graphs_, core::pose::Pose::residue_type(), scorefxn_info_, size_, and core::id::to_string().

Referenced by context_graph(), require_context_graph(), set_scorefxn_info(), tenA_neighbor_graph(), and twelveA_neighbor_graph().

◆ require_scoring()

void core::scoring::Energies::require_scoring ( ) const

inlineprivate

will die if not in the middle of an energy evaluation

References scoring_.

Referenced by domain_map(), and res_moved().

◆ required_context_graphs()

utility::vector1< bool > & core::scoring::Energies::required_context_graphs ( ) const

protected

References required_context_graphs_.

Referenced by core::scoring::symmetry::SymmetricEnergies::require_context_graph_().

◆ res_moved()

bool core::scoring::Energies::res_moved ( int const seqpos ) const

check if rsd has changed internal conformation, necessitating, recomputation of 1d energies like dun,intra,prob,etc

References energy_graph_, and require_scoring().

Referenced by core::scoring::ScoreFunction::asym_eval_onebody_energies(), and core::scoring::ScoreFunction::sym_eval_onebody_energies().

◆ reset_nblist()

void core::scoring::Energies::reset_nblist ( )

References graph_state_, minimization_graph_, MOD, nblist_, scoring_, size_, structure_has_moved(), and use_nblist_.

Referenced by protocols::ncbb::SecStructMinimizeMover::apply(), protocols::normalmode::NormalModeMinimizer::apply(), core::optimization::AtomTreeMinimizer::run(), core::optimization::CartesianMinimizer::run(), and core::optimization::symmetry::SymAtomTreeMinimizer::run().

◆ reset_res_moved()

void core::scoring::Energies::reset_res_moved ( int const seqpos )

References energy_graph_.

Referenced by core::scoring::ScoreFunction::asym_eval_onebody_energies(), and core::scoring::ScoreFunction::sym_eval_onebody_energies().

◆ residue_neighbors_updated()

bool core::scoring::Energies::residue_neighbors_updated ( ) const

inline

References GOOD, and graph_state_.

Referenced by core::select::residue_selector::NeighborhoodResidueSelector::apply(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), core::pack::interaction_graph::SurfacePotential::compute_residue_surface_energy(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), core::scoring::hbonds::fill_hbond_set(), protocols::constel::HBondCommon::is_rmoi_hbonded(), protocols::features::AtomAtomPairFeatures::report_atom_pairs(), protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs(), protocols::features::HBondFeatures::report_features(), protocols::features::TaskOperationFeatures::report_features(), and protocols::features::PairFeatures::report_residue_pairs().

◆ residue_total_energies()

EnergyMap const& core::scoring::Energies::residue_total_energies ( int const seqpos ) const

inline

Returns the unweighted total_energies EnergyMap for Residue <seqpos>

Note: : only evaluated when requested (lazy!), inaccessible during minimization, EnergyMap is an EMapVector

example(s): r3 = pose.energies().residue_total_energies(3) r3[fa_sol] See also: Energies Energies.residue_total_energy Pose ScoreFunction ScoreFunction.show create_score_function EMapVector

References accumulate_residue_total_energies(), energies_updated(), residue_total_energies_, residue_total_energies_uptodate_, size(), and use_nblist().

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::task_operations::SelectByDeltaScoreOperation::apply(), core::select::residue_selector::ScoreTermValueBasedSelector::apply(), protocols::protein_interface_design::best_bbcst_residues(), protocols::hybridization::FragmentBiasAssigner::cal_perrsd_score(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_pep_scores(), protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_and_regional_data(), core::scoring::electron_density::calc_per_rsd_score(), core::simple_metrics::composite_metrics::CompositeEnergyMetric::calculate(), core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::calculate(), core::scoring::electron_density::calculate_rama(), protocols::score_filters::GeometryFilter::compute(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::simple_filters::EnergyPerResidueFilter::compute(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), protocols::sasa_scores::compute_avge_scores(), protocols::enzdes::EnzdesScorefileFilter::compute_metrics_for_residue_subset(), protocols::enzdes::LigInterfaceEnergyFilter::constraint_energy(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::determine_res_to_recompute(), protocols::rna::movers::determine_residues_to_rebuild(), core::pose::Pose::dump_scored_pdb(), protocols::jobdist::PlainPdbJobDistributor::dump_scores(), protocols::design_opt::Supercharge::energy_comparison(), protocols::simple_ddg::ddG::fill_per_residue_energy_vector(), protocols::loop_grower::LoopGrower::full_atom_beam(), core::pose::symmetry::get_buildingblock_and_neighbor_subs(), protocols::moves::get_energies(), protocols::nonlocal::get_per_residue_score(), protocols::relax::get_per_residue_scores(), protocols::enzdes::EnzdesFlexibleRegion::get_region_mm_bend_score(), protocols::score_filters::ScoreCutoffFilter::get_score(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_pose_energies_table(), protocols::make_rot_lib::MakeRotLibMover::minimize_rotamer(), core::pack::interaction_graph::LinearMemNode::project_deltaE_for_substitution(), protocols::mean_field::EnergiesByTaskCalculator::recompute(), protocols::enzdes::LigInterfaceEnergyFilter::report(), protocols::optimize_weights::IterativeOptEDriver::residue_has_unacceptably_bad_dunbrack_energy(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::moves::PyMOLMover::send_energy(), protocols::minimization_packing::EnergyCutRotamerTrialsMinMover::setup_energycut_task(), protocols::enzdes::enzutil::sum_constraint_scoreterms(), protocols::protein_interface_design::sum_total_residue_energy(), protocols::features::strand_assembly::write_p_aa_pp_of_AAs_to_a_file(), and protocols::features::strand_assembly::write_rama_of_AAs_to_a_file().

◆ residue_total_energy()

Real core::scoring::Energies::residue_total_energy ( int const seqpos ) const

inline

Returns the weighted total energy of residue <seqpos>

example(s): pose.energies().residue_total_energy(3) See also: Energies Energies.residue_total_energies Pose ScoreFunction ScoreFunction.show create_score_function

References accumulate_residue_total_energy(), energies_updated(), residue_total_energy_, residue_total_energy_uptodate_, size(), and use_nblist().

Referenced by protocols::evolution::AlignmentAAFinder::apply(), protocols::evolution::AlignmentGapInserter::apply(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_pep_scores(), protocols::peptide_deriver::PeptideDeriverFilter::calculate_per_residue_interface_score(), protocols::antibody::cdr_energy(), protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter::compute(), protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::compute(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::enzdes::EnzdesBaseProtocol::design_targets_score(), protocols::design_opt::Supercharge::energy_comparison(), protocols::hydrate::get_ready_for_sew_packing(), protocols::enzdes::EnzdesFlexibleRegion::get_region_total_score(), protocols::features::ResidueTotalScoresFeatures::insert_residue_total_scores_rows(), protocols::hydrate::remove_high_energy_water_molecules(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), protocols::analysis::InterfaceAnalyzerMover::score_separated_chains(), protocols::moves::PyMOLMover::send_energy(), and protocols::minimization_packing::EnergyCutRotamerTrialsMover::setup_energycut_task().

◆ same_type_as_me()

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

virtual

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 in core::scoring::symmetry::SymmetricEnergies, and core::scoring::solid_surface::SurfaceEnergies.

References same_type_as_me().

Referenced by same_type_as_me(), core::scoring::solid_surface::SurfaceEnergies::same_type_as_me(), and core::scoring::symmetry::SymmetricEnergies::same_type_as_me().

◆ scoring()

bool core::scoring::Energies::scoring ( ) const

inline

are we in the midst of a scoring calculation?

References scoring_.

Referenced by set_scorefxn_info(), tenA_neighbor_graph(), twelveA_neighbor_graph(), update_neighbor_links(), and core::scoring::symmetry::SymmetricEnergies::update_neighbor_links().

◆ scoring_begin()

void core::scoring::Energies::scoring_begin	(	scoring::ScoreFunction const &	sfxn,
		pose::Pose const &	pose
	)

Notification of the start of a scoring calculation.

This is called by ScoreFunction at the start of an energy calculation.

the responsibilities are:

to check for size/scorefxn mismatches,
reset some of the cached energies Expect that Energies::structure_has_moved( ... ) has been called already if the stucture has changed, ie if domain_map != 1

References BAD, core::scoring::EMapVector::clear(), domain_map_, energy_state_, finalized_energies_, graph_state_, core::scoring::ScoreFunction::info(), internalize_new_domain_map(), MOD, prepare_neighbor_graphs(), residue_total_energies_uptodate_, residue_total_energy_uptodate_, scorefxn_info_, scorefxn_weights_, scoring_, set_scorefxn_info(), set_size(), core::pose::Pose::size(), size_, total_energies_, total_energy_, update_neighbor_links(), core::scoring::ScoreFunction::weights(), and core::scoring::EMapVector::zero().

◆ scoring_end()

void core::scoring::Energies::scoring_end ( scoring::ScoreFunction const & scorefxn )

signal from the scorefxn that scoring is over

References energy_state_, GOOD, and scoring_.

Referenced by core::scoring::cryst::PhenixInterface::initialize_target_evaluator().

◆ set_long_range_container()

void core::scoring::Energies::set_long_range_container	(	methods::LongRangeEnergyType	lrtype,
		LREnergyContainerOP	lrec
	)

References long_range_energy_containers_.

◆ set_max_context_neighbor_cutoff()

void core::scoring::Energies::set_max_context_neighbor_cutoff ( Real val ) const

protected

References max_context_neighbor_cutoff_, and protocols::hybridization::val.

Referenced by core::scoring::symmetry::SymmetricEnergies::require_context_graph_().

◆ set_minimization_graph()

void core::scoring::Energies::set_minimization_graph ( MinimizationGraphOP mingraph )

References minimization_graph_.

Referenced by core::scoring::ScoreFunction::asym_setup_for_minimizing(), core::scoring::create_and_store_atom_tree_minimization_graph_asym(), and protocols::ncbb::SecStructMinimizeMultiFunc::setup_minimization_graph().

◆ set_nblist()

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

References nblist_, and use_nblist_.

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

◆ set_owner()

void core::scoring::Energies::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.

References owner(), owner_, and core::id::to_string().

◆ set_scorefxn_info()

void core::scoring::Energies::set_scorefxn_info ( scoring::ScoreFunctionInfoOP info )

private

update the context graphs and the energy graph according to a new score function type

References context_graphs_, energy_graph_, externally_required_context_graphs_, max_context_neighbor_cutoff_, core::scoring::n_shortranged_2b_score_types, core::scoring::num_context_graph_types, require_context_graph_(), required_context_graphs_, scorefxn_info_, and scoring().

Referenced by clear(), and scoring_begin().

◆ set_size()

void core::scoring::Energies::set_size ( Size const size_in )

private

Internal method to resize data that is dependent on the number of residues in the Pose.

References core::scoring::EMapVector::clear(), context_graphs_, domain_map_, energy_graph_, long_range_energy_containers_, onebody_energies_, residue_total_energies_, residue_total_energies_uptodate_, residue_total_energy_, residue_total_energy_uptodate_, size_, and total_energies_.

Referenced by scoring_begin(), and update_residue_neighbors().

◆ set_use_nblist()

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

References domain_map_, energy_state_, GOOD, internalize_new_domain_map(), scoring_, use_nblist_, use_nblist_auto_update(), and use_nblist_auto_update_.

Referenced by protocols::ncbb::SecStructMinimizeMover::apply(), protocols::normalmode::NormalModeMinimizer::apply(), core::optimization::AtomTreeMinimizer::run(), core::optimization::CartesianMinimizer::run(), and core::optimization::symmetry::SymAtomTreeMinimizer::run().

◆ show() [1/4]

void core::scoring::Energies::show ( ) const

References core::scoring::tr().

Referenced by show().

◆ show() [2/4]

void core::scoring::Energies::show ( Size res ) const

Shows the energy information of residue <seqpos>

Note: : wrapper function of energies.show(Size) for Pyrosetta

example(s): pose.energies().show(3) See also: Energies Energies.residue_total_energies Energies.residue_total_energy Pose ScoreFunction ScoreFunction.show create_score_function

References show(), and core::scoring::tr().

◆ show() [3/4]

void core::scoring::Energies::show ( std::ostream & out ) const

Show the per-residue and total energies, only for scores with a non-zero weight in the last energy evaluation

References protocols::comparative_modeling::features::A, accumulate_residue_total_energies(), core::scoring::EMapVector::begin(), core::scoring::EMapVector::end(), energy_state_, core::chemical::element::F, GOOD, core::chemical::element::I, core::scoring::name_from_score_type(), core::conformation::membrane::out, residue_total_energies_, residue_total_energies_uptodate_, scorefxn_weights_, size(), and total_energies_.

Referenced by protocols::simple_moves::ScoreMover::apply(), and core::optimization::AtomTreeMinimizer::run().

◆ show() [4/4]

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

Show the residue energies, only for scores with a non-zero weight in the last energy evaluation

References protocols::comparative_modeling::features::A, accumulate_residue_total_energies(), core::scoring::EMapVector::begin(), core::scoring::EMapVector::end(), energy_state_, core::chemical::element::F, GOOD, core::chemical::element::I, core::scoring::name_from_score_type(), core::conformation::membrane::out, residue_total_energies_, residue_total_energies_uptodate_, scorefxn_weights_, and total_energies_.

◆ show_total_headers()

void core::scoring::Energies::show_total_headers ( std::ostream & out ) const

References core::sequence::end, get_scorefxn_info(), core::conformation::membrane::out, and total_energies().

Referenced by protocols::membrane::MPQuickRelaxMover::apply(), and protocols::relax::RangeRelaxMover::print_score().

◆ show_totals()

void core::scoring::Energies::show_totals ( std::ostream & out ) const

References core::sequence::end, core::chemical::element::F, get_scorefxn_info(), core::conformation::membrane::out, and total_energies().

Referenced by protocols::membrane::MPQuickRelaxMover::apply(), and protocols::relax::RangeRelaxMover::print_score().

◆ size()

Size core::scoring::Energies::size ( ) const

inline

Returns the number of held residue energies.

example(s): r3 = pose.energies().residue_total_energies(3) r3[fa_sol] See also: Energies Energies.residue_total_energies Energies.residue_total_energy Pose ScoreFunction ScoreFunction.show create_score_function

References size_.

Referenced by core::scoring::symmetry::SymmetricEnergies::require_context_graph_(), residue_total_energies(), residue_total_energy(), show(), and core::scoring::symmetry::SymmetricEnergies::update_neighbor_links().

◆ structure_has_moved()

void core::scoring::Energies::structure_has_moved ( Size const nres ) const

called (eg by pose) to notify us of a change to the structure

Triggers clearing of the total energies and the twobody rsd energies PHIL – should also mark the neighbor links as invalid somehow... Called by pose when someone tries to access us, if the Conformation indicates that the structure has moved since the last score evaluation

const b/c called inside const access methods

References BAD, energy_state_, GOOD, graph_state_, MOD, residue_total_energies_uptodate_, residue_total_energy_uptodate_, scoring_, size_, and total_energy_.

Referenced by protocols::legacy_sewing::LegacyAssemblyMover::output_stats(), and reset_nblist().

◆ tenA_neighbor_graph() [1/2]

scoring::TenANeighborGraph & core::scoring::Energies::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.

get the graph encoding # neighbors within 10 Angstroms – see comments for const version of this method

References context_graphs_, GOOD, graph_state_, require_context_graph_(), scoring(), and core::scoring::ten_A_neighbor_graph.

◆ tenA_neighbor_graph() [2/2]

scoring::TenANeighborGraph const & core::scoring::Energies::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.

convenience function – this function violates the idea that the energies object doesn't know the kind of context information its maintaining. There is no reason to add a method like this for future context graphs.

References context_graphs_, GOOD, graph_state_, require_context_graph_(), scoring(), and core::scoring::ten_A_neighbor_graph.

◆ total_energies() [1/2]

EnergyMap & core::scoring::Energies::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.

References total_energies_.

◆ total_energies() [2/2]

EnergyMap const & core::scoring::Energies::total_energies ( ) const

Returns the total_energies EnergyMap after first computing the component energies if they are not up-to-date.

References total_energies_.

◆ total_energies_weighted()

EnergyMap core::scoring::Energies::total_energies_weighted ( ) const

Returns the weighted total energies.

References scorefxn_weights_, and total_energies_.

Referenced by core::simple_metrics::metrics::TotalEnergyMetric::calculate().

◆ total_energy() [1/2]

Real& core::scoring::Energies::total_energy ( )

inline

References total_energy_.

◆ total_energy() [2/2]

Real core::scoring::Energies::total_energy ( ) const

inline

energy access

Returns the total score

example(s): pose.energies().total_energy() See also: Energies Energies.residue_total_energy Energies.residue_total_energies Pose ScoreFunction ScoreFunction.show create_score_function

References total_energy_.

◆ twelveA_neighbor_graph() [1/2]

scoring::TwelveANeighborGraph & core::scoring::Energies::twelveA_neighbor_graph ( )

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

References context_graphs_, GOOD, graph_state_, require_context_graph_(), scoring(), and core::scoring::twelve_A_neighbor_graph.

◆ twelveA_neighbor_graph() [2/2]

scoring::TwelveANeighborGraph const & core::scoring::Energies::twelveA_neighbor_graph ( ) const

get the graph encoding # neighbors within 12 Angstroms

convenience function – this function violates the idea that the energies object doesn't know the kind of context information its maintaining. There is no reason to add a method like this for future context graphs.

References context_graphs_, GOOD, graph_state_, require_context_graph_(), scoring(), and core::scoring::twelve_A_neighbor_graph.

◆ update_component_energies()

void core::scoring::Energies::update_component_energies ( ) const

private

Lazy component evaluation for residue pair energies;.

◆ update_domainmap_for_lr_energy_container()

void core::scoring::Energies::update_domainmap_for_lr_energy_container ( LREnergyContainerOP lrec )

private

Reset the "already computed" status for pairs of residues represented in a particular long-range energy container using the domain map.

References domain_map_, and size_.

Referenced by prepare_neighbor_graphs().

◆ update_neighbor_links()

void core::scoring::Energies::update_neighbor_links ( pose::Pose const & pose )

privatevirtual

Detect the new set of neighbors given the structure of the Pose (find_neighbors()) and add new edges to the neighbor graphs so that the status of the neighbor graphs is current wrt the current conformation.

Add edges to the energy_graph and the context graphs according to domain map.

Precondition: if the graph contains any edges, then all neighbor relationships between pairs of residues that have not moved relative to each other are represented by the presence or absence of edges in the energy graph. If there are no edges in the energy graph, then all pair inforamtion must be calculated Precondition: if two residues have changed relative to one another according to the domain map, then there are no edges between them.

Reimplemented in core::scoring::symmetry::SymmetricEnergies.

References context_graphs_, domain_map_, energy_graph_, fill_point_graph(), core::chemical::ResidueType::is_ligand(), core::pose::symmetry::is_symmetric(), core::chemical::ResidueType::nbr_radius(), point_graph_, core::pose::Pose::residue_type(), scorefxn_info_, scoring(), and core::pose::Pose::size().

Referenced by scoring_begin(), and update_residue_neighbors().

◆ update_residue_neighbors()

void core::scoring::Energies::update_residue_neighbors	(	DomainMap const &	domain_map_in,
		pose::Pose const &	pose
	)

update the residue neighbors

References BAD, domain_map_, GOOD, graph_state_, internalize_new_domain_map(), MOD, prepare_neighbor_graphs(), set_size(), core::pose::Pose::size(), size_, update_neighbor_links(), and use_nblist_.

◆ use_nblist()

bool core::scoring::Energies::use_nblist ( ) const

inline

References use_nblist_.

◆ use_nblist_auto_update()

bool core::scoring::Energies::use_nblist_auto_update ( ) const

inline

References use_nblist_auto_update_.

◆ use_nblist_of_type()

bool core::scoring::Energies::use_nblist_of_type ( EnergiesCacheableDataType::Enum const & type ) const

inline

References nblist_.

◆ weights() [1/2]

EnergyMap core::scoring::Energies::weights ( ) const

Returns an EnergyMap of the ScoreFunction weights from the last scoring.

example(s): we = pose.energies().weights() we[fa_atr] See also: Energies Energies.residue_total_energies Energies.residue_total_energy Pose ScoreFunction ScoreFunction.show create_score_function EMapVector

May not be called during scoring, to discourage access by energy methods.

References scorefxn_weights_, and scoring_.

Referenced by core::io::raw_data::ScoreMap::add_energies_data_from_scored_pose(), protocols::evolution::AlignmentGapInserter::apply(), protocols::recon_design::MSDMover::apply(), protocols::recon_design::MSDMover::apply_mpi(), core::simple_metrics::metrics::InteractionEnergyMetric::calculate(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::calculate(), protocols::hydrate::calculate_water_overcoordinated_hb_correction(), protocols::enzdes::PackRotamersMoverPartGreedy::choose_n_best(), core::pack::compare_mingraph_and_energy_graph(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), protocols::simple_filters::ResidueIEFilter::compute(), protocols::enzdes::EnzdesScorefileFilter::compute_metrics_for_residue_subset(), protocols::enzdes::LigInterfaceEnergyFilter::constraint_energy(), protocols::stepwise::monte_carlo::StepWiseMonteCarlo::do_main_loop(), protocols::jobdist::PlainPdbJobDistributor::dump_scores(), core::io::silent::SilentStruct::energies_from_pose(), core::io::silent::SilentStruct::energies_into_pose(), protocols::enzdes::EnzdesScorefileFilter::examine_pose(), protocols::enzdes::EnzdesFlexibleRegion::extract_lig_designability_score(), protocols::features::get_current_model_score(), protocols::score_filters::ScoreCutoffFilter::get_score(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_pose_energies_table(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::interface_interaction_energy(), protocols::score_filters::ScoreCutoffFilter::output_residue_pair_energies(), protocols::rpc::pose_energies_to_json(), core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::recompute(), protocols::mean_field::EnergiesByTaskCalculator::recompute(), protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::recompute(), protocols::pose_metric_calculators::NonlocalContactsCalculator::recompute(), protocols::hydrate::show_water_hb_network(), protocols::enzdes::enzutil::sum_constraint_scoreterms(), and protocols::protein_interface_design::sum_total_residue_energy().

◆ weights() [2/2]

void core::scoring::Energies::weights ( EnergyMap new_weights )

Setter for the weights in this Energies object.

References scorefxn_weights_.

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<<	(	std::ostream &	out,
		const Energies &	e
	)

friend

Member Data Documentation

◆ context_graphs_

utility::vector1< ContextGraphOP > core::scoring::Energies::context_graphs_

mutableprivate

The collection of context graphs used by the context-dependent energy components which the Energies object is responsible for maintaining. Context graphs are allocated as requested, (e.g. in a call to tenA_neighbor_graph() ), if they have not yet been allocated. If a portion of the code requires a context graph (e.g the packer), it may call require_context_graph( int cgtype ), which will create the context graph immediately.

Referenced by clear_energies(), context_graph(), context_graphs(), copy_context_graphs(), operator=(), prepare_neighbor_graphs(), require_context_graph_(), set_scorefxn_info(), set_size(), tenA_neighbor_graph(), twelveA_neighbor_graph(), and update_neighbor_links().

◆ data_cache_

BasicDataCache core::scoring::Energies::data_cache_

private

BasicDataCache indexed by enum in core/scoring/EnergiesCacheableDataType.hh.

Warning: DataCache must always be initialized with the number of cacheable data types – see the last enum entry.

Referenced by data(), and operator=().

◆ domain_map_

DomainMap core::scoring::Energies::domain_map_

private

Domain map, stores information about the rigid-bodies whose internal conformation is unchanged since the last score calc'n If domain_map_(i) == 0 then residue i has changed internal conformation. – no longer true If domain_map_(i) > 0 and domain_map_(i) == domain_map_(j), then residues i and j are unchanged wrt one another

Referenced by clear(), clear_energies(), delete_graph_edges_using_domain_map(), domain_map(), domain_map_during_minimization(), internalize_new_domain_map(), operator=(), scoring_begin(), set_size(), set_use_nblist(), update_domainmap_for_lr_energy_container(), update_neighbor_links(), and update_residue_neighbors().

◆ energy_graph_

EnergyGraphOP core::scoring::Energies::energy_graph_

mutableprivate

Referenced by accumulate_residue_total_energies(), accumulate_residue_total_energy(), clear_energies(), energy_graph(), energy_graph_no_state_check(), internalize_new_domain_map(), operator=(), prepare_neighbor_graphs(), res_moved(), reset_res_moved(), set_scorefxn_info(), set_size(), and update_neighbor_links().

◆ energy_state_

EnergyState core::scoring::Energies::energy_state_

mutableprivate

Referenced by accumulate_residue_total_energies(), clear_energies(), energies_updated(), operator=(), scoring_begin(), scoring_end(), set_use_nblist(), show(), and structure_has_moved().

◆ externally_required_context_graphs_

utility::vector1< bool > core::scoring::Energies::externally_required_context_graphs_

mutableprivate

those required by non-score function entities (e.g. the packer).

Referenced by copy_context_graphs(), require_context_graph_(), and set_scorefxn_info().

◆ finalized_energies_

EnergyMap core::scoring::Energies::finalized_energies_

private

Energies computed during the finalize() stage of scoring.

Referenced by finalized_energies(), operator=(), and scoring_begin().

◆ graph_state_

EnergyState core::scoring::Energies::graph_state_

mutableprivate

Referenced by clear_energies(), context_graph(), energy_graph(), operator=(), prepare_neighbor_graphs(), reset_nblist(), residue_neighbors_updated(), scoring_begin(), structure_has_moved(), tenA_neighbor_graph(), twelveA_neighbor_graph(), and update_residue_neighbors().

◆ long_range_energy_containers_

utility::vector1< LREnergyContainerOP > core::scoring::Energies::long_range_energy_containers_

private

Referenced by accumulate_residue_total_energies(), accumulate_residue_total_energy(), clear_energies(), copy_lr_energy_containers(), long_range_container(), nonconst_long_range_container(), prepare_neighbor_graphs(), set_long_range_container(), and set_size().

◆ max_context_neighbor_cutoff_

Real core::scoring::Energies::max_context_neighbor_cutoff_

mutableprivate

The maximum neighbor cutoff for all required context graphs;.

Referenced by copy_context_graphs(), fill_point_graph(), max_context_neighbor_cutoff(), require_context_graph_(), set_max_context_neighbor_cutoff(), and set_scorefxn_info().

◆ minimization_graph_

MinimizationGraphOP core::scoring::Energies::minimization_graph_

private

Referenced by minimization_graph(), operator=(), reset_nblist(), and set_minimization_graph().

◆ nblist_

std::map< EnergiesCacheableDataType::Enum, scoring::NeighborListOP > core::scoring::Energies::nblist_

private

atom-atom neighborlists

Referenced by copy_nblists(), nblist(), reset_nblist(), set_nblist(), and use_nblist_of_type().

◆ onebody_energies_

utility::vector1< EnergyMap > core::scoring::Energies::onebody_energies_

private

cached onebody energies – expensive – shortly to be replaced by an FArray2D which can be smarly indexed into to access only the active one-body energy terms.

Referenced by accumulate_residue_total_energies(), accumulate_residue_total_energy(), clear_energies(), internalize_new_domain_map(), onebody_energies(), operator=(), and set_size().

◆ owner_

pose::Pose* core::scoring::Energies::owner_

private

In order to do lazy context-graph creation, the Energies object must be able to access coordinates stored in the pose. This now means an Energies object cannot live independently of a Pose!

Referenced by owner(), require_context_graph_(), and set_owner().

◆ point_graph_

conformation::PointGraphOP core::scoring::Energies::point_graph_

private

Keep this guy between score function evaluations to avoid the expense of recreating it each time; this data does not need to be copied in either the copy-ctor or the assignment operator Its purpose is solely to improve performance and the data is used only inside the neighbor calculation function call.

Referenced by point_graph(), and update_neighbor_links().

◆ required_context_graphs_

utility::vector1< bool > core::scoring::Energies::required_context_graphs_

mutableprivate

OR of the sfxn required context graphs and the externally required ones.

Referenced by copy_context_graphs(), require_context_graph_(), required_context_graphs(), and set_scorefxn_info().

◆ residue_total_energies_

utility::vector1< EnergyMap > core::scoring::Energies::residue_total_energies_

mutableprivate

Referenced by accumulate_residue_total_energies(), clear_energies(), residue_total_energies(), set_size(), and show().

◆ residue_total_energies_uptodate_

bool core::scoring::Energies::residue_total_energies_uptodate_

mutableprivate

cached energy component totals – summed twobody and one body interactions for each residue

Referenced by accumulate_residue_total_energies(), clear_energies(), operator=(), residue_total_energies(), scoring_begin(), set_size(), show(), and structure_has_moved().

◆ residue_total_energy_

utility::vector1< Real > core::scoring::Energies::residue_total_energy_

mutableprivate

Referenced by accumulate_residue_total_energy(), clear_energies(), operator=(), residue_total_energy(), and set_size().

◆ residue_total_energy_uptodate_

bool core::scoring::Energies::residue_total_energy_uptodate_

mutableprivate

cached energy totals – only the weighted sum, no components.

Referenced by accumulate_residue_total_energy(), clear_energies(), operator=(), residue_total_energy(), scoring_begin(), set_size(), and structure_has_moved().

◆ scorefxn_info_

scoring::ScoreFunctionInfoOP core::scoring::Energies::scorefxn_info_

private

info about last score evaluation

Referenced by fill_point_graph(), get_scorefxn_info(), operator=(), require_context_graph_(), scoring_begin(), set_scorefxn_info(), and update_neighbor_links().

◆ scorefxn_weights_

EnergyMap core::scoring::Energies::scorefxn_weights_

private

ScoreFunction weights from the last scoring call.

Referenced by accumulate_residue_total_energies(), accumulate_residue_total_energy(), clear(), operator=(), scoring_begin(), show(), total_energies_weighted(), and weights().

◆ scoring_

bool core::scoring::Energies::scoring_

private

are we within a scoring evaluation?

Referenced by operator=(), require_scoring(), reset_nblist(), scoring(), scoring_begin(), scoring_end(), set_use_nblist(), structure_has_moved(), and weights().

◆ size_

Size core::scoring::Energies::size_

private

our internal nres

Used for dimensioning new Energy1D's, eg and for checking the validity of the NeighborEnergies by comparing against their size

Referenced by accumulate_residue_total_energies(), accumulate_residue_total_energy(), clear(), clear_energies(), internalize_new_domain_map(), operator=(), require_context_graph_(), reset_nblist(), scoring_begin(), set_size(), size(), structure_has_moved(), update_domainmap_for_lr_energy_container(), and update_residue_neighbors().

◆ total_energies_

EnergyMap core::scoring::Energies::total_energies_

mutableprivate

cached total energies

Referenced by clear_energies(), operator=(), scoring_begin(), set_size(), show(), total_energies(), and total_energies_weighted().

◆ total_energy_

Real core::scoring::Energies::total_energy_

mutableprivate

Referenced by operator=(), scoring_begin(), structure_has_moved(), and total_energy().

◆ use_nblist_

bool core::scoring::Energies::use_nblist_

private

Referenced by discard_conformation_domain_map(), nblist(), operator=(), reset_nblist(), set_nblist(), set_use_nblist(), update_residue_neighbors(), and use_nblist().

◆ use_nblist_auto_update_

bool core::scoring::Energies::use_nblist_auto_update_

private

Referenced by operator=(), set_use_nblist(), and use_nblist_auto_update().

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

src/core/scoring/Energies.hh
src/core/scoring/Energies.cc

Public Types

Public Member Functions

Protected Member Functions

Private Types

Private Member Functions

Private Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ AtomID

◆ AtomID_Mask

◆ BasicDataCache

◆ DomainMap

◆ EnergyGraph

◆ EnergyMap

◆ Graph

◆ NeighborList

◆ ScoreFunctionInfo

◆ ScoreType

Member Enumeration Documentation

◆ EnergyState

Constructor & Destructor Documentation

◆ Energies() [1/2]

◆ Energies() [2/2]

◆ ~Energies()

Member Function Documentation

◆ accumulate_residue_energies()

◆ accumulate_residue_total_energies()

◆ accumulate_residue_total_energy()

◆ clear()

◆ clear_energies()

◆ clone()

◆ context_graph() [1/2]

◆ context_graph() [2/2]

◆ context_graphs()

◆ copy_context_graphs()

◆ copy_lr_energy_containers()

◆ copy_nblists()

◆ data() [1/2]

◆ data() [2/2]

◆ delete_graph_edges_using_domain_map()

◆ discard_conformation_domain_map()

◆ domain_map() [1/2]

◆ domain_map() [2/2]

◆ domain_map_during_minimization()

◆ energies_updated()

◆ energy_graph() [1/2]

◆ energy_graph() [2/2]

◆ energy_graph_no_state_check()

◆ fill_point_graph()

◆ finalized_energies() [1/2]

◆ finalized_energies() [2/2]

◆ get_scorefxn_info()

◆ internalize_new_domain_map()

◆ long_range_container()

◆ max_context_neighbor_cutoff()

◆ minimization_graph() [1/2]

◆ minimization_graph() [2/2]

◆ nblist()

◆ nonconst_long_range_container()

◆ onebody_energies() [1/2]

◆ onebody_energies() [2/2]

◆ operator=()

◆ owner()

◆ point_graph()

◆ prepare_neighbor_graphs()

◆ require_context_graph()

◆ require_context_graph_()

◆ require_scoring()

◆ required_context_graphs()

◆ res_moved()

◆ reset_nblist()

◆ reset_res_moved()

◆ residue_neighbors_updated()

◆ residue_total_energies()

◆ residue_total_energy()

◆ same_type_as_me()

◆ scoring()

◆ scoring_begin()

◆ scoring_end()