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core::scoring::Energies Class Reference

A cached energies object. More...

#include <Energies.hh>

Inheritance diagram for core::scoring::Energies:
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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 Energiesoperator= (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...
 
Realtotal_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...
 
EnergyMaptotal_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...
 
EnergyMaponebody_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...
 
EnergyMapfinalized_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...
 
EnergyGraphenergy_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...
 
TenANeighborGraphtenA_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::TwelveANeighborGraphtwelveA_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...
 
BasicDataCachedata ()
 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...
 
EnergyGraphenergy_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::Poseowner () 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::Poseowner_
 
EnergyGraphOP energy_graph_
 
utility::vector1< ContextGraphOPcontext_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< boolexternally_required_context_graphs_
 those required by non-score function entities (e.g. the packer). More...
 
utility::vector1< boolrequired_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< EnergyMaponebody_energies_
 
bool residue_total_energies_uptodate_
 cached energy component totals – summed twobody and one body interactions for each residue More...
 
utility::vector1< EnergyMapresidue_total_energies_
 
bool residue_total_energy_uptodate_
 cached energy totals – only the weighted sum, no components. More...
 
utility::vector1< Realresidue_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.

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

typedef basic::datacache::BasicDataCache core::scoring::Energies::BasicDataCache
typedef utility::graph::Graph core::scoring::Energies::Graph

Member Enumeration Documentation

should push this into energygraph once it stabilizes

Enumerator
BAD 
MOD 
GOOD 

Constructor & Destructor Documentation

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

ctor – ensure correct initial state

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

copy ctor – deep copy

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

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

dtor

Member Function Documentation

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

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

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

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().

Referenced by protocols::cluster::GatherPosesMover::apply(), protocols::flexpack::FlexPacker::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::monte_carlo::GenericMonteCarloMover::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::calculate_free_receptor_score(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), protocols::forge::remodel::RemodelMover::centroid_build(), protocols::forge::components::VarLengthBuild::centroid_build(), protocols::forge::components::BDR::design_refine(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::forge::remodel::RemodelMover::design_refine_cart_relax(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), core::io::silent::BinarySilentStruct::fill_pose(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::fold_attempt(), protocols::forge::build::BuildInstruction::modify(), protocols::simple_moves::ShearMover::move_with_scorefxn(), protocols::frag_picker::FragmentCandidate::output_silent(), protocols::toolbox::pose_manipulation::remove_non_protein_residues(), protocols::constraint_filters::ConstraintScoreFilter::report_sm(), protocols::forge::methods::restore_residues(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::rnp_docking_trial(), protocols::moves::MonteCarlo::score_function(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::search_rigid_body_orientation(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rnp_fold_tree(), and core::util::switch_to_residue_type_set().

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

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_().

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_().

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

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=().

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=().

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

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

References data_cache_.

Referenced by protocols::fldsgn::filters::HelixKinkFilter::apply(), core::scoring::hbonds::HBondEnergy::backbone_backbone_energy(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::calculate(), protocols::fldsgn::topology::check_internal_hbonds(), protocols::fldsgn::topology::check_kink_helix(), core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::clean_up_residuearrayannealableenergy_after_packing(), core::pack::interaction_graph::InteractionGraphFactory::clear_cached_residuearrayannealableenergy_information(), core::scoring::hbonds::HBondEnergy::create_rotamer_trie(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::scoring::methods::WaterAdductHBondEnergy::eval_atom_derivative(), core::scoring::hbonds::NPDHBondEnergy::eval_atom_derivative(), core::scoring::hbonds::HBondEnergy::eval_intrares_derivatives(), core::scoring::hbonds::HBondEnergy::eval_residue_pair_derivatives(), core::scoring::methods::MMLJEnergyInter::evaluate_rotamer_background_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_background_energies(), core::scoring::elec::FA_ElecEnergy::evaluate_rotamer_background_energies(), core::scoring::etable::BaseEtableEnergy< Derived >::evaluate_rotamer_background_energies(), core::scoring::lkball::LK_BallEnergy::evaluate_rotamer_background_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_pair_energies(), core::scoring::hbonds::NPDHBondEnergy::finalize_total_energy(), core::scoring::hbonds::HBondEnergy::finalize_total_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::ScoreFunction::get_sub_score(), core::scoring::ScoreFunction::intersubunit_hbond_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext(), core::pack::interaction_graph::NPDHBSimpleInteractionGraph::set_pose_no_initialize(), core::scoring::ScoreFunction::set_symmetric_residue_neighbors_hbonds(), core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::set_up_residuearrayannealableenergy_for_packing(), core::scoring::methods::WaterAdductHBondEnergy::setup_for_derivatives(), core::scoring::hbonds::HBondEnergy::setup_for_minimizing_for_residue(), core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy::setup_for_packing(), core::scoring::methods::MMLJEnergyInter::setup_for_packing(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), core::scoring::lkball::LK_BallEnergy::setup_for_packing(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_packing(), core::scoring::elec::FA_ElecEnergy::setup_for_packing(), core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy::setup_for_scoring(), core::scoring::hbonds::NPDHBondEnergy::setup_for_scoring(), core::scoring::hbonds::HBondEnergy::setup_for_scoring(), core::scoring::hbonds::HBondEnergy::sidechain_sidechain_energy(), core::scoring::ScoreFunction::symmetrical_allow_hbonds(), core::scoring::methods::MMLJEnergyInter::update_residue_for_packing(), core::scoring::hbonds::HBondEnergy::update_residue_for_packing(), core::scoring::lkball::LK_BallEnergy::update_residue_for_packing(), core::scoring::etable::BaseEtableEnergy< Derived >::update_residue_for_packing(), and core::scoring::elec::FA_ElecEnergy::update_residue_for_packing().

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

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

References data_cache_.

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().

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_.

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::elec::RNA_FA_ElecEnergy::finalize_total_energy(), core::scoring::rna::StackElecEnergy::finalize_total_energy(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), and core::scoring::etable::BaseEtableEnergy< Derived >::finalize_total_energy().

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

Read access for the domain map.

References domain_map_, and require_scoring().

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().

bool core::scoring::Energies::energies_updated ( ) const
inline
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_.

Referenced by core::scoring::methods::FreeDOF_Energy::accumulate_stack_energy(), protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::evolution::AlignmentGapInserter::apply(), core::scoring::ScoreFunction::asym_setup_for_minimizing(), core::simple_metrics::metrics::InteractionEnergyMetric::calculate(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::calculate(), core::scoring::electron_density::calculate_density_nbr(), protocols::enzdes::PackRotamersMoverPartGreedy::choose_n_best(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::clean_up_rna_two_body_energy_tables(), core::pack::compare_mingraph_and_energy_graph(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), core::scoring::CenRotEnvPairPotential::compute_centroid_environment(), core::scoring::SmoothEnvPairPotential::compute_centroid_environment(), core::scoring::EnvPairPotential::compute_centroid_environment(), core::scoring::CenRotEnvPairPotential::compute_dcentroid_environment(), core::scoring::SmoothEnvPairPotential::compute_dcentroid_environment(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::compute_Hbonds_for_residue(), core::pack::create_packer_graph(), protocols::electron_density::BfactorMultifunc::dfunc(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_backbone_backbone(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_repulsive(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_atom_energy(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_deriv(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), protocols::enzdes::EnzdesFlexibleRegion::extract_lig_designability_score(), protocols::stepwise::modeler::packer::figure_out_working_interface_res(), core::scoring::WaterAdductHBondPotential::fill_h2o_hbond_set(), core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::get_atom_lk_energy(), protocols::ligand_docking::LigandBaseProtocol::get_non_bb_clashing_rotamers(), protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover::get_random_o2prime_residue_near_moving_residue(), core::scoring::SecondaryStructurePotential::hspair(), protocols::neighbor::in_nrg_graph(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::interface_interaction_energy(), protocols::constel::HBondCommon::is_rmoi_hbonded(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::let_neighboring_chis_minimize(), core::scoring::electron_density::ElectronDensity::matchRes(), protocols::cryst::ReportGradientsMover::normalization(), protocols::electron_density::BfactorMultifunc::operator()(), protocols::score_filters::ScoreCutoffFilter::output_residue_pair_energies(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::precalculate_bb_bb_energy_for_design(), protocols::scoring::Interface::protein_calculate(), protocols::hbnet::HBNet::rec_trav_native(), core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::recompute(), protocols::pose_metric_calculators::NonlocalContactsCalculator::recompute(), protocols::vardist_solaccess::VarSolDistSasaCalculator::recompute(), protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::recompute(), protocols::features::ModelFeatures::report_features(), protocols::fldsgn::potentials::sspot::HSPairPotential::score(), protocols::fldsgn::potentials::sspot::SSPairPotential::score(), protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::score(), protocols::vip::set_local_movemap(), protocols::loop_grower::LoopComparator::set_scores(), core::scoring::SecondaryStructurePotential::sspair(), core::scoring::ScoreFunction::sym_setup_for_minimizing(), core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap(), protocols::hbnet::HBNet::traverse_native(), and core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions().

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_.

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().

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

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().

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()().

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_.

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

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

References long_range_energy_containers_.

Referenced by core::pack::rotamer_set::symmetry::SymmetricRotamerSets::append_two_body_energy_computations_to_work_vector(), core::pack::rotamer_set::RotamerSets::append_two_body_energy_computations_to_work_vector(), core::scoring::ScoreFunction::asym_setup_for_minimizing(), core::simple_metrics::metrics::InteractionEnergyMetric::calculate(), protocols::minimization_packing::GreenPacker::compute_absent_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_and_two_body_energies(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energies(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_one_body_energies_for_otf_ig(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), core::pack::create_minimization_graph(), core::scoring::disulfides::CentroidDisulfideEnergy::defines_residue_pair_energy(), core::scoring::disulfides::DisulfideMatchingEnergy::defines_residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::ensure_lrenergy_container_is_up_to_date(), core::scoring::ScoreFunction::get_sub_score(), core::pack::interaction_graph::SimpleInteractionGraph::initialize(), protocols::features::ResidueScoresFeatures::insert_two_body_long_range_residue_score_rows(), core::scoring::disulfides::FullatomDisulfideEnergy::old_eval_atom_derivative(), core::optimization::SingleResidueMultifunc::operator()(), protocols::score_filters::ScoreCutoffFilter::output_residue_pair_energies(), core::pack::rotamer_set::RotamerSets::prepare_otf_graph(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::prepare_symm_otf_interaction_graph(), core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::recompute(), protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::recompute(), core::scoring::disulfides::DisulfideMatchingEnergy::residue_pair_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy(), core::pack::RTMin::rtmin(), core::scoring::sym_e::symEnergy::setup_for_scoring(), core::scoring::rna::TNA_SuiteEnergy::setup_for_scoring(), core::scoring::disulfides::DisulfideMatchingEnergy::setup_for_scoring(), core::scoring::disulfides::CentroidDisulfideEnergy::setup_for_scoring(), protocols::ncbb::SecStructMinimizeMultiFunc::setup_minimization_graph(), and core::scoring::ScoreFunction::sym_setup_for_minimizing().

Real core::scoring::Energies::max_context_neighbor_cutoff ( ) const
protected
MinimizationGraphOP core::scoring::Energies::minimization_graph ( )
MinimizationGraphCOP core::scoring::Energies::minimization_graph ( ) const

References minimization_graph_.

scoring::NeighborList const & core::scoring::Energies::nblist ( EnergiesCacheableDataType::Enum const &  type) const
LREnergyContainerOP core::scoring::Energies::nonconst_long_range_container ( methods::LongRangeEnergyType  lrtype)
EnergyMap const& core::scoring::Energies::onebody_energies ( int const  seqpos) const
inline
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_.

Energies & core::scoring::Energies::operator= ( Energies const &  rhs)
virtual
pose::Pose * core::scoring::Energies::owner ( ) const
protected
conformation::PointGraphOP core::scoring::Energies::point_graph ( )
protected
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().

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_().

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().

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().

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

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

References energy_graph_.

bool core::scoring::Energies::residue_neighbors_updated ( ) const
inline
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::task_operations::SelectByDeltaScoreOperation::apply(), core::select::residue_selector::ScoreTermValueBasedSelector::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::loop_grower::LoopGrower::apply(), 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::simple_filters::TaskAwareScoreTypeFilter::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::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::scoring::operator<<(), protocols::mean_field::EnergiesByTaskCalculator::recompute(), 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().

Real core::scoring::Energies::residue_total_energy ( int const  seqpos) const
inline
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 core::scoring::solid_surface::SurfaceEnergies::same_type_as_me(), core::scoring::symmetry::SymmetricEnergies::same_type_as_me(), and same_type_as_me().

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

  1. to check for size/scorefxn mismatches,
  2. 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().

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().

void core::scoring::Energies::set_long_range_container ( methods::LongRangeEnergyType  lrtype,
LREnergyContainerOP  lrec 
)
void core::scoring::Energies::set_max_context_neighbor_cutoff ( Real  val) const
protected
void core::scoring::Energies::set_minimization_graph ( MinimizationGraphOP  mingraph)
void core::scoring::Energies::set_nblist ( EnergiesCacheableDataType::Enum const &  type,
scoring::NeighborListOP  nblist_in 
)

References nblist_, and use_nblist_.

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().

void core::scoring::Energies::set_scorefxn_info ( scoring::ScoreFunctionInfoOP  info)
private
void core::scoring::Energies::set_size ( Size const  size_in)
private
void core::scoring::Energies::set_use_nblist ( pose::Pose const &  pose,
DomainMap const &  domain_map_in,
bool const  use_nblist_auto_update 
)
void core::scoring::Energies::show ( std::ostream &  out) const
void core::scoring::Energies::show ( std::ostream &  out,
Size  res 
) const
void core::scoring::Energies::show ( ) const

References core::scoring::tr().

Referenced by show().

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().

void core::scoring::Energies::show_total_headers ( std::ostream &  out) const
void core::scoring::Energies::show_totals ( std::ostream &  out) const
Size core::scoring::Energies::size ( ) const
inline
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().

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.

Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), core::scoring::geometric_solvation::add_to_individual_sol_energies(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set(), protocols::legacy_sewing::LegacyAssemblyConstraintsMover::apply(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), protocols::fldsgn::filters::InterlockingAromaFilter::compute(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::compute_Hbonds_for_residue(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_sho_acceptor_atom_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_sho_donor_atom_energy(), core::pack::hbonds::create_init_and_create_edges_for_hbond_graph(), core::scoring::hbonds::HBondEnergy::eval_intrares_energy(), core::scoring::methods::PairEnergy::eval_residue_pair_derivatives(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_background_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_pair_energies(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), core::scoring::WaterAdductHBondPotential::fill_h2o_hbond_set(), core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold(), core::scoring::hbonds::fill_intra_res_hbond_set(), core::select::fill_tenA_neighbor_residues(), core::pack::hbonds::find_satisfying_interactions_with_background(), protocols::enzdes::EnzdesFlexibleRegion::get_10A_neighbors(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::enzdes::EnzdesFlexBBProtocol::get_tenA_neighbor_residues(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::initialize_graphs(), protocols::features::HBondFeatures::insert_hbond_dehydron_row(), protocols::constel::HBondCommon::is_rmoi_hbonded(), protocols::ligand_docking::ComputeLigandRDF::ligand_protein_rdf(), protocols::match::NumNeighborsMPM::modified_match_positions(), core::pose::rna::output_ligands(), core::pose::rna::output_other_contacts(), core::scoring::elec::FA_GrpElecEnergy::precalc_context(), protocols::ligand_docking::ComputeLigandRDF::protein_protein_rdf(), protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs(), protocols::features::ProteinBackboneAtomAtomPairFeatures::report_features(), protocols::features::ResidueBurialFeatures::report_features(), protocols::features::PairFeatures::report_residue_pairs(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::io::sequence_comparation::DesignContrast::setNeighbors(), core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), and core::scoring::hbonds::HBondEnergy::sidechain_sidechain_energy().

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.

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_.

Referenced by core::io::raw_data::ScoreMap::add_energies_data_from_scored_pose(), protocols::rbsegment_relax::AutoRBMover::apply(), protocols::protein_interface_design::movers::DockWithHotspotMover::apply(), protocols::flexpack::FlexPacker::apply(), protocols::simple_moves::DisulfideInsertionMover::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::symmetry::SymDockingSlideIntoContact::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::moves::MCShowMover::apply(), protocols::membrane::MPQuickRelaxMover::apply(), protocols::relax::RangeRelaxMover::apply(), protocols::dna_dock::DNAClashCheckFilter::apply(), protocols::ddg::ddGMover::apply(), protocols::dna_dock::PropagateClashCheckFilter::apply(), protocols::symmetry::FaSymDockingSlideTogether::apply(), protocols::docking::DockingProtocol::apply(), protocols::docking::DockingSlideIntoContact::apply(), protocols::docking::FaDockingSlideIntoContact::apply(), protocols::abinitio::ComputeTotalDistCst::apply(), protocols::docking::SlideIntoContact::apply(), core::scoring::ScoreFunction::asym_eval_long_range_twobody_energies(), core::simple_metrics::composite_metrics::CompositeEnergyMetric::calculate(), protocols::ncbb::calculate_statistics(), protocols::ub_e2c::ubi_e2c_modeler::centroid_filter(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::chain_break_screening_general(), protocols::stepwise::modeler::check_scores_from_parts(), protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker::check_screen(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::check_screen(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_binding_data(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), protocols::enzdes::RepackWithoutLigandFilter::compute(), protocols::features::StructureScoresFeatures::compute_energies(), protocols::enzdes::LigInterfaceEnergyFilter::constraint_energy(), core::scoring::ScoreFunction::correct_finalize_score(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_five(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_four(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_one(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_three(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_two(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_zero(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::determine_best_constraint(), protocols::stepwise::monte_carlo::StepWiseMonteCarlo::do_main_loop(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::pose::Pose::dump_scored_pdb(), protocols::jobdist::PlainPdbJobDistributor::dump_scores(), protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_output(), core::io::silent::SilentStruct::energies_from_pose(), core::io::silent::SilentStruct::energies_into_pose(), core::pose::energy_from_pose(), protocols::abinitio::FoldConstraints::evaluate_constraint_energy(), protocols::abinitio::ConstraintFragmentSampler::evaluate_constraint_energy(), protocols::enzdes::EnzdesScorefileFilter::examine_pose(), protocols::LoopRebuild::extend_barcode_regions_if_chain_break(), protocols::simple_ddg::ddG::fill_energy_vector(), protocols::ub_e2c::ubi_e2c_modeler::fullatom_filter(), protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region(), protocols::motif_grafting::movers::MotifGraftMover::get_clash_score_from_pose(), protocols::trajectory::DbTrajectoryReader::get_pose(), protocols::score_filters::ScoreCutoffFilter::get_score(), protocols::ligand_docking::InterfaceScoreCalculator::get_scores(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_pose_energies_table(), protocols::enzdes::PackRotamersMoverPartGreedy::greedy_around(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::tcr::TCRmodel::make_model(), core::import_pose::atom_tree_diffs::map_of_weighted_scores(), core::pack::min_pack_optimize(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::ub_e2c::ubi_e2c_modeler::monoub_centroid_filter(), protocols::ub_e2c::ubi_e2c_modeler::monoub_fullatom_filter(), protocols::nmr::pcs::PCSLigandTransformMover::move_ligand_close_to_surface(), core::scoring::DockingScoreFunction::operator()(), core::scoring::MinScoreScoreFunction::operator()(), core::scoring::ScoreFunction::operator()(), core::scoring::operator<<(), protocols::legacy_sewing::LegacyAssemblyMover::output_stats(), protocols::rpc::pose_energies_to_json(), protocols::optimize_weights::IterativeOptEDriver::print_energies(), protocols::relax::RangeRelaxMover::print_score(), protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::recompute(), protocols::loop_modeling::utilities::TrajectoryLogger::record_endpoint(), protocols::ddg::ddGMover::relax_wildtype_structure(), protocols::score_filters::ScoreCutoffFilter::report(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::run(), core::scoring::ScoreFunction::score_by_scoretype(), protocols::abinitio::abscript::score_cst(), protocols::moves::MonteCarlo::score_function(), protocols::optimize_weights::IterativeOptEDriver::score_ligand_interface(), protocols::hbnet::HBNet::score_network_on_pose(), core::scoring::ScoreFunction::show(), core::scoring::ScoreFunction::show_line(), show_total_headers(), show_totals(), protocols::optimize_weights::IterativeOptEDriver::single_structure_data_for_pose(), protocols::symmetry::SymmetrySlider::slide_score(), protocols::flexpep_docking::FlexPepDockingProtocol::SlideIntoContact(), protocols::motifs::IRCollection::successful_loop_closure(), protocols::enzdes::enzutil::sum_constraint_scoreterms(), core::scoring::ScoreFunction::sym_eval_long_range_twobody_energies(), protocols::symmetry::SymmetrySlider::SymmetrySlider(), and protocols::hydrate::water_specific_hbond_energy().

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_.

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_.

Referenced by protocols::moves::JumpOutMover::apply(), protocols::recces::scratch::ThermalMinimizer::apply(), protocols::simple_filters::EvaluatedTrialMover::apply(), protocols::recon_design::MSDMover::apply(), protocols::surface_docking::SurfaceDockingProtocol::apply(), protocols::helical_bundle::BundleGridSampler::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::membrane::MPQuickRelaxMover::apply(), protocols::relax::RangeRelaxMover::apply(), protocols::moves::TrialMover::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::recon_design::MSDMover::apply_mpi(), protocols::canonical_sampling::BiasedMonteCarlo::boltzmann(), protocols::stepwise::modeler::StepWiseMinimizer::do_full_minimizing(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), protocols::symmetric_docking::SymDockProtocol::docking_highres_filter(), protocols::moves::MonteCarlo::eval_lowest_score_pose(), protocols::multistate_design::SingleStateFitnessFunction::evaluate(), protocols::canonical_sampling::WTEBiasEnergy::extract_collective_var(), protocols::jd3::job_summaries::EnergyJobSummary::extract_energy(), protocols::jd3::job_summaries::StandardPoseJobSummary::extract_energy(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::filter_by_constraints_energy(), protocols::cyclic_peptide::CrosslinkerMover::filter_by_total_score(), protocols::vip::VIP_Report::get_GOE_relaxed_report(), protocols::vip::VIP_Report::get_GOE_repack_report(), protocols::trajectory::DbTrajectoryReader::get_pose(), core::util::ChainbreakUtil::has_chainbreak(), protocols::make_rot_lib::MakeRotLibMover::minimize_rotamer(), core::scoring::ScoreFunction::operator()(), protocols::surface_docking::FullatomRelaxMover::output_solution_state(), protocols::vip::VIP_Mover::relax_favorable_poses(), protocols::moves::MonteCarlo::set_lowest_score_pose(), protocols::vip::VIP_Mover::sort_fill_energies(), protocols::canonical_sampling::TemperatureController::temperature_move(), core::pose::total_energy_from_pose(), protocols::vip::VIP_Mover::try_point_mutants(), protocols::canonical_sampling::MetricRecorder::update_after_boltzmann(), protocols::rna::setup::RNA_CSA_JobDistributor::update_bank(), and protocols::canonical_sampling::PDBTrajectoryRecorder::write_model().

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

References total_energy_.

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

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

Lazy component evaluation for residue pair energies;.

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().

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().

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

References use_nblist_.

Referenced by accumulate_residue_total_energies(), core::scoring::ScoreFunction::asym_eval_long_range_twobody_energies(), core::scoring::etable::BaseEtableEnergy< Derived >::backbone_backbone_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::backbone_sidechain_energy(), core::scoring::MultipoleElecPotential::calculate_and_store_all_derivs(), core::scoring::ScoreFunction::correct_finalize_score(), core::scoring::methods::MMLJEnergyInter::eval_atom_derivative(), core::scoring::elec::RNA_FA_ElecEnergy::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergy::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative(), core::scoring::elec::FA_GrpElecEnergy::eval_intrares_energy(), core::scoring::etable::TableLookupEtableEnergy::eval_intrares_energy(), core::scoring::etable::AnalyticEtableEnergy::eval_intrares_energy(), core::scoring::VdWTinkerPotential::eval_residue_pair_derivatives(), core::pack::interaction_graph::HPatchEnergy::finalize_total_energy(), core::pack::interaction_graph::SurfaceEnergy::finalize_total_energy(), core::scoring::elec::RNA_FA_ElecEnergy::finalize_total_energy(), core::scoring::rna::StackElecEnergy::finalize_total_energy(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), core::scoring::hbonds::HBondEnergy::finalize_total_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::finalize_total_energy(), core::scoring::ScoreFunction::operator()(), core::scoring::rna::StackElecEnergy::residue_pair_energy(), core::scoring::elec::RNA_FA_ElecEnergy::residue_pair_energy(), core::scoring::elec::FA_GrpElecEnergy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::residue_pair_energy(), residue_total_energies(), residue_total_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_derivatives(), core::scoring::methods::MMLJEnergyInter::setup_for_minimizing(), core::scoring::rna::RNA_FullAtomStackingEnergy::setup_for_minimizing(), core::scoring::elec::RNA_FA_ElecEnergy::setup_for_minimizing(), core::scoring::methods::LK_PolarNonPolarEnergy::setup_for_minimizing(), core::scoring::elec::FA_GrpElecEnergy::setup_for_minimizing(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing(), core::scoring::elec::FA_ElecEnergy::setup_for_minimizing(), core::scoring::rna::StackElecEnergy::setup_for_minimizing(), core::scoring::methods::P_AA_ss_Energy::setup_for_scoring(), core::scoring::rna::StackElecEnergy::setup_for_scoring(), core::scoring::rna::RNA_FullAtomStackingEnergy::setup_for_scoring(), core::scoring::methods::LK_PolarNonPolarEnergy::setup_for_scoring(), core::scoring::elec::RNA_FA_ElecEnergy::setup_for_scoring(), core::scoring::hbonds::HBondEnergy::setup_for_scoring(), core::scoring::elec::FA_GrpElecEnergy::setup_for_scoring(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_scoring(), core::scoring::elec::FA_ElecEnergy::setup_for_scoring(), core::scoring::ScoreFunction::setup_for_scoring(), core::scoring::MultipoleElecPotential::setup_for_scoring(), core::scoring::etable::BaseEtableEnergy< Derived >::sidechain_sidechain_energy(), and core::scoring::ScoreFunction::sym_eval_long_range_twobody_energies().

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

References use_nblist_auto_update_.

Referenced by core::scoring::rna::StackElecEnergy::eval_atom_derivative(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_atom_derivative(), core::scoring::elec::RNA_FA_ElecEnergy::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergy::eval_atom_derivative(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_derivatives(), core::scoring::elec::FA_GrpElecEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_derivatives(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy_ext(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_energy_ext(), core::scoring::rna::StackElecEnergy::eval_residue_pair_derivatives(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_residue_pair_derivatives(), core::scoring::elec::FA_GrpElecEnergy::eval_residue_pair_derivatives(), core::scoring::elec::RNA_FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_residue_pair_derivatives(), core::scoring::elec::RNA_FA_ElecEnergy::finalize_total_energy(), core::scoring::rna::StackElecEnergy::finalize_total_energy(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::finalize_total_energy(), core::scoring::rna::StackElecEnergy::minimize_in_whole_structure_context(), core::scoring::etable::BaseEtableEnergy< Derived >::minimize_in_whole_structure_context(), core::scoring::elec::RNA_FA_ElecEnergy::minimize_in_whole_structure_context(), core::scoring::elec::FA_GrpElecEnergy::minimize_in_whole_structure_context(), core::scoring::elec::FA_ElecEnergy::minimize_in_whole_structure_context(), core::scoring::elec::RNA_FA_ElecEnergy::residue_pair_energy_ext(), core::scoring::rna::StackElecEnergy::residue_pair_energy_ext(), core::scoring::elec::FA_GrpElecEnergy::residue_pair_energy_ext(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy_ext(), core::scoring::etable::BaseEtableEnergy< Derived >::residue_pair_energy_ext(), set_use_nblist(), core::scoring::methods::MMLJEnergyInter::setup_for_minimizing(), core::scoring::rna::RNA_FullAtomStackingEnergy::setup_for_minimizing(), core::scoring::elec::RNA_FA_ElecEnergy::setup_for_minimizing(), core::scoring::methods::LK_PolarNonPolarEnergy::setup_for_minimizing(), core::scoring::elec::FA_GrpElecEnergy::setup_for_minimizing(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing(), core::scoring::elec::FA_ElecEnergy::setup_for_minimizing(), core::scoring::rna::StackElecEnergy::setup_for_minimizing(), core::scoring::methods::MMLJEnergyIntra::setup_for_minimizing_for_residue(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing_for_residue(), core::scoring::elec::RNA_FA_ElecEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::rna::StackElecEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::elec::FA_GrpElecEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing_for_residue_pair(), and core::scoring::elec::FA_ElecEnergy::setup_for_minimizing_for_residue_pair().

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

References nblist_.

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::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::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(), protocols::mean_field::EnergiesByTaskCalculator::recompute(), core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::recompute(), protocols::pose_metric_calculators::NonlocalContactsCalculator::recompute(), protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::recompute(), protocols::hydrate::show_water_hb_network(), protocols::enzdes::enzutil::sum_constraint_scoreterms(), and protocols::protein_interface_design::sum_total_residue_energy().

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

Setter for the weights in this Energies object.

References scorefxn_weights_.

Friends And Related Function Documentation

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

Member Data Documentation

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().

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=().

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().

EnergyGraphOP core::scoring::Energies::energy_graph_
mutableprivate
EnergyState core::scoring::Energies::energy_state_
mutableprivate
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().

EnergyMap core::scoring::Energies::finalized_energies_
private

Energies computed during the finalize() stage of scoring.

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

EnergyState core::scoring::Energies::graph_state_
mutableprivate
utility::vector1< LREnergyContainerOP > core::scoring::Energies::long_range_energy_containers_
private
Real core::scoring::Energies::max_context_neighbor_cutoff_
mutableprivate
MinimizationGraphOP core::scoring::Energies::minimization_graph_
private
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().

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().

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().

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().

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().

utility::vector1< EnergyMap > core::scoring::Energies::residue_total_energies_
mutableprivate
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().

utility::vector1< Real > core::scoring::Energies::residue_total_energy_
mutableprivate
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().

scoring::ScoreFunctionInfoOP core::scoring::Energies::scorefxn_info_
private
EnergyMap core::scoring::Energies::scorefxn_weights_
private
bool core::scoring::Energies::scoring_
private
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().

EnergyMap core::scoring::Energies::total_energies_
mutableprivate

cached total energies

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

Real core::scoring::Energies::total_energy_
mutableprivate
bool core::scoring::Energies::use_nblist_
private
bool core::scoring::Energies::use_nblist_auto_update_
private

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