Rosetta 3.4
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core::scoring::Energies Class Reference

A cached energies object. More...

#include <Energies.hh>

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List of all members.

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 graph::Graph Graph
typedef scoring::EnergyMap EnergyMap

Public Member Functions

 Energies ()
 ctor -- ensure correct initial state
 Energies (Energies const &src)
 copy ctor -- deep copy
virtual Energies const & operator= (Energies const &rhs)
 assignment operator -- deep copy
virtual bool same_type_as_me (Energies const &other, bool recurse=true) const
virtual ~Energies ()
 dtor
virtual EnergiesOP clone () const
void set_owner (pose::PoseAP 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.
Real total_energy () const
 Returns the total score.
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.
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.
EnergyMap const & onebody_energies (int const seqpos) const
 Read access to the components of the one-body energies.
EnergyMaponebody_energies (int const seqpos)
 Write access to the components of the one-body energies. This access is intended only for the ScoreFunction.
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.
EnergyMapfinalized_energies ()
 Write access to the components of the "finalized" energies. This access is intended only for the ScoreFunction.
EnergyMap const & residue_total_energies (int const seqpos) const
 Returns the unweighted total_energies EnergyMap for Residue <seqpos>
Real residue_total_energy (int const seqpos) const
 Returns the weighted total energy of residue <seqpos>
EnergyGraph const & energy_graph () const
 Read access to the EnergyGraph.
EnergyGraphenergy_graph ()
 Write access to the EnergyGraph.
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.
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.
scoring::TwelveANeighborGraph
const & 
twelveA_neighbor_graph () const
 get the graph encoding # neighbors within 12 Angstroms
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.
scoring::ContextGraphCOP context_graph (scoring::ContextGraphType type) const
 const access to a particular context graph
scoring::ContextGraphOP context_graph (scoring::ContextGraphType type)
 non-const access to a particular context graph
void require_context_graph (scoring::ContextGraphType) const
 Allows non-scorefunction components of Rosetta to impose requirements on the context graphs that this object maintains.
EnergyMap weights () const
 Returns an EnergyMap of the ScoreFunction weights from the last scoring.
void weights (EnergyMap new_weights)
 Setter for the weights in this Energies object.
void update_residue_neighbors (DomainMap const &domain_map_in, pose::Pose const &pose)
 update the residue neighbors
bool residue_neighbors_updated () const
bool energies_updated () const
 Returns true if the score is up-to-date.
bool res_moved (int const seqpos) const
 check if rsd has changed internal conformation, necessitating, recomputation of 1d energies like dun,intra,prob,etc
void reset_res_moved (int const seqpos)
void clear_energies ()
 for debugging -- forget all stored energies, does not change size
Size size () const
 Returns the number of held residue energies.
bool scoring () const
 are we in the midst of a scoring calculation?
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>
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
void scoring_begin (scoring::ScoreFunction const &sfxn, pose::Pose const &pose)
 Notification of the start of a scoring calculation.
void scoring_end (scoring::ScoreFunction const &scorefxn)
 signal from the scorefxn that scoring is over
scoring::ScoreFunctionInfo const & get_scorefxn_info () const
 get scorefxn info
void clear ()
 kill everything (that nobody forgot about)
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.
BasicDataCachedata ()
 BasicDataCache indexed by enum in core/scoring/EnergiesCacheableDataType.hh.
bool discard_conformation_domain_map () const
 instructs Pose whether the domain map info in the Conformation object should be discarded
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.
DomainMap const & domain_map () const
 Read access for the domain map.
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
EnergyGraphenergy_graph_no_state_check ()
 Write access to the EnergyGraph.
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::PoseAP 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.

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

Constructor & Destructor Documentation

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

ctor -- ensure correct initial state

Referenced by clone().

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

copy ctor -- deep copy

core::scoring::Energies::~Energies ( ) [virtual]

dtor


Member Function Documentation

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

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

References core::scoring::EMapVector::clear().

Referenced by clear().

EnergiesOP core::scoring::Energies::clone ( ) const [virtual]

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

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

References Energies().

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

const access to a particular context graph

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

non-const access to a particular context graph

utility::vector1< ContextGraphOP > & core::scoring::Energies::context_graphs ( ) const [protected]
BasicDataCache const& core::scoring::Energies::data ( ) const [inline]

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

Referenced by protocols::fldsgn::filters::HelixKinkFilter::apply(), core::scoring::hbonds::HBondEnergy::backbone_backbone_energy(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), protocols::fldsgn::topology::check_internal_hbonds(), protocols::fldsgn::topology::check_kink_helix(), core::scoring::methods::WaterAdductHBondEnergy::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::hackelec::HackElecEnergy::evaluate_rotamer_background_energies(), core::scoring::etable::BaseEtableEnergy< Derived >::evaluate_rotamer_background_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_pair_energies(), core::scoring::hbonds::HBondEnergy::finalize_total_energy(), core::scoring::ScoreFunction::get_sub_score(), core::scoring::symmetry::SymmetricScoreFunction::intersubunit_hbond_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), core::scoring::symmetry::SymmetricScoreFunction::set_symmetric_residue_neighbors_hbonds(), core::scoring::methods::WaterAdductHBondEnergy::setup_for_derivatives(), core::scoring::geometric_solvation::GeometricSolEnergy::setup_for_derivatives(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::setup_for_derivatives(), core::scoring::hbonds::HBondEnergy::setup_for_minimizing_for_residue(), core::scoring::methods::MMLJEnergyInter::setup_for_packing(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), core::scoring::hackelec::HackElecEnergy::setup_for_packing(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_packing(), core::scoring::hbonds::HBondEnergy::setup_for_scoring(), core::scoring::geometric_solvation::GeometricSolEnergy::setup_for_scoring(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::setup_for_scoring(), core::scoring::symmetry::SymmetricScoreFunction::symmetrical_allow_hbonds(), core::scoring::methods::MMLJEnergyInter::update_residue_for_packing(), core::scoring::hbonds::HBondEnergy::update_residue_for_packing(), core::scoring::hackelec::HackElecEnergy::update_residue_for_packing(), and core::scoring::etable::BaseEtableEnergy< Derived >::update_residue_for_packing().

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

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

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.

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

Referenced by core::scoring::hackelec::HackElecEnergy::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.

int core::scoring::Energies::domain_map_during_minimization ( int const  pos) const [inline, protected]

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.

bool core::scoring::Energies::energies_updated ( ) const [inline]
Energies::EnergyGraph & core::scoring::Energies::energy_graph ( )

Write access to the EnergyGraph.

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

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.

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), core::pack::compare_mingraph_and_energy_graph(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), core::scoring::SmoothEnvPairPotential::compute_centroid_environment(), core::scoring::EnvPairPotential::compute_centroid_environment(), core::scoring::SmoothEnvPairPotential::compute_dcentroid_environment(), protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::compute_Hbonds_for_residue(), core::pack::create_packer_graph(), core::scoring::geometric_solvation::GeometricSolEnergy::eval_atom_derivative(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_atom_derivative(), 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::GeometricSolEnergy::eval_atom_energy(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_atom_energy(), protocols::enzdes::EnzdesFlexibleRegion::extract_lig_designability_score(), core::scoring::WaterAdductHBondPotential::fill_h2o_hbond_set(), core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold(), protocols::ligand_docking::LigandBaseProtocol::get_non_bb_clashing_rotamers(), protocols::simple_filters::RotamerBoltzmannWeight::interface_interaction_energy(), core::scoring::electron_density::ElectronDensity::matchRes(), protocols::simple_filters::ScoreCutoffFilter::output_residue_pair_energies(), protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::recompute(), core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::recompute(), protocols::fldsgn::potentials::sspot::SSPairPotential::score(), protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::score(), protocols::fldsgn::potentials::sspot::HSPairPotential::score(), protocols::vip::set_local_movemap(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_minimizing(), core::scoring::ScoreFunction::setup_for_minimizing(), core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap(), and core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions().

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.

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.

Referenced by core::scoring::symmetry::SymmetricScoreFunction::correct_finalize_score(), core::scoring::symmetry::SymmetricScoreFunction::operator()(), 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.

scoring::ScoreFunctionInfo const& core::scoring::Energies::get_scorefxn_info ( ) const [inline]
LREnergyContainerCOP core::scoring::Energies::long_range_container ( methods::LongRangeEnergyType  lrtype) const

Referenced by 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::FullatomDisulfideEnergy::defines_residue_pair_energy(), core::scoring::disulfides::DisulfideMatchingEnergy::defines_residue_pair_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::defines_residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::old_eval_atom_derivative(), protocols::simple_filters::ScoreCutoffFilter::output_residue_pair_energies(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::precompute_two_body_energies(), core::pack::rotamer_set::RotamerSets::precompute_two_body_energies(), protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::recompute(), core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::recompute(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy(), core::scoring::disulfides::DisulfideMatchingEnergy::residue_pair_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::pack::RTMin::rtmin(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_minimizing(), core::scoring::ScoreFunction::setup_for_minimizing(), core::scoring::sym_e::symEnergy::setup_for_scoring(), core::scoring::disulfides::FullatomDisulfideEnergy::setup_for_scoring(), core::scoring::disulfides::DisulfideMatchingEnergy::setup_for_scoring(), and core::scoring::disulfides::CentroidDisulfideEnergy::setup_for_scoring().

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

Energies const & core::scoring::Energies::operator= ( Energies const &  rhs) [virtual]
pose::PoseAP core::scoring::Energies::owner ( ) const [protected]

Referenced by set_owner().

conformation::PointGraphOP core::scoring::Energies::point_graph ( ) [protected]

get access to the point graph. For derived classes

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.

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

void core::scoring::Energies::reset_nblist ( )
void core::scoring::Energies::reset_res_moved ( int const  seqpos)
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 energies_updated(), size(), and use_nblist().

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_pep_scores(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), protocols::enzdes::LigInterfaceEnergyFilter::constraint_energy(), protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::determine_res_to_recompute(), core::pose::Pose::dump_scored_pdb(), protocols::jobdist::PlainPdbJobDistributor::dump_scores(), core::io::pdb::extract_scores(), protocols::nonlocal::get_per_residue_score(), protocols::relax::get_per_residue_scores(), protocols::enzdes::EnzdesFlexibleRegion::get_region_mm_bend_score(), protocols::simple_filters::ScoreCutoffFilter::get_score(), core::scoring::operator<<(), protocols::simple_filters::EnergyPerResidueFilter::report(), protocols::protein_interface_design::EnergyPerResidueFilter::report(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::moves::PyMolMover::send_energy(), protocols::enzdes::enzutil::sum_constraint_scoreterms(), and protocols::protein_interface_design::sum_total_residue_energy().

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

References same_type_as_me().

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

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

are we in the midst of a scoring calculation?

Referenced by tenA_neighbor_graph(), and twelveA_neighbor_graph().

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 core::scoring::ScoreFunction::info(), core::pose::Pose::total_residue(), and core::scoring::ScoreFunction::weights().

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

signal from the scorefxn that scoring is over

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 
)
void core::scoring::Energies::set_owner ( pose::PoseAP  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().

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,
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, core::scoring::EMapVector::begin(), core::scoring::EMapVector::end(), and core::scoring::name_from_score_type().

void core::scoring::Energies::show ( ) const [inline]

References show().

Referenced by show().

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, core::scoring::EMapVector::begin(), core::scoring::EMapVector::end(), core::scoring::name_from_score_type(), and size().

Referenced by protocols::simple_moves::ScoreMover::apply().

void core::scoring::Energies::show ( Size  res) const [inline]

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().

Referenced by show().

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]

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

Referenced by core::scoring::operator<<(), residue_total_energies(), residue_total_energy(), and show().

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

Referenced by 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 scoring(), and core::scoring::ten_A_neighbor_graph.

Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), core::scoring::geometric_solvation::add_to_individual_sol_energies(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO::alter_rotamer_set(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), protocols::fldsgn::filters::InterlockingAromaFilter::compute(), protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::compute_Hbonds_for_residue(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_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(), core::scoring::WaterAdductHBondPotential::fill_h2o_hbond_set(), core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold(), protocols::enzdes::EnzdesFlexibleRegion::get_12A_neighbors(), protocols::loops::get_tenA_neighbor_residues(), protocols::enzdes::EnzdesFlexBBProtocol::get_tenA_neighbor_residues(), protocols::features::HBondFeatures::insert_hbond_dehydron_row(), protocols::match::NumNeighborsMPM::modified_match_positions(), protocols::features::PairFeatures::report_residue_pairs(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::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 scoring(), and core::scoring::ten_A_neighbor_graph.

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.

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.

Referenced by protocols::surface_docking::FaSlideAwayFromSurface::apply(), protocols::surface_docking::FaSlideIntoSurface::apply(), protocols::surface_docking::SlideIntoSurface::apply(), protocols::simple_moves::symmetry::FaSymDockingSlideTogether::apply(), protocols::simple_moves::symmetry::SymDockingSlideIntoContact::apply(), protocols::rbsegment_relax::AutoRBMover::apply(), protocols::moves::MCShowMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::flexpack::FlexPacker::apply(), protocols::docking::DockingProtocol::apply(), protocols::docking::FaDockingSlideIntoContact::apply(), protocols::docking::DockingSlideIntoContact::apply(), protocols::ddg::ddGMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::antibody2::Ab_ModelCDRH3::apply(), protocols::abinitio::ComputeTotalDistCst::apply(), protocols::moves::MonteCarlo::boltzmann(), protocols::ub_e2c::ubi_e2c_modeler::centroid_filter(), protocols::enzdes::RepackWithoutLigandFilter::compute(), protocols::enzdes::LigInterfaceEnergyFilter::constraint_energy(), core::scoring::symmetry::SymmetricScoreFunction::correct_finalize_score(), protocols::symmetric_docking::SymDockProtocol::docking_lowres_filter(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), core::optimization::AtomTreeMultifunc::dump(), core::pose::Pose::dump_scored_pdb(), protocols::jobdist::PlainPdbJobDistributor::dump_scores(), core::io::silent::SilentStruct::energies_from_pose(), core::io::silent::SilentStruct::energies_into_pose(), core::pose::energy_from_pose(), core::scoring::symmetry::SymmetricScoreFunction::eval_long_range_twobody_energies(), core::scoring::ScoreFunction::eval_long_range_twobody_energies(), protocols::enzdes::EnzdesScorefileFilter::examine_pose(), core::io::pdb::extract_scores(), protocols::swa::StepWiseFilterer::filter(), protocols::swa::protein::StepWiseProteinFilterer::filter(), protocols::swa::rna::floating_base_chain_break_screening(), protocols::swa::rna::floating_base_chain_closure_setup(), protocols::swa::rna::floating_base_full_atom_van_der_Waals_screening(), protocols::ub_e2c::ubi_e2c_modeler::fullatom_filter(), protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region(), protocols::simple_filters::ScoreCutoffFilter::get_score(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), core::import_pose::atom_tree_diffs::map_of_weighted_scores(), core::pack::min_pack(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), core::scoring::symmetry::SymmetricScoreFunction::operator()(), core::scoring::ScoreFunction::operator()(), core::scoring::DockingScoreFunction::operator()(), core::scoring::operator<<(), protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::recompute(), protocols::simple_filters::ScoreCutoffFilter::report(), protocols::moves::MonteCarlo::score_function(), protocols::jd2::ScoreMap::score_map_from_scored_pose(), core::scoring::ScoreFunction::show(), core::scoring::ScoreFunction::show_line(), show_total_headers(), show_totals(), protocols::simple_moves::symmetry::SymmetrySlider::slide_score(), protocols::motifs::IRCollection::successful_loop_closure(), protocols::enzdes::enzutil::sum_constraint_scoreterms(), and protocols::simple_moves::symmetry::SymmetrySlider::SymmetrySlider().

Real& core::scoring::Energies::total_energy ( ) [inline]
Real core::scoring::Energies::total_energy ( ) const [inline]
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 scoring(), and core::scoring::twelve_A_neighbor_graph.

Referenced by core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), and core::scoring::methods::BurialEnergy::residue_energy().

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 scoring(), and core::scoring::twelve_A_neighbor_graph.

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

update the residue neighbors

References core::pose::Pose::total_residue().

bool core::scoring::Energies::use_nblist ( ) const [inline]

Referenced by core::scoring::etable::BaseEtableEnergy< Derived >::backbone_backbone_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::backbone_sidechain_energy(), core::scoring::symmetry::SymmetricScoreFunction::correct_finalize_score(), core::scoring::methods::MMLJEnergyIntra::eval_atom_derivative(), core::scoring::methods::MMLJEnergyInter::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative(), core::scoring::etable::EtableEnergy::eval_intrares_energy(), core::scoring::symmetry::SymmetricScoreFunction::eval_long_range_twobody_energies(), core::scoring::ScoreFunction::eval_long_range_twobody_energies(), core::scoring::hbonds::HBondEnergy::finalize_total_energy(), core::scoring::hackelec::HackElecEnergy::finalize_total_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::finalize_total_energy(), core::pack::interaction_graph::SurfaceEnergy::finalize_total_energy(), core::pack::interaction_graph::HPatchEnergy::finalize_total_energy(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::symmetry::SymmetricScoreFunction::operator()(), core::scoring::ScoreFunction::operator()(), core::scoring::hackelec::HackElecEnergy::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::MMLJEnergyIntra::setup_for_minimizing(), core::scoring::methods::MMLJEnergyInter::setup_for_minimizing(), core::scoring::hackelec::HackElecEnergy::setup_for_minimizing(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing(), core::scoring::ScoreFunction::setup_for_scoring(), core::scoring::hbonds::HBondEnergy::setup_for_scoring(), core::scoring::hackelec::HackElecEnergy::setup_for_scoring(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_scoring(), and core::scoring::etable::BaseEtableEnergy< Derived >::sidechain_sidechain_energy().

bool core::scoring::Energies::use_nblist_auto_update ( ) const [inline]
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.

Referenced by protocols::protein_interface_design::ReportSequenceDifferences::calculate(), core::pack::compare_mingraph_and_energy_graph(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), protocols::enzdes::LigInterfaceEnergyFilter::constraint_energy(), 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(), core::io::pdb::extract_scores(), protocols::simple_filters::ScoreCutoffFilter::get_score(), protocols::simple_filters::RotamerBoltzmannWeight::interface_interaction_energy(), protocols::simple_filters::ScoreCutoffFilter::output_residue_pair_energies(), protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::recompute(), core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::recompute(), protocols::jd2::ScoreMap::score_map_from_scored_pose(), 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.


Friends And Related Function Documentation

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

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