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core::scoring::symmetry::SymmetricEnergies Class Reference

#include <SymmetricEnergies.hh>

Inheritance diagram for core::scoring::symmetry::SymmetricEnergies:
Inheritance graph
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Public Types

typedef
conformation::symmetry::SymmetricConformation 
SymmetricConformation
 
typedef
conformation::symmetry::SymmetryInfoCOP 
SymmetryInfoCOP
 
typedef numeric::xyzMatrix< RealMatrix
 
- Public Types inherited from core::scoring::Energies
typedef scoring::EnergyGraph EnergyGraph
 
typedef scoring::NeighborList NeighborList
 
typedef scoring::ScoreType ScoreType
 
typedef scoring::ScoreFunctionInfo ScoreFunctionInfo
 
typedef
basic::datacache::BasicDataCache 
BasicDataCache
 
typedef id::AtomID AtomID
 
typedef id::AtomID_Mask AtomID_Mask
 
typedef kinematics::DomainMap DomainMap
 
typedef utility::graph::Graph Graph
 
typedef scoring::EnergyMap EnergyMap
 

Public Member Functions

 SymmetricEnergies ()
 ctor – ensure correct initial state More...
 
 SymmetricEnergies (Energies const &src)
 copy ctor – deep copy More...
 
 SymmetricEnergies (Energies &src)
 copy ctor – deep copy More...
 
Energiesoperator= (Energies const &rhs) override
 assignment operator – deep copy More...
 
bool same_type_as_me (Energies const &other, bool recurse=true) const override
 
 ~SymmetricEnergies () override
 
EnergiesOP clone () const override
 
void set_derivative_graph (MinimizationGraphOP dg)
 
MinimizationGraphOP derivative_graph ()
 
MinimizationGraphCOP derivative_graph () const
 
- Public Member Functions inherited from core::scoring::Energies
 Energies ()
 ctor – ensure correct initial state More...
 
 Energies (Energies const &src)
 copy ctor – deep copy More...
 
 ~Energies () override
 dtor More...
 
void set_owner (pose::Pose *owner)
 Pose must claim its Energies object; this should happen once, at the time the Pose is allocated. Future copying of the Energies object will not change ownership. The purpose of ownership is to allow lazy context-graph creation. When context graphs are requested that have not been created, they must be created and their edges must be updated to represent the current conformation of the pose. More...
 
Real total_energy () const
 energy access More...
 
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
 

Private Member Functions

void update_neighbor_links (pose::Pose const &pose) override
 Add edges to the energy_graph and the context graphs according to domain map. More...
 
void fill_point_graph (pose::Pose const &pose, conformation::PointGraphOP pg) const override
 determine distance cutoff threshold based on scorefxn_info_ and then add edges to the PointGraph class More...
 
void require_context_graph_ (scoring::ContextGraphType type, bool external) const override
 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. More...
 

Private Attributes

MinimizationGraphOP derivative_graph_
 

Additional Inherited Members

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

Member Typedef Documentation

Constructor & Destructor Documentation

core::scoring::symmetry::SymmetricEnergies::SymmetricEnergies ( )

ctor – ensure correct initial state

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

copy ctor – deep copy

core::scoring::symmetry::SymmetricEnergies::SymmetricEnergies ( Energies src)

copy ctor – deep copy

core::scoring::symmetry::SymmetricEnergies::~SymmetricEnergies ( )
overridedefault

Member Function Documentation

EnergiesOP core::scoring::symmetry::SymmetricEnergies::clone ( ) const
overridevirtual

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

Reimplemented from core::scoring::Energies.

MinimizationGraphOP core::scoring::symmetry::SymmetricEnergies::derivative_graph ( )

References derivative_graph_.

MinimizationGraphCOP core::scoring::symmetry::SymmetricEnergies::derivative_graph ( ) const

References derivative_graph_.

void core::scoring::symmetry::SymmetricEnergies::fill_point_graph ( pose::Pose const &  pose,
conformation::PointGraphOP  pg 
) const
overrideprivatevirtual
Energies & core::scoring::symmetry::SymmetricEnergies::operator= ( Energies const &  rhs)
overridevirtual

assignment operator – deep copy

Reimplemented from core::scoring::Energies.

References core::scoring::Energies::operator=().

void core::scoring::symmetry::SymmetricEnergies::require_context_graph_ ( scoring::ContextGraphType  type,
bool  external 
) const
overrideprivatevirtual
bool core::scoring::symmetry::SymmetricEnergies::same_type_as_me ( Energies const &  other,
bool  recurse = true 
) const
overridevirtual

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

Reimplemented from core::scoring::Energies.

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

void core::scoring::symmetry::SymmetricEnergies::set_derivative_graph ( MinimizationGraphOP  dg)

References derivative_graph_.

void core::scoring::symmetry::SymmetricEnergies::update_neighbor_links ( pose::Pose const &  pose)
overrideprivatevirtual

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 from core::scoring::Energies.

References core::scoring::EnergyGraph::add_energy_edge(), core::pose::Pose::conformation(), core::scoring::Energies::context_graphs(), core::scoring::Energies::domain_map_during_minimization(), core::scoring::Energies::energy_graph_no_state_check(), fill_point_graph(), core::scoring::Energies::get_scorefxn_info(), core::chemical::ResidueType::nbr_radius(), core::scoring::Energies::point_graph(), core::pose::Pose::residue_type(), core::scoring::Energies::scoring(), core::scoring::Energies::size(), and core::pose::Pose::size().

Member Data Documentation

MinimizationGraphOP core::scoring::symmetry::SymmetricEnergies::derivative_graph_
private

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