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core::scoring::solid_surface::SurfaceEnergies Class Reference

#include <SurfaceEnergies.hh>

Inheritance diagram for core::scoring::solid_surface::SurfaceEnergies:
Inheritance graph
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Public Types

typedef Energies parent
 
- Public Types inherited from core::scoring::Energies
typedef scoring::EnergyGraph EnergyGraph
 
typedef scoring::NeighborList NeighborList
 
typedef scoring::ScoreType ScoreType
 
typedef scoring::ScoreFunctionInfo ScoreFunctionInfo
 
typedef
basic::datacache::BasicDataCache 
BasicDataCache
 
typedef id::AtomID AtomID
 
typedef id::AtomID_Mask AtomID_Mask
 
typedef kinematics::DomainMap DomainMap
 
typedef utility::graph::Graph Graph
 
typedef scoring::EnergyMap EnergyMap
 

Public Member Functions

 SurfaceEnergies ()
 ctor – ensure correct initial state More...
 
 SurfaceEnergies (SurfaceEnergies const &src)
 copy ctor – deep copy More...
 
Energiesoperator= (Energies const &rhs) override
 assignment operator – deep copy More...
 
bool same_type_as_me (Energies const &other, bool recurse=true) const override
 
 ~SurfaceEnergies () override
 dtor More...
 
EnergiesOP clone () const override
 
void set_total_residue (Size total_residue)
 The SurfaceEnergies object needs to know how many residues are in its pose; it also has to be told which residues are considered part of the surface and which residues are not part of the surface. More...
 
void reset_surface_residue_information ()
 Wipe away all the information in the SurfacEnergies object describing which residues are considered part of the surface and which residues are not part of the surface. (Afterwards, all residues are going to be considered part of the surface). More...
 
void set_residue_range_not_surface (Size seqpos_begin, Size seqpos_end)
 Tell the SurfacEnergies that the following residues are considered not part of the surface. More...
 
bool residue_is_surface (Size seqpos) const
 Does the SurfaceEnergies object consider a particular residue to be part of the surface? More...
 
- Public Member Functions inherited from core::scoring::Energies
 Energies ()
 ctor – ensure correct initial state More...
 
 Energies (Energies const &src)
 copy ctor – deep copy More...
 
 ~Energies () override
 dtor More...
 
void set_owner (pose::Pose *owner)
 Pose must claim its Energies object; this should happen once, at the time the Pose is allocated. Future copying of the Energies object will not change ownership. The purpose of ownership is to allow lazy context-graph creation. When context graphs are requested that have not been created, they must be created and their edges must be updated to represent the current conformation of the pose. More...
 
Real total_energy () const
 energy access More...
 
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 fill_point_graph (pose::Pose const &pose, conformation::PointGraphOP pg) const override
 Create a point graph representing the xyz coordinates of the "neighbor atoms." (Each residue_type indicates one of its atoms to be used for neighbor detection – e.g. CB for most amino acids, CA for GLY.) The point graph will then be used in a call to find_neighbors to add upper-edges to neighboring residues. More...
 

Private Attributes

Size total_residue_
 Create a new surface grid, bounding box and dimension for the surface residues. This might get called if the range on the score function changes or if the surface moves. (NOTE: currently not prepared to handle the case where the surface moves!) More...
 
utility::vector1< std::pair
< Size, Size > > 
non_surface_ranges_
 
utility::vector1< boolis_surface_
 
Real neighbor_cutoff_
 

Additional Inherited Members

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

Detailed Description

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

Member Typedef Documentation

Constructor & Destructor Documentation

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

ctor – ensure correct initial state

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

copy ctor – deep copy

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

dtor

Member Function Documentation

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

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

Reimplemented from core::scoring::Energies.

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

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

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

Reimplemented from core::scoring::Energies.

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

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

assignment operator – deep copy

Reimplemented from core::scoring::Energies.

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

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

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

References is_surface_, non_surface_ranges_, and total_residue_.

Referenced by set_total_residue().

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

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

References is_surface_.

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

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

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

Reimplemented from core::scoring::Energies.

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

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

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

References is_surface_, non_surface_ranges_, and total_residue_.

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

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

References reset_surface_residue_information(), and total_residue_.

Member Data Documentation

utility::vector1< bool > core::scoring::solid_surface::SurfaceEnergies::is_surface_
private
Real core::scoring::solid_surface::SurfaceEnergies::neighbor_cutoff_
mutableprivate

Referenced by operator=().

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

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

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

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


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