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core::fragment::picking_old::vall::eval::EnergyEval Class Reference

scores a fragment by inserting its backbone angles into a Pose and evaluating its energy using a given ScoreFunction More...

#include <EnergyEval.hh>

Inheritance diagram for core::fragment::picking_old::vall::eval::EnergyEval:
Inheritance graph
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Public Types

typedef Super::VallFragmentScore VallFragmentScore
 
typedef core::pose::Pose Pose
 
typedef
core::scoring::ScoreFunction 
ScoreFunction
 
typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
 
typedef
core::scoring::ScoreFunctionCOP 
ScoreFunctionCOP
 
typedef std::string String
 
typedef core::Real Real
 
typedef Super::PageConstIterator PageConstIterator
 typedef for ExtentEvaluator concept More...
 
typedef Super::Extent Extent
 typedef for ExtentEvaluator concept More...
 
typedef PageConstIterator VallResidueConstIterator
 
- Public Types inherited from core::fragment::picking_old::vall::eval::VallFragmentEval
typedef
core::fragment::picking_old::vall::scores::VallFragmentScore 
VallFragmentScore
 
typedef
VallFragmentScore::PageConstIterator 
PageConstIterator
 typedef for ExtentEvaluator concept More...
 
typedef
core::fragment::picking_old::concepts::Extent
< VallSection::PageConstIterator
Extent
 typedef for ExtentEvaluator concept More...
 
typedef PageConstIterator VallResidueConstIterator
 

Public Member Functions

 EnergyEval ()
 default constructor More...
 
 EnergyEval (Pose const &pose, Size const insert_position, ScoreFunction const &score_function, bool const randomize=false)
 constructor More...
 
 EnergyEval (EnergyEval const &rval)
 default copy constructor More...
 
 ~EnergyEval () override
 default destructor More...
 
EnergyEvaloperator= (EnergyEval const &rval)
 copy assignment More...
 
VallFragmentEvalOP clone () const override
 clone this object More...
 
bool eval_impl (Extent const &extent, VallFragmentScore &fs) override
 for a fragment extent, evaluate and store results in a VallFragmentScore More...
 
Pose const & pose () const
 the Pose to evaluate More...
 
Size insert_position () const
 insert angles into the Pose starting from this position More...
 
ScoreFunctionCOP score_function () const
 the ScoreFunction used to evaluate the pose More...
 
bool randomize () const
 adding random noise between [0, 0.000001) to the energy? More...
 
void pose (Pose const &p)
 the Pose to evaluate More...
 
void insert_position (Size const position)
 insert angles into the Pose starting from this position More...
 
void score_function (ScoreFunction const &fx)
 the ScoreFunction used to evaluate the pose More...
 
void randomize (bool const flag)
 set flag to add random noise between [0, 0.000001) to the energy More...
 
void pre_catalog_op (VallLibrary const &) override
 operation to be perform before catalog() starts More...
 
- Public Member Functions inherited from core::fragment::picking_old::vall::eval::VallFragmentEval
 VallFragmentEval ()
 default constructor More...
 
 VallFragmentEval (VallFragmentEval const &rval)
 default copy constructor More...
 
 ~VallFragmentEval () override
 default destructor More...
 
VallFragmentEvaloperator= (VallFragmentEval const &rval)
 copy assignment More...
 
bool operator() (Extent const &extent, VallFragmentScore &fs)
 called by VallLibrarian: for a fragment extent, evaluate and store results in a VallFragmentScore More...
 
virtual void post_catalog_op (VallLibrary const &)
 operation to be performed after catalog() finished More...
 

Private Types

typedef VallFragmentEval Super
 

Private Attributes

Pose pose_
 insert backbone angles into this Pose More...
 
Size insert_position_
 insert backbone angles into pose starting from this position More...
 
ScoreFunctionOP score_function_
 evaluate the Pose using this ScoreFunction More...
 
bool randomize_
 flag to add random noise between [0, 0.000001) into the energy More...
 

Detailed Description

scores a fragment by inserting its backbone angles into a Pose and evaluating its energy using a given ScoreFunction

Remarks
Useful for e.g. evaluating a chainbreak score, constraint score, etc.
Warning
Class currently assumes insertion of backbone angles into protein residues.

Member Typedef Documentation

typedef for ExtentEvaluator concept

typedef for ExtentEvaluator concept

Constructor & Destructor Documentation

core::fragment::picking_old::vall::eval::EnergyEval::EnergyEval ( )

default constructor

core::fragment::picking_old::vall::eval::EnergyEval::EnergyEval ( Pose const &  pose,
Size const  insert_position,
ScoreFunction const &  score_function,
bool const  randomize = false 
)

constructor

Parameters
[in]poseinsert backbone angles using a copy of this Pose
[in]insert_positioninsert backbone angles starting from this position in the Pose
[in]score_functionevaluate the Pose using a copy of this ScoreFunction
[in]randomizeflags that indicates whether a small amount of noise between [0, 0.000001) will be added to the energy
core::fragment::picking_old::vall::eval::EnergyEval::EnergyEval ( EnergyEval const &  rval)

default copy constructor

core::fragment::picking_old::vall::eval::EnergyEval::~EnergyEval ( )
overridedefault

default destructor

Member Function Documentation

VallFragmentEvalOP core::fragment::picking_old::vall::eval::EnergyEval::clone ( ) const
overridevirtual
bool core::fragment::picking_old::vall::eval::EnergyEval::eval_impl ( Extent const &  extent,
VallFragmentScore fs 
)
overridevirtual
Size core::fragment::picking_old::vall::eval::EnergyEval::insert_position ( ) const
inline

insert angles into the Pose starting from this position

References insert_position_.

void core::fragment::picking_old::vall::eval::EnergyEval::insert_position ( Size const  position)
inline

insert angles into the Pose starting from this position

References insert_position_.

EnergyEval & core::fragment::picking_old::vall::eval::EnergyEval::operator= ( EnergyEval const &  rval)
Pose const& core::fragment::picking_old::vall::eval::EnergyEval::pose ( ) const
inline

the Pose to evaluate

References pose_.

void core::fragment::picking_old::vall::eval::EnergyEval::pose ( Pose const &  p)
inline

the Pose to evaluate

References pose_.

void core::fragment::picking_old::vall::eval::EnergyEval::pre_catalog_op ( VallLibrary const &  )
overridevirtual

operation to be perform before catalog() starts

Reimplemented from core::fragment::picking_old::vall::eval::VallFragmentEval.

References score_function_, and core::fragment::picking_old::vall::eval::TR().

bool core::fragment::picking_old::vall::eval::EnergyEval::randomize ( ) const
inline

adding random noise between [0, 0.000001) to the energy?

References randomize_.

void core::fragment::picking_old::vall::eval::EnergyEval::randomize ( bool const  flag)
inline

set flag to add random noise between [0, 0.000001) to the energy

References randomize_.

ScoreFunctionCOP core::fragment::picking_old::vall::eval::EnergyEval::score_function ( ) const
inline

the ScoreFunction used to evaluate the pose

References score_function_.

void core::fragment::picking_old::vall::eval::EnergyEval::score_function ( ScoreFunction const &  fx)
inline

the ScoreFunction used to evaluate the pose

References core::scoring::ScoreFunction::clone(), and score_function_.

Member Data Documentation

Size core::fragment::picking_old::vall::eval::EnergyEval::insert_position_
private

insert backbone angles into pose starting from this position

Referenced by eval_impl(), insert_position(), and operator=().

Pose core::fragment::picking_old::vall::eval::EnergyEval::pose_
private

insert backbone angles into this Pose

Referenced by eval_impl(), operator=(), and pose().

bool core::fragment::picking_old::vall::eval::EnergyEval::randomize_
private

flag to add random noise between [0, 0.000001) into the energy

Referenced by eval_impl(), operator=(), and randomize().

ScoreFunctionOP core::fragment::picking_old::vall::eval::EnergyEval::score_function_
private

evaluate the Pose using this ScoreFunction

Referenced by eval_impl(), operator=(), pre_catalog_op(), and score_function().


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