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:

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Collaboration diagram for core::fragment::picking_old::vall::eval::EnergyEval:

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Public Types
typedef Super::VallFragmentScore	VallFragmentScore

typedef core::pose::Pose	Pose

typedef core::scoring::ScoreFunction	ScoreFunction

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...

virtual	~EnergyEval ()
	default destructor More...

EnergyEval &	operator= (EnergyEval const &rval)
	copy assignment More...

virtual VallFragmentEvalOP	clone () const
	clone this object More...

virtual bool	eval_impl (Extent const &extent, VallFragmentScore &fs)
	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...

ScoreFunction const &	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...

virtual void	pre_catalog_op (VallLibrary const &)
	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...

virtual	~VallFragmentEval ()
	default destructor More...

VallFragmentEval &	operator= (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...

ScoreFunction	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.

Definition at line 54 of file EnergyEval.hh.

Member Typedef Documentation

typedef Super::Extent core::fragment::picking_old::vall::eval::EnergyEval::Extent

typedef for ExtentEvaluator concept

Definition at line 83 of file EnergyEval.hh.

typedef Super::PageConstIterator core::fragment::picking_old::vall::eval::EnergyEval::PageConstIterator

typedef for ExtentEvaluator concept

Definition at line 79 of file EnergyEval.hh.

typedef core::pose::Pose core::fragment::picking_old::vall::eval::EnergyEval::Pose

Definition at line 68 of file EnergyEval.hh.

typedef core::Real core::fragment::picking_old::vall::eval::EnergyEval::Real

Definition at line 72 of file EnergyEval.hh.

typedef core::scoring::ScoreFunction core::fragment::picking_old::vall::eval::EnergyEval::ScoreFunction

Definition at line 69 of file EnergyEval.hh.

typedef std::string core::fragment::picking_old::vall::eval::EnergyEval::String

Definition at line 71 of file EnergyEval.hh.

typedef VallFragmentEval core::fragment::picking_old::vall::eval::EnergyEval::Super

private

Definition at line 60 of file EnergyEval.hh.

typedef Super::VallFragmentScore core::fragment::picking_old::vall::eval::EnergyEval::VallFragmentScore

Definition at line 66 of file EnergyEval.hh.

typedef PageConstIterator core::fragment::picking_old::vall::eval::EnergyEval::VallResidueConstIterator

Definition at line 89 of file EnergyEval.hh.

Constructor & Destructor Documentation

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

default constructor

Definition at line 44 of file EnergyEval.cc.

Referenced by clone().

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]	pose	insert backbone angles using a copy of this Pose
[in]	insert_position	insert backbone angles starting from this position in the Pose
[in]	score_function	evaluate the Pose using a copy of this ScoreFunction
[in]	randomize	flags that indicates whether a small amount of noise between [0, 0.000001) will be added to the energy

Definition at line 59 of file EnergyEval.cc.

core::fragment::picking_old::vall::eval::EnergyEval::EnergyEval ( EnergyEval const & rval)

default copy constructor

Definition at line 74 of file EnergyEval.cc.

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

virtual

default destructor

Definition at line 84 of file EnergyEval.cc.

Member Function Documentation

VallFragmentEvalOP core::fragment::picking_old::vall::eval::EnergyEval::clone ( ) const

virtual

clone this object

Implements core::fragment::picking_old::vall::eval::VallFragmentEval.

Definition at line 102 of file EnergyEval.cc.

References EnergyEval().

bool core::fragment::picking_old::vall::eval::EnergyEval::eval_impl	(	Extent const &	extent,
		VallFragmentScore &	fs
	)

virtual

for a fragment extent, evaluate and store results in a VallFragmentScore

Returns: true, so score is always stored during VallLibrarian::catalog()

Implements core::fragment::picking_old::vall::eval::VallFragmentEval.

Definition at line 109 of file EnergyEval.cc.

References core::fragment::picking_old::concepts::Extent< PageIterator >::begin, core::fragment::picking_old::concepts::Extent< PageIterator >::end, insert_position_, pose_, randomize_, core::fragment::picking_old::vall::eval::RG(), core::fragment::picking_old::vall::scores::VallFragmentScore::score, score_function_, core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), and core::pose::Pose::set_psi().

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

inline

insert angles into the Pose starting from this position

Definition at line 163 of file EnergyEval.hh.

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

Definition at line 194 of file EnergyEval.hh.

References insert_position_.

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

copy assignment

Definition at line 88 of file EnergyEval.cc.

References insert_position_, core::fragment::picking_old::vall::eval::VallFragmentEval::operator=(), pose_, randomize_, and score_function_.

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

inline

the Pose to evaluate

Definition at line 156 of file EnergyEval.hh.

References pose_.

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

inline

the Pose to evaluate

Definition at line 187 of file EnergyEval.hh.

References pose_.

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

virtual

operation to be perform before catalog() starts

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

Definition at line 134 of file EnergyEval.cc.

References score_function_, core::scoring::ScoreFunction::show_line_headers(), 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?

Definition at line 177 of file EnergyEval.hh.

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

Definition at line 208 of file EnergyEval.hh.

References randomize_.

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

inline

the ScoreFunction used to evaluate the pose

Definition at line 170 of file EnergyEval.hh.

References score_function_.

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

inline

the ScoreFunction used to evaluate the pose

Definition at line 201 of file EnergyEval.hh.

References 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

Definition at line 229 of file EnergyEval.hh.

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

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

private

insert backbone angles into this Pose

Definition at line 225 of file EnergyEval.hh.

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

Definition at line 237 of file EnergyEval.hh.

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

ScoreFunction core::fragment::picking_old::vall::eval::EnergyEval::score_function_

private

evaluate the Pose using this ScoreFunction

Definition at line 233 of file EnergyEval.hh.

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

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

src/core/fragment/picking_old/vall/eval/EnergyEval.hh
src/core/fragment/picking_old/vall/eval/EnergyEval.cc

Public Types

Public Member Functions

Private Types

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation