scores a fragment based on sum of secondary structure identity and sequence identity More...

#include <ABEGOEval.hh>

Inheritance diagram for core::fragment::picking_old::vall::eval::ABEGOEval:

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

Public Types
typedef Super::VallFragmentScore	VallFragmentScore

typedef std::string	String

typedef core::Real	Real

typedef core::util::ABEGOManager	ABEGOManager

typedef core::util::ABEGOManagerOP	ABEGOManagerOP

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
	ABEGOEval ()
	default constructor More...

	ABEGOEval (utility::vector1< String > const &input, Real const penalty=1.0, bool const randomize=true)
	full values constructor More...

	ABEGOEval (ABEGOEval const &rval)
	default copy constructor More...

virtual	~ABEGOEval ()
	default destructor More...

ABEGOEval &	operator= (ABEGOEval 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...

utility::vector1< String > const &	abego_str () const
	get secondary structure string More...

void	abego_str (utility::vector1< String > const &abego)
	set abego vector of string More...

Real	penalty () const
	get secondary structure penalty More...

bool	randomize () const
	adding random noise to score? 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
utility::vector1< String >	abego_
	abego string to match against More...

Real	penalty_
	abego penalty if non-matching More...

bool	randomize_
	flag to add random noise between [0, 0.001) into score More...

ABEGOManagerOP	am_

Detailed Description

scores a fragment based on sum of secondary structure identity and sequence identity

Definition at line 43 of file ABEGOEval.hh.

Member Typedef Documentation

typedef core::util::ABEGOManager core::fragment::picking_old::vall::eval::ABEGOEval::ABEGOManager

Definition at line 60 of file ABEGOEval.hh.

typedef core::util::ABEGOManagerOP core::fragment::picking_old::vall::eval::ABEGOEval::ABEGOManagerOP

Definition at line 61 of file ABEGOEval.hh.

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

typedef for ExtentEvaluator concept

Definition at line 71 of file ABEGOEval.hh.

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

typedef for ExtentEvaluator concept

Definition at line 67 of file ABEGOEval.hh.

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

Definition at line 58 of file ABEGOEval.hh.

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

Definition at line 57 of file ABEGOEval.hh.

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

private

Definition at line 49 of file ABEGOEval.hh.

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

Definition at line 55 of file ABEGOEval.hh.

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

Definition at line 77 of file ABEGOEval.hh.

Constructor & Destructor Documentation

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

default constructor

Definition at line 46 of file ABEGOEval.cc.

References abego_, and am_.

Referenced by clone().

core::fragment::picking_old::vall::eval::ABEGOEval::ABEGOEval	(	utility::vector1< String > const &	abego,
		Real const	penalty = `1.0`,
		bool const	randomize = `true`
	)

full values constructor

Parameters

ss	secondary structure string to match against
aa	amino acid structure string to match against
abego	abego string to match against

Definition at line 58 of file ABEGOEval.cc.

References am_.

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

default copy constructor

Definition at line 73 of file ABEGOEval.cc.

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

virtual

default destructor

Definition at line 83 of file ABEGOEval.cc.

Member Function Documentation

utility::vector1< String > const& core::fragment::picking_old::vall::eval::ABEGOEval::abego_str ( ) const

inline

get secondary structure string

Definition at line 138 of file ABEGOEval.hh.

References abego_.

void core::fragment::picking_old::vall::eval::ABEGOEval::abego_str ( utility::vector1< String > const & abego)

inline

set abego vector of string

Definition at line 144 of file ABEGOEval.hh.

References core::scoring::abego, and abego_.

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

virtual

clone this object

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

Definition at line 100 of file ABEGOEval.cc.

References ABEGOEval().

bool core::fragment::picking_old::vall::eval::ABEGOEval::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 107 of file ABEGOEval.cc.

References abego_, am_, core::fragment::picking_old::concepts::Extent< PageIterator >::begin, core::fragment::picking_old::concepts::Extent< PageIterator >::distance(), core::fragment::picking_old::concepts::Extent< PageIterator >::end, penalty_, randomize_, and core::fragment::picking_old::vall::scores::VallFragmentScore::score.

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

copy assignment

Definition at line 87 of file ABEGOEval.cc.

References abego_, am_, core::fragment::picking_old::vall::eval::VallFragmentEval::operator=(), penalty_, and randomize_.

Real core::fragment::picking_old::vall::eval::ABEGOEval::penalty ( ) const

inline

get secondary structure penalty

Definition at line 150 of file ABEGOEval.hh.

References penalty_.

void core::fragment::picking_old::vall::eval::ABEGOEval::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 140 of file ABEGOEval.cc.

References core::scoring::abego, and abego_.

bool core::fragment::picking_old::vall::eval::ABEGOEval::randomize ( ) const

inline

adding random noise to score?

Definition at line 156 of file ABEGOEval.hh.

References randomize_.

Member Data Documentation

utility::vector1< String > core::fragment::picking_old::vall::eval::ABEGOEval::abego_

private

abego string to match against

Definition at line 173 of file ABEGOEval.hh.

Referenced by abego_str(), ABEGOEval(), eval_impl(), operator=(), and pre_catalog_op().

ABEGOManagerOP core::fragment::picking_old::vall::eval::ABEGOEval::am_

private

Definition at line 181 of file ABEGOEval.hh.

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

Real core::fragment::picking_old::vall::eval::ABEGOEval::penalty_

private

abego penalty if non-matching

Definition at line 176 of file ABEGOEval.hh.

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

bool core::fragment::picking_old::vall::eval::ABEGOEval::randomize_

private

flag to add random noise between [0, 0.001) into score

Definition at line 179 of file ABEGOEval.hh.

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

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

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

Public Types

Public Member Functions

Private Types

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation