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

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:

Public Types
typedef Super::VallFragmentScore	VallFragmentScore
typedef std::string	String
typedef core::Real	Real
typedef core::sequence::ABEGOManager	ABEGOManager
typedef core::sequence::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...
	~ABEGOEval () override
	default destructor More...
ABEGOEval &	operator= (ABEGOEval 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...
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...
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...
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

Member Typedef Documentation

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

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

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

typedef for ExtentEvaluator concept

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

typedef for ExtentEvaluator concept

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

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

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

private

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

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

Constructor & Destructor Documentation

core::fragment::picking_old::vall::eval::ABEGOEval::ABEGOEval

(

)

default constructor

References abego_, and am_.

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

References am_.

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

default

default copy constructor

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

overridedefault

default destructor

Member Function Documentation

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

inline

get secondary structure string

References abego_.

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

inline

set abego vector of string

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

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

overridevirtual

clone this object

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

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

overridevirtual

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.

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_, protocols::sic_dock::range(), core::scoring::rg, and core::fragment::picking_old::vall::scores::VallFragmentScore::score.

ABEGOEval & core::fragment::picking_old::vall::eval::ABEGOEval::operator=

(

ABEGOEval const &

rval

)

copy assignment

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

References penalty_.

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

overridevirtual

operation to be perform before catalog() starts

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

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

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

inline

adding random noise to score?

References randomize_.

Member Data Documentation

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

private

abego string to match against

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

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

private

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

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

private

abego penalty if non-matching

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

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