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

#include <IdentityEval.hh>

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

Public Types
typedef Super::VallFragmentScore	VallFragmentScore

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
	IdentityEval ()
	default constructor More...

	IdentityEval (String const &ss, String const &aa, Real const ss_penalty=1.0, Real const aa_penalty=1.0, bool const randomize=true)
	full values constructor More...

	IdentityEval (String const &ss, Real const ss_penalty=1.0, bool const randomize=true)
	secondary structure constructor More...

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

	~IdentityEval () override
	default destructor More...

IdentityEval &	operator= (IdentityEval 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...

String const &	ss_str () const
	get secondary structure string More...

void	ss_str (String const &ss)
	set secondary structure string More...

String const &	aa_str () const
	get amino acid string More...

void	aa_str (String const &aa)
	set amino acid string More...

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

void	ss_penalty (Real const penalty)
	set secondary structure penalty More...

Real	aa_penalty () const
	get amino acid penalty More...

void	aa_penalty (Real const penalty)
	set amino acid penalty More...

bool	randomize () const
	adding random noise to score? More...

void	randomize (bool const flag)
	set flag to add random noise between [0, 0.001) 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
String	ss_
	secondary structure string to match against More...

String	aa_
	amino acid string to match against More...

Real	ss_penalty_
	secondary structure penalty if non-matching More...

Real	aa_penalty_
	amino acid penalty if non-matching More...

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

Detailed Description

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

Member Typedef Documentation

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

typedef for ExtentEvaluator concept

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

typedef for ExtentEvaluator concept

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

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

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

private

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

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

Constructor & Destructor Documentation

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

default constructor

core::fragment::picking_old::vall::eval::IdentityEval::IdentityEval	(	String const &	ss,
		String const &	aa,
		Real const	ss_penalty = `1.0`,
		Real const	aa_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

References aa_, and ss_.

core::fragment::picking_old::vall::eval::IdentityEval::IdentityEval	(	String const &	ss,
		Real const	ss_penalty = `1.0`,
		bool const	randomize = `true`
	)

secondary structure constructor

References aa_, and ss_.

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

default

default copy constructor

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

overridedefault

default destructor

Member Function Documentation

Real core::fragment::picking_old::vall::eval::IdentityEval::aa_penalty ( ) const

inline

get amino acid penalty

References aa_penalty_.

void core::fragment::picking_old::vall::eval::IdentityEval::aa_penalty ( Real const penalty )

inline

set amino acid penalty

References aa_penalty_.

String const& core::fragment::picking_old::vall::eval::IdentityEval::aa_str ( ) const

inline

get amino acid string

References aa_.

void core::fragment::picking_old::vall::eval::IdentityEval::aa_str ( String const & aa )

inline

set amino acid string

References protocols::cluster::calibur::aa, and aa_.

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

overridevirtual

clone this object

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

bool core::fragment::picking_old::vall::eval::IdentityEval::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 aa_, aa_penalty_, core::fragment::picking_old::concepts::Extent< PageIterator >::begin, core::fragment::picking_old::concepts::Extent< PageIterator >::distance(), core::fragment::picking_old::concepts::Extent< PageIterator >::end, randomize_, core::scoring::rg, core::fragment::picking_old::vall::scores::VallFragmentScore::score, ss_, and ss_penalty_.

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

copy assignment

References aa_, aa_penalty_, core::fragment::picking_old::vall::eval::VallFragmentEval::operator=(), randomize_, ss_, and ss_penalty_.

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

overridevirtual

operation to be perform before catalog() starts

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

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

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

inline

adding random noise to score?

References randomize_.

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

inline

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

References randomize_.

Real core::fragment::picking_old::vall::eval::IdentityEval::ss_penalty ( ) const

inline

get secondary structure penalty

References ss_penalty_.

void core::fragment::picking_old::vall::eval::IdentityEval::ss_penalty ( Real const penalty )

inline

set secondary structure penalty

References ss_penalty_.

String const& core::fragment::picking_old::vall::eval::IdentityEval::ss_str ( ) const

inline

get secondary structure string

References ss_.

void core::fragment::picking_old::vall::eval::IdentityEval::ss_str ( String const & ss )

inline

set secondary structure string

References ss_.

Member Data Documentation

String core::fragment::picking_old::vall::eval::IdentityEval::aa_

private

amino acid string to match against

Referenced by aa_str(), eval_impl(), IdentityEval(), operator=(), and pre_catalog_op().

Real core::fragment::picking_old::vall::eval::IdentityEval::aa_penalty_

private

amino acid penalty if non-matching

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

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

private

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

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

String core::fragment::picking_old::vall::eval::IdentityEval::ss_

private

secondary structure string to match against

Referenced by eval_impl(), IdentityEval(), operator=(), pre_catalog_op(), and ss_str().

Real core::fragment::picking_old::vall::eval::IdentityEval::ss_penalty_

private

secondary structure penalty if non-matching

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

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

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

Public Types

Public Member Functions

Private Types

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation