protocols::frag_picker::scores::JCoupling Class Reference

scores a fragment by the JCouplings More...

#include <JCoupling.hh>

Inheritance diagram for protocols::frag_picker::scores::JCoupling:

Collaboration diagram for protocols::frag_picker::scores::JCoupling:

Public Member Functions
	JCoupling (Size, Real, bool, JCouplingIO &)
	creates a More...
void	do_caching (VallChunkOP)
void	clean_up ()
bool	cached_score (FragmentCandidateOP, FragmentScoreMapOP)
bool	score (FragmentCandidateOP, FragmentScoreMapOP)
Public Member Functions inherited from protocols::frag_picker::scores::CachingScoringMethod
	CachingScoringMethod (Size priority, Real lowest_acceptable_value, bool use_lowest, std::string name)
Public Member Functions inherited from protocols::frag_picker::scores::FragmentScoringMethod
	FragmentScoringMethod (Size priority, Real lowest_acceptable_value, bool use_lowest, std::string name)
std::string &	get_score_name ()
	Returns a name of this scoring method. More...
Size	get_id ()
	Returns an integer index assigned to this scoring method by a scoring manager. More...
void	set_id (Size id)
	Sets a new integer index for this scoring method. More...
Size	get_priority ()
	Returns a priority of this scoring method. More...
Real	get_min_allowed_score ()
	Returns the lowest acceptable score value for this scoring method. More...
bool	get_use_lowest ()
	Returns the boolean choice on using the above lowest acceptable score value. More...
void	set_min_allowed_score (Real lowest_acceptable_value)
	Sets a new value of the lowest acceptable score. More...

Private Attributes
JCouplingIO	data_
Size	len_
Real	A_
Real	B_
Real	C_
Real	THETA_

Additional Inherited Members
Protected Attributes inherited from protocols::frag_picker::scores::FragmentScoringMethod
Size	id_
Size	priority_
std::string	name_
Real	lowest_acceptable_value_
bool	use_lowest_

Detailed Description

scores a fragment by the JCouplings

Constructor & Destructor Documentation

protocols::frag_picker::scores::JCoupling::JCoupling	(	Size	priority,
		Real	lowest_acceptable_value,
		bool	use_lowest,
		JCouplingIO &	reader
	)

creates a

Detailed:

References A_, B_, C_, data_, protocols::frag_picker::JCouplingIO::get_length(), protocols::frag_picker::JCouplingIO::get_parameters(), len_, and THETA_.

Member Function Documentation

bool protocols::frag_picker::scores::JCoupling::cached_score ( FragmentCandidateOP  fragment, FragmentScoreMapOP  scores  )

virtual

Reimplemented from protocols::frag_picker::scores::CachingScoringMethod.

References score().

void protocols::frag_picker::scores::JCoupling::clean_up ( )

virtual

Implements protocols::frag_picker::scores::CachingScoringMethod.

void protocols::frag_picker::scores::JCoupling::do_caching ( VallChunkOP  current_chunk)

virtual

Implements protocols::frag_picker::scores::CachingScoringMethod.

bool protocols::frag_picker::scores::JCoupling::score ( FragmentCandidateOP  fragment, FragmentScoreMapOP  scores  )

virtual

Reimplemented from protocols::frag_picker::scores::CachingScoringMethod.

References A_, B_, C_, data_, protocols::frag_picker::JCouplingIO::get_data(), protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, THETA_, and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

Referenced by cached_score().

Member Data Documentation

Real protocols::frag_picker::scores::JCoupling::A_

private

Referenced by JCoupling(), and score().

Real protocols::frag_picker::scores::JCoupling::B_

private

Referenced by JCoupling(), and score().

Real protocols::frag_picker::scores::JCoupling::C_

private

Referenced by JCoupling(), and score().

JCouplingIO protocols::frag_picker::scores::JCoupling::data_

private

Referenced by JCoupling(), and score().

Size protocols::frag_picker::scores::JCoupling::len_

private

Referenced by JCoupling().

Real protocols::frag_picker::scores::JCoupling::THETA_

private

Referenced by JCoupling(), and score().

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

• src/protocols/frag_picker/scores/JCoupling.hh
• src/protocols/frag_picker/scores/JCoupling.cc