protocols::frag_picker::scores::ProfileScoreSubMatrix Class Reference

a fragment candidate More...

#include <ProfileScoreSubMatrix.hh>

Inheritance diagram for protocols::frag_picker::scores::ProfileScoreSubMatrix:

Public Member Functions
	ProfileScoreSubMatrix (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, std::string sequence, core::Size longest_vall_chunk, std::string subMatrixFile)
	~ProfileScoreSubMatrix () override
void	do_caching (VallChunkOP) override
void	clean_up () override
bool	score (FragmentCandidateOP, FragmentScoreMapOP) override
bool	cached_score (FragmentCandidateOP, FragmentScoreMapOP) override
Public Member Functions inherited from protocols::frag_picker::scores::CachingScoringMethod
	CachingScoringMethod (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, std::string name)
Public Member Functions inherited from protocols::frag_picker::scores::FragmentScoringMethod
	FragmentScoringMethod (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, std::string name)
std::string &	get_score_name ()
	Returns a name of this scoring method. More...
core::Size	get_id ()
	Returns an integer index assigned to this scoring method by a scoring manager. More...
void	set_id (core::Size id)
	Sets a new integer index for this scoring method. More...
core::Size	get_priority ()
	Returns a priority of this scoring method. More...
core::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 (core::Real lowest_acceptable_value)
	Sets a new value of the lowest acceptable score. More...

Protected Attributes
Matrix	scores_
Protected Attributes inherited from protocols::frag_picker::scores::FragmentScoringMethod
core::Size	id_
core::Size	priority_
std::string	name_
core::Real	lowest_acceptable_value_
bool	use_lowest_

Private Member Functions
void	clear ()

Private Attributes
std::string	sequence_
std::string	subMatrixFile_
utility::vector1< utility::vector1< core::Real > >	sub_matrix_
std::string	cached_scores_id_

Detailed Description

a fragment candidate

Constructor & Destructor Documentation

ProfileScoreSubMatrix()

protocols::frag_picker::scores::ProfileScoreSubMatrix::ProfileScoreSubMatrix	(	core::Size	priority,
		core::Real	lowest_acceptable_value,
		bool	use_lowest,
		std::string	sequence,
		core::Size	longest_vall_chunk,
		std::string	subMatrixFile
	)

References core::sequence::MatrixScoringScheme::read_from_file(), scores_, core::sequence::MatrixScoringScheme::scoring_matrix(), sequence_, sub_matrix_, and subMatrixFile_.

~ProfileScoreSubMatrix()

protocols::frag_picker::scores::ProfileScoreSubMatrix::~ProfileScoreSubMatrix ( )

overridedefault

Member Function Documentation

cached_score()

bool protocols::frag_picker::scores::ProfileScoreSubMatrix::cached_score ( FragmentCandidateOP  f, FragmentScoreMapOP  empty_map  )

overridevirtual

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

References cached_scores_id_, do_caching(), protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, scores_, and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

Referenced by score().

clean_up()

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

inlineoverridevirtual

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

clear()

void protocols::frag_picker::scores::ProfileScoreSubMatrix::clear ( )

private

do_caching()

void protocols::frag_picker::scores::ProfileScoreSubMatrix::do_caching ( VallChunkOP  chunk )

overridevirtual

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

References core::chemical::aa_from_oneletter_code(), cached_scores_id_, scores_, sequence_, sub_matrix_, and protocols::frag_picker::scores::trProfScoreSubMatrix().

Referenced by cached_score().

score()

bool protocols::frag_picker::scores::ProfileScoreSubMatrix::score ( FragmentCandidateOP  f, FragmentScoreMapOP  empty_map  )

overridevirtual

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

References cached_score().

Member Data Documentation

cached_scores_id_

std::string protocols::frag_picker::scores::ProfileScoreSubMatrix::cached_scores_id_

private

Referenced by cached_score(), and do_caching().

scores_

Matrix protocols::frag_picker::scores::ProfileScoreSubMatrix::scores_

protected

Referenced by cached_score(), do_caching(), and ProfileScoreSubMatrix().

sequence_

std::string protocols::frag_picker::scores::ProfileScoreSubMatrix::sequence_

private

Referenced by do_caching(), and ProfileScoreSubMatrix().

sub_matrix_

utility::vector1< utility::vector1< core::Real > > protocols::frag_picker::scores::ProfileScoreSubMatrix::sub_matrix_

private

Referenced by do_caching(), and ProfileScoreSubMatrix().

subMatrixFile_

std::string protocols::frag_picker::scores::ProfileScoreSubMatrix::subMatrixFile_

private

Referenced by ProfileScoreSubMatrix().

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

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