protocols::frag_picker::scores::ProfileScoreDistWeight Class Reference

a fragment candidate More...

#include <ProfileScoreDistWeight.hh>

Inheritance diagram for protocols::frag_picker::scores::ProfileScoreDistWeight:

Public Member Functions
	ProfileScoreDistWeight (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, core::sequence::SequenceProfileOP query_profile, core::fragment::SecondaryStructureOP query_ss_prediction, std::string query_sequence, core::Size longest_vall_chunk)
void	do_caching (VallChunkOP) override
void	clean_up () 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)
bool	score (FragmentCandidateOP, FragmentScoreMapOP) override
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
utility::vector1 < utility::vector1 < utility::vector1< core::Real > > >	distance_weights_
std::string	query_sequence_
std::map< char, core::Size >	ss_type_map_
std::map< char, core::Size >	aa_order_map_
core::sequence::SequenceProfileOP	query_profile_
core::fragment::SecondaryStructureOP	query_ss_
std::string	cached_scores_id_

Detailed Description

a fragment candidate

Constructor & Destructor Documentation

protocols::frag_picker::scores::ProfileScoreDistWeight::ProfileScoreDistWeight	(	core::Size	priority,
		core::Real	lowest_acceptable_value,
		bool	use_lowest,
		core::sequence::SequenceProfileOP	query_profile,
		core::fragment::SecondaryStructureOP	query_ss_prediction,
		std::string	query_sequence,
		core::Size	longest_vall_chunk
	)

References aa_order_map_, distance_weights_, scores_, and ss_type_map_.

Member Function Documentation

bool protocols::frag_picker::scores::ProfileScoreDistWeight::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_.

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

inlineoverridevirtual

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

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

private

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

overridevirtual

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

References aa_order_map_, cached_scores_id_, distance_weights_, query_sequence_, query_ss_, protocols::frag_picker::scores::CachingScoringMethod::score(), scores_, and protocols::frag_picker::scores::trProfScoreDistWeight().

Referenced by cached_score().

Member Data Documentation

std::map<char,core::Size> protocols::frag_picker::scores::ProfileScoreDistWeight::aa_order_map_

private

Referenced by do_caching(), and ProfileScoreDistWeight().

std::string protocols::frag_picker::scores::ProfileScoreDistWeight::cached_scores_id_

private

Referenced by cached_score(), and do_caching().

utility::vector1< utility::vector1< utility::vector1 <core::Real> > > protocols::frag_picker::scores::ProfileScoreDistWeight::distance_weights_

private

Referenced by do_caching(), and ProfileScoreDistWeight().

core::sequence::SequenceProfileOP protocols::frag_picker::scores::ProfileScoreDistWeight::query_profile_

private

std::string protocols::frag_picker::scores::ProfileScoreDistWeight::query_sequence_

private

Referenced by do_caching().

core::fragment::SecondaryStructureOP protocols::frag_picker::scores::ProfileScoreDistWeight::query_ss_

private

Referenced by do_caching().

Matrix protocols::frag_picker::scores::ProfileScoreDistWeight::scores_

protected

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

std::map<char,core::Size> protocols::frag_picker::scores::ProfileScoreDistWeight::ss_type_map_

private

Referenced by ProfileScoreDistWeight().

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

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