protocols::frag_picker::scores::ProfileScoreL1 Class Reference

a fragment candidate More...

#include <ProfileScoreL1.hh>

Public Member Functions
	ProfileScoreL1 (Size, Real, bool, sequence::SequenceProfileOP, utility::vector1< Size > &, Size)
	~ProfileScoreL1 ()
void	do_caching_simple (VallChunkOP)
void	do_caching (VallChunkOP)
void	clean_up ()
bool	score (FragmentCandidateOP, FragmentScoreMapOP)
bool	cached_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...

Protected Attributes
Matrix	scores_
utility::vector1< Matrix >	cache_
Protected Attributes inherited from protocols::frag_picker::scores::FragmentScoringMethod
Size	id_
Size	priority_
std::string	name_
Real	lowest_acceptable_value_
bool	use_lowest_

Private Member Functions
void	clear ()

Private Attributes
sequence::SequenceProfileOP	query_profile_
std::string	cached_scores_id_

Detailed Description

a fragment candidate

Constructor & Destructor Documentation

protocols::frag_picker::scores::ProfileScoreL1::ProfileScoreL1	(	Size	priority,
		Real	lowest_acceptable_value,
		bool	use_lowest,
		sequence::SequenceProfileOP	query_profile,
		utility::vector1< Size > &	frag_sizes,
		Size	longest_vall_chunk
	)

References cache_, protocols::frag_picker::scores::create_cache(), query_profile_, scores_, size(), protocols::frag_picker::scores::trProfScoreL1, and utility_exit_with_message.

protocols::frag_picker::scores::ProfileScoreL1::~ProfileScoreL1

(

)

Member Function Documentation

bool protocols::frag_picker::scores::ProfileScoreL1::cached_score ( FragmentCandidateOP  f, FragmentScoreMapOP  empty_map  )

virtual

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

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

void protocols::frag_picker::scores::ProfileScoreL1::clean_up ( )

inlinevirtual

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

void protocols::frag_picker::scores::ProfileScoreL1::clear ( )

private

void protocols::frag_picker::scores::ProfileScoreL1::do_caching ( VallChunkOP  chunk )

virtual

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

References cache_, cached_scores_id_, protocols::frag_picker::VallChunk::chunk_key(), do_caching_simple(), protocols::frag_picker::VallChunk::get_pdb_id(), protocols::frag_picker::scores::rolling_score(), scores_, size(), protocols::frag_picker::VallChunk::size(), and protocols::frag_picker::scores::trProfScoreL1.

Referenced by cached_score().

void protocols::frag_picker::scores::ProfileScoreL1::do_caching_simple

(

VallChunkOP

chunk

)

References protocols::frag_picker::VallChunk::at(), protocols::frag_picker::VallChunk::get_pdb_id(), j, query_profile_, score(), scores_, protocols::frag_picker::VallChunk::size(), and protocols::frag_picker::scores::trProfScoreL1.

Referenced by do_caching().

bool protocols::frag_picker::scores::ProfileScoreL1::score ( FragmentCandidateOP  f, FragmentScoreMapOP  empty_map  )

virtual

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

References protocols::frag_picker::VallChunk::at(), chunk, protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, profile, query_profile_, and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

Referenced by do_caching_simple().

Member Data Documentation

utility::vector1< Matrix > protocols::frag_picker::scores::ProfileScoreL1::cache_

protected

Referenced by cached_score(), do_caching(), and ProfileScoreL1().

std::string protocols::frag_picker::scores::ProfileScoreL1::cached_scores_id_

private

Referenced by cached_score(), and do_caching().

sequence::SequenceProfileOP protocols::frag_picker::scores::ProfileScoreL1::query_profile_

private

Referenced by do_caching_simple(), ProfileScoreL1(), and score().

Matrix protocols::frag_picker::scores::ProfileScoreL1::scores_

protected

Referenced by do_caching(), do_caching_simple(), and ProfileScoreL1().

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

• symlinks/rosetta/src/protocols/frag_picker/scores/ProfileScoreL1.hh
• symlinks/rosetta/src/protocols/frag_picker/scores/ProfileScoreL1.cc