protocols::frag_picker::scores::PartialSecondarySimilarity Class Reference

scores a fragment by secondary structure similarity The score for each position is P(H), P(L) or P(E) if a vall residue is within Helix, Loop or Extended secondary stucture element, respectively. P(H), P(L) and P(E) denotes the probability that a given residue in a query is within Helix, Loop or Extended secondary stucture element. The total score of a fragment is a simple sum of all positions; for N-mer fragment is a sum of N terms
If P(H), P(L) and P(E) probabilities takes only 1.0 and 0.0 values, result of this scoring function should be the same as SecondaryIdentity, although the later one is faster. More...

#include <PartialSecondarySimilarity.hh>

Inheritance diagram for protocols::frag_picker::scores::PartialSecondarySimilarity:

Collaboration diagram for protocols::frag_picker::scores::PartialSecondarySimilarity:

Public Member Functions
	PartialSecondarySimilarity (Size priority, Real lowest_acceptable_value, bool use_lowest, core::fragment::SecondaryStructureOP query_prediction, std::string prediction_name, Size sequence_length, Size longest_vall_chunk)
	~PartialSecondarySimilarity ()
void	do_caching (VallChunkOP)
bool	cached_score (FragmentCandidateOP f, FragmentScoreMapOP empty_map)
void	clean_up ()
virtual bool	score (FragmentCandidateOP, FragmentScoreMapOP)
	Computes the score. More...
std::string &	get_prediction_name ()
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_

Private Attributes
std::string	prediction_name_
utility::vector1< Real >	norm_query_H_
utility::vector1< Real >	norm_query_E_
utility::vector1< Real >	norm_query_L_
utility::vector1 < utility::vector1< Real > >	raw_probs_
Size	query_len_
std::string	cached_scores_id_

Detailed Description

scores a fragment by secondary structure similarity The score for each position is P(H), P(L) or P(E) if a vall residue is within Helix, Loop or Extended secondary stucture element, respectively. P(H), P(L) and P(E) denotes the probability that a given residue in a query is within Helix, Loop or Extended secondary stucture element. The total score of a fragment is a simple sum of all positions; for N-mer fragment is a sum of N terms
If P(H), P(L) and P(E) probabilities takes only 1.0 and 0.0 values, result of this scoring function should be the same as SecondaryIdentity, although the later one is faster.

Definition at line 45 of file PartialSecondarySimilarity.hh.

Constructor & Destructor Documentation

protocols::frag_picker::scores::PartialSecondarySimilarity::PartialSecondarySimilarity	(	Size	priority,
		Real	lowest_acceptable_value,
		bool	use_lowest,
		core::fragment::SecondaryStructureOP	query_prediction,
		std::string	prediction_name,
		Size	sequence_length,
		Size	longest_vall_chunk
	)

Definition at line 140 of file PartialSecondarySimilarity.cc.

References norm_query_E_, norm_query_H_, norm_query_L_, query_len_, raw_probs_, and scores_.

protocols::frag_picker::scores::PartialSecondarySimilarity::~PartialSecondarySimilarity ( )

inline

Definition at line 52 of file PartialSecondarySimilarity.hh.

Member Function Documentation

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

virtual

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

Definition at line 118 of file PartialSecondarySimilarity.cc.

References score().

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

inlinevirtual

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

Definition at line 57 of file PartialSecondarySimilarity.hh.

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

virtual

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

Definition at line 43 of file PartialSecondarySimilarity.cc.

References cached_scores_id_, query_len_, raw_probs_, scores_, and protocols::frag_picker::scores::trPartialSecondarySimilarity().

std::string& protocols::frag_picker::scores::PartialSecondarySimilarity::get_prediction_name ( )

inline

Definition at line 63 of file PartialSecondarySimilarity.hh.

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

virtual

Computes the score.

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

Definition at line 68 of file PartialSecondarySimilarity.cc.

References protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, raw_probs_, and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

Referenced by cached_score().

Member Data Documentation

std::string protocols::frag_picker::scores::PartialSecondarySimilarity::cached_scores_id_

private

Definition at line 77 of file PartialSecondarySimilarity.hh.

Referenced by do_caching().

utility::vector1< Real > protocols::frag_picker::scores::PartialSecondarySimilarity::norm_query_E_

private

Definition at line 71 of file PartialSecondarySimilarity.hh.

Referenced by PartialSecondarySimilarity().

utility::vector1< Real > protocols::frag_picker::scores::PartialSecondarySimilarity::norm_query_H_

private

Definition at line 70 of file PartialSecondarySimilarity.hh.

Referenced by PartialSecondarySimilarity().

utility::vector1< Real > protocols::frag_picker::scores::PartialSecondarySimilarity::norm_query_L_

private

Definition at line 72 of file PartialSecondarySimilarity.hh.

Referenced by PartialSecondarySimilarity().

std::string protocols::frag_picker::scores::PartialSecondarySimilarity::prediction_name_

private

Definition at line 68 of file PartialSecondarySimilarity.hh.

Size protocols::frag_picker::scores::PartialSecondarySimilarity::query_len_

private

Definition at line 75 of file PartialSecondarySimilarity.hh.

Referenced by do_caching(), and PartialSecondarySimilarity().

utility::vector1< utility::vector1< Real > > protocols::frag_picker::scores::PartialSecondarySimilarity::raw_probs_

private

Definition at line 74 of file PartialSecondarySimilarity.hh.

Referenced by do_caching(), PartialSecondarySimilarity(), and score().

Matrix protocols::frag_picker::scores::PartialSecondarySimilarity::scores_

protected

Definition at line 63 of file PartialSecondarySimilarity.hh.

Referenced by do_caching(), and PartialSecondarySimilarity().

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

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