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 <SecondarySimilarity.hh>

Inheritance diagram for protocols::frag_picker::scores::SecondarySimilarity:

[legend]

Public Member Functions
	SecondarySimilarity (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, core::fragment::SecondaryStructureOP query_prediction, std::string const &prediction_name, core::Size sequence_length, utility::vector1< core::Size > &frag_sizes, core::Size longest_vall_chunk)

	~SecondarySimilarity () override

void	do_caching (VallChunkOP) override

void	do_caching_simple (VallChunkOP)

bool	cached_score (FragmentCandidateOP f, FragmentScoreMapOP empty_map) override

void	clean_up () override

bool	score (FragmentCandidateOP, FragmentScoreMapOP) override
	Computes the score. More...

core::fragment::SecondaryStructureOP	get_secondary_prediction ()
	returns the secondary structure porediction object that is used by this score More...

std::string &	get_prediction_name ()

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_

utility::vector1< Matrix >	cache_

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 Attributes
std::string	prediction_name_

core::fragment::SecondaryStructureOP	query_ss_

utility::vector1 < utility::vector1< core::Real > >	raw_probs_

core::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.

Constructor & Destructor Documentation

protocols::frag_picker::scores::SecondarySimilarity::SecondarySimilarity	(	core::Size	priority,
		core::Real	lowest_acceptable_value,
		bool	use_lowest,
		core::fragment::SecondaryStructureOP	query_prediction,
		std::string const &	prediction_name,
		core::Size	sequence_length,
		utility::vector1< core::Size > &	frag_sizes,
		core::Size	longest_vall_chunk
	)

References cache_, protocols::frag_picker::scores::create_cache(), query_len_, query_ss_, raw_probs_, and scores_.

protocols::frag_picker::scores::SecondarySimilarity::~SecondarySimilarity ( )

inlineoverride

Member Function Documentation

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

overridevirtual

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

References cache_, 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::SecondarySimilarity::clean_up ( )

inlineoverridevirtual

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

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

overridevirtual

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

References cache_, cached_scores_id_, do_caching_simple(), protocols::frag_picker::scores::rolling_score(), scores_, and protocols::frag_picker::scores::trSecondarySimilarity().

void protocols::frag_picker::scores::SecondarySimilarity::do_caching_simple ( VallChunkOP chunk )

References query_len_, query_ss_, raw_probs_, scores_, and protocols::frag_picker::scores::trSecondarySimilarity().

Referenced by do_caching().

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

inline

core::fragment::SecondaryStructureOP protocols::frag_picker::scores::SecondarySimilarity::get_secondary_prediction ( )

inline

returns the secondary structure porediction object that is used by this score

References query_ss_.

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

overridevirtual

Computes the score.

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

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

Member Data Documentation

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

protected

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

std::string protocols::frag_picker::scores::SecondarySimilarity::cached_scores_id_

private

Referenced by do_caching().

std::string protocols::frag_picker::scores::SecondarySimilarity::prediction_name_

private

core::Size protocols::frag_picker::scores::SecondarySimilarity::query_len_

private

Referenced by do_caching_simple(), and SecondarySimilarity().

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

private

Referenced by do_caching_simple(), get_secondary_prediction(), score(), and SecondarySimilarity().

utility::vector1< utility::vector1< core::Real > > protocols::frag_picker::scores::SecondarySimilarity::raw_probs_

private

Referenced by do_caching_simple(), and SecondarySimilarity().

Matrix protocols::frag_picker::scores::SecondarySimilarity::scores_

protected

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

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

src/protocols/frag_picker/scores/SecondarySimilarity.hh
src/protocols/frag_picker/scores/SecondarySimilarity.cc

Public Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation