protocols::frag_picker::scores::TalosSSSimilarity 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 <TalosSSSimilarity.hh>

Inheritance diagram for protocols::frag_picker::scores::TalosSSSimilarity:

Collaboration diagram for protocols::frag_picker::scores::TalosSSSimilarity:

List of all members.

Public Member Functions
	TalosSSSimilarity (Size priority, Real lowest_acceptable_value, bool use_lowest, core::fragment::SecondaryStructureOP query_prediction, std::string prediction_name, Size sequence_length, utility::vector1< Size > &frag_sizes, Size longest_vall_chunk)
	~TalosSSSimilarity ()
void	do_caching (VallChunkOP)
void	do_caching_simple (VallChunkOP)
bool	cached_score (FragmentCandidateOP f, FragmentScoreMapOP empty_map)
void	clean_up ()
virtual bool	score (FragmentCandidateOP, FragmentScoreMapOP)
	Computes the score.
core::fragment::SecondaryStructureOP	get_secondary_prediction ()
	returns the secondary structure porediction object that is used by this score
std::string &	get_prediction_name ()
Protected Attributes
Matrix	scores_
utility::vector1< Matrix >	cache_

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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.

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Constructor & Destructor Documentation

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

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

protocols::frag_picker::scores::TalosSSSimilarity::~TalosSSSimilarity

(

)

[inline]

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Member Function Documentation

bool protocols::frag_picker::scores::TalosSSSimilarity::cached_score	(	FragmentCandidateOP	f,
		FragmentScoreMapOP	empty_map
	)		[virtual]

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

void protocols::frag_picker::scores::TalosSSSimilarity::clean_up

(

)

[inline, virtual]

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

void protocols::frag_picker::scores::TalosSSSimilarity::do_caching

(

VallChunkOP

chunk

)

[virtual]

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

References protocols::frag_picker::scores::rolling_score(), and protocols::frag_picker::scores::trTalosSSSimilarity().

void protocols::frag_picker::scores::TalosSSSimilarity::do_caching_simple

(

VallChunkOP

chunk

)

References protocols::frag_picker::scores::trTalosSSSimilarity().

std::string& protocols::frag_picker::scores::TalosSSSimilarity::get_prediction_name

(

)

[inline]

core::fragment::SecondaryStructureOP protocols::frag_picker::scores::TalosSSSimilarity::get_secondary_prediction

(

)

[inline]

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

bool protocols::frag_picker::scores::TalosSSSimilarity::score	(	FragmentCandidateOP	f,
		FragmentScoreMapOP	empty_map
	)		[virtual]

Computes the score.

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

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Member Data Documentation

utility::vector1< Matrix > protocols::frag_picker::scores::TalosSSSimilarity::cache_ [protected]

Referenced by TalosSSSimilarity().

Matrix protocols::frag_picker::scores::TalosSSSimilarity::scores_ [protected]

Referenced by TalosSSSimilarity().

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

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