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

Inheritance diagram for protocols::frag_picker::scores::SecondarySimilarity:
Inheritance graph
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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< Matrixcache_
 
- 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 
)
protocols::frag_picker::scores::SecondarySimilarity::~SecondarySimilarity ( )
inlineoverride

Member Function Documentation

bool protocols::frag_picker::scores::SecondarySimilarity::cached_score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map 
)
overridevirtual
void protocols::frag_picker::scores::SecondarySimilarity::clean_up ( )
inlineoverridevirtual
void protocols::frag_picker::scores::SecondarySimilarity::do_caching ( VallChunkOP  chunk)
overridevirtual
void protocols::frag_picker::scores::SecondarySimilarity::do_caching_simple ( VallChunkOP  chunk)
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

Member Data Documentation

utility::vector1< Matrix > protocols::frag_picker::scores::SecondarySimilarity::cache_
protected
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
core::fragment::SecondaryStructureOP protocols::frag_picker::scores::SecondarySimilarity::query_ss_
private
utility::vector1< utility::vector1< core::Real > > protocols::frag_picker::scores::SecondarySimilarity::raw_probs_
private
Matrix protocols::frag_picker::scores::SecondarySimilarity::scores_
protected

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