Rosetta Protocols  2014.35
Public Member Functions | Protected Attributes | Private Attributes | List of all members
protocols::frag_picker::scores::PartialSecondarySimilarity Class Reference

scores a fragment by secondary structure similarity More...

#include <PartialSecondarySimilarity.hh>

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::stringget_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::stringget_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_
- Protected Attributes inherited from protocols::frag_picker::scores::FragmentScoringMethod
Size id_
Size priority_
std::string name_
Real lowest_acceptable_value_
bool use_lowest_

Private Attributes

std::string prediction_name_
utility::vector1< Realnorm_query_H_
utility::vector1< Realnorm_query_E_
utility::vector1< Realnorm_query_L_
< utility::vector1< Real > > 
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::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 
protocols::frag_picker::scores::PartialSecondarySimilarity::~PartialSecondarySimilarity ( )

Member Function Documentation

bool protocols::frag_picker::scores::PartialSecondarySimilarity::cached_score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map 
void protocols::frag_picker::scores::PartialSecondarySimilarity::clean_up ( )
void protocols::frag_picker::scores::PartialSecondarySimilarity::do_caching ( VallChunkOP  chunk)
std::string& protocols::frag_picker::scores::PartialSecondarySimilarity::get_prediction_name ( )
bool protocols::frag_picker::scores::PartialSecondarySimilarity::score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map 

Member Data Documentation

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

Referenced by do_caching().

utility::vector1< Real > protocols::frag_picker::scores::PartialSecondarySimilarity::norm_query_E_
utility::vector1< Real > protocols::frag_picker::scores::PartialSecondarySimilarity::norm_query_H_
utility::vector1< Real > protocols::frag_picker::scores::PartialSecondarySimilarity::norm_query_L_
std::string protocols::frag_picker::scores::PartialSecondarySimilarity::prediction_name_
Size protocols::frag_picker::scores::PartialSecondarySimilarity::query_len_
utility::vector1< utility::vector1< Real > > protocols::frag_picker::scores::PartialSecondarySimilarity::raw_probs_
Matrix protocols::frag_picker::scores::PartialSecondarySimilarity::scores_

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