Rosetta 3.4
Public Member Functions | Protected Attributes
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>

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List of all members.

Public Member Functions

 SecondarySimilarity (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)
 ~SecondarySimilarity ()
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< Matrixcache_

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 ( 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 
)
protocols::frag_picker::scores::SecondarySimilarity::~SecondarySimilarity ( ) [inline]

Member Function Documentation

bool protocols::frag_picker::scores::SecondarySimilarity::cached_score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map 
) [virtual]
void protocols::frag_picker::scores::SecondarySimilarity::clean_up ( ) [inline, virtual]
void protocols::frag_picker::scores::SecondarySimilarity::do_caching ( VallChunkOP  chunk) [virtual]
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

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

Member Data Documentation


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