Rosetta 3.4
Public Member Functions | Static Public Attributes
protocols::frag_picker::scores::SecondaryIdentity Class Reference

SequenceIdentity score counts how many residues share the same secondary structure. More...

#include <SecondaryIdentity.hh>

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List of all members.

Public Member Functions

 SecondaryIdentity (Size priority, Real lowest_acceptable_value, bool use_lowest, std::string &query_secondary_structure, std::string prediction_name)
virtual bool score (FragmentCandidateOP, FragmentScoreMapOP)
 Computes the score.
bool describe_score (FragmentCandidateOP, FragmentScoreMapOP, std::ostream &)
 prints a detailed explanation how a fragment score has been computed
std::string & get_prediction_name ()

Static Public Attributes

static const int REWARD = 0
 will be added if the two residues are in the same secondary structure
static const int PENALTY = 1
 will be added if the two residues are NOT in the same secondary structure

Detailed Description

SequenceIdentity score counts how many residues share the same secondary structure.

Detailed: Resulting score is the number of residues
on corresponding positions in a vall fragment and a query sequence that are annotated with the same secondary structure

Constructor & Destructor Documentation

protocols::frag_picker::scores::SecondaryIdentity::SecondaryIdentity ( Size  priority,
Real  lowest_acceptable_value,
bool  use_lowest,
std::string &  query_secondary_structure,
std::string  prediction_name 
) [inline]

Member Function Documentation

bool protocols::frag_picker::scores::SecondaryIdentity::describe_score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map,
std::ostream &  out 
)

prints a detailed explanation how a fragment score has been computed

Detailed: besides extensive output, the method should return the same result as score()

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

std::string& protocols::frag_picker::scores::SecondaryIdentity::get_prediction_name ( ) [inline]
bool protocols::frag_picker::scores::SecondaryIdentity::score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map 
) [virtual]

Member Data Documentation

will be added if the two residues are NOT in the same secondary structure

Referenced by describe_score(), and score().

will be added if the two residues are in the same secondary structure

Detailed: the REWARD value is 0 because we are minimizing the score and the perfect match should be 0

Referenced by describe_score(), and score().


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