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protocols::frag_picker::scores::SecondaryIdentity Class Reference

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

#include <SecondaryIdentity.hh>

Inheritance diagram for protocols::frag_picker::scores::SecondaryIdentity:
Inheritance graph
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Public Member Functions

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

Static Public Attributes

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

Private Attributes

std::string & query_
 
std::string prediction_name_
 

Additional Inherited Members

- 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_
 

Detailed Description

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

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 ( core::Size  priority,
core::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

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

References core::chemical::element::F, and core::chemical::element::I.

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

Member Data Documentation

const int protocols::frag_picker::scores::SecondaryIdentity::PENALTY = 1
static

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

std::string protocols::frag_picker::scores::SecondaryIdentity::prediction_name_
private
std::string& protocols::frag_picker::scores::SecondaryIdentity::query_
private
const int protocols::frag_picker::scores::SecondaryIdentity::REWARD = 0
static

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

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


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