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:

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

Computes the score.

Implements protocols::frag_picker::scores::FragmentScoringMethod.

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

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

• src/protocols/frag_picker/scores/SecondaryIdentity.hh
• src/protocols/frag_picker/scores/SecondaryIdentity.cc