protocols::frag_picker::scores::SolventAccessibility Class Reference

scores a fragment by its predicted solvent accessibility More...

#include <SolventAccessibility.hh>

Inheritance diagram for protocols::frag_picker::scores::SolventAccessibility:

Public Member Functions
	SolventAccessibility (Size priority, Real lowest_acceptable_value, bool use_lowest, std::string &fastaQuerySequence, utility::vector1< core::Real > &predicted_sa)
	creates a predicted solvent accessibility based scoring function. More...
	~SolventAccessibility ()
void	do_caching (VallChunkOP)
void	clean_up ()
bool	score (FragmentCandidateOP, FragmentScoreMapOP)
bool	cached_score (FragmentCandidateOP, FragmentScoreMapOP)
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::string &	get_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...

Private Attributes
std::string	cached_scores_id_
std::string &	query_
utility::vector1< Real >	predicted_sa_norm_

Additional Inherited Members
Protected Attributes inherited from protocols::frag_picker::scores::FragmentScoringMethod
Size	id_
Size	priority_
std::string	name_
Real	lowest_acceptable_value_
bool	use_lowest_

Detailed Description

scores a fragment by its predicted solvent accessibility

Constructor & Destructor Documentation

protocols::frag_picker::scores::SolventAccessibility::SolventAccessibility ( Size  priority, Real  lowest_acceptable_value, bool  use_lowest, std::string &  fastaQuerySequence, utility::vector1< core::Real > &  predicted_sa  )

inline

creates a predicted solvent accessibility based scoring function.

References protocols::frag_picker::sa_faraggi_max().

protocols::frag_picker::scores::SolventAccessibility::~SolventAccessibility ( )

inline

Member Function Documentation

bool protocols::frag_picker::scores::SolventAccessibility::cached_score ( FragmentCandidateOP  fragment, FragmentScoreMapOP  scores  )

virtual

Reimplemented from protocols::frag_picker::scores::CachingScoringMethod.

References score().

void protocols::frag_picker::scores::SolventAccessibility::clean_up ( )

inlinevirtual

Implements protocols::frag_picker::scores::CachingScoringMethod.

void protocols::frag_picker::scores::SolventAccessibility::do_caching ( VallChunkOP  current_chunk )

virtual

Implements protocols::frag_picker::scores::CachingScoringMethod.

bool protocols::frag_picker::scores::SolventAccessibility::score ( FragmentCandidateOP  f, FragmentScoreMapOP  empty_map  )

virtual

Reimplemented from protocols::frag_picker::scores::CachingScoringMethod.

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

Referenced by cached_score().

Member Data Documentation

std::string protocols::frag_picker::scores::SolventAccessibility::cached_scores_id_

private

utility::vector1<Real> protocols::frag_picker::scores::SolventAccessibility::predicted_sa_norm_

private

Referenced by score().

std::string& protocols::frag_picker::scores::SolventAccessibility::query_

private

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

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