protocols::frag_picker::scores::HydrophobicitySimilarity Class Reference

scores a fragment by its hydrophobicity similarity More...

#include <HydrophobicitySimilarity.hh>

Inheritance diagram for protocols::frag_picker::scores::HydrophobicitySimilarity:

Collaboration diagram for protocols::frag_picker::scores::HydrophobicitySimilarity:

Public Member Functions
	HydrophobicitySimilarity (Size priority, Real lowest_acceptable_value, bool use_lowest, std::string &fastaQuerySequence)
	creates a hydrophobicity-based scoring function. More...
	~HydrophobicitySimilarity ()
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_

Static Private Attributes
static std::map< char, bool >	is_hydrophobic_

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 hydrophobicity similarity

Definition at line 37 of file HydrophobicitySimilarity.hh.

Constructor & Destructor Documentation

protocols::frag_picker::scores::HydrophobicitySimilarity::HydrophobicitySimilarity ( Size  priority, Real  lowest_acceptable_value, bool  use_lowest, std::string &  fastaQuerySequence  )

inline

creates a hydrophobicity-based scoring function.

Definition at line 41 of file HydrophobicitySimilarity.hh.

References is_hydrophobic_.

protocols::frag_picker::scores::HydrophobicitySimilarity::~HydrophobicitySimilarity ( )

inline

Definition at line 93 of file HydrophobicitySimilarity.hh.

Member Function Documentation

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

virtual

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

Definition at line 38 of file HydrophobicitySimilarity.cc.

References score().

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

inlinevirtual

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

Definition at line 96 of file HydrophobicitySimilarity.hh.

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

virtual

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

Definition at line 31 of file HydrophobicitySimilarity.cc.

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

virtual

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

Definition at line 45 of file HydrophobicitySimilarity.cc.

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

Referenced by cached_score().

Member Data Documentation

std::string protocols::frag_picker::scores::HydrophobicitySimilarity::cached_scores_id_

private

Definition at line 101 of file HydrophobicitySimilarity.hh.

std::map< char, bool > protocols::frag_picker::scores::HydrophobicitySimilarity::is_hydrophobic_

staticprivate

Definition at line 103 of file HydrophobicitySimilarity.hh.

Referenced by HydrophobicitySimilarity(), and score().

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

private

Definition at line 102 of file HydrophobicitySimilarity.hh.

Referenced by score().

---

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

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