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protocols::frag_picker::scores::HydrophobicityProfileSimilarity Class Reference

scores a fragment by its hydrophobicity similarity More...

#include <HydrophobicityProfileSimilarity.hh>

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

 HydrophobicityProfileSimilarity (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, std::string &fastaQuerySequence, core::sequence::SequenceProfileOP query_profile)
 creates a hydrophobicity-based scoring function. More...
 
 ~HydrophobicityProfileSimilarity () override
 
void do_caching (VallChunkOP) override
 
void clean_up () override
 
bool score (FragmentCandidateOP, FragmentScoreMapOP) override
 
bool cached_score (FragmentCandidateOP, FragmentScoreMapOP) override
 
- Public Member Functions inherited from protocols::frag_picker::scores::CachingScoringMethod
 CachingScoringMethod (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, std::string 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...
 

Private Attributes

std::string cached_scores_id_
 
std::string & query_
 
core::sequence::SequenceProfileOP query_profile_
 

Static Private Attributes

static std::map< char, boolis_hydrophobic_
 

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

scores a fragment by its hydrophobicity similarity

Constructor & Destructor Documentation

protocols::frag_picker::scores::HydrophobicityProfileSimilarity::HydrophobicityProfileSimilarity ( core::Size  priority,
core::Real  lowest_acceptable_value,
bool  use_lowest,
std::string &  fastaQuerySequence,
core::sequence::SequenceProfileOP  query_profile 
)
inline

creates a hydrophobicity-based scoring function.

References is_hydrophobic_, and query_profile_.

protocols::frag_picker::scores::HydrophobicityProfileSimilarity::~HydrophobicityProfileSimilarity ( )
inlineoverride

Member Function Documentation

bool protocols::frag_picker::scores::HydrophobicityProfileSimilarity::cached_score ( FragmentCandidateOP  fragment,
FragmentScoreMapOP  scores 
)
overridevirtual
void protocols::frag_picker::scores::HydrophobicityProfileSimilarity::clean_up ( )
inlineoverridevirtual
void protocols::frag_picker::scores::HydrophobicityProfileSimilarity::do_caching ( VallChunkOP  current_chunk)
overridevirtual
bool protocols::frag_picker::scores::HydrophobicityProfileSimilarity::score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map 
)
overridevirtual

Member Data Documentation

std::string protocols::frag_picker::scores::HydrophobicityProfileSimilarity::cached_scores_id_
private
std::map< char, bool > protocols::frag_picker::scores::HydrophobicityProfileSimilarity::is_hydrophobic_
staticprivate
std::string& protocols::frag_picker::scores::HydrophobicityProfileSimilarity::query_
private

Referenced by score().

core::sequence::SequenceProfileOP protocols::frag_picker::scores::HydrophobicityProfileSimilarity::query_profile_
private

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