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:

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, bool >	is_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

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

References score().

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

inlineoverridevirtual

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

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

overridevirtual

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

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

overridevirtual

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

References core::chemical::aa_from_oneletter_code(), protocols::frag_picker::scores::FragmentScoringMethod::id_, is_hydrophobic_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, query_, query_profile_, and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

Referenced by cached_score().

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

Referenced by HydrophobicityProfileSimilarity(), and score().

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

private

Referenced by score().

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

private

Referenced by HydrophobicityProfileSimilarity(), and score().

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

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