protocols::frag_picker::scores::TorsionBinSimilarity Class Reference

scores a fragment by torsion bin similarity More...

#include <TorsionBinSimilarity.hh>

Inheritance diagram for protocols::frag_picker::scores::TorsionBinSimilarity:

Collaboration diagram for protocols::frag_picker::scores::TorsionBinSimilarity:

Public Member Functions
	TorsionBinSimilarity (Size priority, Real lowest_acceptable_value, bool use_lowest, utility::vector1< utility::vector1< core::Real > > query_bin_probs, Size sequence_length, Size longest_vall_chunk)
void	do_caching (VallChunkOP)
void	clean_up ()
virtual bool	cached_score (FragmentCandidateOP, FragmentScoreMapOP)
	Computes the score. More...
Public Member Functions inherited from protocols::frag_picker::scores::CachingScoringMethod
	CachingScoringMethod (Size priority, Real lowest_acceptable_value, bool use_lowest, std::string name)
virtual bool	score (FragmentCandidateOP fragment, FragmentScoreMapOP scores)
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...

Protected Attributes
Matrix	scores_

Private Member Functions
char	torsion2big_bin_ (core::Real const phi, core::Real const psi, core::Real const omega) const
Size	bin_index_ (char const bin_name) const

Private Attributes
std::string	name_
Size	query_len_
utility::vector1 < utility::vector1< core::Real > >	query_bin_probs_
std::string	cached_scores_id_

Detailed Description

scores a fragment by torsion bin similarity

Definition at line 41 of file TorsionBinSimilarity.hh.

Constructor & Destructor Documentation

protocols::frag_picker::scores::TorsionBinSimilarity::TorsionBinSimilarity ( Size  priority, Real  lowest_acceptable_value, bool  use_lowest, utility::vector1< utility::vector1< core::Real > >  query_bin_probs, Size  sequence_length, Size  longest_vall_chunk  )

inline

Definition at line 44 of file TorsionBinSimilarity.hh.

References query_len_, and scores_.

Member Function Documentation

core::Size protocols::frag_picker::scores::TorsionBinSimilarity::bin_index_ ( char const  bin_name) const

private

Definition at line 113 of file TorsionBinSimilarity.cc.

Referenced by do_caching().

bool protocols::frag_picker::scores::TorsionBinSimilarity::cached_score ( FragmentCandidateOP  f, FragmentScoreMapOP  empty_map  )

virtual

Computes the score.

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

Definition at line 63 of file TorsionBinSimilarity.cc.

References cached_scores_id_, do_caching(), protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, scores_, core::scoring::total_score, and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

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

inlinevirtual

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

Definition at line 67 of file TorsionBinSimilarity.hh.

void protocols::frag_picker::scores::TorsionBinSimilarity::do_caching ( VallChunkOP  chunk)

virtual

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

Definition at line 38 of file TorsionBinSimilarity.cc.

References bin_index_(), cached_scores_id_, core::scoring::omega, protocols::swa::phi(), protocols::swa::psi(), query_bin_probs_, query_len_, scores_, torsion2big_bin_(), and protocols::frag_picker::scores::tr().

Referenced by cached_score().

char protocols::frag_picker::scores::TorsionBinSimilarity::torsion2big_bin_ ( core::Real const  phi, core::Real const  psi, core::Real const  omega  ) const

private

Definition at line 90 of file TorsionBinSimilarity.cc.

Referenced by do_caching().

Member Data Documentation

std::string protocols::frag_picker::scores::TorsionBinSimilarity::cached_scores_id_

private

Definition at line 88 of file TorsionBinSimilarity.hh.

Referenced by cached_score(), and do_caching().

std::string protocols::frag_picker::scores::TorsionBinSimilarity::name_

private

Definition at line 85 of file TorsionBinSimilarity.hh.

utility::vector1< utility::vector1< core::Real > > protocols::frag_picker::scores::TorsionBinSimilarity::query_bin_probs_

private

Definition at line 87 of file TorsionBinSimilarity.hh.

Referenced by do_caching().

Size protocols::frag_picker::scores::TorsionBinSimilarity::query_len_

private

Definition at line 86 of file TorsionBinSimilarity.hh.

Referenced by do_caching(), and TorsionBinSimilarity().

Matrix protocols::frag_picker::scores::TorsionBinSimilarity::scores_

protected

Definition at line 82 of file TorsionBinSimilarity.hh.

Referenced by cached_score(), do_caching(), and TorsionBinSimilarity().

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

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