protocols::frag_picker::scores::ProfileScoreDistWeight Class Reference

a fragment candidate More...

#include <ProfileScoreDistWeight.hh>

Public Member Functions
	ProfileScoreDistWeight (Size priority, Real lowest_acceptable_value, bool use_lowest, sequence::SequenceProfileOP query_profile, core::fragment::SecondaryStructureOP query_ss_prediction, std::string query_sequence, Size longest_vall_chunk)
void	do_caching (VallChunkOP)
void	clean_up ()
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)
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_
Protected Attributes inherited from protocols::frag_picker::scores::FragmentScoringMethod
Size	id_
Size	priority_
std::string	name_
Real	lowest_acceptable_value_
bool	use_lowest_

Private Member Functions
void	clear ()

Private Attributes
utility::vector1 < utility::vector1 < utility::vector1< Real > > >	distance_weights_
std::string	query_sequence_
std::map< char, Size >	ss_type_map_
std::map< char, Size >	aa_order_map_
sequence::SequenceProfileOP	query_profile_
core::fragment::SecondaryStructureOP	query_ss_
std::string	cached_scores_id_

Detailed Description

a fragment candidate

Constructor & Destructor Documentation

protocols::frag_picker::scores::ProfileScoreDistWeight::ProfileScoreDistWeight ( Size  priority, Real  lowest_acceptable_value, bool  use_lowest, sequence::SequenceProfileOP  query_profile, core::fragment::SecondaryStructureOP  query_ss_prediction, std::string  query_sequence, Size  longest_vall_chunk  )

inline

References aa_order_map_, distance_weights_, getline(), query_profile_, query_sequence_, query_ss_, scores_, ss1, ss2, ss_type_map_, and utility_exit_with_message.

Member Function Documentation

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

virtual

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

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

inlinevirtual

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

void protocols::frag_picker::scores::ProfileScoreDistWeight::clear ( )

private

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

virtual

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

References protocols::frag_picker::VallChunk::at(), protocols::frag_picker::VallChunk::chunk_key(), basic::FRAGMENTPICKING_PROFILE_CAHING, protocols::frag_picker::VallChunk::get_pdb_id(), j, PROF_START, PROF_STOP, s, score, protocols::frag_picker::VallChunk::size(), and protocols::frag_picker::scores::trProfScoreDistWeight.

Member Data Documentation

std::map<char,Size> protocols::frag_picker::scores::ProfileScoreDistWeight::aa_order_map_

private

Referenced by ProfileScoreDistWeight().

std::string protocols::frag_picker::scores::ProfileScoreDistWeight::cached_scores_id_

private

utility::vector1< utility::vector1< utility::vector1 <Real> > > protocols::frag_picker::scores::ProfileScoreDistWeight::distance_weights_

private

Referenced by ProfileScoreDistWeight().

sequence::SequenceProfileOP protocols::frag_picker::scores::ProfileScoreDistWeight::query_profile_

private

Referenced by ProfileScoreDistWeight().

std::string protocols::frag_picker::scores::ProfileScoreDistWeight::query_sequence_

private

Referenced by ProfileScoreDistWeight().

core::fragment::SecondaryStructureOP protocols::frag_picker::scores::ProfileScoreDistWeight::query_ss_

private

Referenced by ProfileScoreDistWeight().

Matrix protocols::frag_picker::scores::ProfileScoreDistWeight::scores_

protected

Referenced by ProfileScoreDistWeight().

std::map<char,Size> protocols::frag_picker::scores::ProfileScoreDistWeight::ss_type_map_

private

Referenced by ProfileScoreDistWeight().

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

• symlinks/rosetta/src/protocols/frag_picker/scores/ProfileScoreDistWeight.hh
• symlinks/rosetta/src/protocols/frag_picker/scores/ProfileScoreDistWeight.cc