protocols::frag_picker::scores::RamaScore Class Reference

RamaScore score counts identical residues. More...

#include <RamaScore.hh>

Public Member Functions
	RamaScore (Size, Real, bool, std::string &, std::string)
	RamaScore (Size, Real, bool, std::string &, core::fragment::SecondaryStructureOP, std::string)
void	SetupRamaTables ()
void	do_caching (VallChunkOP)
void	clean_up ()
bool	score (FragmentCandidateOP f, FragmentScoreMapOP empty_map)
bool	cached_score (FragmentCandidateOP f, FragmentScoreMapOP empty_map)
bool	describe_score (FragmentCandidateOP f, FragmentScoreMapOP empty_map, std::ostream &out)
	prints a detailed explanation how a fragment score has been computed More...
std::string &	get_prediction_name ()
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
Real	minScoreAllowed_
std::string &	query_
core::fragment::SecondaryStructureOP	query_ss_
std::string	prediction_name_
std::string	cached_scores_id_
utility::vector1 < utility::vector1< Real > >	scores_

Static Private Attributes
static utility::vector1 < utility::vector1 < utility::vector1< Real > > >	sequence_rama_tables_

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

RamaScore score counts identical residues.

Detailed: Resulting score is the number of identical residues

on corresponding positions in a vall fragment and a query sequence

Constructor & Destructor Documentation

protocols::frag_picker::scores::RamaScore::RamaScore	(	Size	priority,
		Real	lowest_acceptable_value,
		bool	use_lowest,
		std::string &	fastaQuery,
		std::string	prediction_name
	)

References core::fragment::SecondaryStructure::extend(), query_, query_ss_, core::fragment::SecondaryStructure::set_fractions(), and SetupRamaTables().

protocols::frag_picker::scores::RamaScore::RamaScore	(	Size	priority,
		Real	lowest_acceptable_value,
		bool	use_lowest,
		std::string &	fastaQuery,
		core::fragment::SecondaryStructureOP	query_prediction,
		std::string	prediction_name
	)

References SetupRamaTables().

Member Function Documentation

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

virtual

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

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

Referenced by score().

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

virtual

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

bool protocols::frag_picker::scores::RamaScore::describe_score	(	FragmentCandidateOP	f,
		FragmentScoreMapOP	empty_map,
		std::ostream &	out
	)

prints a detailed explanation how a fragment score has been computed

Detailed: besides extensive output, the method should return the same result as score()

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

virtual

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

References protocols::frag_picker::VallChunk::at(), cached_scores_id_, protocols::frag_picker::VallChunk::chunk_key(), query_, runtime_assert, scores_, sequence_rama_tables_, and protocols::frag_picker::VallChunk::size().

Referenced by cached_score().

std::string& protocols::frag_picker::scores::RamaScore::get_prediction_name ( )

inline

References prediction_name_.

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

virtual

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

References cached_score().

void protocols::frag_picker::scores::RamaScore::SetupRamaTables

(

)

References B, C, getline(), core::fragment::SecondaryStructure::helix_fraction(), core::fragment::SecondaryStructure::loop_fraction(), basic::database::open(), utility::io::ozstream::open(), option, query_, query_ss_, frags::rama_B, frags::rama_C, frags::rama_norm, runtime_assert, s, sequence_rama_tables_, ss_type, core::fragment::SecondaryStructure::strand_fraction(), protocols::analysis::total, user, and frags::write_rama_tables.

Referenced by RamaScore().

Member Data Documentation

std::string protocols::frag_picker::scores::RamaScore::cached_scores_id_

private

Referenced by cached_score(), and do_caching().

Real protocols::frag_picker::scores::RamaScore::minScoreAllowed_

private

std::string protocols::frag_picker::scores::RamaScore::prediction_name_

private

Referenced by get_prediction_name().

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

private

Referenced by do_caching(), RamaScore(), and SetupRamaTables().

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

private

Referenced by RamaScore(), and SetupRamaTables().

utility::vector1< utility::vector1< Real > > protocols::frag_picker::scores::RamaScore::scores_

private

Referenced by cached_score(), and do_caching().

utility::vector1< utility::vector1< utility::vector1< Real > > > protocols::frag_picker::scores::RamaScore::sequence_rama_tables_

staticprivate

Referenced by do_caching(), and SetupRamaTables().

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

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