holds particular score components, weights and calculates the total score for a fragment candidate More...

#include <FragmentScoreManager.hh>

Inheritance diagram for protocols::frag_picker::scores::FragmentScoreManager:

Public Member Functions
	~FragmentScoreManager () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...

	FragmentScoreManager ()
	creates an empty manager More...

FragmentScoreMapOP	create_empty_map ()
	creates an empty score map More...

void	add_scoring_method (FragmentScoringMethodOP, core::Real)
	registers a new scoring method in this manager More...

core::Size	count_components ()
	says how many scoring methods have already been registered More...

FragmentScoringMethodOP	get_component (core::Size index)
	Returns a desired scoring method. More...

utility::vector1< core::Real >	get_weights ()
	returns a vector of weights that are used to compute the total score More...

FragmentScoringMethodOP	get_component_by_name (std::string score_name)
	Returns a desired scoring method from its name rather than index. More...

void	show_scoring_methods (std::ostream &out)
	prints a nice table showing the registered scores More...

core::Real	total_score (FragmentScoreMapOP)
	calculates the total score More...

virtual bool	score_fragment_from_cache (FragmentCandidateOP, FragmentScoreMapOP)
	calculates all the small scores for a given fragment More...

virtual bool	score_fragment (FragmentCandidateOP, FragmentScoreMapOP)
	calculates all the small scores for a given fragment More...

void	use_late_scoring_for_zeros (const bool if_true)
	those score metohods that have weight = 0.0 will be computed after the fragments are picked More...

bool	if_late_scoring_for_zeros ()
	says if late scoring is used or not More...

bool	score_zero_scores (FragmentCandidateOP, FragmentScoreMapOP)
	calculates all these small scores for a given fragment whose weight is 0.0 More...

void	register_score_maker (MakeFragmentScoringMethodOP)
	registers a maker object that will be used to create a scoring method object More...

void	create_scoring_method (std::string const &, core::Size, core::Real, core::Real, bool, FragmentPickerOP, std::string)
	creates a new scoring method object More...

void	create_scores (std::string const &, FragmentPickerOP)
	reads a config file and creates scoring methods More...

void	do_caching (VallChunkOP chunk)
	calls do_caching() for each FragmentScoringMethod object, if it is possible More...

void	clean_up ()
	calls clean_up() for each FragmentScoringMethod object, if it is possible More...

void	set_width (FragmentScoringMethodOP which_score, core::Size width)
	sets up a new number of characters spend to print fragment score value More...

void	set_precision (FragmentScoringMethodOP which_score, core::Size precision)
	sets up a new precision used to print fragment score value More...

virtual void	describe_fragments (utility::vector1< std::pair< FragmentCandidateOP, scores::FragmentScoreMapOP > > const &, std::ostream &)
	prints a flat table with all scores for all the fragments in a given vector More...

Public Attributes
core::Size	default_width_
	default width used to print a score value, equal to 6 More...

core::Size	default_precision_
	default precision used to print a score value, equal to 1 More...

Static Public Attributes
static const core::Size	TOTAL_PRECISION = 3
	precision used to display the total score for each fragment More...

Protected Attributes
utility::vector1 < FragmentScoringMethodOP >	scores_

std::map < FragmentScoringMethodOP, core::Size >	width_

std::map < FragmentScoringMethodOP, core::Size >	precision_

Private Attributes
utility::vector1< core::Real >	score_weights_

std::map< std::string, MakeFragmentScoringMethodOP >	registered_makers_

bool	zeros_score_later_

Detailed Description

holds particular score components, weights and calculates the total score for a fragment candidate

a fragment picker object needs exactly one fragment manager to pick fragments. Adding new scoring methods is supposed to be done FragmentPicker, which calls proper method from this class.

Constructor & Destructor Documentation

protocols::frag_picker::scores::FragmentScoreManager::~FragmentScoreManager ( )

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

protocols::frag_picker::scores::FragmentScoreManager::FragmentScoreManager ( )

creates an empty manager

References default_precision_, default_width_, register_score_maker(), and zeros_score_later_.

Member Function Documentation

void protocols::frag_picker::scores::FragmentScoreManager::add_scoring_method	(	FragmentScoringMethodOP	scoring_term,
		core::Real	weight
	)

registers a new scoring method in this manager

References default_precision_, default_width_, precision_, score_weights_, scores_, protocols::frag_picker::scores::sort_scores(), and width_.

Referenced by create_scoring_method().

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

calls clean_up() for each FragmentScoringMethod object, if it is possible

FragmentPicker calls this method when a given chunk has been processed

References protocols::frag_picker::scores::CachingScoringMethod::clean_up(), protocols::hybridization::score, and scores_.

core::Size protocols::frag_picker::scores::FragmentScoreManager::count_components ( )

inline

says how many scoring methods have already been registered

References scores_.

FragmentScoreMapOP protocols::frag_picker::scores::FragmentScoreManager::create_empty_map ( )

creates an empty score map

this is the recommended way to create FragmentScoreMap objects since FragmentScoreManager knows exactly what is the correct size of the map i.e. how many scoring terms have been registered.

References score_weights_.

void protocols::frag_picker::scores::FragmentScoreManager::create_scores	(	std::string const &	file_name,
		FragmentPickerOP	picker
	)

reads a config file and creates scoring methods

References create_scoring_method().

void protocols::frag_picker::scores::FragmentScoreManager::create_scoring_method	(	std::string const &	score_name,
		core::Size	priority,
		core::Real	weight,
		core::Real	lowest,
		bool	use_lowest,
		FragmentPickerOP	picker,
		std::string	config_line
	)

creates a new scoring method object

References add_scoring_method(), and registered_makers_.

Referenced by create_scores().

void protocols::frag_picker::scores::FragmentScoreManager::describe_fragments	(	utility::vector1< std::pair< FragmentCandidateOP, scores::FragmentScoreMapOP > > const &	pairs,
		std::ostream &	out
	)

virtual

prints a flat table with all scores for all the fragments in a given vector

Reimplemented in protocols::frag_picker::scores::PValuedFragmentScoreManager.

References core::chemical::element::F, core::chemical::element::I, precision_, scores_, TOTAL_PRECISION, total_score(), protocols::frag_picker::scores::tr(), and width_.

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

calls do_caching() for each FragmentScoringMethod object, if it is possible

FragmentPicker calls this method when a new chunk is to be processed

References protocols::frag_picker::scores::CachingScoringMethod::do_caching(), protocols::hybridization::score, score_weights_, scores_, and zeros_score_later_.

FragmentScoringMethodOP protocols::frag_picker::scores::FragmentScoreManager::get_component ( core::Size index )

inline

Returns a desired scoring method.

Allowed index values are [1,count_components()]

References scores_.

FragmentScoringMethodOP protocols::frag_picker::scores::FragmentScoreManager::get_component_by_name ( std::string score_name )

inline

Returns a desired scoring method from its name rather than index.

Allowed inputs include the name of any scoring method as defined by get_score_name().

References core::conformation::membrane::out, and scores_.

utility::vector1<core::Real> protocols::frag_picker::scores::FragmentScoreManager::get_weights ( )

inline

returns a vector of weights that are used to compute the total score

References score_weights_.

bool protocols::frag_picker::scores::FragmentScoreManager::if_late_scoring_for_zeros ( )

inline

says if late scoring is used or not

late scoring means that some scores (those with weight=0, such as crmsd) are evaluated only for the selected fragments rather than for all the candidates

References zeros_score_later_.

void protocols::frag_picker::scores::FragmentScoreManager::register_score_maker ( MakeFragmentScoringMethodOP scoring_term_maker )

registers a maker object that will be used to create a scoring method object

References registered_makers_.

Referenced by FragmentScoreManager().

bool protocols::frag_picker::scores::FragmentScoreManager::score_fragment	(	FragmentCandidateOP	candidate,
		FragmentScoreMapOP	empty_map
	)

virtual

calculates all the small scores for a given fragment

results are properly stored inside a FragmentScoreMap object

Reimplemented in protocols::frag_picker::scores::PValuedFragmentScoreManager.

References protocols::hybridization::score, score_weights_, scores_, and zeros_score_later_.

Referenced by protocols::frag_picker::scores::PValuedFragmentScoreManager::score_fragment().

bool protocols::frag_picker::scores::FragmentScoreManager::score_fragment_from_cache	(	FragmentCandidateOP	candidate,
		FragmentScoreMapOP	empty_map
	)

virtual

calculates all the small scores for a given fragment

results are properly stored inside a FragmentScoreMap object

Reimplemented in protocols::frag_picker::scores::PValuedFragmentScoreManager.

References protocols::hybridization::score, score_weights_, scores_, and zeros_score_later_.

Referenced by protocols::frag_picker::scores::PValuedFragmentScoreManager::score_fragment_from_cache().

bool protocols::frag_picker::scores::FragmentScoreManager::score_zero_scores	(	FragmentCandidateOP	candidate,
		FragmentScoreMapOP	empty_map
	)

calculates all these small scores for a given fragment whose weight is 0.0

When use_late_scoring_for_zeros() was used to set the flag to true, all fragment scoring methods neglects zero-weighted scores. These will be evaluated by this function, that may be called after fragments are picked. This way some time consuming computations (e.g. crmsd for fragments) may be computed only for the selected fragments rather than for all of them

References score_weights_, and scores_.

void protocols::frag_picker::scores::FragmentScoreManager::set_precision	(	FragmentScoringMethodOP	which_score,
		core::Size	precision
	)

inline

sets up a new precision used to print fragment score value

References core::io::raw_data::precision(), and precision_.

void protocols::frag_picker::scores::FragmentScoreManager::set_width	(	FragmentScoringMethodOP	which_score,
		core::Size	width
	)

inline

sets up a new number of characters spend to print fragment score value

References width_.

void protocols::frag_picker::scores::FragmentScoreManager::show_scoring_methods ( std::ostream & out )

prints a nice table showing the registered scores

the table shows also the order in which the scores are evaluated

References score_weights_, and scores_.

core::Real protocols::frag_picker::scores::FragmentScoreManager::total_score ( FragmentScoreMapOP f )

calculates the total score

References score_weights_, and protocols::analysis::total.

Referenced by protocols::frag_picker::scores::PValuedFragmentScoreManager::describe_fragments(), and describe_fragments().

void protocols::frag_picker::scores::FragmentScoreManager::use_late_scoring_for_zeros ( const bool if_true )

inline

those score metohods that have weight = 0.0 will be computed after the fragments are picked

if weight for a score is 0.0 than it does not affect the total score and thus has no effect on fragments sorting, quota, etc. Such scores may be computed after fragment picking is finished

References zeros_score_later_.

Member Data Documentation

core::Size protocols::frag_picker::scores::FragmentScoreManager::default_precision_

default precision used to print a score value, equal to 1

Referenced by add_scoring_method(), and FragmentScoreManager().

core::Size protocols::frag_picker::scores::FragmentScoreManager::default_width_

default width used to print a score value, equal to 6

Referenced by add_scoring_method(), and FragmentScoreManager().

std::map<FragmentScoringMethodOP, core::Size> protocols::frag_picker::scores::FragmentScoreManager::precision_

protected

Referenced by add_scoring_method(), protocols::frag_picker::scores::PValuedFragmentScoreManager::describe_fragments(), describe_fragments(), and set_precision().

std::map<std::string, MakeFragmentScoringMethodOP> protocols::frag_picker::scores::FragmentScoreManager::registered_makers_

private

Referenced by create_scoring_method(), and register_score_maker().

utility::vector1<core::Real> protocols::frag_picker::scores::FragmentScoreManager::score_weights_

private

Referenced by add_scoring_method(), create_empty_map(), do_caching(), get_weights(), score_fragment(), score_fragment_from_cache(), score_zero_scores(), show_scoring_methods(), and total_score().

utility::vector1<FragmentScoringMethodOP> protocols::frag_picker::scores::FragmentScoreManager::scores_

protected

Referenced by add_scoring_method(), clean_up(), count_components(), protocols::frag_picker::scores::PValuedFragmentScoreManager::describe_fragments(), describe_fragments(), do_caching(), get_component(), get_component_by_name(), protocols::frag_picker::scores::PValuedFragmentScoreManager::score_fragment(), score_fragment(), protocols::frag_picker::scores::PValuedFragmentScoreManager::score_fragment_from_cache(), score_fragment_from_cache(), score_zero_scores(), and show_scoring_methods().

const core::Size protocols::frag_picker::scores::FragmentScoreManager::TOTAL_PRECISION = 3

static

precision used to display the total score for each fragment

Referenced by protocols::frag_picker::scores::PValuedFragmentScoreManager::describe_fragments(), and describe_fragments().

std::map<FragmentScoringMethodOP, core::Size> protocols::frag_picker::scores::FragmentScoreManager::width_

protected

Referenced by add_scoring_method(), protocols::frag_picker::scores::PValuedFragmentScoreManager::describe_fragments(), describe_fragments(), and set_width().

bool protocols::frag_picker::scores::FragmentScoreManager::zeros_score_later_

private

Referenced by do_caching(), FragmentScoreManager(), if_late_scoring_for_zeros(), score_fragment(), score_fragment_from_cache(), and use_late_scoring_for_zeros().

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

src/protocols/frag_picker/scores/FragmentScoreManager.hh
src/protocols/frag_picker/scores/FragmentScoreManager.cc

Public Member Functions

Public Attributes

Static Public Attributes

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation