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:

Collaboration diagram for protocols::frag_picker::scores::FragmentScoreManager:

Public Member Functions
	FragmentScoreManager ()
	creates an empty manager
FragmentScoreMapOP	create_empty_map ()
	creates an empty score map
void	add_scoring_method (FragmentScoringMethodOP, Real)
	registers a new scoring method in this manager
Size	count_components ()
	says how many scoring methods have already been registered
FragmentScoringMethodOP	get_component (Size index)
	Returns a desired scoring method.
utility::vector1< Real >	get_weights ()
	returns a vector of weights that are used to compute the total score
void	show_scoring_methods (std::ostream &out)
	prints a nice table showing the registered scores
Real	total_score (FragmentScoreMapOP)
	calculates the total score
virtual bool	score_fragment_from_cache (FragmentCandidateOP, FragmentScoreMapOP)
	calculates all the small scores for a given fragment
virtual bool	score_fragment (FragmentCandidateOP, FragmentScoreMapOP)
	calculates all the small scores for a given fragment
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
bool	if_late_scoring_for_zeros ()
	says if late scoring is used or not
bool	score_zero_scores (FragmentCandidateOP, FragmentScoreMapOP)
	calculates all these small scores for a given fragment whose weight is 0.0
void	register_score_maker (MakeFragmentScoringMethodOP)
	registers a maker object that will be used to create a scoring method object
void	create_scoring_method (std::string const &, Size, Real, Real, bool, FragmentPickerOP, std::string)
	creates a new scoring method object
void	create_scores (std::string const &, FragmentPickerOP)
	reads a config file and creates scoring methods
void	do_caching (VallChunkOP chunk)
	calls do_caching() for each FragmentScoringMethod object, if it is possible
void	clean_up ()
	calls clean_up() for each FragmentScoringMethod object, if it is possible
void	set_width (FragmentScoringMethodOP which_score, Size width)
	sets up a new number of characters spend to print fragment score value
void	set_precision (FragmentScoringMethodOP which_score, Size precision)
	sets up a new precision used to print fragment score value
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
Public Attributes
Size	default_width_
	default width used to print a score value, equal to 6
Size	default_precision_
	default precision used to print a score value, equal to 1
Static Public Attributes
static const Size	TOTAL_PRECISION = 3
	precision used to display the total score for each fragment
Protected Attributes
utility::vector1 < FragmentScoringMethodOP >	scores_
std::map < FragmentScoringMethodOP, Size >	width_
std::map < FragmentScoringMethodOP, Size >	precision_

Detailed Description

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

Detailed: 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 ( )

creates an empty manager

References default_precision_, default_width_, and register_score_maker().

Member Function Documentation

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

registers a new scoring method in this manager

References default_precision_, default_width_, precision_, 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

Detailed: FragmentPicker calls this method when a given chunk has been processed

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

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

Detailed: 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.

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,
		Size	priority,
		Real	weight,
		Real	lowest,
		bool	use_lowest,
		FragmentPickerOP	picker,
		std::string	config_line
	)

creates a new scoring method object

References add_scoring_method().

Referenced by create_scores().

virtual void protocols::frag_picker::scores::FragmentScoreManager::describe_fragments	(	utility::vector1< std::pair< FragmentCandidateOP, scores::FragmentScoreMapOP > > const &	,
		std::ostream &
	)		`[virtual]`

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

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

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

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

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

References protocols::frag_picker::scores::CachingScoringMethod::do_caching(), and scores_.

FragmentScoringMethodOP protocols::frag_picker::scores::FragmentScoreManager::get_component ( Size index ) [inline]

Returns a desired scoring method.

Detailed: Allowed index values are [1,count_components()]

References scores_.

utility::vector1<Real> protocols::frag_picker::scores::FragmentScoreManager::get_weights ( ) [inline]

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

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

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

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 scores_.

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::frag_picker::scores::CachingScoringMethod::cached_score(), and scores_.

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

Detailed: 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 scores_.

void protocols::frag_picker::scores::FragmentScoreManager::set_precision	(	FragmentScoringMethodOP	which_score,
		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,
		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

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

References scores_.

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

calculates the total score

Referenced by protocols::frag_picker::scores::PValuedFragmentScoreManager::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

Detailed: 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