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

#include <PValuedFragmentScoreManager.hh>

Inheritance diagram for protocols::frag_picker::scores::PValuedFragmentScoreManager:

Public Member Functions
	PValuedFragmentScoreManager ()
	creates an empty manager More...

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

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

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

Public Member Functions inherited from protocols::frag_picker::scores::FragmentScoreManager
	~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...

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...

Private Attributes
utility::vector1 < utility::vector1 < AdaptiveScoreHistogramOP > >	statistics_

Additional Inherited Members
Public Attributes inherited from protocols::frag_picker::scores::FragmentScoreManager
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 inherited from protocols::frag_picker::scores::FragmentScoreManager
static const core::Size	TOTAL_PRECISION = 3
	precision used to display the total score for each fragment More...

Protected Attributes inherited from protocols::frag_picker::scores::FragmentScoreManager
utility::vector1 < FragmentScoringMethodOP >	scores_

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

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

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::PValuedFragmentScoreManager::PValuedFragmentScoreManager ( )

inline

creates an empty manager

Member Function Documentation

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

overridevirtual

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

print the scores and associated p-values

If the manager allows for annotations, they will be printed as well

Reimplemented from protocols::frag_picker::scores::FragmentScoreManager.

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

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

overridevirtual

calculates all the small scores for a given fragment

results are properly stored inside a FragmentScoreMap object

Reimplemented from protocols::frag_picker::scores::FragmentScoreManager.

References protocols::frag_picker::scores::FragmentScoreManager::score_fragment(), protocols::frag_picker::scores::FragmentScoreManager::scores_, and statistics_.

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

overridevirtual

calculates all the small scores for a given fragment

results are properly stored inside a FragmentScoreMap object

Reimplemented from protocols::frag_picker::scores::FragmentScoreManager.

References protocols::frag_picker::scores::FragmentScoreManager::score_fragment_from_cache(), protocols::frag_picker::scores::FragmentScoreManager::scores_, and statistics_.

Member Data Documentation

utility::vector1<utility::vector1<AdaptiveScoreHistogramOP> > protocols::frag_picker::scores::PValuedFragmentScoreManager::statistics_

private

Referenced by describe_fragments(), score_fragment(), and score_fragment_from_cache().

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

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

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation