represents a single pool used by quota selector More...

#include <ABEGO_SS_Pool.hh>

Inheritance diagram for protocols::frag_picker::quota::ABEGO_SS_Pool:

Public Member Functions
	ABEGO_SS_Pool (core::Size, std::string, utility::vector1< std::pair< core::Size, core::Size > >, utility::vector1< core::Size >, utility::vector1< core::Real >, core::Real, core::Size, core::Size)
	Creates a pool of a given size and name. More...

bool	accepts (char ss_type, char abego_type)

	~ABEGO_SS_Pool () override

core::Size	total_size () const override
	Says how many fragments (in total) may fit into this pool. More...

core::Size	current_size () const override
	Says how many fragments are currently in this pool. More...

core::Size	size_left () const override
	Says how many fragments can still be inserted into this pool. More...

bool	could_be_accepted (ScoredCandidate candidate) const override

void	resize (core::Size new_size)

void	set_fraction (core::Real new_fraction) override
	Sets the fraction of this quota pool in the entire population of fragments. More...

void	push (ScoredCandidate candidate) override
	Push a fragment candidate into the container. More...

bool	add (ScoredCandidate) override
	Insert a fragment candidate to the container. More...

void	clear () override
	removes all candidates from the container More...

core::Size	count_candidates (core::Size) const override
	Check how many candidates have been already collected for a given position. More...

core::Size	count_candidates () const override
	Check how many candidates have been already collected for all positions. More...

core::Size	query_length () const override
	Check the size of query sequence that this object knows. More...

void	insert (core::Size, CandidatesCollectorOP collector) override
	Inserts candidates from another Collector for a give position in the query Candidates may or may not get inserted depending on the candidate. More...

ScoredCandidatesVector1 &	get_candidates (core::Size) override
	Returns all the candidate in this pool. More...

void	print_report (std::ostream &, scores::FragmentScoreManagerOP) const override
	Describes what has been collected. More...

core::Real	quota_score (ScoredCandidate candidate) const override
	provides the score for a candidate that was used to sort a quota pool More...

Public Member Functions inherited from protocols::frag_picker::quota::QuotaPool
	QuotaPool (std::string const &pool_name, core::Real quota_fraction)
	Creates a pool of a given size and name. More...

	~QuotaPool () override

std::string const &	get_pool_name () const
	returns the name assigned to this quota pool More...

virtual void	show_availability (std::ostream &where) const
	prints information on which fragments can be accepted by this pool and how many of them More...

core::Real	get_fraction () const
	returns the fraction of this quota pool in the entire population of fragments More...

Private Attributes
core::Size	total_size_

core::Size	this_size_

core::Size	buffer_factor_

ABEGO_SS_MapOP	ss_abego_types_

utility::vector1< core::Size >	components_

utility::vector1< core::Real >	weights_

BoundedQuotaContainerOP	storage_

Static Private Attributes
static char	all_abego_ []

static char	all_ss_ []

Detailed Description

represents a single pool used by quota selector

Constructor & Destructor Documentation

protocols::frag_picker::quota::ABEGO_SS_Pool::ABEGO_SS_Pool	(	core::Size	total_size,
		std::string	pool_name,
		utility::vector1< std::pair< core::Size, core::Size > >	ss_abego_types,
		utility::vector1< core::Size >	which_components,
		utility::vector1< core::Real >	weights,
		core::Real	fraction,
		core::Size	n_scores,
		core::Size	buffer_factor = `5`
	)

Creates a pool of a given size and name.

Parameters

size	- total number of fragments from all the pools at a given position
name	- name assigned to this pool. This in general may be any string that later allows one control pool's behavior from a flag file
abego_ss_pairs	- what types of secondary structure and ABEGO this pool is accepting
score_components_id	- which scores will be used to sort this pool
weights	- weights for the scores that in general may be different than these used for fragment picking
fraction	- fraction of this pool in the entire population
total_size	- how many fragments will be selected (in total in all pools)
name	- name assigned to this pool. This in general may be any string that later allows one control pool's behavior from a flag file
ss_type	- what is the type of secondary structur this pool is accepting
fraction	- fraction of the total number of fragments that goes into this pool

References buffer_factor_, components_, ss_abego_types_, storage_, this_size_, total_size(), total_size_, protocols::frag_picker::quota::trABEGO_SS_Pool(), and weights_.

protocols::frag_picker::quota::ABEGO_SS_Pool::~ABEGO_SS_Pool ( )

overridedefault

Member Function Documentation

bool protocols::frag_picker::quota::ABEGO_SS_Pool::accepts	(	char	ss_type,
		char	abego_type
	)

inline

References ss_abego_types_.

bool protocols::frag_picker::quota::ABEGO_SS_Pool::add ( ScoredCandidate candidate )

overridevirtual

Insert a fragment candidate to the container.

Implements protocols::frag_picker::CandidatesCollector.

References could_be_accepted(), and storage_.

void protocols::frag_picker::quota::ABEGO_SS_Pool::clear ( )

inlineoverridevirtual

removes all candidates from the container

Implements protocols::frag_picker::quota::QuotaPool.

References storage_.

bool protocols::frag_picker::quota::ABEGO_SS_Pool::could_be_accepted ( ScoredCandidate candidate ) const

overridevirtual

Implements protocols::frag_picker::quota::QuotaPool.

References ss_abego_types_, and protocols::frag_picker::quota::torsion2big_bin_id().

Referenced by add().

core::Size protocols::frag_picker::quota::ABEGO_SS_Pool::count_candidates ( core::Size ) const

inlineoverridevirtual

Check how many candidates have been already collected for a given position.

This is a very special case - collector will be used only for a given position. Thus it returns the total number of inserted candidates, as count_candidates() does

Implements protocols::frag_picker::CandidatesCollector.

References current_size().

core::Size protocols::frag_picker::quota::ABEGO_SS_Pool::count_candidates ( ) const

inlineoverridevirtual

Check how many candidates have been already collected for all positions.

Implements protocols::frag_picker::quota::QuotaPool.

References current_size().

core::Size protocols::frag_picker::quota::ABEGO_SS_Pool::current_size ( ) const

inlineoverridevirtual

Says how many fragments are currently in this pool.

Implements protocols::frag_picker::quota::QuotaPool.

References storage_.

Referenced by count_candidates(), print_report(), and size_left().

ScoredCandidatesVector1& protocols::frag_picker::quota::ABEGO_SS_Pool::get_candidates ( core::Size )

inlineoverridevirtual

Returns all the candidate in this pool.

Implements protocols::frag_picker::CandidatesCollector.

References storage_.

void protocols::frag_picker::quota::ABEGO_SS_Pool::insert	(	core::Size	,
		CandidatesCollectorOP	collector
	)

inlineoverridevirtual

Inserts candidates from another Collector for a give position in the query Candidates may or may not get inserted depending on the candidate.

Implements protocols::frag_picker::CandidatesCollector.

References core::pack::dunbrack::c, and storage_.

void protocols::frag_picker::quota::ABEGO_SS_Pool::print_report	(	std::ostream &	out,
		scores::FragmentScoreManagerOP
	)		const

overridevirtual

Describes what has been collected.

Implements protocols::frag_picker::CandidatesCollector.

References current_size(), and protocols::frag_picker::quota::QuotaPool::get_pool_name().

void protocols::frag_picker::quota::ABEGO_SS_Pool::push ( ScoredCandidate candidate )

inlineoverridevirtual

Push a fragment candidate into the container.

Implements protocols::frag_picker::quota::QuotaPool.

References storage_.

core::Size protocols::frag_picker::quota::ABEGO_SS_Pool::query_length ( ) const

inlineoverridevirtual

Check the size of query sequence that this object knows.

This is a very special case - collector will be used only for a given position and it does NOT know the tolal size. Thus it returns always 0

Implements protocols::frag_picker::CandidatesCollector.

core::Real protocols::frag_picker::quota::ABEGO_SS_Pool::quota_score ( ScoredCandidate candidate ) const

inlineoverridevirtual

provides the score for a candidate that was used to sort a quota pool

This base class returns the most recent total score for a fragment

Reimplemented from protocols::frag_picker::quota::QuotaPool.

References components_, and weights_.

void protocols::frag_picker::quota::ABEGO_SS_Pool::resize ( core::Size new_size )

inline

References buffer_factor_, and storage_.

void protocols::frag_picker::quota::ABEGO_SS_Pool::set_fraction ( core::Real new_fraction )

inlineoverridevirtual

Sets the fraction of this quota pool in the entire population of fragments.

Reimplemented from protocols::frag_picker::quota::QuotaPool.

References buffer_factor_, protocols::frag_picker::quota::QuotaPool::set_fraction(), storage_, this_size_, and total_size_.

core::Size protocols::frag_picker::quota::ABEGO_SS_Pool::size_left ( ) const

inlineoverridevirtual

Says how many fragments can still be inserted into this pool.

Implements protocols::frag_picker::quota::QuotaPool.

References current_size(), and total_size().

core::Size protocols::frag_picker::quota::ABEGO_SS_Pool::total_size ( ) const

inlineoverridevirtual

Says how many fragments (in total) may fit into this pool.

Implements protocols::frag_picker::quota::QuotaPool.

References storage_.

Referenced by ABEGO_SS_Pool(), and size_left().

Member Data Documentation

char protocols::frag_picker::quota::ABEGO_SS_Pool::all_abego_[]

staticprivate

char protocols::frag_picker::quota::ABEGO_SS_Pool::all_ss_[]

staticprivate

core::Size protocols::frag_picker::quota::ABEGO_SS_Pool::buffer_factor_

private

Referenced by ABEGO_SS_Pool(), resize(), and set_fraction().

utility::vector1<core::Size> protocols::frag_picker::quota::ABEGO_SS_Pool::components_

private

Referenced by ABEGO_SS_Pool(), and quota_score().

ABEGO_SS_MapOP protocols::frag_picker::quota::ABEGO_SS_Pool::ss_abego_types_

private

Referenced by ABEGO_SS_Pool(), accepts(), and could_be_accepted().

BoundedQuotaContainerOP protocols::frag_picker::quota::ABEGO_SS_Pool::storage_

private

Referenced by ABEGO_SS_Pool(), add(), clear(), current_size(), get_candidates(), insert(), push(), resize(), set_fraction(), and total_size().

core::Size protocols::frag_picker::quota::ABEGO_SS_Pool::this_size_

private

Referenced by ABEGO_SS_Pool(), and set_fraction().

core::Size protocols::frag_picker::quota::ABEGO_SS_Pool::total_size_

private

Referenced by ABEGO_SS_Pool(), and set_fraction().

utility::vector1<core::Real> protocols::frag_picker::quota::ABEGO_SS_Pool::weights_

private

Referenced by ABEGO_SS_Pool(), and quota_score().

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

src/protocols/frag_picker/quota/ABEGO_SS_Pool.hh
src/protocols/frag_picker/quota/ABEGO_SS_Pool.cc

Public Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation