#include <HedgeArchive.hh>

Public Member Functions
	HedgeArchive (std::string name)

virtual bool	add_evaluated_structure (core::io::silent::SilentStructOP, jd2::archive::Batch const &batch)
	add an evaluated decoy to Archive (i.e, evaluated_decoy = evaluate( some_decoy ) ); More...

virtual void	generate_batch ()
	create a new batch with manager().start_new_batch() and manager().finalize_batch(); More...

virtual void	rescore ()
	recompute all score-values of all decoys and re-order the archive by (new) select_score More...

virtual void	save_status (std::ostream &) const
	save and restore status of archive to file-system More...

virtual void	restore_status (std::istream &)

virtual void	init_from_decoy_set (core::io::silent::SilentFileData const &)
	overloaded to make input decoys appear the same as decoys coming from batches More...

void	collect (jd2::archive::Batch const &batch, core::io::silent::SilentStructOPs &) const

Public Member Functions inherited from protocols::jd2::archive::EvaluatedArchive
	EvaluatedArchive (ArchiveManagerAP ptr)
	Constructor and Destructor. More...

	EvaluatedArchive ()

	~EvaluatedArchive ()

virtual bool	add_structure (core::io::silent::SilentStructOP from_batch, Batch const &)
	add decoy to Archive evaluate decoy and call add_evaluated_structure More...

core::Real	select_score (core::io::silent::SilentStructOP evaluated_decoy)
	compute score according to select_weights — this can contain any evaluator columns More...

void	setup_default_evaluators ()
	set common evaluators: eg. ConstraintEvaluator if -cst_file is present More...

virtual bool	restore_from_file ()
	overloaded that we can sort the pool after reading More...

virtual void	read_structures (core::io::silent::SilentFileData &, Batch const &batch)
	only overloaded this to add some verbosity each time we read structures More...

void	start_evaluation_timer () const

core::io::silent::SilentStructOP	evaluate_silent_struct (core::io::silent::SilentStructOP from_batch) const
	yields an "evaluated" silent-struct which can be queried with select_score will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct More...

bool	evaluate_local () const
	specify if decoys are evaluated on the master or (non-local i.e., on the individual slave nodes) More...

void	set_evaluate_local (bool setting)

void	add_evaluation (evaluation::PoseEvaluatorCOP, core::Real weight=0.0)
	add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score() More...

void	remove_evaluation (std::string const &column)
	remove Evaluator More...

bool	has_evaluator (std::string const &column)
	is a certain elvaluator present ? More...

void	set_weight (std::string const &column, core::Real weight)
	set weight of an evaluator or a column otherwise present in silent-structs (i.e, score, chainbreak, external evaluation like score_final ) More...

core::Real	get_weight (std::string const &column) const

void	set_scorefxn (core::scoring::ScoreFunctionOP scorefxn_)
	set scorefxn used for evaluation More...

core::scoring::ScoreFunction const &	scorefxn () const

virtual WeightMap const &	score_variations () const

virtual core::Real	score_variation (std::string const &col) const

WeightMap const &	weights () const

EvaluatorMap const &	evaluators () const

void	set_weights (WeightMap const &setting)

void	set_evaluators (EvaluatorMap const &, WeightMap const &)

virtual void	save_to_file (std::string suffix="")
	overloaded to save / restore the variance_archive_ More...

Public Member Functions inherited from protocols::jd2::archive::ArchiveBase
	ArchiveBase (ArchiveManagerAP ptr=NULL)

	~ArchiveBase ()

virtual bool	finished () const
	is archive converged ? More...

virtual void	initialize ()

core::Size	nstruct () const
	how many structures should be in archive .. varies from decoys().size() in startup phase. More...

void	set_nstruct (core::Size set)
	set target size of pool More...

virtual void	idle ()
	called when nothing is happening More...

core::Size &	accepts_since_last_batch ()

core::Size	accepts_since_last_batch () const

core::Size	proposed_since_last_batch () const

core::Real	current_acceptance_ratio () const

void	reset_accept_counter ()

core::Size	total_proposed ()

core::Size	total_accepts ()

bool	statistics_valid ()

SilentStructs const &	decoys () const

SilentStructs &	decoys ()

Public Member Functions inherited from protocols::jd2::archive::AbstractArchiveBase
virtual	~AbstractArchiveBase ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

	AbstractArchiveBase (ArchiveManagerAP ptr)

	AbstractArchiveBase ()

virtual bool	still_interested (jd2::archive::Batch const &) const
	old-batches might be outdated and should not be computed anymore return true for this query if this is the case for old_batch More...

void	set_name (std::string const &set)
	set name of archive ( used also for save_to_file and restore_from_file ) More...

std::string const &	name () const

ArchiveManager &	manager ()
	access to the ArchiveManager (control of batches) More...

virtual void	set_manager (ArchiveManagerAP manager)

Protected Member Functions
void	incorporate_batch (core::Size batch_id)

Protected Member Functions inherited from protocols::jd2::archive::EvaluatedArchive
core::scoring::ScoreFunctionOP	scorefxn_non_const ()

virtual void	score (core::pose::Pose &pose) const
	score a pose More...

virtual void	invalidate_score_variations ()

Protected Member Functions inherited from protocols::jd2::archive::ArchiveBase
virtual void	count_structure (Batch const &batch, bool accepted)
	count the structure for the acceptance statistics only count if not from expired batch More...

void	count_removed_structures (core::Size n_removed)
	count the structure for the acceptance statistics only count if not from expired batch More...

void	set_max_nstruct (core::Size setting)

void	add_structure_at_position (SilentStructs::iterator iss, core::io::silent::SilentStructOP new_decoy)
	call to insert structure at position given by iterator More...

Protected Member Functions inherited from protocols::jd2::archive::AbstractArchiveBase
ArchiveManagerAP	manager_ptr ()

Private Types
typedef jd2::archive::EvaluatedArchive	Parent

typedef std::list< std::pair < core::Real, core::io::silent::SilentStructOP > >	SilentStructs

typedef std::map< core::Size, SilentStructs >	BatchStructuresMap

typedef std::set< core::Size >	BatchList

Private Member Functions
void	save_decoys (SilentStructs const &decoys, core::Size batch_id) const

void	remove_decoys (core::Size batch_id) const

Private Attributes
core::Real	score_cut_per_batch_

core::Real	add_fuzzy_

BatchStructuresMap	incoming_structures_

BatchList	old_batches_

Additional Inherited Members
Public Types inherited from protocols::jd2::archive::EvaluatedArchive
typedef std::map< std::string, core::Real >	WeightMap
	typedefs for Evaluators and Weights More...

typedef std::map< std::string, evaluation::PoseEvaluatorCOP >	EvaluatorMap

Static Public Member Functions inherited from protocols::jd2::archive::EvaluatedArchive
static void	register_options ()
	Archive specific options. More...

Static Public Member Functions inherited from protocols::jd2::archive::ArchiveBase
static void	register_options ()

Protected Types inherited from protocols::jd2::archive::ArchiveBase
typedef std::list < core::io::silent::SilentStructOP >	SilentStructs

typedef SilentStructs::const_iterator	const_decoy_iterator

typedef SilentStructs::const_iterator	decoy_iterator

Static Protected Attributes inherited from protocols::jd2::archive::ArchiveBase
static std::string const	TAG_IN_FILE

static std::string const	SOURCE_FILE