#include <VarianceStatisticsArchive.hh>

Inheritance diagram for protocols::jd2::archive::VarianceStatisticsArchive:

Public Member Functions
	VarianceStatisticsArchive (std::string name)

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

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

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

void	set_insertion_prob (core::Real setting)

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

	EvaluatedArchive ()

	~EvaluatedArchive () override

bool	add_structure (core::io::silent::SilentStructOP new_decoy, core::io::silent::SilentStructOP alternative_decoy, Batch const &batch) override
	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...

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

void	read_structures (core::io::silent::SilentFileData &sfd, core::io::silent::SilentFileData &alternative_decoys, Batch const &batch) override
	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)

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

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 &)

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

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

	~ArchiveBase () override

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

void	initialize () override

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...

void	save_decoys (std::string const &dirname, std::string const &name, SilentStructs const &decoys)
	helper routine to save decoys properly More...

void	load_decoys (std::string const &filename, SilentStructs &decoys)

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

virtual void	restore_status (std::istream &)

void	idle () override
	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
	~AbstractArchiveBase () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...

	AbstractArchiveBase (BaseArchiveManagerAP 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...

virtual core::Size	generate_batch (jd2::archive::Batch &, core::Size)
	create a batch for the current stage, return ct != 0 if more batches should be created at current stage. (e.g., harvest_batches) 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

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

virtual void	set_manager (BaseArchiveManagerAP manager)

Private Types
typedef EvaluatedArchive	Parent

typedef utility::vector1 < core::io::silent::SilentStructOP >	SilentStructVector

Private Attributes
core::Real	insertion_prob_

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

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)

core::Size	max_nstruct ()

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

virtual void	erase_decoy (std::string const &tag)

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

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

static std::string const	SOURCE_FILE

Member Typedef Documentation

typedef EvaluatedArchive protocols::jd2::archive::VarianceStatisticsArchive::Parent

private

typedef utility::vector1< core::io::silent::SilentStructOP > protocols::jd2::archive::VarianceStatisticsArchive::SilentStructVector

private

Constructor & Destructor Documentation

protocols::jd2::archive::VarianceStatisticsArchive::VarianceStatisticsArchive ( std::string name )

References protocols::jd2::archive::AbstractArchiveBase::set_name().

Member Function Documentation

bool protocols::jd2::archive::VarianceStatisticsArchive::add_evaluated_structure	(	core::io::silent::SilentStructOP	evaluated_decoy,
		core::io::silent::SilentStructOP	alternative_decoy,
		Batch const &
	)