Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input. More...

#include <EvaluatedArchive.hh>

Inheritance diagram for protocols::jd2::archive::EvaluatedArchive:

[legend]

Public Types
typedef std::map< std::string, core::Real >	WeightMap
	typedefs for Evaluators and Weights More...

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

Public Member Functions
	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 @detail 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	init_from_decoy_set (core::io::silent::SilentFileData const &sfd) override=0
	overloaded to make input decoys appear the same as decoys coming from batches 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 @detail will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct More...

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

void	generate_batch () override=0
	create a new batch with manager().start_new_batch() and manager().finalize_batch(); More...

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)

Static Public Member Functions
static void	register_options ()
	Archive specific options. More...

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

Protected Member Functions
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 ()

Private Types
typedef ArchiveBase	Parent

Private Member Functions
virtual core::io::silent::SilentStructOP	evaluate_pose (core::io::silent::SilentStructOP result, core::pose::Pose &input_pose) const
	call score( pose ) and collect energies into result this is low-level function: it expects that result already contains the coordinates of the pose for convenience the pointer result is also return value More...

void	sort ()
	re-sort decoys based on select_score More...

Private Attributes
core::scoring::ScoreFunctionOP	scorefxn_
	scorefxn_ for evaluate( SilentStruct, Pose const& ) More...

WeightMap	select_weights_
	Evaluators and weights for select_score and evaluate. More...

EvaluatorMap	evaluators_

WeightMap	dummy_score_variations_

bool	scores_are_clean_
	keep track wether cached scores in archive_select_score are up-to-date More...

bool	b_evaluate_incoming_decoys_
	local evaluation or is evaluation outsourced to slave nodes? More...

time_t	start_eval_time_

VarianceStatisticsArchiveOP	variance_archive_

Static Private Attributes
static bool	options_registered_
	keep track whether our options have been registered at start up More...

Additional Inherited Members
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

Detailed Description

Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input.

This job distributor is meant for running jobs where the machine you are using has a large number of processors, the number of jobs is much greater than the number of processors, or the runtimes of the individual jobs could vary greatly. It dedicates the head node (whichever processor gets processor rank #0) to handling job requests from the slave nodes (all nonzero ranks). Unlike the MPIWorkPartitionJobDistributor, this JD will not work at all without MPI and the implementations of all but the interface functions have been put inside of ifdef directives. Generally each function has a master and slave version, and the interface functions call one or the other depending on processor rank.

Member Typedef Documentation

◆ EvaluatorMap

typedef std::map< std::string, evaluation::PoseEvaluatorCOP > protocols::jd2::archive::EvaluatedArchive::EvaluatorMap

◆ Parent

typedef ArchiveBase protocols::jd2::archive::EvaluatedArchive::Parent

private

◆ WeightMap

typedef std::map< std::string, core::Real > protocols::jd2::archive::EvaluatedArchive::WeightMap

typedefs for Evaluators and Weights

Constructor & Destructor Documentation

◆ EvaluatedArchive() [1/2]

protocols::jd2::archive::EvaluatedArchive::EvaluatedArchive ( ArchiveManagerAP ptr )

Constructor and Destructor.

References options_registered_, and setup_default_evaluators().

◆ EvaluatedArchive() [2/2]

protocols::jd2::archive::EvaluatedArchive::EvaluatedArchive ( )

References OBSOLETE, options_registered_, and setup_default_evaluators().

◆ ~EvaluatedArchive()

protocols::jd2::archive::EvaluatedArchive::~EvaluatedArchive ( )

overridedefault

Member Function Documentation

◆ add_evaluated_structure()

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

virtual

add an evaluated decoy to Archive (i.e, evaluated_decoy = evaluate( some_decoy ) );

Reimplemented in protocols::abinitio::HedgeArchive, protocols::jd2::archive::VarianceStatisticsArchive, and protocols::jd2::archive::NormalizedEvaluatedArchive.

References protocols::jd2::archive::ArchiveBase::add_structure_at_position(), protocols::jd2::archive::ArchiveBase::decoys(), core::sequence::end, protocols::jd2::archive::ArchiveBase::nstruct(), select_score(), start_eval_time_, and protocols::jd2::tr().

Referenced by protocols::jd2::archive::NormalizedEvaluatedArchive::add_evaluated_structure(), and add_structure().

◆ add_evaluation()

void protocols::jd2::archive::EvaluatedArchive::add_evaluation	(	evaluation::PoseEvaluatorCOP	eval,
		core::Real	weight = `0.0`
	)

add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()

References core::energy_methods::eval(), evaluators_, protocols::jd2::archive::AbstractArchiveBase::name(), scores_are_clean_, set_weight(), and protocols::jd2::tr().

◆ add_structure()

bool protocols::jd2::archive::EvaluatedArchive::add_structure	(	core::io::silent::SilentStructOP	new_decoy,
		core::io::silent::SilentStructOP	alternative_decoy,
		Batch const &	batch
	)

overridevirtual

add decoy to Archive @detail evaluate decoy and call add_evaluated_structure

Reimplemented from protocols::jd2::archive::ArchiveBase.

References add_evaluated_structure(), evaluate_silent_struct(), and protocols::jd2::tr().

◆ evaluate_local()

bool protocols::jd2::archive::EvaluatedArchive::evaluate_local ( ) const

inline

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

References b_evaluate_incoming_decoys_.

◆ evaluate_pose()

core::io::silent::SilentStructOP protocols::jd2::archive::EvaluatedArchive::evaluate_pose	(	core::io::silent::SilentStructOP	result,
		core::pose::Pose &	input_pose
	)		const

privatevirtual

call score( pose ) and collect energies into result this is low-level function: it expects that result already contains the coordinates of the pose for convenience the pointer result is also return value

@detail evaluate a pose ... store info in iss (and return the same for convenience )

References evaluators_, score(), and protocols::jd2::tr().

Referenced by evaluate_silent_struct().

◆ evaluate_silent_struct()

core::io::silent::SilentStructOP protocols::jd2::archive::EvaluatedArchive::evaluate_silent_struct ( core::io::silent::SilentStructOP iss ) const

yields an "evaluated" silent-struct which can be queried with select_score @detail will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct

evaluate decoy... if non-local evaluation just copy silent-struct

References core::scoring::Energies::clear(), core::pose::Pose::data(), core::pose::Pose::energies(), evaluate_local(), evaluate_pose(), start_eval_time_, start_evaluation_timer(), and protocols::jd2::tr().

Referenced by add_structure(), protocols::abinitio::IterativeBase::add_structure(), and rescore().

◆ evaluators()

EvaluatorMap const& protocols::jd2::archive::EvaluatedArchive::evaluators ( ) const

inline

References evaluators_.

Referenced by protocols::abinitio::IterativeBase::collect_hedge_structures(), protocols::abinitio::IterativeBase::rescore(), protocols::jd2::archive::NormalizedEvaluatedArchive::rescore(), and set_evaluators().

◆ get_weight()

core::Real protocols::jd2::archive::EvaluatedArchive::get_weight ( std::string const & column ) const

References select_weights_.

Referenced by protocols::abinitio::IterativeBase::do_dynamic_patching(), protocols::abinitio::IterativeBase::reassign_noesy_data(), protocols::abinitio::IterativeBase::replace_noesy_filter_constraints(), and protocols::abinitio::IterativeBase::restore_status().

◆ has_evaluator()

bool protocols::jd2::archive::EvaluatedArchive::has_evaluator ( std::string const & column )

is a certain elvaluator present ?

References evaluators_.

◆ init_from_decoy_set()

void protocols::jd2::archive::EvaluatedArchive::init_from_decoy_set ( core::io::silent::SilentFileData const & sfd )

overridepure virtual

overloaded to make input decoys appear the same as decoys coming from batches

Reimplemented from protocols::jd2::archive::ArchiveBase.

Implemented in protocols::abinitio::IterativeBase, protocols::jd2::archive::VarianceStatisticsArchive, protocols::abinitio::IterativeAbrelax, and protocols::abinitio::HedgeArchive.

◆ invalidate_score_variations()

virtual void protocols::jd2::archive::EvaluatedArchive::invalidate_score_variations ( )

inlineprotectedvirtual

Reimplemented in protocols::jd2::archive::NormalizedEvaluatedArchive.

Referenced by protocols::jd2::archive::VarianceStatisticsArchive::add_evaluated_structure(), and set_weight().

◆ read_structures()

void protocols::jd2::archive::EvaluatedArchive::read_structures	(	core::io::silent::SilentFileData &	sfd,
		core::io::silent::SilentFileData &	alternative_decoys,
		Batch const &	batch
	)

overridevirtual

only overloaded this to add some verbosity each time we read structures

Reimplemented from protocols::jd2::archive::ArchiveBase.

References protocols::jd2::archive::Batch::batch(), evaluate_local(), protocols::jd2::archive::AbstractArchiveBase::name(), protocols::jd2::archive::ArchiveBase::read_structures(), score_variations(), scorefxn(), select_weights_, core::scoring::ScoreFunction::show_pretty(), and protocols::jd2::tr().

Referenced by protocols::abinitio::IterativeBase::read_structures().

◆ register_options()

void protocols::jd2::archive::EvaluatedArchive::register_options ( )

static

Archive specific options.

References protocols::evaluation::options_registered_, and protocols::moves::Mover::register_options().

◆ remove_evaluation()

void protocols::jd2::archive::EvaluatedArchive::remove_evaluation ( std::string const & column )

remove Evaluator

References evaluators_, protocols::jd2::archive::AbstractArchiveBase::name(), scores_are_clean_, select_weights_, and protocols::jd2::tr().

Referenced by protocols::abinitio::IterativeBase::init_from_decoy_set(), protocols::abinitio::IterativeFullatom::initialize(), and protocols::abinitio::IterativeBase::rescore_nonlocal_archive().

◆ rescore()

void protocols::jd2::archive::EvaluatedArchive::rescore ( )

virtual

recompute all score-values of all decoys and re-order the archive by (new) select_score

@detail rescore and sort archive

Reimplemented in protocols::jd2::archive::NormalizedEvaluatedArchive, protocols::abinitio::IterativeBase, and protocols::abinitio::HedgeArchive.

References protocols::jd2::archive::ArchiveBase::decoys(), evaluate_silent_struct(), protocols::jd2::archive::AbstractArchiveBase::name(), score_variations(), scores_are_clean_, select_weights_, sort(), and protocols::jd2::tr().

Referenced by protocols::jd2::archive::NormalizedEvaluatedArchive::rescore(), and select_score().

◆ restore_from_file()

bool protocols::jd2::archive::EvaluatedArchive::restore_from_file ( )

overridevirtual

overloaded that we can sort the pool after reading

@detail restore archive and sort

Reimplemented from protocols::jd2::archive::ArchiveBase.

Reimplemented in protocols::jd2::archive::NormalizedEvaluatedArchive.

References protocols::jd2::archive::ArchiveBase::restore_from_file(), scores_are_clean_, and sort().

Referenced by protocols::jd2::archive::NormalizedEvaluatedArchive::restore_from_file().

◆ save_to_file()

void protocols::jd2::archive::EvaluatedArchive::save_to_file ( std::string suffix = "" )

overridevirtual

overloaded to save / restore the variance_archive_

Reimplemented from protocols::jd2::archive::ArchiveBase.

Reimplemented in protocols::jd2::archive::NormalizedEvaluatedArchive.

References protocols::jd2::archive::ArchiveBase::save_to_file().

Referenced by protocols::jd2::archive::NormalizedEvaluatedArchive::save_to_file().

◆ score()

void protocols::jd2::archive::EvaluatedArchive::score ( core::pose::Pose & pose ) const

protectedvirtual

score a pose

@detail before we can apply score-fxn we have to add extra data: RDC, NOES, (not supported yet: PCS, ... )

Reimplemented in protocols::abinitio::IterativeBase.

References scorefxn().

Referenced by evaluate_pose(), and protocols::abinitio::IterativeBase::score().

◆ score_variation()

core::Real protocols::jd2::archive::EvaluatedArchive::score_variation ( std::string const & col ) const

virtual

Reimplemented in protocols::jd2::archive::NormalizedEvaluatedArchive.

◆ score_variations()

EvaluatedArchive::WeightMap const & protocols::jd2::archive::EvaluatedArchive::score_variations ( ) const

virtual

Reimplemented in protocols::jd2::archive::NormalizedEvaluatedArchive.

References dummy_score_variations_.

Referenced by read_structures(), rescore(), and select_score().

◆ scorefxn()

core::scoring::ScoreFunction const & protocols::jd2::archive::EvaluatedArchive::scorefxn ( ) const

References scorefxn_.

Referenced by protocols::abinitio::IterativeBase::do_dynamic_patching(), protocols::abinitio::IterativeBase::initialize(), protocols::abinitio::IterativeFullatom::initialize(), read_structures(), protocols::abinitio::IterativeBase::rescore(), protocols::jd2::archive::NormalizedEvaluatedArchive::rescore(), score(), and set_scorefxn().

◆ scorefxn_non_const()

core::scoring::ScoreFunctionOP protocols::jd2::archive::EvaluatedArchive::scorefxn_non_const ( )

protected

References scorefxn_.

Referenced by protocols::abinitio::IterativeBase::init_from_decoy_set().

◆ select_score()

Real protocols::jd2::archive::EvaluatedArchive::select_score ( core::io::silent::SilentStructOP evaluated_decoy )

compute score according to select_weights — this can contain any evaluator columns

@detail compute the score of an evaluated decoy

References evaluate_local(), protocols::jd2::archive::AbstractArchiveBase::name(), rescore(), score_variations(), scores_are_clean_, select_weights_, SPECIAL_INITIAL_DECOY_PENALTY(), core::simple_metrics::metrics::sum, and protocols::jd2::tr().

Referenced by add_evaluated_structure(), protocols::abinitio::HedgeArchive::add_evaluated_structure(), protocols::abinitio::IterativeBase::add_structure(), protocols::abinitio::IterativeBase::collect_hedgeing_decoys_from_batches(), and protocols::abinitio::HedgeArchive::restore_status().

◆ set_evaluate_local()

void protocols::jd2::archive::EvaluatedArchive::set_evaluate_local ( bool setting )

inline

References b_evaluate_incoming_decoys_.

Referenced by protocols::abinitio::HedgeArchive::HedgeArchive(), protocols::abinitio::IterativeBase::init_from_decoy_set(), and protocols::abinitio::IterativeBase::rescore_nonlocal_archive().

◆ set_evaluators()

void protocols::jd2::archive::EvaluatedArchive::set_evaluators	(	EvaluatorMap const &	evaluators,
		WeightMap const &	weights
	)

References add_evaluation(), evaluators(), evaluators_, and weights().

◆ set_scorefxn()

void protocols::jd2::archive::EvaluatedArchive::set_scorefxn ( core::scoring::ScoreFunctionOP scorefxn_ )

set scorefxn used for evaluation

References scorefxn(), scorefxn_, and scores_are_clean_.

Referenced by protocols::abinitio::IterativeBase::initialize(), protocols::abinitio::IterativeFullatom::initialize(), and protocols::abinitio::IterativeBase::rescore_nonlocal_archive().

◆ set_weight()

void protocols::jd2::archive::EvaluatedArchive::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 )

References dummy_score_variations_, invalidate_score_variations(), protocols::jd2::archive::AbstractArchiveBase::name(), scores_are_clean_, select_weights_, and protocols::jd2::tr().

Referenced by add_evaluation(), protocols::abinitio::IterativeBase::init_from_decoy_set(), protocols::abinitio::IterativeBase::initialize(), protocols::abinitio::IterativeFullatom::initialize(), protocols::abinitio::IterativeBase::rescore_nonlocal_archive(), set_weights(), protocols::abinitio::IterativeBase::setup_autoNOE(), and setup_default_evaluators().

◆ set_weights()

void protocols::jd2::archive::EvaluatedArchive::set_weights ( WeightMap const & setting )

References select_weights_, and set_weight().

◆ setup_default_evaluators()

void protocols::jd2::archive::EvaluatedArchive::setup_default_evaluators ( )

set common evaluators: eg. ConstraintEvaluator if -cst_file is present

References set_weight(), and SPECIAL_INITIAL_DECOY_PENALTY().

Referenced by EvaluatedArchive(), and protocols::abinitio::IterativeBase::setup_default_evaluators().

◆ sort()

void protocols::jd2::archive::EvaluatedArchive::sort ( )

private

re-sort decoys based on select_score

References protocols::jd2::archive::ArchiveBase::decoys().

Referenced by rescore(), and restore_from_file().

◆ start_evaluation_timer()

void protocols::jd2::archive::EvaluatedArchive::start_evaluation_timer ( ) const

References start_eval_time_, and protocols::jd2::tr().

Referenced by evaluate_silent_struct().

◆ weights()

WeightMap const& protocols::jd2::archive::EvaluatedArchive::weights ( ) const

inline

References select_weights_.

Referenced by protocols::abinitio::IterativeBase::collect_hedge_structures(), protocols::jd2::archive::NormalizedEvaluatedArchive::determine_score_variations(), protocols::abinitio::get_core(), protocols::abinitio::IterativeBase::rescore(), protocols::jd2::archive::NormalizedEvaluatedArchive::rescore(), and set_evaluators().

Member Data Documentation

◆ b_evaluate_incoming_decoys_

bool protocols::jd2::archive::EvaluatedArchive::b_evaluate_incoming_decoys_

private

local evaluation or is evaluation outsourced to slave nodes?

Referenced by evaluate_local(), and set_evaluate_local().

◆ dummy_score_variations_

WeightMap protocols::jd2::archive::EvaluatedArchive::dummy_score_variations_

private

Referenced by score_variations(), and set_weight().

◆ evaluators_

EvaluatorMap protocols::jd2::archive::EvaluatedArchive::evaluators_

private

Referenced by add_evaluation(), evaluate_pose(), evaluators(), has_evaluator(), remove_evaluation(), and set_evaluators().

◆ options_registered_

bool protocols::jd2::archive::EvaluatedArchive::options_registered_

staticprivate

keep track whether our options have been registered at start up

Referenced by EvaluatedArchive().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::jd2::archive::EvaluatedArchive::scorefxn_

private

scorefxn_ for evaluate( SilentStruct, Pose const& )

Referenced by scorefxn(), scorefxn_non_const(), and set_scorefxn().

◆ scores_are_clean_

bool protocols::jd2::archive::EvaluatedArchive::scores_are_clean_

mutableprivate

keep track wether cached scores in archive_select_score are up-to-date

Referenced by add_evaluation(), remove_evaluation(), rescore(), restore_from_file(), select_score(), set_scorefxn(), and set_weight().

◆ select_weights_

WeightMap protocols::jd2::archive::EvaluatedArchive::select_weights_

private

Evaluators and weights for select_score and evaluate.

Referenced by get_weight(), read_structures(), remove_evaluation(), rescore(), select_score(), set_weight(), set_weights(), and weights().

◆ start_eval_time_

time_t protocols::jd2::archive::EvaluatedArchive::start_eval_time_

mutableprivate

Referenced by add_evaluated_structure(), evaluate_silent_struct(), and start_evaluation_timer().

◆ variance_archive_

VarianceStatisticsArchiveOP protocols::jd2::archive::EvaluatedArchive::variance_archive_

private

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

src/protocols/jd2/archive/EvaluatedArchive.hh
src/protocols/jd2/archive/EvaluatedArchive.cc

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Types

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ EvaluatorMap

◆ Parent

◆ WeightMap

Constructor & Destructor Documentation

◆ EvaluatedArchive() [1/2]

◆ EvaluatedArchive() [2/2]

◆ ~EvaluatedArchive()

Member Function Documentation

◆ add_evaluated_structure()

◆ add_evaluation()

◆ add_structure()

◆ evaluate_local()

◆ evaluate_pose()

◆ evaluate_silent_struct()

◆ evaluators()

◆ get_weight()

◆ has_evaluator()

◆ init_from_decoy_set()

◆ invalidate_score_variations()

◆ read_structures()

◆ register_options()

◆ remove_evaluation()

◆ rescore()

◆ restore_from_file()

◆ save_to_file()

◆ score()

◆ score_variation()

◆ score_variations()

◆ scorefxn()

◆ scorefxn_non_const()

◆ select_score()

◆ set_evaluate_local()

◆ set_evaluators()

◆ set_scorefxn()

◆ set_weight()

◆ set_weights()

◆ setup_default_evaluators()

◆ sort()

◆ start_evaluation_timer()

◆ weights()

Member Data Documentation

◆ b_evaluate_incoming_decoys_

◆ dummy_score_variations_

◆ evaluators_

◆ options_registered_

◆ scorefxn_

◆ scores_are_clean_

◆ select_weights_

◆ start_eval_time_

◆ variance_archive_