#include <IterativeAbrelax.hh>

Inheritance diagram for protocols::abinitio::IterativeAbrelax:

Public Member Functions
	IterativeAbrelax ()

void	initialize () override

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

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	old-batches might be outdated and should not be computed anymore return true for this query if this is the case for old_batch More...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

core::Size	generate_batch (jd2::archive::Batch &, core::Size repeat_id) override
	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	idle () override
	do some computations on archive that can be done while we are waiting More...

void	save_to_file (std::string suffix="") override
	save archive to file .. you can put 'suffix' at end of dirname to save other snapshots than the 'current' More...

void	save_status (std::ostream &) const override

bool	restore_from_file () override
	restore archive 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	read_structures (core::io::silent::SilentFileData &sfd, core::io::silent::SilentFileData &alternative_decoys, jd2::archive::Batch const &batch) override
	read 'returned_decoys' from 'batch' into archive. More...

void	set_manager (jd2::archive::BaseArchiveManagerAP manager) override

Public Member Functions inherited from protocols::abinitio::IterativeBase
	IterativeBase (std::string name)

	~IterativeBase () override

bool	finished () const override
	archive is finished when at last stage More...

void	initialize () override
	do initializing work that requires fully setup object here More...

void	set_finish_stage (IterationStage setting)
	where to stop ? More...

void	test_for_stage_end ()
	calls increment_stage() if appropriate More...

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

virtual bool	ready_for_batch () const
	we are always ready to generate a new batch More...

bool	still_interested (jd2::archive::Batch const &batch) const override
	we are not interested in batches that were generated in old stages More...

void	generate_batch () override
	generate a new batch, use different recipe according to current stage More...

core::Size	generate_batch (jd2::archive::Batch &, core::Size repeat_id) override

void	idle () override
	while waiting for jobs to finish More...

void	rescore () override

void	save_status (std::ostream &) const override

void	restore_status (std::istream &) override

bool	add_structure (core::io::silent::SilentStructOP new_decoy, core::io::silent::SilentStructOP alternative_decoy, jd2::archive::Batch const &) override
	overloaded to handel special convergence check 'pool_converged_rmsd' More...

void	setup_default_evaluators ()
	setup JumpNrEvaluator More...

void	read_structures (core::io::silent::SilentFileData &sfd, core::io::silent::SilentFileData &alternative_decoys, jd2::archive::Batch const &batch) override
	overloaded so we can test for end of IterationStage after reading More...

virtual void	gen_evaluation_output (jd2::archive::Batch &batch, bool fullatom=false)
	generate flags and stuff for the out-sourced evaluation —> such that score_final column is returned for each decoy note needs to be public, since IterativeCentroid calls this from IterativeFullatom to prepare evaluation for soon to be full-atom decoys More...

virtual void	gen_diversity_pool (jd2::archive::Batch &, bool fullatom=false)

virtual void	gen_dynamic_patches (jd2::archive::Batch &batch)

virtual void	update_noesy_filter_files (std::string const &current, bool fullatom)

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

	NormalizedEvaluatedArchive ()

	~NormalizedEvaluatedArchive () override

void	init_from_options ()

void	initialize () override

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

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

bool	determine_score_variations () const
	determine variation of scores (those that are non-zeros in select_weights_ ) More...

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

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

WeightMap const &	score_variations () const override

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

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...

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)

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

WeightMap const &	weights () const

EvaluatorMap const &	evaluators () const

void	set_weights (WeightMap const &setting)

void	set_evaluators (EvaluatorMap const &, WeightMap const &)

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

	~ArchiveBase () override

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

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 ()

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...

Static Public Member Functions
static void	register_options ()

Static Public Member Functions inherited from protocols::abinitio::IterativeBase
static void	register_options ()

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

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 ()

Private Types
typedef IterativeBase	Parent

Private Attributes
IterativeCentroid	centroid_archive_

IterativeFullatom	fullatom_archive_

bool	fullatom_

Static Private Attributes
static bool	options_registered_

Additional Inherited Members
Public Types inherited from protocols::abinitio::IterativeBase
enum	IterationStage { ENUMERATION = 1, TOPO_RESAMPLING, PURE_TOPO_RESAMPLING, STAGE2_RESAMPLING, NOESY_PHASEII_TOPO, NOESY_PHASEII_S2_RESAMPLING, CEN2FULLATOM, LAST_CENTROID_START = CEN2FULLATOM, RIGID_CORE_RESAMPLING, FINISHED }

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

Protected Types inherited from protocols::abinitio::IterativeBase
typedef utility::vector1 < core::io::silent::SilentStructOP >	SilentStructVector

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::abinitio::IterativeBase
void	set_noesy_assign_float_cycle (core::Real setting)

bool	super_quick_relax_of_centroids () const

void	gen_resample_topologies (jd2::archive::Batch &batch)
	----------— helper functions to be used from generate_batch() -----------------— More...

void	gen_start_structures (jd2::archive::Batch &batch)
	in the comp. modelling protocol the topo-resampling stage might also contain a RigidChunkClaimer... provide start-structures for this as -in:file:silent More...

void	gen_enumerate_pairings (jd2::archive::Batch &batch)

void	gen_resample_stage2 (jd2::archive::Batch &batch)
	restart runs from stage2-structures that correspond to those in the pool More...

void	gen_resample_fragments (jd2::archive::Batch &batch)

void	gen_cen2fullatom (jd2::archive::Batch &batch)

void	gen_cen2fullatom_non_pool_decoys (jd2::archive::Batch &batch)

void	collect_hedgeing_decoys_from_batches (jd2::archive::Batch const &batch, core::io::silent::SilentStructOPs &start_decoys, core::Real score_cut_per_batch)

void	add_fullatom_flags (jd2::archive::Batch &batch)

void	reassign_noesy_data (jd2::archive::Batch &batch)
	actually run the assignment machinery (only after batch is started to keep archive from hogging the queue... ) More...

void	gen_noe_assignments (jd2::archive::Batch &batch)
	generate cst-input from current assigned noesy data More...

PairingStatisticsOP	compute_beta_topology ()
	some helpers for the helpers More...

void	guess_pairings_from_secondary_structure (core::fragment::FragSet const &frags, std::string const &out_pairings_file, std::string const &out_frag_ss_file) const

void	compute_cores ()

std::string const &	fa_score () const
	these are set by the cmd-line options iterative::fa_score and iterative::fa_score_patch More...

std::string const &	fa_score_patch () const

std::string const &	cen_score () const
	these are set by the cmd-line options iterative::cen_score and iterative::cen_score_patch More...

std::string const &	cen_score_patch () const

core::Real	overall_cstfilter_weight () const
	this is set from score::atom_pair_constraint of the pool-scorefunction More...

void	set_overall_cstfilter_weight (core::Real setting)
	this is set from score::atom_pair_constraint of the pool-scorefunction More...

loops::Loops const &	core (core::Size i)
	OBSOLET cores are computed by compute_cores() in idle() More...

IterationStage	stage () const
	current stage? More...

std::string const &	target_sequence () const
	needed for writing of psi-pred fiels (guess_pairings_from_secondary_structure) More...

void	set_stage (IterationStage setting)

void	cluster ()
	cluster structures with min_diversity_list_[ stage_ ] as cluster:radius More...

std::string const &	chemshift_column () const

void	test_broker_settings (jd2::archive::Batch const &batch)
	Helper functions. More...

void	setup_filter_cst (core::Real weight)

virtual void	collect_alternative_decoys (SilentStructs, std::string, SilentStructVector &)

Protected Member Functions inherited from protocols::jd2::archive::NormalizedEvaluatedArchive
void	invalidate_score_variations () override

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

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 ()

Protected Attributes inherited from protocols::abinitio::IterativeBase
bool	never_switched_noe_filter_

loops::Loops	scored_core_

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 IterativeBase protocols::abinitio::IterativeAbrelax::Parent

private

Constructor & Destructor Documentation

protocols::abinitio::IterativeAbrelax::IterativeAbrelax ( )

References centroid_archive_, fullatom_, protocols::abinitio::IterativeBase::LAST_CENTROID_START, and protocols::abinitio::IterativeBase::set_finish_stage().

Member Function Documentation

bool protocols::abinitio::IterativeAbrelax::finished ( ) const

overridevirtual

is archive converged ?

Implements protocols::jd2::archive::AbstractArchiveBase.

References centroid_archive_, protocols::abinitio::IterativeBase::finished(), fullatom_, and fullatom_archive_.

void protocols::abinitio::IterativeAbrelax::generate_batch ( )

overridevirtual

ready for new batch .... if queue is empty batch will be generated any way, but otherwise we only generate if this yields true. logic here: new batch at beginning, but only if we are in startup phase ( not a reload of a full archive ) otherwise make new batch if sufficiently many structures have been accepted since last batch

generate new batch... type of batch depends on stage_. we switch to next stage based on some convergence criteria: right now it is how many decoys were accepted from last batch.. if this number drops sufficiently —> next stage... (maybe need to put a safeguard in here: ratio small but at least XXX decoys proposed since last batch... )

Implements protocols::jd2::archive::ArchiveBase.

References centroid_archive_, fullatom_, fullatom_archive_, protocols::abinitio::IterativeFullatom::generate_batch(), protocols::abinitio::IterativeBase::generate_batch(), and protocols::abinitio::IterativeFullatom::ready_for_batch().

core::Size protocols::abinitio::IterativeAbrelax::generate_batch	(	jd2::archive::Batch &	,
		core::Size
	)

overridevirtual

create a batch for the current stage, return ct != 0 if more batches should be created at current stage. (e.g., harvest_batches)

Reimplemented from protocols::jd2::archive::AbstractArchiveBase.

References centroid_archive_, fullatom_, fullatom_archive_, protocols::abinitio::IterativeFullatom::generate_batch(), protocols::abinitio::IterativeBase::generate_batch(), and protocols::abinitio::IterativeFullatom::ready_for_batch().

void protocols::abinitio::IterativeAbrelax::idle ( )

overridevirtual

do some computations on archive that can be done while we are waiting

Implements protocols::jd2::archive::AbstractArchiveBase.

References centroid_archive_, fullatom_, fullatom_archive_, protocols::abinitio::IterativeBase::idle(), protocols::jd2::archive::AbstractArchiveBase::name(), and tr().

void protocols::abinitio::IterativeAbrelax::init_from_decoy_set ( core::io::silent::SilentFileData const & sfd )

overridevirtual

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

Implements protocols::jd2::archive::EvaluatedArchive.

References centroid_archive_, and protocols::abinitio::IterativeBase::init_from_decoy_set().

void protocols::abinitio::IterativeAbrelax::initialize ( )

overridevirtual

Implements protocols::jd2::archive::AbstractArchiveBase.

References centroid_archive_, fullatom_, fullatom_archive_, protocols::abinitio::IterativeFullatom::initialize(), and protocols::abinitio::IterativeBase::initialize().

void protocols::abinitio::IterativeAbrelax::read_structures	(	core::io::silent::SilentFileData &	returned_decoys,
		core::io::silent::SilentFileData &	alternative_decoys,
		jd2::archive::Batch const &	batch
	)