#include <IterativeFullatom.hh>

Inheritance diagram for protocols::abinitio::IterativeFullatom:

Collaboration diagram for protocols::abinitio::IterativeFullatom:

Public Member Functions
	IterativeFullatom ()

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

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

virtual void	generate_batch ()

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

	~IterativeBase ()

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

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

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

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

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

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

virtual void	rescore ()

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

virtual void	restore_status (std::istream &)

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

void	setup_default_evaluators ()
	setup JumpNrEvaluator More...

virtual void	read_structures (core::io::silent::SilentFileData &returned_decoys, jd2::archive::Batch const &batch)
	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 ()

void	init_from_options ()

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

virtual bool	restore_from_file ()
	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...

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

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

virtual WeightMap const &	score_variations () const

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

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

	EvaluatedArchive ()

	~EvaluatedArchive ()

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	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=NULL)

	~ArchiveBase ()

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...

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 ()

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)

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 ()

Protected Member Functions
void	gen_resample_core (jd2::archive::Batch &batch, bool flex)

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)

void	setup_filter_cst (core::Real weight)

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

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)

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 IterativeBase	Parent

Private Attributes
core::Real	perturb_start_structures_

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 }

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 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

Detailed Description

Definition at line 46 of file IterativeFullatom.hh.

Member Typedef Documentation

typedef IterativeBase protocols::abinitio::IterativeFullatom::Parent

private

Definition at line 47 of file IterativeFullatom.hh.

Constructor & Destructor Documentation

protocols::abinitio::IterativeFullatom::IterativeFullatom ( )

Definition at line 84 of file IterativeFullatom.cc.

References perturb_start_structures_.

Member Function Documentation

void protocols::abinitio::IterativeFullatom::gen_resample_core	(	jd2::archive::Batch &	batch,
		bool	flex
	)

protected

============================================================================ --------— methods to make new batches ---------—

--— each method should only "append" to broker and flags --—

Definition at line 190 of file IterativeFullatom.cc.

References protocols::abinitio::IterativeBase::add_fullatom_flags(), core::io::silent::SilentFileData::add_structure(), protocols::jd2::archive::Batch::broker_file(), protocols::abinitio::IterativeBase::core(), protocols::jd2::archive::ArchiveBase::decoys(), protocols::jd2::archive::Batch::dir(), protocols::jd2::archive::Batch::flag_file(), protocols::jd2::archive::Batch::nstruct(), protocols::loops::Loops::num_loop(), perturb_start_structures_, protocols::jd2::archive::Batch::set_has_silent_in(), protocols::jd2::archive::Batch::silent_in(), core::io::silent::SilentFileData::write_all(), and protocols::loops::Loops::write_loops_to_file().

Referenced by generate_batch().

void protocols::abinitio::IterativeFullatom::generate_batch ( )

virtual

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... )

Reimplemented from protocols::abinitio::IterativeBase.

Definition at line 147 of file IterativeFullatom.cc.

References protocols::jd2::archive::Batch::batch(), protocols::abinitio::IterativeBase::cluster(), protocols::jd2::archive::ArchiveManager::finalize_batch(), protocols::abinitio::IterativeBase::gen_evaluation_output(), protocols::abinitio::IterativeBase::gen_noe_assignments(), gen_resample_core(), protocols::abinitio::IterativeBase::gen_resample_fragments(), protocols::jd2::archive::AbstractArchiveBase::manager(), protocols::jd2::archive::AbstractArchiveBase::name(), protocols::abinitio::IterativeBase::reassign_noesy_data(), protocols::abinitio::IterativeBase::RIGID_CORE_RESAMPLING, protocols::jd2::archive::Batch::set_intermediate_structs(), protocols::abinitio::IterativeBase::stage(), and tr().