#include <IterativeBase.hh>

Inheritance diagram for protocols::abinitio::IterativeBase:

[legend]

Public Types
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

Public Member Functions
	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 @detail 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 @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...

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 @detail 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...

virtual void	set_manager (BaseArchiveManagerAP manager)

Static Public Member Functions
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 Types
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
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
bool	never_switched_noe_filter_

loops::Loops	scored_core_

Private Types
typedef jd2::archive::NormalizedEvaluatedArchive	Parent

Private Member Functions
void	collect_hedge_structures (core::io::silent::SilentStructOP evaluated_decoy, jd2::archive::Batch const &batch)

void	score (core::pose::Pose &pose) const override
	score a pose with Pool-Scoring function (adds necessary data to pose (RDC, constraints, etc ) ) More...

core::Real	target_accept_ratio () const
	what is the expected lowest acceptance ratio at the current stage ? More...

void	add_core_evaluator (loops::Loops const &core, std::string const &core_tag)
	[OBSOLET] add score_coreX and rms_coreX evaluators (and columns) with 0.0 weight More...

void	increment_stage ()
	necessary steps to go to next stage... e.g., saving snapshot of archive More...

void	replace_noesy_filter_constraints ()

void	rescore_nonlocal_archive ()

void	setup_autoNOE ()

void	do_dynamic_patching (jd2::archive::Batch &batch, utility::io::ozstream &flags, std::string score, utility::options::FileVectorOptionKey const &key) const

Private Attributes
IterationStage	stage_
	--------------— – private data members – -----------------— More...

IterationStage	finish_stage_
	end-condition More...

core::Size	first_batch_this_stage_
	indices of prominent batches ( STATUS file ) More...

core::Size	first_fullatom_batch_

bool	bEnumeratedLastTime_
	toggle to keep track of the enumerate-pairings mode .. want to run this only every 2nd batch More...

core::Size	last_accepted_decoys_in_idle_
	[OBSOLET?] keep track when idle() has been run ... More...

loops::Loops	core15_
	core-regions — used in IterativeFullatom for the "rigid-core" sampling step... More...

loops::Loops	core2_

loops::Loops	core3_

loops::Loops	core4_

utility::vector1< int >	max_nstruct_list_
	--------— some cmd-line controlled settings --------------— More...

utility::vector1< core::Real >	min_diversity_list_
	cluster:radius for minimum diversity in stage X More...

utility::vector1< core::Real >	target_accept_ratio_
	minimum acceptance ratio .. current_accept_ratio < target_accept_ratio[ stage_ ] --> increment_stage More...

core::pose::PoseCOP	reference_pose_
	for RMSD ... e.g., in:file:native More...

std::string	cen_score_
	from cmd-line cen-score and patch names More...

std::string	cen_score_patch_

std::string	fa_score_
	from cmd-line fa-score and patch names More...

std::string	fa_score_patch_

core::Real	overall_cstfilter_weight_
	this is set from score::atom_pair_constraint of the pool-scorefunction More...

std::string	target_sequence_

protocols::noesy_assign::NoesyModuleOP	noesy_module_

core::Real	noesy_assign_float_cycle_

std::string	first_noesy_cst_file_

std::string	first_noesy_fa_cst_file_

std::string	current_noesy_sampling_file_

bool	bCombineNoesyCst_

size_t	noesy_assign_hash_

boost::hash< std::string >	hasher

std::string	chemshift_column_
	even in centroid mode the end of abinitio will have a fast relax... enables cs-score and noe-assignment More...

bool	bDoBetaJumping_

bool	super_quick_relax_of_centroids_
	even in centroid mode the end of abinitio will have a fast relax... enables cs-score and noe-assignment More...

bool	use_dynamic_weights_for_sampling_
	use the score_variations from EvaluatedArchive to determine new sampling weights More...

core::Size	delay_noesy_reassign_

HedgeArchiveOP	hedge_archive_

core::scoring::ResidualDipolarCouplingOP	rdc_data_
	cache some of the experimental data so we don't reload from file for each evaluation More...

core::scoring::constraints::ConstraintSetOP	cst_data_

core::scoring::constraints::ConstraintSetOP	cst_fa_data_

utility::options::OptionCollectionCOP	vanilla_options_
	---------------— register cmdline options ------------------------— More...

Static Private Attributes
static bool	options_registered_

Additional Inherited Members
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

◆ Parent

typedef jd2::archive::NormalizedEvaluatedArchive protocols::abinitio::IterativeBase::Parent

private

◆ SilentStructVector

typedef utility::vector1< core::io::silent::SilentStructOP > protocols::abinitio::IterativeBase::SilentStructVector

protected

Member Enumeration Documentation

◆ IterationStage

enum protocols::abinitio::IterativeBase::IterationStage

Enumerator
ENUMERATION
TOPO_RESAMPLING
PURE_TOPO_RESAMPLING
STAGE2_RESAMPLING
NOESY_PHASEII_TOPO
NOESY_PHASEII_S2_RESAMPLING
CEN2FULLATOM
LAST_CENTROID_START
RIGID_CORE_RESAMPLING
FINISHED

Constructor & Destructor Documentation

◆ IterativeBase()

protocols::abinitio::IterativeBase::IterativeBase ( std::string name )

References delay_noesy_reassign_, FINISHED, max_nstruct_list_, mem_tr, min_diversity_list_, never_switched_noe_filter_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::sequence::read_fasta_file(), reference_pose_, protocols::jd2::archive::AbstractArchiveBase::set_name(), target_accept_ratio_, target_sequence_, tr(), and warn_obsolete_flags().

◆ ~IterativeBase()

protocols::abinitio::IterativeBase::~IterativeBase ( )

overridedefault

Member Function Documentation

◆ add_core_evaluator()

void protocols::abinitio::IterativeBase::add_core_evaluator	(	loops::Loops const &	core,
		std::string const &	core_tag
	)

private

[OBSOLET] add score_coreX and rms_coreX evaluators (and columns) with 0.0 weight

References protocols::jd2::archive::EvaluatedArchive::add_evaluation(), protocols::jd2::archive::AbstractArchiveBase::name(), and reference_pose_.

Referenced by compute_cores().

◆ add_fullatom_flags()

void protocols::abinitio::IterativeBase::add_fullatom_flags ( jd2::archive::Batch & batch )

protected

References protocols::jd2::archive::Batch::broker_file(), first_fullatom_batch_, protocols::jd2::archive::Batch::flag_file(), and protocols::jd2::archive::Batch::id().

Referenced by gen_cen2fullatom(), gen_cen2fullatom_non_pool_decoys(), and protocols::abinitio::IterativeFullatom::gen_resample_core().

◆ add_structure()

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

overridevirtual

overloaded to handel special convergence check 'pool_converged_rmsd'

overload to check for pool_convergence data in incoming decoys

add structure to Archive.. return false if structure is rejected.

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

References protocols::jd2::archive::NormalizedEvaluatedArchive::add_evaluated_structure(), CEN2FULLATOM, protocols::ligand_docking::check_score(), collect_hedge_structures(), protocols::jd2::archive::ArchiveBase::decoys(), core::sequence::end, protocols::jd2::archive::ArchiveBase::erase_decoy(), protocols::jd2::archive::EvaluatedArchive::evaluate_silent_struct(), first_batch_this_stage_, protocols::jd2::archive::Batch::id(), min_diversity_list_, protocols::jd2::archive::EvaluatedArchive::select_score(), stage(), stage_, and tr().

◆ cen_score()

std::string const& protocols::abinitio::IterativeBase::cen_score ( ) const

inlineprotected

these are set by the cmd-line options iterative::cen_score and iterative::cen_score_patch

References cen_score_.

Referenced by initialize().

◆ cen_score_patch()

std::string const& protocols::abinitio::IterativeBase::cen_score_patch ( ) const

inlineprotected

References cen_score_patch_.

Referenced by initialize().

◆ chemshift_column()

std::string const& protocols::abinitio::IterativeBase::chemshift_column ( ) const

inlineprotected

References chemshift_column_.

Referenced by protocols::abinitio::IterativeFullatom::initialize().

◆ cluster()

void protocols::abinitio::IterativeBase::cluster ( )

protected

cluster structures with min_diversity_list_[ stage_ ] as cluster:radius

Referenced by protocols::abinitio::IterativeFullatom::generate_batch().

◆ collect_alternative_decoys()

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

inlineprotectedvirtual

Reimplemented in protocols::abinitio::IterativeCentroid.

Referenced by gen_resample_stage2().

◆ collect_hedge_structures()

void protocols::abinitio::IterativeBase::collect_hedge_structures	(	core::io::silent::SilentStructOP	evaluated_decoy,
		jd2::archive::Batch const &	batch
	)

private

References protocols::jd2::archive::EvaluatedArchive::evaluators(), hedge_archive_, protocols::jd2::archive::AbstractArchiveBase::name(), and protocols::jd2::archive::EvaluatedArchive::weights().

Referenced by add_structure().

◆ collect_hedgeing_decoys_from_batches()

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

protected

References protocols::jd2::archive::Batch::batch(), core::io::silent::SilentFileData::begin(), core::io::silent::SilentFileData::end(), first_fullatom_batch_, protocols::jd2::archive::AbstractArchiveBase::manager(), protocols::jd2::archive::Batch::nstruct(), core::io::silent::SilentFileData::read_file(), core::scoring::rg, protocols::jd2::archive::EvaluatedArchive::select_score(), protocols::analysis::total, and tr().

Referenced by gen_cen2fullatom_non_pool_decoys().

◆ compute_beta_topology()

PairingStatisticsOP protocols::abinitio::IterativeBase::compute_beta_topology ( )

protected

some helpers for the helpers

============================================================================ --------— methods to compute stuff from archive ---------—

--------— these may be called from idle() ---------—

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

Referenced by gen_resample_topologies().

◆ compute_cores()

void protocols::abinitio::IterativeBase::compute_cores ( )

protected

References add_core_evaluator(), core15_, core2_, core3_, core4_, protocols::jd2::archive::ArchiveBase::decoys(), core::sequence::end, core::energy_methods::eval(), protocols::abinitio::get_core(), protocols::mean_field::min(), protocols::jd2::archive::ArchiveBase::nstruct(), and tr().

Referenced by idle(), and restore_status().

◆ core()

loops::Loops const & protocols::abinitio::IterativeBase::core ( core::Size i )

protected

OBSOLET cores are computed by compute_cores() in idle()

References core15_, core2_, core3_, and core4_.

Referenced by protocols::abinitio::IterativeFullatom::gen_resample_core().

◆ do_dynamic_patching()

void protocols::abinitio::IterativeBase::do_dynamic_patching	(	jd2::archive::Batch &	batch,
		utility::io::ozstream &	flags,
		std::string	score,
		utility::options::FileVectorOptionKey const &	key
	)		const

private

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

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

References core::scoring::atom_pair_constraint, protocols::jd2::archive::Batch::dir(), core::scoring::ScoreFunction::get_weight(), protocols::jd2::archive::EvaluatedArchive::get_weight(), core::scoring::rdc, score(), protocols::jd2::archive::NormalizedEvaluatedArchive::score_variation(), protocols::jd2::archive::NormalizedEvaluatedArchive::score_variations(), protocols::jd2::archive::EvaluatedArchive::scorefxn(), and tr().

Referenced by gen_dynamic_patches().

◆ fa_score()

std::string const& protocols::abinitio::IterativeBase::fa_score ( ) const

inlineprotected

these are set by the cmd-line options iterative::fa_score and iterative::fa_score_patch

References fa_score_.

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

◆ fa_score_patch()

std::string const& protocols::abinitio::IterativeBase::fa_score_patch ( ) const

inlineprotected

References fa_score_patch_.

Referenced by protocols::abinitio::IterativeFullatom::initialize().

◆ finished()

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

inlineoverridevirtual

archive is finished when at last stage

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

References finish_stage_, and stage_.

Referenced by protocols::abinitio::IterativeAbrelax::finished().

◆ gen_cen2fullatom()

void protocols::abinitio::IterativeBase::gen_cen2fullatom ( jd2::archive::Batch & batch )

protected

References add_fullatom_flags(), core::io::silent::SilentFileData::add_structure(), protocols::jd2::archive::Batch::broker_file(), protocols::jd2::archive::ArchiveBase::decoys(), core::sequence::end, protocols::jd2::archive::Batch::flag_file(), protocols::mean_field::max(), protocols::jd2::archive::Batch::nstruct(), protocols::jd2::archive::Batch::set_has_silent_in(), protocols::jd2::archive::Batch::silent_in(), and core::io::silent::SilentFileData::write_all().

Referenced by generate_batch().

◆ gen_cen2fullatom_non_pool_decoys()

void protocols::abinitio::IterativeBase::gen_cen2fullatom_non_pool_decoys ( jd2::archive::Batch & batch )

protected

References add_fullatom_flags(), core::io::silent::SilentFileData::add_structure(), protocols::jd2::archive::Batch::broker_file(), collect_hedgeing_decoys_from_batches(), protocols::jd2::archive::Batch::flag_file(), hedge_archive_, protocols::mean_field::max(), protocols::jd2::archive::Batch::nstruct(), protocols::jd2::archive::Batch::set_has_silent_in(), protocols::jd2::archive::Batch::silent_in(), tr(), and core::io::silent::SilentFileData::write_all().

Referenced by generate_batch().

◆ gen_diversity_pool()

void protocols::abinitio::IterativeBase::gen_diversity_pool	(	jd2::archive::Batch &	batch,
		bool	fullatom = `false`
	)

virtual

Reimplemented in protocols::abinitio::IterativeCentroid.

References core::io::silent::SilentFileData::add_structure(), protocols::jd2::archive::ArchiveBase::decoys(), protocols::jd2::archive::Batch::dir(), protocols::jd2::archive::Batch::flag_file(), protocols::mean_field::max(), min_diversity_list_, core::io::silent::SilentFileData::size(), stage(), and core::io::silent::SilentFileData::write_all().

Referenced by gen_evaluation_output().

◆ gen_dynamic_patches()

void protocols::abinitio::IterativeBase::gen_dynamic_patches ( jd2::archive::Batch & batch )

virtual

References do_dynamic_patching(), protocols::jd2::archive::Batch::flag_file(), and use_dynamic_weights_for_sampling_.

Referenced by generate_batch().

◆ gen_enumerate_pairings()

void protocols::abinitio::IterativeBase::gen_enumerate_pairings ( jd2::archive::Batch & batch )

protected

References bEnumeratedLastTime_, protocols::jd2::archive::Batch::broker_file(), protocols::jd2::archive::Batch::dir(), guess_pairings_from_secondary_structure(), core::fragment::FragmentIO::read_data(), and tr().

Referenced by generate_batch().

◆ gen_evaluation_output()

void protocols::abinitio::IterativeBase::gen_evaluation_output	(	jd2::archive::Batch &	batch,
		bool	fullatom = `false`
	)

virtual

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

References protocols::noesy_assign::NoesyModule::cmdline_options_activated(), current_noesy_sampling_file_, protocols::jd2::archive::Batch::dir(), protocols::jd2::archive::EvaluatedArchive::evaluate_local(), first_noesy_cst_file_, first_noesy_fa_cst_file_, protocols::jd2::archive::Batch::flag_file(), gen_diversity_pool(), min_diversity_list_, protocols::jd2::archive::AbstractArchiveBase::name(), stage(), super_quick_relax_of_centroids_, tr(), and update_noesy_filter_files().

Referenced by generate_batch(), and protocols::abinitio::IterativeFullatom::generate_batch().

◆ gen_noe_assignments()

void protocols::abinitio::IterativeBase::gen_noe_assignments ( jd2::archive::Batch & batch )

protected

generate cst-input from current assigned noesy data

References bCombineNoesyCst_, protocols::jd2::archive::Batch::broker_file(), CEN2FULLATOM, protocols::noesy_assign::NoesyModule::cmdline_options_activated(), core::chemical::combine(), current_noesy_sampling_file_, mem_tr, protocols::jd2::archive::AbstractArchiveBase::name(), core::scoring::constraints::skip_redundant_constraints(), stage(), and tr().

Referenced by generate_batch(), and protocols::abinitio::IterativeFullatom::generate_batch().

◆ gen_resample_fragments()

void protocols::abinitio::IterativeBase::gen_resample_fragments ( jd2::archive::Batch & batch )

protected

References core::fragment::FragSet::add(), protocols::jd2::archive::ArchiveBase::decoys(), protocols::jd2::archive::Batch::dir(), protocols::jd2::archive::Batch::flag_file(), mem_tr, core::fragment::FragmentIO::read_data(), core::fragment::steal_constant_length_frag_set_from_pose(), and core::fragment::FragmentIO::write_data().

Referenced by generate_batch(), and protocols::abinitio::IterativeFullatom::generate_batch().

◆ gen_resample_stage2()

void protocols::abinitio::IterativeBase::gen_resample_stage2 ( jd2::archive::Batch & batch )

protected

restart runs from stage2-structures that correspond to those in the pool

References core::io::silent::SilentFileData::add_structure(), protocols::jd2::archive::Batch::broker_file(), collect_alternative_decoys(), protocols::jd2::archive::ArchiveBase::decoys(), protocols::jd2::archive::Batch::flag_file(), protocols::jd2::archive::Batch::id(), protocols::mean_field::max(), mem_tr, protocols::jd2::archive::Batch::nstruct(), core::scoring::rg, protocols::jd2::archive::Batch::set_has_silent_in(), protocols::jd2::archive::Batch::silent_in(), tr(), and core::io::silent::SilentFileData::write_all().

Referenced by generate_batch().

◆ gen_resample_topologies()

void protocols::abinitio::IterativeBase::gen_resample_topologies ( jd2::archive::Batch & batch )

protected

----------— helper functions to be used from generate_batch() -----------------—

figure out beta-sheet topologies from pooled decoys and run with jumping

References bDoBetaJumping_, protocols::jd2::archive::Batch::broker_file(), compute_beta_topology(), protocols::jd2::archive::Batch::dir(), protocols::jd2::archive::ArchiveBase::total_accepts(), and tr().

Referenced by generate_batch().

◆ gen_start_structures()

void protocols::abinitio::IterativeBase::gen_start_structures ( jd2::archive::Batch & batch )

protected

in the comp. modelling protocol the topo-resampling stage might also contain a RigidChunkClaimer... provide start-structures for this as -in:file:silent

◆ generate_batch() [1/2]

void protocols::abinitio::IterativeBase::generate_batch ( )

overridevirtual

generate a new batch, use different recipe according to current stage

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

Reimplemented in protocols::abinitio::IterativeFullatom.

References protocols::jd2::archive::BaseArchiveManager::finalize_batch(), protocols::jd2::archive::AbstractArchiveBase::manager(), mem_tr, reassign_noesy_data(), and tr().

Referenced by protocols::abinitio::IterativeAbrelax::generate_batch(), and protocols::abinitio::IterativeFullatom::generate_batch().

◆ generate_batch() [2/2]

core::Size protocols::abinitio::IterativeBase::generate_batch	(	jd2::archive::Batch &	batch,
		core::Size	repeat_id
	)

overridevirtual

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::jd2::archive::AbstractArchiveBase.

Reimplemented in protocols::abinitio::IterativeFullatom.

References protocols::jd2::archive::Batch::batch(), CEN2FULLATOM, gen_cen2fullatom(), gen_cen2fullatom_non_pool_decoys(), gen_dynamic_patches(), gen_enumerate_pairings(), gen_evaluation_output(), gen_noe_assignments(), gen_resample_fragments(), gen_resample_stage2(), gen_resample_topologies(), mem_tr, protocols::jd2::archive::AbstractArchiveBase::name(), NOESY_PHASEII_S2_RESAMPLING, NOESY_PHASEII_TOPO, PURE_TOPO_RESAMPLING, protocols::jd2::archive::Batch::set_intermediate_structs(), STAGE2_RESAMPLING, stage_, test_broker_settings(), TOPO_RESAMPLING, and tr().

◆ guess_pairings_from_secondary_structure()

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

protected

References protocols::loops::Loops::push_back(), core::fragment::SecondaryStructure::sheet_fraction(), protocols::loops::Loops::size(), protocols::loops::start, target_sequence(), core::fragment::SecondaryStructure::total_residue(), tr(), and core::fragment::SecondaryStructure::write_psipred_ss2().

Referenced by gen_enumerate_pairings().

◆ idle()

void protocols::abinitio::IterativeBase::idle ( )

overridevirtual

while waiting for jobs to finish

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

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

References protocols::jd2::archive::ArchiveBase::accepts_since_last_batch(), protocols::noesy_assign::NoesyModule::cmdline_options_activated(), compute_cores(), protocols::jd2::archive::ArchiveBase::decoys(), core::sequence::end, protocols::jd2::archive::EvaluatedArchive::evaluate_local(), last_accepted_decoys_in_idle_, never_switched_noe_filter_, replace_noesy_filter_constraints(), rescore(), STAGE2_RESAMPLING, stage_, protocols::jd2::archive::ArchiveBase::total_accepts(), and tr().

Referenced by protocols::abinitio::IterativeAbrelax::idle().

◆ increment_stage()

void protocols::abinitio::IterativeBase::increment_stage ( )

private

necessary steps to go to next stage... e.g., saving snapshot of archive

got to next stage

References bDoBetaJumping_, protocols::jd2::archive::BaseArchiveManager::cancel_batches_previous_to(), core::fragment::FragmentIO::clean_frag_cache(), finish_stage_, first_batch_this_stage_, protocols::jd2::archive::BaseArchiveManager::last_batch_id(), protocols::jd2::archive::AbstractArchiveBase::manager(), protocols::jd2::archive::AbstractArchiveBase::manager_ptr(), max_nstruct_list_, NOESY_PHASEII_TOPO, PURE_TOPO_RESAMPLING, protocols::jd2::archive::ArchiveBase::reset_accept_counter(), protocols::jd2::archive::NormalizedEvaluatedArchive::save_to_file(), stage_, protocols::jd2::archive::ArchiveBase::total_proposed(), and tr().

Referenced by test_for_stage_end().

◆ init_from_decoy_set()

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

overridevirtual

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

@detail load decoys into archive from -archive:input_pool or so

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

References protocols::jd2::archive::EvaluatedArchive::add_evaluation(), protocols::jd2::archive::EvaluatedArchive::evaluate_local(), protocols::jd2::archive::ArchiveBase::init_from_decoy_set(), protocols::jd2::archive::EvaluatedArchive::remove_evaluation(), protocols::jd2::archive::EvaluatedArchive::scorefxn_non_const(), protocols::jd2::archive::EvaluatedArchive::set_evaluate_local(), protocols::jd2::archive::EvaluatedArchive::set_weight(), and tr().

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

◆ initialize()

void protocols::abinitio::IterativeBase::initialize ( )

overridevirtual

do initializing work that requires fully setup object here

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

Reimplemented in protocols::abinitio::IterativeFullatom.

References protocols::jd2::archive::EvaluatedArchive::add_evaluation(), core::scoring::atom_pair_constraint, bDoBetaJumping_, cen_score(), cen_score_patch(), chemshift_column_, core::scoring::ScoreFunctionFactory::create_score_function(), protocols::abinitio::decide_on_beta_jumping_from_frags(), protocols::jd2::archive::EvaluatedArchive::evaluate_local(), protocols::abinitio::fix_chainbreak_patch(), core::scoring::ScoreFunction::get_weight(), protocols::jd2::archive::NormalizedEvaluatedArchive::initialize(), mem_tr, overall_cstfilter_weight(), PURE_TOPO_RESAMPLING, core::scoring::rdc, protocols::jd2::archive::EvaluatedArchive::scorefxn(), set_overall_cstfilter_weight(), protocols::jd2::archive::EvaluatedArchive::set_scorefxn(), core::scoring::ScoreFunction::set_weight(), protocols::jd2::archive::EvaluatedArchive::set_weight(), setup_autoNOE(), setup_filter_cst(), stage_, super_quick_relax_of_centroids_, test_for_stage_end(), and tr().

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

◆ overall_cstfilter_weight()

core::Real protocols::abinitio::IterativeBase::overall_cstfilter_weight ( ) const

inlineprotected

this is set from score::atom_pair_constraint of the pool-scorefunction

References overall_cstfilter_weight_.

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

◆ read_structures()

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

overridevirtual

overloaded so we can test for end of IterationStage after reading

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

References protocols::jd2::archive::AbstractArchiveBase::name(), protocols::jd2::archive::EvaluatedArchive::read_structures(), test_for_stage_end(), and tr().

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

◆ ready_for_batch()

virtual bool protocols::abinitio::IterativeBase::ready_for_batch ( ) const

inlinevirtual

we are always ready to generate a new batch

Reimplemented in protocols::abinitio::IterativeFullatom.

◆ reassign_noesy_data()

void protocols::abinitio::IterativeBase::reassign_noesy_data ( jd2::archive::Batch & batch )

protected

actually run the assignment machinery (only after batch is started to keep archive from hogging the queue... )

END gen_xxx ( batch ) methods

Referenced by generate_batch().

◆ register_options()

void protocols::abinitio::IterativeBase::register_options ( )

static

References protocols::evaluation::options_registered_, protocols::evaluation::register_options(), protocols::moves::Mover::register_options(), and core::scoring::constraints::skip_redundant_constraints().

◆ replace_noesy_filter_constraints()

void protocols::abinitio::IterativeBase::replace_noesy_filter_constraints ( )

private

References protocols::jd2::archive::EvaluatedArchive::add_evaluation(), protocols::noesy_assign::NoesyModule::cmdline_options_activated(), current_noesy_sampling_file_, protocols::jd2::archive::ArchiveBase::decoys(), first_noesy_cst_file_, first_noesy_fa_cst_file_, protocols::jd2::archive::EvaluatedArchive::get_weight(), core::pose::Pose::is_fullatom(), overall_cstfilter_weight_, rescore_nonlocal_archive(), core::scoring::constraints::skip_redundant_constraints(), tr(), and update_noesy_filter_files().

Referenced by idle().

◆ rescore()

void protocols::abinitio::IterativeBase::rescore ( )

overridevirtual

---------------------— end stage control @detail rescore and sort archive

Reimplemented from protocols::jd2::archive::EvaluatedArchive.

References protocols::jd2::archive::EvaluatedArchive::evaluators(), hedge_archive_, protocols::jd2::archive::NormalizedEvaluatedArchive::rescore(), protocols::jd2::archive::EvaluatedArchive::scorefxn(), and protocols::jd2::archive::EvaluatedArchive::weights().

Referenced by idle(), reassign_noesy_data(), and rescore_nonlocal_archive().

◆ rescore_nonlocal_archive()

void protocols::abinitio::IterativeBase::rescore_nonlocal_archive ( )

private

Referenced by replace_noesy_filter_constraints().

◆ restore_status()

void protocols::abinitio::IterativeBase::restore_status ( std::istream & is )

overridevirtual

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

References protocols::jd2::archive::EvaluatedArchive::add_evaluation(), bCombineNoesyCst_, compute_cores(), current_noesy_sampling_file_, protocols::jd2::archive::EvaluatedArchive::evaluate_local(), first_batch_this_stage_, first_fullatom_batch_, first_noesy_cst_file_, first_noesy_fa_cst_file_, protocols::jd2::archive::EvaluatedArchive::get_weight(), hedge_archive_, protocols::loops::PoseNumberedLoopFileReader::hijack_loop_reading_code_set_loop_line_begin_token(), protocols::jd2::archive::AbstractArchiveBase::name(), noesy_assign_float_cycle_, overall_cstfilter_weight_, protocols::loops::PoseNumberedLoopFileReader::read_pose_numbered_loops_file(), protocols::jd2::archive::ArchiveBase::restore_status(), core::scoring::constraints::skip_redundant_constraints(), stage(), STAGE2_RESAMPLING, stage_, tr(), and update_noesy_filter_files().

◆ save_status()

void protocols::abinitio::IterativeBase::save_status ( std::ostream & os ) const

overridevirtual

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

References current_noesy_sampling_file_, first_batch_this_stage_, first_fullatom_batch_, first_noesy_cst_file_, first_noesy_fa_cst_file_, hedge_archive_, noesy_assign_float_cycle_, protocols::jd2::archive::ArchiveBase::save_status(), and stage_.

Referenced by protocols::abinitio::IterativeAbrelax::save_status(), and update_noesy_filter_files().

◆ score()

void protocols::abinitio::IterativeBase::score ( core::pose::Pose & pose ) const

overrideprivatevirtual

score a pose with Pool-Scoring function (adds necessary data to pose (RDC, constraints, etc ) )

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

Reimplemented from protocols::jd2::archive::EvaluatedArchive.

References core::scoring::rdc, rdc_data_, protocols::jd2::archive::EvaluatedArchive::score(), and core::scoring::store_RDC_in_pose().

Referenced by do_dynamic_patching().

◆ set_finish_stage()

void protocols::abinitio::IterativeBase::set_finish_stage ( IterationStage setting )

inline

where to stop ?

References finish_stage_.

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

◆ set_noesy_assign_float_cycle()

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

inlineprotected

References noesy_assign_float_cycle_.

Referenced by protocols::abinitio::IterativeFullatom::initialize().

◆ set_overall_cstfilter_weight()

void protocols::abinitio::IterativeBase::set_overall_cstfilter_weight ( core::Real setting )

inlineprotected

this is set from score::atom_pair_constraint of the pool-scorefunction

References overall_cstfilter_weight_.

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

◆ set_stage()

void protocols::abinitio::IterativeBase::set_stage ( IterationStage setting )

inlineprotected

References stage_.

Referenced by protocols::abinitio::IterativeFullatom::initialize().

◆ setup_autoNOE()

void protocols::abinitio::IterativeBase::setup_autoNOE ( )

private

References protocols::jd2::archive::EvaluatedArchive::add_evaluation(), bCombineNoesyCst_, protocols::noesy_assign::NoesyModule::cmdline_options_activated(), current_noesy_sampling_file_, protocols::jd2::archive::EvaluatedArchive::evaluate_local(), hasher, noesy_assign_hash_, overall_cstfilter_weight_, protocols::jd2::archive::EvaluatedArchive::set_weight(), super_quick_relax_of_centroids_, and tr().

Referenced by initialize().

◆ setup_default_evaluators()

void protocols::abinitio::IterativeBase::setup_default_evaluators ( )

setup JumpNrEvaluator

References protocols::jd2::archive::EvaluatedArchive::add_evaluation(), and protocols::jd2::archive::EvaluatedArchive::setup_default_evaluators().

◆ setup_filter_cst()

void protocols::abinitio::IterativeBase::setup_filter_cst ( core::Real weight )

protected

References protocols::topology_broker::add_cmdline_claims(), protocols::jd2::archive::EvaluatedArchive::add_evaluation(), protocols::jd2::archive::AbstractArchiveBase::name(), and tr().

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

◆ stage()

IterationStage protocols::abinitio::IterativeBase::stage ( ) const

inlineprotected

current stage?

References stage_.

Referenced by add_structure(), gen_diversity_pool(), gen_evaluation_output(), gen_noe_assignments(), protocols::abinitio::IterativeFullatom::generate_batch(), protocols::abinitio::IterativeFullatom::ready_for_batch(), reassign_noesy_data(), and restore_status().

◆ still_interested()

bool protocols::abinitio::IterativeBase::still_interested ( jd2::archive::Batch const & batch ) const

overridevirtual

we are not interested in batches that were generated in old stages

--------------— stage control -------------------—

batch is expired ?

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

References first_batch_this_stage_, protocols::jd2::archive::Batch::id(), and protocols::jd2::archive::AbstractArchiveBase::still_interested().

Referenced by protocols::abinitio::IterativeAbrelax::still_interested().

◆ super_quick_relax_of_centroids()

bool protocols::abinitio::IterativeBase::super_quick_relax_of_centroids ( ) const

inlineprotected

References super_quick_relax_of_centroids_.

Referenced by protocols::abinitio::IterativeFullatom::initialize().

◆ target_accept_ratio()

core::Real protocols::abinitio::IterativeBase::target_accept_ratio ( ) const

inlineprivate

what is the expected lowest acceptance ratio at the current stage ?

References stage_, and target_accept_ratio_.

Referenced by test_for_stage_end().

◆ target_sequence()

std::string const& protocols::abinitio::IterativeBase::target_sequence ( ) const

inlineprotected

needed for writing of psi-pred fiels (guess_pairings_from_secondary_structure)

References target_sequence_.

Referenced by guess_pairings_from_secondary_structure().

◆ test_broker_settings()

void protocols::abinitio::IterativeBase::test_broker_settings ( jd2::archive::Batch const & batch )

protected

Helper functions.

References protocols::topology_broker::add_cmdline_claims(), protocols::jd2::archive::Batch::all_broker_files(), protocols::jd2::archive::Batch::flag_file(), and tr().

Referenced by generate_batch().

◆ test_for_stage_end()

void protocols::abinitio::IterativeBase::test_for_stage_end ( )

calls increment_stage() if appropriate

are we ready to switch to next stage ?

References protocols::jd2::archive::ArchiveBase::current_acceptance_ratio(), increment_stage(), max_nstruct_list_, protocols::jd2::archive::ArchiveBase::proposed_since_last_batch(), stage_, target_accept_ratio(), protocols::jd2::archive::ArchiveBase::total_proposed(), and tr().

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

◆ update_noesy_filter_files()

void protocols::abinitio::IterativeBase::update_noesy_filter_files	(	std::string const &	current,
		bool	fullatom
	)

virtual

Reimplemented in protocols::abinitio::IterativeCentroid.

References current_noesy_sampling_file_, first_noesy_cst_file_, first_noesy_fa_cst_file_, protocols::jd2::archive::AbstractArchiveBase::name(), save_status(), super_quick_relax_of_centroids_, and tr().

Referenced by gen_evaluation_output(), replace_noesy_filter_constraints(), and restore_status().

Member Data Documentation

◆ bCombineNoesyCst_

bool protocols::abinitio::IterativeBase::bCombineNoesyCst_

private

Referenced by gen_noe_assignments(), reassign_noesy_data(), restore_status(), and setup_autoNOE().

◆ bDoBetaJumping_

bool protocols::abinitio::IterativeBase::bDoBetaJumping_

private

Referenced by gen_resample_topologies(), increment_stage(), and initialize().

◆ bEnumeratedLastTime_

bool protocols::abinitio::IterativeBase::bEnumeratedLastTime_

private

toggle to keep track of the enumerate-pairings mode .. want to run this only every 2nd batch

------------------------------— other ---------------------------------—

Referenced by gen_enumerate_pairings().

◆ cen_score_

std::string protocols::abinitio::IterativeBase::cen_score_

private

from cmd-line cen-score and patch names

Referenced by cen_score().

◆ cen_score_patch_

std::string protocols::abinitio::IterativeBase::cen_score_patch_

private

Referenced by cen_score_patch().

◆ chemshift_column_

std::string protocols::abinitio::IterativeBase::chemshift_column_

private

even in centroid mode the end of abinitio will have a fast relax... enables cs-score and noe-assignment

Referenced by chemshift_column(), and initialize().

◆ core15_

loops::Loops protocols::abinitio::IterativeBase::core15_

private

core-regions — used in IterativeFullatom for the "rigid-core" sampling step...

Referenced by compute_cores(), and core().

◆ core2_

loops::Loops protocols::abinitio::IterativeBase::core2_

private

Referenced by compute_cores(), and core().

◆ core3_

loops::Loops protocols::abinitio::IterativeBase::core3_

private

Referenced by compute_cores(), and core().

◆ core4_

loops::Loops protocols::abinitio::IterativeBase::core4_

private

Referenced by compute_cores(), and core().

◆ cst_data_

core::scoring::constraints::ConstraintSetOP protocols::abinitio::IterativeBase::cst_data_

mutableprivate

◆ cst_fa_data_

core::scoring::constraints::ConstraintSetOP protocols::abinitio::IterativeBase::cst_fa_data_

mutableprivate

◆ current_noesy_sampling_file_

std::string protocols::abinitio::IterativeBase::current_noesy_sampling_file_

private

Referenced by gen_evaluation_output(), gen_noe_assignments(), reassign_noesy_data(), replace_noesy_filter_constraints(), restore_status(), save_status(), setup_autoNOE(), and update_noesy_filter_files().

◆ delay_noesy_reassign_

core::Size protocols::abinitio::IterativeBase::delay_noesy_reassign_

private

Referenced by IterativeBase(), and reassign_noesy_data().

◆ fa_score_

std::string protocols::abinitio::IterativeBase::fa_score_

private

from cmd-line fa-score and patch names

Referenced by fa_score().

◆ fa_score_patch_

std::string protocols::abinitio::IterativeBase::fa_score_patch_

private

Referenced by fa_score_patch().

◆ finish_stage_

IterationStage protocols::abinitio::IterativeBase::finish_stage_

private

end-condition

Referenced by finished(), increment_stage(), and set_finish_stage().

◆ first_batch_this_stage_

core::Size protocols::abinitio::IterativeBase::first_batch_this_stage_

private

indices of prominent batches ( STATUS file )

Referenced by add_structure(), increment_stage(), restore_status(), save_status(), and still_interested().

◆ first_fullatom_batch_

core::Size protocols::abinitio::IterativeBase::first_fullatom_batch_

private

Referenced by add_fullatom_flags(), collect_hedgeing_decoys_from_batches(), restore_status(), and save_status().

◆ first_noesy_cst_file_

std::string protocols::abinitio::IterativeBase::first_noesy_cst_file_

private

Referenced by gen_evaluation_output(), replace_noesy_filter_constraints(), restore_status(), save_status(), and update_noesy_filter_files().

◆ first_noesy_fa_cst_file_

std::string protocols::abinitio::IterativeBase::first_noesy_fa_cst_file_

private

Referenced by gen_evaluation_output(), replace_noesy_filter_constraints(), restore_status(), save_status(), and update_noesy_filter_files().

◆ hasher

boost::hash<std::string> protocols::abinitio::IterativeBase::hasher

private

Referenced by reassign_noesy_data(), and setup_autoNOE().

◆ hedge_archive_

HedgeArchiveOP protocols::abinitio::IterativeBase::hedge_archive_

private

Referenced by collect_hedge_structures(), gen_cen2fullatom_non_pool_decoys(), rescore(), restore_status(), and save_status().

◆ last_accepted_decoys_in_idle_

core::Size protocols::abinitio::IterativeBase::last_accepted_decoys_in_idle_

private

[OBSOLET?] keep track when idle() has been run ...

Referenced by idle().

◆ max_nstruct_list_

utility::vector1< int > protocols::abinitio::IterativeBase::max_nstruct_list_

private

--------— some cmd-line controlled settings --------------—

how many structures are maximally produced in stage X

Referenced by increment_stage(), IterativeBase(), and test_for_stage_end().

◆ min_diversity_list_

utility::vector1< core::Real > protocols::abinitio::IterativeBase::min_diversity_list_

private

cluster:radius for minimum diversity in stage X

Referenced by add_structure(), gen_diversity_pool(), gen_evaluation_output(), and IterativeBase().

◆ never_switched_noe_filter_

bool protocols::abinitio::IterativeBase::never_switched_noe_filter_

protected

Referenced by idle(), and IterativeBase().

◆ noesy_assign_float_cycle_

core::Real protocols::abinitio::IterativeBase::noesy_assign_float_cycle_

private

Referenced by restore_status(), save_status(), and set_noesy_assign_float_cycle().

◆ noesy_assign_hash_

size_t protocols::abinitio::IterativeBase::noesy_assign_hash_

private

Referenced by reassign_noesy_data(), and setup_autoNOE().

◆ noesy_module_

protocols::noesy_assign::NoesyModuleOP protocols::abinitio::IterativeBase::noesy_module_

private

Referenced by reassign_noesy_data().

◆ options_registered_

bool protocols::abinitio::IterativeBase::options_registered_

staticprivate

◆ overall_cstfilter_weight_

core::Real protocols::abinitio::IterativeBase::overall_cstfilter_weight_

private

this is set from score::atom_pair_constraint of the pool-scorefunction

Referenced by overall_cstfilter_weight(), reassign_noesy_data(), replace_noesy_filter_constraints(), restore_status(), set_overall_cstfilter_weight(), and setup_autoNOE().

◆ rdc_data_

core::scoring::ResidualDipolarCouplingOP protocols::abinitio::IterativeBase::rdc_data_

mutableprivate

cache some of the experimental data so we don't reload from file for each evaluation

Referenced by score().

◆ reference_pose_

core::pose::PoseCOP protocols::abinitio::IterativeBase::reference_pose_

private

for RMSD ... e.g., in:file:native

Referenced by add_core_evaluator(), IterativeBase(), and reassign_noesy_data().

◆ scored_core_

loops::Loops protocols::abinitio::IterativeBase::scored_core_

protected

◆ stage_

IterationStage protocols::abinitio::IterativeBase::stage_

private

--------------— – private data members – -----------------—

---------------------------— stage - control -----------------------—

current stage

Referenced by add_structure(), finished(), generate_batch(), idle(), increment_stage(), initialize(), rescore_nonlocal_archive(), restore_status(), save_status(), set_stage(), stage(), target_accept_ratio(), and test_for_stage_end().

◆ super_quick_relax_of_centroids_

bool protocols::abinitio::IterativeBase::super_quick_relax_of_centroids_

private

even in centroid mode the end of abinitio will have a fast relax... enables cs-score and noe-assignment

Referenced by gen_evaluation_output(), initialize(), rescore_nonlocal_archive(), setup_autoNOE(), super_quick_relax_of_centroids(), and update_noesy_filter_files().

◆ target_accept_ratio_

utility::vector1< core::Real > protocols::abinitio::IterativeBase::target_accept_ratio_

private

minimum acceptance ratio .. current_accept_ratio < target_accept_ratio[ stage_ ] --> increment_stage

Referenced by IterativeBase(), and target_accept_ratio().

◆ target_sequence_

std::string protocols::abinitio::IterativeBase::target_sequence_

private

Referenced by IterativeBase(), reassign_noesy_data(), and target_sequence().

◆ use_dynamic_weights_for_sampling_

bool protocols::abinitio::IterativeBase::use_dynamic_weights_for_sampling_

private

use the score_variations from EvaluatedArchive to determine new sampling weights

Referenced by gen_dynamic_patches().

◆ vanilla_options_

utility::options::OptionCollectionCOP protocols::abinitio::IterativeBase::vanilla_options_

private

---------------— register cmdline options ------------------------—

Referenced by reassign_noesy_data().

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

src/protocols/abinitio/IterativeBase.hh
src/protocols/abinitio/IterativeBase.cc

Public Types

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Private Types

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ Parent

◆ SilentStructVector

Member Enumeration Documentation

◆ IterationStage

Constructor & Destructor Documentation

◆ IterativeBase()

◆ ~IterativeBase()

Member Function Documentation

◆ add_core_evaluator()

◆ add_fullatom_flags()

◆ add_structure()

◆ cen_score()

◆ cen_score_patch()

◆ chemshift_column()

◆ cluster()

◆ collect_alternative_decoys()

◆ collect_hedge_structures()

◆ collect_hedgeing_decoys_from_batches()

◆ compute_beta_topology()

--------— these may be called from idle() ---------—

◆ compute_cores()

◆ core()

◆ do_dynamic_patching()

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

◆ fa_score()

◆ fa_score_patch()

◆ finished()

◆ gen_cen2fullatom()

◆ gen_cen2fullatom_non_pool_decoys()

◆ gen_diversity_pool()

◆ gen_dynamic_patches()

◆ gen_enumerate_pairings()

◆ gen_evaluation_output()

◆ gen_noe_assignments()

◆ gen_resample_fragments()

◆ gen_resample_stage2()

◆ gen_resample_topologies()

◆ gen_start_structures()

◆ generate_batch() [1/2]

◆ generate_batch() [2/2]

◆ guess_pairings_from_secondary_structure()

◆ idle()

◆ increment_stage()

◆ init_from_decoy_set()

◆ initialize()

◆ overall_cstfilter_weight()

◆ read_structures()

◆ ready_for_batch()

◆ reassign_noesy_data()

END gen_xxx ( batch ) methods

◆ register_options()

◆ replace_noesy_filter_constraints()

◆ rescore()

◆ rescore_nonlocal_archive()

◆ restore_status()

◆ save_status()

◆ score()

◆ set_finish_stage()

◆ set_noesy_assign_float_cycle()

◆ set_overall_cstfilter_weight()

◆ set_stage()

◆ setup_autoNOE()

◆ setup_default_evaluators()

◆ setup_filter_cst()

◆ stage()

◆ still_interested()

◆ super_quick_relax_of_centroids()

◆ target_accept_ratio()