#include <IterativeBase.hh>

Inheritance diagram for protocols::abinitio::IterativeBase:

Collaboration diagram for protocols::abinitio::IterativeBase:

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 Member Functions
	IterativeBase (std::string name)

	~IterativeBase ()

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

virtual void	initialize ()
	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...

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	ready_for_batch () const
	we are always ready to generate a new batch 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	generate_batch ()

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::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	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 ()

Protected Attributes
bool	never_switched_noe_filter_

loops::Loops	scored_core_

Private Types
typedef jd2::archive::NormalizedEvaluatedArchive	Parent

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

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

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

void	collect_alternative_decoys (SilentStructs primary_decoys, std::string alternative_decoy_file, SilentStructVector &output_decoys)
	Helper functions. 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

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

std::string	chemshift_column_

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::OptionCollection const	vanilla_options_
	---------------— register cmdline options ------------------------— More...

Static Private Attributes
static bool	options_registered_

Additional Inherited Members
Protected Types inherited from protocols::jd2::archive::ArchiveBase
typedef std::list < core::io::silent::SilentStructOP >	SilentStructs

typedef SilentStructs::const_iterator	const_decoy_iterator

typedef SilentStructs::const_iterator	decoy_iterator

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

static std::string const	SOURCE_FILE

Detailed Description

Definition at line 57 of file IterativeBase.hh.

Member Typedef Documentation

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

private

Definition at line 58 of file IterativeBase.hh.

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

private

Definition at line 59 of file IterativeBase.hh.

Member Enumeration Documentation

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

Definition at line 61 of file IterativeBase.hh.

Constructor & Destructor Documentation

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

Definition at line 372 of file IterativeBase.cc.

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

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

Definition at line 546 of file IterativeBase.cc.

Member Function Documentation

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

Definition at line 1978 of file IterativeBase.cc.

References protocols::jd2::archive::EvaluatedArchive::add_evaluation(), protocols::loops::Loops::get_residues(), protocols::jd2::archive::AbstractArchiveBase::name(), reference_pose_, and protocols::loops::Loops::write_loops_to_file().

Referenced by compute_cores().

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

protected

Definition at line 1854 of file IterativeBase.cc.

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().

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

virtual

overloaded to handel special convergence check 'pool_converged_rmsd'

overload to check for pool_convergence data in incoming decoys

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

Definition at line 678 of file IterativeBase.cc.

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::EvaluatedArchive::evaluate_silent_struct(), first_batch_this_stage_, protocols::jd2::archive::Batch::id(), min_diversity_list_, protocols::jd2::archive::EvaluatedArchive::select_score(), core::io::serialization::size(), stage(), stage_, and tr().

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

Definition at line 189 of file IterativeBase.hh.

References cen_score_.

Referenced by initialize().

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

inlineprotected

Definition at line 192 of file IterativeBase.hh.

References cen_score_patch_.

Referenced by initialize().

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

inlineprotected

Definition at line 234 of file IterativeBase.hh.

References chemshift_column_.

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

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

protected

cluster structures with min_diversity_list_[ stage_ ] as cluster:radius

Definition at line 2061 of file IterativeBase.cc.

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

void protocols::abinitio::IterativeBase::collect_alternative_decoys	(	SilentStructs	primary_decoys,
		std::string	alternative_decoy_file,
		SilentStructVector &	output_decoys
	)

private

Helper functions.

Definition at line 2130 of file IterativeBase.cc.

References core::io::silent::SilentFileData::_read_file(), core::io::silent::SilentFileData::begin(), core::io::silent::SilentFileData::end(), core::io::silent::SilentFileData::size(), protocols::jd2::archive::ArchiveBase::SOURCE_FILE, protocols::jd2::archive::ArchiveBase::TAG_IN_FILE, and tr().

Referenced by gen_resample_stage2().

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

private

Definition at line 667 of file IterativeBase.cc.

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

Referenced by add_structure().

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

Definition at line 1411 of file IterativeBase.cc.

References protocols::jd2::archive::Batch::batch(), protocols::jd2::archive::ArchiveManager::batches(), first_fullatom_batch_, protocols::jd2::archive::AbstractArchiveBase::manager(), protocols::jd2::archive::Batch::nstruct(), protocols::abinitio::RG(), protocols::jd2::archive::EvaluatedArchive::select_score(), and tr().

Referenced by gen_cen2fullatom_non_pool_decoys().

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() ---------—

Definition at line 1890 of file IterativeBase.cc.

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

Referenced by gen_resample_topologies().

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

protected

Definition at line 1940 of file IterativeBase.cc.

References add_core_evaluator(), core15_, core2_, core3_, core4_, protocols::jd2::archive::ArchiveBase::decoys(), core::sequence::end, protocols::abinitio::get_core(), protocols::jd2::archive::ArchiveBase::nstruct(), protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz_from_silent_file(), protocols::toolbox::DecoySetEvaluation::reserve(), core::io::serialization::size(), and tr().

Referenced by idle(), and restore_status().

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

inlineprotected

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

Definition at line 207 of file IterativeBase.hh.

References core15_, core2_, core3_, and core4_.

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

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 --—

Definition at line 842 of file IterativeBase.cc.

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

Referenced by gen_dynamic_patches().

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

Definition at line 181 of file IterativeBase.hh.

References fa_score_.

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

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

inlineprotected

Definition at line 184 of file IterativeBase.hh.

References fa_score_patch_.

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

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

inlinevirtual

archive is finished when at last stage

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

Reimplemented in protocols::abinitio::IterativeAbrelax.

Definition at line 80 of file IterativeBase.hh.

References finish_stage_, and stage_.

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

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

protected

Definition at line 1380 of file IterativeBase.cc.

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::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().

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

protected

Definition at line 1484 of file IterativeBase.cc.

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::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().

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

virtual

Reimplemented in protocols::abinitio::IterativeCentroid.

Definition at line 978 of file IterativeBase.cc.

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

Referenced by gen_evaluation_output().

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

virtual

Definition at line 897 of file IterativeBase.cc.

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

Referenced by generate_batch().

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

protected

Definition at line 1035 of file IterativeBase.cc.

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().

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

Definition at line 910 of file IterativeBase.cc.

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

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

protected

generate cst-input from current assigned noesy data

Definition at line 1270 of file IterativeBase.cc.

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

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

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

protected

Definition at line 1205 of file IterativeBase.cc.

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

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

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

protected

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

Definition at line 1112 of file IterativeBase.cc.

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::jd2::archive::Batch::nstruct(), protocols::abinitio::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().

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

Definition at line 1078 of file IterativeBase.cc.

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().

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

Definition at line 1015 of file IterativeBase.cc.

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

virtual

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

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.

Reimplemented in protocols::abinitio::IterativeAbrelax, and protocols::abinitio::IterativeFullatom.

Definition at line 756 of file IterativeBase.cc.

References protocols::jd2::archive::Batch::batch(), CEN2FULLATOM, protocols::jd2::archive::ArchiveManager::finalize_batch(), 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(), protocols::jd2::archive::AbstractArchiveBase::manager(), protocols::jd2::archive::AbstractArchiveBase::name(), NOESY_PHASEII_S2_RESAMPLING, NOESY_PHASEII_TOPO, PURE_TOPO_RESAMPLING, reassign_noesy_data(), protocols::jd2::archive::Batch::set_intermediate_structs(), STAGE2_RESAMPLING, stage_, test_broker_settings(), TOPO_RESAMPLING, and tr().

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

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

Definition at line 1700 of file IterativeBase.cc.

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

Referenced by gen_enumerate_pairings().

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

virtual

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

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

Reimplemented in protocols::abinitio::IterativeAbrelax.

Definition at line 557 of file IterativeBase.cc.

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(), core::io::serialization::size(), STAGE2_RESAMPLING, stage_, protocols::jd2::archive::ArchiveBase::total_accepts(), and tr().

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

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

private

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

got to next stage

Definition at line 623 of file IterativeBase.cc.

References bDoBetaJumping_, protocols::jd2::archive::ArchiveManager::cancel_batches_previous_to(), core::fragment::FragmentIO::clean_frag_cache(), finish_stage_, first_batch_this_stage_, protocols::jd2::archive::ArchiveManager::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().

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

virtual

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

load decoys into archive from -archive:input_pool or so

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

Reimplemented in protocols::abinitio::IterativeAbrelax.

Definition at line 2213 of file IterativeBase.cc.

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().

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

virtual

do initializing work that requires fully setup object here

Reimplemented from protocols::jd2::archive::NormalizedEvaluatedArchive.

Reimplemented in protocols::abinitio::IterativeAbrelax, and protocols::abinitio::IterativeFullatom.

Definition at line 478 of file IterativeBase.cc.

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(), protocols::jd2::archive::NormalizedEvaluatedArchive::initialize(), overall_cstfilter_weight(), PURE_TOPO_RESAMPLING, core::scoring::rdc, protocols::jd2::archive::EvaluatedArchive::scorefxn(), set_overall_cstfilter_weight(), protocols::jd2::archive::EvaluatedArchive::set_scorefxn(), 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::IterativeFullatom::initialize(), and protocols::abinitio::IterativeAbrelax::initialize().

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

inlineprotected

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

Definition at line 197 of file IterativeBase.hh.

References overall_cstfilter_weight_.

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

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

virtual

overloaded so we can test for end of IterationStage after reading

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

Reimplemented in protocols::abinitio::IterativeAbrelax.

Definition at line 592 of file IterativeBase.cc.

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().

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

inlinevirtual

we are always ready to generate a new batch

Reimplemented in protocols::abinitio::IterativeFullatom.

Definition at line 97 of file IterativeBase.hh.

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

Definition at line 1530 of file IterativeBase.cc.

References protocols::jd2::archive::EvaluatedArchive::add_evaluation(), bCombineNoesyCst_, CEN2FULLATOM, protocols::noesy_assign::NoesyModule::cmdline_options_activated(), current_noesy_sampling_file_, protocols::noesy_assign::PeakAssignmentParameters::dcut_, protocols::jd2::archive::ArchiveBase::decoys(), delay_noesy_reassign_, protocols::jd2::archive::Batch::dir(), protocols::jd2::archive::EvaluatedArchive::evaluate_local(), core::chemical::FA_STANDARD, protocols::swa::rna::file_exists(), protocols::noesy_assign::PeakAssignmentParameters::get_nonconst_instance(), protocols::jd2::archive::EvaluatedArchive::get_weight(), hasher, protocols::jd2::archive::Batch::id(), core::pose::make_pose_from_sequence(), protocols::jd2::archive::AbstractArchiveBase::manager(), noesy_assign_hash_, NOESY_CST_FILE_NAME(), noesy_module_, protocols::jd2::archive::ArchiveBase::nstruct(), overall_cstfilter_weight_, reference_pose_, rescore(), protocols::noesy_assign::PeakAssignmentParameters::reset(), protocols::jd2::archive::ArchiveManager::save_archive(), protocols::noesy_assign::PeakAssignmentParameters::set_cycle(), protocols::noesy_assign::PeakAssignmentParameters::show(), protocols::noesy_assign::PeakAssignmentParameters::show_on_tracer(), core::io::serialization::size(), core::scoring::constraints::skip_redundant_constraints(), stage(), STAGE2_RESAMPLING, target_sequence_, protocols::jd2::archive::ArchiveBase::total_proposed(), tr(), protocols::noesy_assign::PeakAssignmentParameters::use_local_distviol_, and vanilla_options_.

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

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

static

Definition at line 195 of file IterativeBase.cc.

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

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

private

Definition at line 1753 of file IterativeBase.cc.

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().

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

virtual

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

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

Definition at line 656 of file IterativeBase.cc.

References core::io::serialization::clone(), 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().

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

private

Definition at line 1778 of file IterativeBase.cc.

Referenced by replace_noesy_filter_constraints().

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

virtual

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

Definition at line 1985 of file IterativeBase.cc.

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().

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

virtual

save and restore status of archive to file-system

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

Reimplemented in protocols::abinitio::IterativeAbrelax.

Definition at line 2041 of file IterativeBase.cc.

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().

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

privatevirtual

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

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

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

Definition at line 2118 of file IterativeBase.cc.

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

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

inline

where to stop ?

Definition at line 86 of file IterativeBase.hh.

References finish_stage_.

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

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

inlineprotected

Definition at line 144 of file IterativeBase.hh.

References noesy_assign_float_cycle_.

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

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

inlineprotected

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

Definition at line 202 of file IterativeBase.hh.

References overall_cstfilter_weight_.

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

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

inlineprotected

Definition at line 226 of file IterativeBase.hh.

References stage_.

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

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

private

Definition at line 2264 of file IterativeBase.cc.

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(), protocols::swa::rna::file_exists(), hasher, noesy_assign_hash_, overall_cstfilter_weight_, protocols::jd2::archive::EvaluatedArchive::set_weight(), super_quick_relax_of_centroids_, and tr().

Referenced by initialize().

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

setup JumpNrEvaluator

Definition at line 2055 of file IterativeBase.cc.

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

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

protected

Definition at line 2237 of file IterativeBase.cc.

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

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

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

inlineprotected

current stage?

Definition at line 217 of file IterativeBase.hh.

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().

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

virtual

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

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

batch is expired ?

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

Reimplemented in protocols::abinitio::IterativeAbrelax.

Definition at line 587 of file IterativeBase.cc.

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

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

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

inlineprotected

Definition at line 148 of file IterativeBase.hh.

References super_quick_relax_of_centroids_.

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

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

inlineprivate

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

Definition at line 250 of file IterativeBase.hh.

References stage_, and target_accept_ratio_.

Referenced by test_for_stage_end().

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

inlineprotected

needed for writing of psi-pred fiels (guess_pairings_from_secondary_structure)

Definition at line 222 of file IterativeBase.hh.

References target_sequence_.

Referenced by guess_pairings_from_secondary_structure().

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

protected

Definition at line 2190 of file IterativeBase.cc.

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().

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

calls increment_stage() if appropriate

are we ready to switch to next stage ?

Definition at line 600 of file IterativeBase.cc.

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

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

virtual

Reimplemented in protocols::abinitio::IterativeCentroid.

Definition at line 1244 of file IterativeBase.cc.

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

bool protocols::abinitio::IterativeBase::bCombineNoesyCst_

private

Definition at line 331 of file IterativeBase.hh.

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

bool protocols::abinitio::IterativeBase::bDoBetaJumping_

private

Definition at line 342 of file IterativeBase.hh.

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

bool protocols::abinitio::IterativeBase::bEnumeratedLastTime_

private

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

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

Definition at line 286 of file IterativeBase.hh.

Referenced by gen_enumerate_pairings().

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

private

from cmd-line cen-score and patch names

Definition at line 312 of file IterativeBase.hh.

Referenced by cen_score().

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

private

Definition at line 313 of file IterativeBase.hh.

Referenced by cen_score_patch().

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

private

Definition at line 341 of file IterativeBase.hh.

Referenced by chemshift_column(), and initialize().

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

private

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

Definition at line 292 of file IterativeBase.hh.

Referenced by compute_cores(), and core().

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

private

Definition at line 293 of file IterativeBase.hh.

Referenced by compute_cores(), and core().

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

private

Definition at line 294 of file IterativeBase.hh.

Referenced by compute_cores(), and core().

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

private

Definition at line 295 of file IterativeBase.hh.

Referenced by compute_cores(), and core().

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

mutableprivate

Definition at line 356 of file IterativeBase.hh.

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

mutableprivate

Definition at line 357 of file IterativeBase.hh.

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

private

Definition at line 330 of file IterativeBase.hh.

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().

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

private

Definition at line 351 of file IterativeBase.hh.

Referenced by IterativeBase(), and reassign_noesy_data().

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

private

from cmd-line fa-score and patch names

Definition at line 316 of file IterativeBase.hh.

Referenced by fa_score().

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

private

Definition at line 317 of file IterativeBase.hh.

Referenced by fa_score_patch().

IterationStage protocols::abinitio::IterativeBase::finish_stage_

private

end-condition

Definition at line 278 of file IterativeBase.hh.

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

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

private

indices of prominent batches ( STATUS file )

Definition at line 281 of file IterativeBase.hh.

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

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

private

Definition at line 282 of file IterativeBase.hh.

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

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

private

Definition at line 327 of file IterativeBase.hh.

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

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

private

Definition at line 328 of file IterativeBase.hh.

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

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

private

Definition at line 336 of file IterativeBase.hh.

Referenced by reassign_noesy_data(), and setup_autoNOE().

HedgeArchiveOP protocols::abinitio::IterativeBase::hedge_archive_

private

Definition at line 353 of file IterativeBase.hh.

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

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

private

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

Definition at line 289 of file IterativeBase.hh.

Referenced by idle().

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

private

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

how many structures are maximally produced in stage X

Definition at line 300 of file IterativeBase.hh.

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

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

private

cluster:radius for minimum diversity in stage X

Definition at line 303 of file IterativeBase.hh.

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

bool protocols::abinitio::IterativeBase::never_switched_noe_filter_

protected

Definition at line 145 of file IterativeBase.hh.

Referenced by idle(), and IterativeBase().

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

private

Definition at line 325 of file IterativeBase.hh.

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

size_t protocols::abinitio::IterativeBase::noesy_assign_hash_

private

Definition at line 335 of file IterativeBase.hh.

Referenced by reassign_noesy_data(), and setup_autoNOE().

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

private

Definition at line 324 of file IterativeBase.hh.

Referenced by reassign_noesy_data().

bool protocols::abinitio::IterativeBase::options_registered_

staticprivate

Definition at line 364 of file IterativeBase.hh.

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

private

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

Definition at line 320 of file IterativeBase.hh.

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

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

Definition at line 355 of file IterativeBase.hh.

Referenced by score().

bool protocols::abinitio::IterativeBase::recover_centroid_structure_for_pool_

private

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

Definition at line 339 of file IterativeBase.hh.

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

private

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

Definition at line 309 of file IterativeBase.hh.

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

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

protected

Definition at line 146 of file IterativeBase.hh.

IterationStage protocols::abinitio::IterativeBase::stage_

private

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

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

Definition at line 275 of file IterativeBase.hh.

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().

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

Definition at line 345 of file IterativeBase.hh.

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

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

private

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

Definition at line 306 of file IterativeBase.hh.

Referenced by IterativeBase(), and target_accept_ratio().

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

private

Definition at line 322 of file IterativeBase.hh.

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

bool protocols::abinitio::IterativeBase::use_dynamic_weights_for_sampling_

private

use the score_variations from EvaluatedArchive to determine new sampling weights

Definition at line 349 of file IterativeBase.hh.

Referenced by gen_dynamic_patches().

utility::options::OptionCollection const protocols::abinitio::IterativeBase::vanilla_options_

private

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

Definition at line 360 of file IterativeBase.hh.

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

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

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

END gen_xxx ( batch ) methods

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