protocols::jd2::archive::ArchiveBase Class Reference

#include <ArchiveBase.hh>

Inheritance diagram for protocols::jd2::archive::ArchiveBase:

Public Member Functions
	ArchiveBase (ArchiveManagerAP ptr=nullptr)
	~ArchiveBase () override
bool	finished () const override
	is archive converged ? More...
void	initialize () override
void	generate_batch () override=0
	create a new batch with manager().start_new_batch() and manager().finalize_batch(); More...
virtual bool	add_structure (core::io::silent::SilentStructOP new_decoy, core::io::silent::SilentStructOP alternative_decoy, Batch const &)
	add structure to Archive.. return false if structure is rejected. 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_to_file (std::string suffix="") override
	save and restore archive to file-system 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)
bool	restore_from_file () override
	restore archive More...
void	save_status (std::ostream &) const override
	save and restore status of archive to file-system More...
virtual void	restore_status (std::istream &)
void	idle () override
	called when nothing is happening More...
void	init_from_decoy_set (core::io::silent::SilentFileData const &sfd) override
	read externally provided structures from decoy_file into archive More...
void	read_structures (core::io::silent::SilentFileData &, core::io::silent::SilentFileData &alternative_decoys, Batch const &batch) override
	SilentFileData contains the new structures belonging to this batch. More...
core::Size &	accepts_since_last_batch ()
core::Size	accepts_since_last_batch () const
core::Size	proposed_since_last_batch () const
core::Real	current_acceptance_ratio () const
void	reset_accept_counter ()
core::Size	total_proposed ()
core::Size	total_accepts ()
bool	statistics_valid ()
SilentStructs const &	decoys () const
SilentStructs &	decoys ()
Public Member Functions inherited from protocols::jd2::archive::AbstractArchiveBase
	~AbstractArchiveBase () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
	AbstractArchiveBase (BaseArchiveManagerAP ptr)
	AbstractArchiveBase ()
virtual bool	still_interested (jd2::archive::Batch const &) const
	old-batches might be outdated and should not be computed anymore return true for this query if this is the case for old_batch More...
virtual core::Size	generate_batch (jd2::archive::Batch &, core::Size)
	create a batch for the current stage, return ct != 0 if more batches should be created at current stage. (e.g., harvest_batches) More...
void	set_name (std::string const &set)
	set name of archive ( used also for save_to_file and restore_from_file ) More...
std::string const &	name () const
BaseArchiveManager &	manager ()
	access to the ArchiveManager (control of batches) More...
virtual void	set_manager (BaseArchiveManagerAP manager)

Static Public Member Functions
static void	register_options ()

Protected Types
typedef std::list < core::io::silent::SilentStructOP >	SilentStructs
typedef SilentStructs::const_iterator	const_decoy_iterator
typedef SilentStructs::const_iterator	decoy_iterator

Protected Member Functions
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 ()

Static Protected Attributes
static std::string const	TAG_IN_FILE
static std::string const	SOURCE_FILE

Private Types
typedef std::deque< bool >	AcceptHistoryQueue

Private Attributes
core::Size	max_nstruct_
core::Size	nstruct_
SilentStructs	decoys_
core::Size	accepts_since_last_batch_
core::Size	total_accepts_
core::Size	proposed_since_last_batch_
core::Size	total_proposed_
AcceptHistoryQueue	acceptance_history_
core::Real	floating_acceptance_ratio_
core::Size	min_structures_for_acceptance_statistics_

Static Private Attributes
static bool	options_registered_

Member Typedef Documentation

typedef std::deque< bool > protocols::jd2::archive::ArchiveBase::AcceptHistoryQueue

private

typedef SilentStructs::const_iterator protocols::jd2::archive::ArchiveBase::const_decoy_iterator

protected

typedef SilentStructs::const_iterator protocols::jd2::archive::ArchiveBase::decoy_iterator

protected

typedef std::list< core::io::silent::SilentStructOP > protocols::jd2::archive::ArchiveBase::SilentStructs

protected

Constructor & Destructor Documentation

protocols::jd2::archive::ArchiveBase::ArchiveBase

(

ArchiveManagerAP

ptr = nullptr

)

References floating_acceptance_ratio_, max_nstruct_, min_structures_for_acceptance_statistics_, nstruct_, and options_registered_.

protocols::jd2::archive::ArchiveBase::~ArchiveBase ( )

overridedefault

Member Function Documentation

core::Size& protocols::jd2::archive::ArchiveBase::accepts_since_last_batch ( )

inline

-— methods to keep statistics of acceptance

References accepts_since_last_batch_.

Referenced by count_removed_structures(), protocols::abinitio::IterativeBase::idle(), and total_accepts().

core::Size protocols::jd2::archive::ArchiveBase::accepts_since_last_batch ( ) const

inline

References accepts_since_last_batch_.

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

virtual

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

Reimplemented in protocols::abinitio::IterativeBase, and protocols::jd2::archive::EvaluatedArchive.

References add_structure_at_position(), and decoys_.

Referenced by read_structures().

void protocols::jd2::archive::ArchiveBase::add_structure_at_position ( SilentStructs::iterator  iss, core::io::silent::SilentStructOP  new_decoy, core::io::silent::SilentStructOP  alternative_decoy  )

protectedvirtual

call to insert structure at position given by iterator

Reimplemented in protocols::abinitio::IterativeCentroid.

References decoys_, and max_nstruct_.

Referenced by protocols::jd2::archive::EvaluatedArchive::add_evaluated_structure(), add_structure(), and protocols::abinitio::HedgeArchive::incorporate_batch().

void protocols::jd2::archive::ArchiveBase::count_removed_structures ( core::Size  n_removed )

protected

count the structure for the acceptance statistics only count if not from expired batch

References acceptance_history_, accepts_since_last_batch(), decoys(), floating_acceptance_ratio_, min_structures_for_acceptance_statistics_, and nstruct_.

void protocols::jd2::archive::ArchiveBase::count_structure ( Batch const &  batch, bool  accepted  )

protectedvirtual

count the structure for the acceptance statistics only count if not from expired batch

References acceptance_history_, accepts_since_last_batch_, floating_acceptance_ratio_, min_structures_for_acceptance_statistics_, proposed_since_last_batch_, and protocols::jd2::archive::AbstractArchiveBase::still_interested().

Referenced by read_structures().

core::Real protocols::jd2::archive::ArchiveBase::current_acceptance_ratio ( ) const

inline

References floating_acceptance_ratio_.

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

SilentStructs const& protocols::jd2::archive::ArchiveBase::decoys ( ) const

inline

References decoys_.

Referenced by protocols::jd2::archive::VarianceStatisticsArchive::add_evaluated_structure(), protocols::jd2::archive::EvaluatedArchive::add_evaluated_structure(), protocols::abinitio::IterativeBase::add_structure(), protocols::abinitio::HedgeArchive::collect(), protocols::abinitio::IterativeBase::compute_beta_topology(), protocols::abinitio::IterativeBase::compute_cores(), count_removed_structures(), protocols::jd2::archive::NormalizedEvaluatedArchive::determine_score_variations(), protocols::abinitio::IterativeBase::gen_cen2fullatom(), protocols::abinitio::IterativeBase::gen_diversity_pool(), protocols::abinitio::IterativeFullatom::gen_resample_core(), protocols::abinitio::IterativeBase::gen_resample_fragments(), protocols::abinitio::IterativeBase::gen_resample_stage2(), protocols::abinitio::IterativeBase::idle(), protocols::abinitio::HedgeArchive::incorporate_batch(), read_structures(), protocols::abinitio::IterativeBase::reassign_noesy_data(), protocols::abinitio::IterativeBase::replace_noesy_filter_constraints(), protocols::jd2::archive::EvaluatedArchive::rescore(), protocols::abinitio::IterativeBase::rescore_nonlocal_archive(), save_to_file(), and protocols::jd2::archive::EvaluatedArchive::sort().

SilentStructs& protocols::jd2::archive::ArchiveBase::decoys ( )

inline

References decoys_.

void protocols::jd2::archive::ArchiveBase::erase_decoy ( std::string const &  tag )

protectedvirtual

Reimplemented in protocols::abinitio::IterativeCentroid.

References decoys_.

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

bool protocols::jd2::archive::ArchiveBase::finished ( ) const

inlineoverridevirtual

is archive converged ?

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

void protocols::jd2::archive::ArchiveBase::generate_batch ( )

overridepure virtual

create a new batch with manager().start_new_batch() and manager().finalize_batch();

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

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

void protocols::jd2::archive::ArchiveBase::idle ( )

inlineoverridevirtual

called when nothing is happening

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

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

overridevirtual

read externally provided structures from decoy_file into archive

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

Reimplemented in protocols::jd2::archive::EvaluatedArchive, and protocols::jd2::archive::VarianceStatisticsArchive.

References core::io::silent::SilentFileData::add_structure(), core::io::silent::SilentFileData::begin(), core::chemical::CENTROID, core::pose::Pose::clone(), core::io::silent::SilentFileData::end(), read_structures(), and protocols::jd2::tr().

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

void protocols::jd2::archive::ArchiveBase::initialize ( )

inlineoverridevirtual

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

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

void protocols::jd2::archive::ArchiveBase::load_decoys	(	std::string const &	filename,
		SilentStructs &	decoys
	)

References core::io::silent::SilentFileData::begin(), core::io::silent::SilentFileData::end(), protocols::jd2::mem_tr, and core::io::silent::SilentFileData::read_file().

Referenced by restore_from_file().

core::Size protocols::jd2::archive::ArchiveBase::max_nstruct ( )

inlineprotected

References max_nstruct_.

core::Size protocols::jd2::archive::ArchiveBase::nstruct ( ) const

inline

how many structures should be in archive .. varies from decoys().size() in startup phase.

References nstruct_.

Referenced by protocols::jd2::archive::VarianceStatisticsArchive::add_evaluated_structure(), protocols::jd2::archive::EvaluatedArchive::add_evaluated_structure(), protocols::abinitio::IterativeBase::compute_cores(), and protocols::abinitio::IterativeBase::reassign_noesy_data().

core::Size protocols::jd2::archive::ArchiveBase::proposed_since_last_batch ( ) const

inline

References proposed_since_last_batch_.

Referenced by protocols::abinitio::IterativeBase::test_for_stage_end(), and total_proposed().

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

overridevirtual

SilentFileData contains the new structures belonging to this batch.

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

Reimplemented in protocols::jd2::archive::EvaluatedArchive.

References protocols::hotspot_hashing::accept, add_structure(), protocols::jd2::archive::Batch::batch(), core::io::silent::SilentFileData::begin(), count_structure(), decoys(), protocols::jd2::archive::Batch::decoys_returned(), core::io::silent::SilentFileData::end(), core::io::silent::SilentFileData::get_iterator_for_tag(), protocols::jd2::archive::Batch::id(), protocols::jd2::archive::Batch::intermediate_structs(), protocols::jd2::mem_tr, protocols::jd2::archive::Batch::silent_out(), core::io::silent::SilentFileData::size(), SOURCE_FILE, TAG_IN_FILE, and protocols::jd2::tr().

Referenced by init_from_decoy_set(), and protocols::jd2::archive::EvaluatedArchive::read_structures().

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

static

References protocols::evaluation::options_registered_.

void protocols::jd2::archive::ArchiveBase::reset_accept_counter ( )

inline

References acceptance_history_, accepts_since_last_batch_, floating_acceptance_ratio_, proposed_since_last_batch_, total_accepts_, and total_proposed_.

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

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

overridevirtual

restore archive

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

Reimplemented in protocols::jd2::archive::EvaluatedArchive, and protocols::jd2::archive::NormalizedEvaluatedArchive.

References decoys_, protocols::abinitio::filename(), load_decoys(), protocols::jd2::mem_tr, protocols::jd2::archive::AbstractArchiveBase::name(), restore_status(), and protocols::jd2::tr().

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

void protocols::jd2::archive::ArchiveBase::restore_status ( std::istream &  is )

virtual

Reimplemented in protocols::abinitio::IterativeBase, and protocols::abinitio::HedgeArchive.

References acceptance_history_, accepts_since_last_batch_, floating_acceptance_ratio_, protocols::jd2::mem_tr, proposed_since_last_batch_, total_accepts_, and total_proposed_.

Referenced by restore_from_file(), protocols::abinitio::HedgeArchive::restore_status(), and protocols::abinitio::IterativeBase::restore_status().

void protocols::jd2::archive::ArchiveBase::save_decoys	(	std::string const &	dirname,
		std::string const &	name,
		SilentStructs const &	decoys
	)

helper routine to save decoys properly

References protocols::abinitio::filename(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by save_to_file().

void protocols::jd2::archive::ArchiveBase::save_status ( std::ostream &  os ) const

overridevirtual

save and restore status of archive to file-system

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

References acceptance_history_, accepts_since_last_batch_, floating_acceptance_ratio_, proposed_since_last_batch_, total_accepts_, and total_proposed_.

Referenced by protocols::abinitio::HedgeArchive::save_status(), protocols::abinitio::IterativeBase::save_status(), and save_to_file().

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

overridevirtual

save and restore archive to file-system

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

Reimplemented in protocols::jd2::archive::EvaluatedArchive, and protocols::jd2::archive::NormalizedEvaluatedArchive.

References decoys(), decoys_, protocols::jd2::archive::AbstractArchiveBase::name(), save_decoys(), save_status(), and protocols::jd2::tr().

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

void protocols::jd2::archive::ArchiveBase::set_max_nstruct ( core::Size  setting )

inlineprotected

References max_nstruct_.

Referenced by protocols::abinitio::HedgeArchive::HedgeArchive(), and protocols::abinitio::HedgeArchive::incorporate_batch().

void protocols::jd2::archive::ArchiveBase::set_nstruct ( core::Size  set )

inline

set target size of pool

References nstruct_.

bool protocols::jd2::archive::ArchiveBase::statistics_valid ( )

inline

References acceptance_history_, and min_structures_for_acceptance_statistics_.

core::Size protocols::jd2::archive::ArchiveBase::total_accepts ( )

inline

References accepts_since_last_batch(), and total_accepts_.

Referenced by protocols::abinitio::IterativeBase::gen_resample_topologies(), and protocols::abinitio::IterativeBase::idle().

core::Size protocols::jd2::archive::ArchiveBase::total_proposed ( )

inline

References proposed_since_last_batch(), and total_proposed_.

Referenced by protocols::jd2::archive::NormalizedEvaluatedArchive::add_evaluated_structure(), protocols::abinitio::IterativeBase::increment_stage(), protocols::abinitio::IterativeBase::reassign_noesy_data(), and protocols::abinitio::IterativeBase::test_for_stage_end().

Member Data Documentation

AcceptHistoryQueue protocols::jd2::archive::ArchiveBase::acceptance_history_

private

Referenced by count_removed_structures(), count_structure(), reset_accept_counter(), restore_status(), save_status(), and statistics_valid().

core::Size protocols::jd2::archive::ArchiveBase::accepts_since_last_batch_

private

Referenced by accepts_since_last_batch(), count_structure(), reset_accept_counter(), restore_status(), and save_status().

SilentStructs protocols::jd2::archive::ArchiveBase::decoys_

private

Referenced by add_structure(), add_structure_at_position(), decoys(), erase_decoy(), restore_from_file(), and save_to_file().

core::Real protocols::jd2::archive::ArchiveBase::floating_acceptance_ratio_

private

Referenced by ArchiveBase(), count_removed_structures(), count_structure(), current_acceptance_ratio(), reset_accept_counter(), restore_status(), and save_status().

core::Size protocols::jd2::archive::ArchiveBase::max_nstruct_

private

Referenced by add_structure_at_position(), ArchiveBase(), max_nstruct(), and set_max_nstruct().

core::Size protocols::jd2::archive::ArchiveBase::min_structures_for_acceptance_statistics_

private

Referenced by ArchiveBase(), count_removed_structures(), count_structure(), and statistics_valid().

core::Size protocols::jd2::archive::ArchiveBase::nstruct_

private

Referenced by ArchiveBase(), count_removed_structures(), nstruct(), and set_nstruct().

bool protocols::jd2::archive::ArchiveBase::options_registered_

staticprivate

Referenced by ArchiveBase().

core::Size protocols::jd2::archive::ArchiveBase::proposed_since_last_batch_

private

Referenced by count_structure(), proposed_since_last_batch(), reset_accept_counter(), restore_status(), and save_status().

std::string const protocols::jd2::archive::ArchiveBase::SOURCE_FILE

staticprotected

Referenced by read_structures().

std::string const protocols::jd2::archive::ArchiveBase::TAG_IN_FILE

staticprotected

Referenced by read_structures().

core::Size protocols::jd2::archive::ArchiveBase::total_accepts_

private

Referenced by reset_accept_counter(), restore_status(), save_status(), and total_accepts().

core::Size protocols::jd2::archive::ArchiveBase::total_proposed_

private

Referenced by reset_accept_counter(), restore_status(), save_status(), and total_proposed().

---

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

• src/protocols/jd2/archive/ArchiveBase.hh
• src/protocols/jd2/archive/ArchiveBase.cc