protocols::jd2::archive::NormalizedEvaluatedArchive Class Reference

Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input. More...

#include <NormalizedEvaluatedArchive.hh>

Public Member Functions
	NormalizedEvaluatedArchive (ArchiveManagerAP ptr)
	Constructor and Destructor. More...
	NormalizedEvaluatedArchive ()
	~NormalizedEvaluatedArchive ()
void	init_from_options ()
virtual void	initialize ()
virtual bool	add_evaluated_structure (core::io::silent::SilentStructOP from_batch, core::io::silent::SilentStructOP alternative_decoy, Batch const &)
	add decoy to Archive 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 ()
virtual bool	add_structure (core::io::silent::SilentStructOP new_decoy, core::io::silent::SilentStructOP alternative_decoy, Batch const &batch)
	add decoy to Archive 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...
virtual void	read_structures (core::io::silent::SilentFileData &sfd, core::io::silent::SilentFileData &alternative_decoys, Batch const &batch)
	only overloaded this to add some verbosity each time we read structures More...
virtual void	init_from_decoy_set (core::io::silent::SilentFileData const &sfd)=0
	overloaded to make input decoys appear the same as decoys coming from batches 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 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 ()
virtual bool	finished () const
	is archive converged ? More...
virtual void	generate_batch ()=0
	create a new batch with manager().start_new_batch() and manager().finalize_batch(); 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)
virtual void	save_status (std::ostream &) const
	save and restore status of archive to file-system More...
virtual void	restore_status (std::istream &)
virtual void	idle ()
	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
virtual	~AbstractArchiveBase ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. 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 ()
	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
virtual void	invalidate_score_variations ()
Protected Member Functions inherited from protocols::jd2::archive::EvaluatedArchive
core::scoring::ScoreFunctionOP	scorefxn_non_const ()
virtual void	score (core::pose::Pose &pose) const
	score a pose More...
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 ()

Private Types
typedef EvaluatedArchive	Parent

Private Member Functions
bool	is_start_zero_score (std::string const &) const

Private Attributes
WeightMap	score_variations_
bool	score_variations_are_clean_
VarianceStatisticsArchiveOP	variance_archive_
core::Size	min_decoys_for_statistics_
core::Size	nstruct_for_statistics_
bool	keep_adding_to_statistics_
bool	use_variance_archive_
core::Real	insertion_prob_
bool	activated_
bool	lower_quartile_
utility::vector1< std::string >	positive_scores_

Static Private Attributes
static bool	options_registered_
	keep track whether our options have been registered at start up More...

Additional Inherited Members
Public Types inherited from protocols::jd2::archive::EvaluatedArchive
typedef std::map< std::string, core::Real >	WeightMap
	typedefs for Evaluators and Weights More...
typedef std::map< std::string, evaluation::PoseEvaluatorCOP >	EvaluatorMap
Protected Types inherited from protocols::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

Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input.

This job distributor is meant for running jobs where the machine you are using has a large number of processors, the number of jobs is much greater than the number of processors, or the runtimes of the individual jobs could vary greatly. It dedicates the head node (whichever processor gets processor rank #0) to handling job requests from the slave nodes (all nonzero ranks). Unlike the MPIWorkPartitionJobDistributor, this JD will not work at all without MPI and the implementations of all but the interface functions have been put inside of ifdef directives. Generally each function has a master and slave version, and the interface functions call one or the other depending on processor rank.

Member Typedef Documentation

typedef EvaluatedArchive protocols::jd2::archive::NormalizedEvaluatedArchive::Parent

private

Constructor & Destructor Documentation

protocols::jd2::archive::NormalizedEvaluatedArchive::NormalizedEvaluatedArchive

(

ArchiveManagerAP

ptr

)

Constructor and Destructor.

References init_from_options(), options_registered_, runtime_assert, and score_variations_are_clean_.

protocols::jd2::archive::NormalizedEvaluatedArchive::NormalizedEvaluatedArchive

(

)

References protocols::evaluation::options_registered_, and runtime_assert.

protocols::jd2::archive::NormalizedEvaluatedArchive::~NormalizedEvaluatedArchive

(

)

Member Function Documentation

bool protocols::jd2::archive::NormalizedEvaluatedArchive::add_evaluated_structure ( core::io::silent::SilentStructOP  from_batch, core::io::silent::SilentStructOP  alternative_decoy, Batch const &  batch  )

virtual

add decoy to Archive

evaluate decoy and call add_evaluated_structure

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

References protocols::jd2::archive::EvaluatedArchive::add_evaluated_structure(), keep_adding_to_statistics_, nstruct_for_statistics_, score_variations_are_clean_, protocols::jd2::archive::ArchiveBase::total_proposed(), protocols::jd2::tr, and variance_archive_.

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

bool protocols::jd2::archive::NormalizedEvaluatedArchive::determine_score_variations

(

)

const

determine variation of scores (those that are non-zeros in select_weights_ )

determine variations of the non-zero weighted (select_weight_) scores by taking the difference Q3-Q1 (upper / lower quartil)

References activated_, protocols::jd2::archive::ArchiveBase::decoys(), is_start_zero_score(), lower_quartile_, min_decoys_for_statistics_, protocols::jd2::archive::AbstractArchiveBase::name(), runtime_assert, score_variations_, score_variations_are_clean_, protocols::jd2::tr, variance_archive_, and protocols::jd2::archive::EvaluatedArchive::weights().

Referenced by score_variation(), and score_variations().

void protocols::jd2::archive::NormalizedEvaluatedArchive::init_from_options

(

)

References activated_, insertion_prob_, keep_adding_to_statistics_, lower_quartile_, min_decoys_for_statistics_, nstruct_for_statistics_, option, positive_scores_, protocols::loops::start, and use_variance_archive_.

Referenced by NormalizedEvaluatedArchive().

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

virtual

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

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

References insertion_prob_, protocols::jd2::archive::AbstractArchiveBase::name(), nstruct_for_statistics_, use_variance_archive_, and variance_archive_.

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

virtual void protocols::jd2::archive::NormalizedEvaluatedArchive::invalidate_score_variations ( )

inlineprotectedvirtual

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

References score_variations_are_clean_.

bool protocols::jd2::archive::NormalizedEvaluatedArchive::is_start_zero_score ( std::string const &  str ) const

private

References positive_scores_.

Referenced by determine_score_variations().

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

static

Archive specific options.

References NEW_OPT, NEW_OPT2, protocols::evaluation::options_registered_, protocols::moves::Mover::register_options(), and protocols::loops::start.

void protocols::jd2::archive::NormalizedEvaluatedArchive::rescore ( )

virtual

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

rescore and sort archive

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

References clone(), protocols::jd2::archive::EvaluatedArchive::evaluators(), protocols::jd2::archive::EvaluatedArchive::rescore(), score_variations_are_clean_, protocols::jd2::archive::EvaluatedArchive::scorefxn(), variance_archive_, and protocols::jd2::archive::EvaluatedArchive::weights().

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

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

virtual

overloaded that we can sort the pool after reading

restore archive and sort

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

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

References protocols::jd2::archive::EvaluatedArchive::restore_from_file(), runtime_assert, score_variations_are_clean_, use_variance_archive_, and variance_archive_.

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

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

virtual

overloaded to save / restore the variance_archive_

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

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

References protocols::jd2::archive::EvaluatedArchive::save_to_file(), and variance_archive_.

Referenced by protocols::abinitio::IterativeBase::increment_stage(), protocols::abinitio::IterativeBase::rescore_nonlocal_archive(), and protocols::abinitio::IterativeAbrelax::save_to_file().

core::Real protocols::jd2::archive::NormalizedEvaluatedArchive::score_variation ( std::string const &  col ) const

virtual

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

References determine_score_variations(), score_variations_, score_variations_are_clean_, and protocols::jd2::tr.

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

NormalizedEvaluatedArchive::WeightMap const & protocols::jd2::archive::NormalizedEvaluatedArchive::score_variations ( ) const

virtual

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

References determine_score_variations(), score_variations_, score_variations_are_clean_, and protocols::jd2::tr.

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

Member Data Documentation

bool protocols::jd2::archive::NormalizedEvaluatedArchive::activated_

private

Referenced by determine_score_variations(), and init_from_options().

core::Real protocols::jd2::archive::NormalizedEvaluatedArchive::insertion_prob_

private

Referenced by init_from_options(), and initialize().

bool protocols::jd2::archive::NormalizedEvaluatedArchive::keep_adding_to_statistics_

private

Referenced by add_evaluated_structure(), and init_from_options().

bool protocols::jd2::archive::NormalizedEvaluatedArchive::lower_quartile_

private

Referenced by determine_score_variations(), and init_from_options().

core::Size protocols::jd2::archive::NormalizedEvaluatedArchive::min_decoys_for_statistics_

private

Referenced by determine_score_variations(), and init_from_options().

core::Size protocols::jd2::archive::NormalizedEvaluatedArchive::nstruct_for_statistics_

private

Referenced by add_evaluated_structure(), init_from_options(), and initialize().

bool protocols::jd2::archive::NormalizedEvaluatedArchive::options_registered_

staticprivate

keep track whether our options have been registered at start up

Referenced by NormalizedEvaluatedArchive().

utility::vector1< std::string > protocols::jd2::archive::NormalizedEvaluatedArchive::positive_scores_

private

Referenced by init_from_options(), and is_start_zero_score().

WeightMap protocols::jd2::archive::NormalizedEvaluatedArchive::score_variations_

mutableprivate

Referenced by determine_score_variations(), score_variation(), and score_variations().

bool protocols::jd2::archive::NormalizedEvaluatedArchive::score_variations_are_clean_

mutableprivate

Referenced by add_evaluated_structure(), determine_score_variations(), invalidate_score_variations(), NormalizedEvaluatedArchive(), rescore(), restore_from_file(), score_variation(), and score_variations().

bool protocols::jd2::archive::NormalizedEvaluatedArchive::use_variance_archive_

private

Referenced by init_from_options(), initialize(), and restore_from_file().

VarianceStatisticsArchiveOP protocols::jd2::archive::NormalizedEvaluatedArchive::variance_archive_

private

Referenced by add_evaluated_structure(), determine_score_variations(), initialize(), rescore(), restore_from_file(), and save_to_file().

---

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

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