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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>

Inheritance diagram for protocols::jd2::archive::NormalizedEvaluatedArchive:
Inheritance graph
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Public Member Functions

 NormalizedEvaluatedArchive (ArchiveManagerAP ptr)
 Constructor and Destructor. More...
 
 NormalizedEvaluatedArchive ()
 
 ~NormalizedEvaluatedArchive () override
 
void init_from_options ()
 
void initialize () override
 
bool add_evaluated_structure (core::io::silent::SilentStructOP from_batch, core::io::silent::SilentStructOP alternative_decoy, Batch const &) override
 add decoy to Archive evaluate decoy and call add_evaluated_structure More...
 
bool restore_from_file () override
 overloaded that we can sort the pool after reading More...
 
bool determine_score_variations () const
 determine variation of scores (those that are non-zeros in select_weights_ ) More...
 
void save_to_file (std::string suffix="") override
 overloaded to save / restore the variance_archive_ More...
 
void rescore () override
 recompute all score-values of all decoys and re-order the archive by (new) select_score More...
 
WeightMap const & score_variations () const override
 
core::Real score_variation (std::string const &col) const override
 
- Public Member Functions inherited from protocols::jd2::archive::EvaluatedArchive
 EvaluatedArchive (ArchiveManagerAP ptr)
 Constructor and Destructor. More...
 
 EvaluatedArchive ()
 
 ~EvaluatedArchive () override
 
bool add_structure (core::io::silent::SilentStructOP new_decoy, core::io::silent::SilentStructOP alternative_decoy, Batch const &batch) override
 add decoy to Archive evaluate decoy and call add_evaluated_structure More...
 
core::Real select_score (core::io::silent::SilentStructOP evaluated_decoy)
 compute score according to select_weights — this can contain any evaluator columns More...
 
void setup_default_evaluators ()
 set common evaluators: eg. ConstraintEvaluator if -cst_file is present More...
 
void read_structures (core::io::silent::SilentFileData &sfd, core::io::silent::SilentFileData &alternative_decoys, Batch const &batch) override
 only overloaded this to add some verbosity each time we read structures More...
 
void init_from_decoy_set (core::io::silent::SilentFileData const &sfd) override=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 will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct More...
 
bool evaluate_local () const
 specify if decoys are evaluated on the master or (non-local i.e., on the individual slave nodes) More...
 
void set_evaluate_local (bool setting)
 
void add_evaluation (evaluation::PoseEvaluatorCOP, core::Real weight=0.0)
 add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score() More...
 
void remove_evaluation (std::string const &column)
 remove Evaluator More...
 
bool has_evaluator (std::string const &column)
 is a certain elvaluator present ? More...
 
void set_weight (std::string const &column, core::Real weight)
 set weight of an evaluator or a column otherwise present in silent-structs (i.e, score, chainbreak, external evaluation like score_final ) More...
 
core::Real get_weight (std::string const &column) const
 
void set_scorefxn (core::scoring::ScoreFunctionOP scorefxn_)
 set scorefxn used for evaluation More...
 
core::scoring::ScoreFunction
const & 
scorefxn () const
 
WeightMap const & weights () const
 
EvaluatorMap const & evaluators () const
 
void set_weights (WeightMap const &setting)
 
void set_evaluators (EvaluatorMap const &, WeightMap const &)
 
- Public Member Functions inherited from protocols::jd2::archive::ArchiveBase
 ArchiveBase (ArchiveManagerAP ptr=nullptr)
 
 ~ArchiveBase () override
 
bool finished () const override
 is archive converged ? More...
 
void generate_batch () override=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)
 
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...
 
core::Sizeaccepts_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
 
SilentStructsdecoys ()
 
- 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
 
BaseArchiveManagermanager ()
 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

void invalidate_score_variations () override
 
- 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

Constructor & Destructor Documentation

protocols::jd2::archive::NormalizedEvaluatedArchive::NormalizedEvaluatedArchive ( ArchiveManagerAP  ptr)

Constructor and Destructor.

References init_from_options(), options_registered_, and score_variations_are_clean_.

protocols::jd2::archive::NormalizedEvaluatedArchive::NormalizedEvaluatedArchive ( )
protocols::jd2::archive::NormalizedEvaluatedArchive::~NormalizedEvaluatedArchive ( )
overridedefault

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 
)
overridevirtual
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(), 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 ( )
void protocols::jd2::archive::NormalizedEvaluatedArchive::initialize ( )
overridevirtual
void protocols::jd2::archive::NormalizedEvaluatedArchive::invalidate_score_variations ( )
inlineoverrideprotectedvirtual
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
void protocols::jd2::archive::NormalizedEvaluatedArchive::rescore ( )
overridevirtual
bool protocols::jd2::archive::NormalizedEvaluatedArchive::restore_from_file ( )
overridevirtual
void protocols::jd2::archive::NormalizedEvaluatedArchive::save_to_file ( std::string  suffix = "")
overridevirtual
core::Real protocols::jd2::archive::NormalizedEvaluatedArchive::score_variation ( std::string const &  col) const
overridevirtual
NormalizedEvaluatedArchive::WeightMap const & protocols::jd2::archive::NormalizedEvaluatedArchive::score_variations ( ) const
overridevirtual

Member Data Documentation

bool protocols::jd2::archive::NormalizedEvaluatedArchive::activated_
private
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
bool protocols::jd2::archive::NormalizedEvaluatedArchive::lower_quartile_
private
core::Size protocols::jd2::archive::NormalizedEvaluatedArchive::min_decoys_for_statistics_
private
core::Size protocols::jd2::archive::NormalizedEvaluatedArchive::nstruct_for_statistics_
private
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
WeightMap protocols::jd2::archive::NormalizedEvaluatedArchive::score_variations_
mutableprivate
bool protocols::jd2::archive::NormalizedEvaluatedArchive::score_variations_are_clean_
mutableprivate
bool protocols::jd2::archive::NormalizedEvaluatedArchive::use_variance_archive_
private
VarianceStatisticsArchiveOP protocols::jd2::archive::NormalizedEvaluatedArchive::variance_archive_
private

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