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protocols::abinitio::HedgeArchive Class Reference

#include <HedgeArchive.hh>

Inheritance diagram for protocols::abinitio::HedgeArchive:
Inheritance graph

Public Member Functions

 HedgeArchive (std::string name)
bool add_evaluated_structure (core::io::silent::SilentStructOP, core::io::silent::SilentStructOP alternative_decoy, jd2::archive::Batch const &batch) override
 add an evaluated decoy to Archive (i.e, evaluated_decoy = evaluate( some_decoy ) ); More...
void generate_batch () override
 create a new batch with manager().start_new_batch() and manager().finalize_batch(); More...
void rescore () override
 recompute all score-values of all decoys and re-order the archive by (new) select_score More...
void save_status (std::ostream &) const override
 save and restore status of archive to file-system More...
void restore_status (std::istream &) override
void init_from_decoy_set (core::io::silent::SilentFileData const &) override
 overloaded to make input decoys appear the same as decoys coming from batches More...
void collect (jd2::archive::Batch const &batch, core::io::silent::SilentStructOPs &) const
- 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...
bool restore_from_file () override
 overloaded that we can sort the pool after reading More...
void read_structures (core::io::silent::SilentFileData &sfd, core::io::silent::SilentFileData &alternative_decoys, Batch const &batch) override
 only overloaded this to add some verbosity each time we read structures More...
void start_evaluation_timer () const
core::io::silent::SilentStructOP evaluate_silent_struct (core::io::silent::SilentStructOP from_batch) const
 yields an "evaluated" silent-struct which can be queried with select_score 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...
const & 
scorefxn () const
virtual WeightMap const & score_variations () const
virtual core::Real score_variation (std::string const &col) const
WeightMap const & weights () const
EvaluatorMap const & evaluators () const
void set_weights (WeightMap const &setting)
void set_evaluators (EvaluatorMap const &, WeightMap const &)
void save_to_file (std::string suffix="") override
 overloaded to save / restore the variance_archive_ More...
- Public Member Functions inherited from protocols::jd2::archive::ArchiveBase
 ArchiveBase (ArchiveManagerAP ptr=nullptr)
 ~ArchiveBase () override
bool finished () const override
 is archive converged ? More...
void initialize () override
core::Size nstruct () const
 how many structures should be in archive .. varies from decoys().size() in startup phase. More...
void set_nstruct (core::Size set)
 set target size of pool More...
void save_decoys (std::string const &dirname, std::string const &name, SilentStructs const &decoys)
 helper routine to save decoys properly More...
void load_decoys (std::string const &filename, SilentStructs &decoys)
void save_status (std::ostream &) const override
 save and restore status of archive to file-system More...
void idle () override
 called when nothing is happening More...
core::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)

Protected Member Functions

void incorporate_batch (core::Size batch_id)
- 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...
virtual void invalidate_score_variations ()
- 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 std::list< std::pair
< core::Real,
core::io::silent::SilentStructOP > > 
typedef std::map< core::Size,
typedef std::set< core::SizeBatchList

Private Member Functions

void save_pending_decoys (SilentStructs const &decoys, core::Size batch_id) const
void remove_pending_decoys (core::Size batch_id) const

Private Attributes

core::Real score_cut_per_batch_
core::Real add_fuzzy_
BatchStructuresMap incoming_structures_
BatchList old_batches_

Additional Inherited Members

- Public Types inherited from protocols::jd2::archive::EvaluatedArchive
typedef std::map< std::string,
 typedefs for Evaluators and Weights More...
typedef std::map< std::string,
- Static Public Member Functions inherited from protocols::jd2::archive::EvaluatedArchive
static void register_options ()
 Archive specific options. More...
- Static Public Member Functions inherited from protocols::jd2::archive::ArchiveBase
static void register_options ()
- Protected Types inherited from protocols::jd2::archive::ArchiveBase
typedef std::list
< core::io::silent::SilentStructOP
- Static Protected Attributes inherited from protocols::jd2::archive::ArchiveBase
static std::string const TAG_IN_FILE
static std::string const SOURCE_FILE

Member Typedef Documentation

Constructor & Destructor Documentation

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

Member Function Documentation

bool protocols::abinitio::HedgeArchive::add_evaluated_structure ( core::io::silent::SilentStructOP  evaluated_decoy,
core::io::silent::SilentStructOP  alternative_decoy,
jd2::archive::Batch const &   
void protocols::abinitio::HedgeArchive::collect ( jd2::archive::Batch const &  batch,
core::io::silent::SilentStructOPs start_decoys 
) const
void protocols::abinitio::HedgeArchive::generate_batch ( )

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

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

void protocols::abinitio::HedgeArchive::incorporate_batch ( core::Size  batch_id)
void protocols::abinitio::HedgeArchive::init_from_decoy_set ( core::io::silent::SilentFileData const &  )

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

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

void protocols::abinitio::HedgeArchive::remove_pending_decoys ( core::Size  batch_id) const
void protocols::abinitio::HedgeArchive::rescore ( )

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.

void protocols::abinitio::HedgeArchive::restore_status ( std::istream &  is)
void protocols::abinitio::HedgeArchive::save_pending_decoys ( SilentStructs const &  decoys,
core::Size  batch_id 
) const
void protocols::abinitio::HedgeArchive::save_status ( std::ostream &  os) const

Member Data Documentation

core::Real protocols::abinitio::HedgeArchive::add_fuzzy_

Referenced by incorporate_batch().

BatchStructuresMap protocols::abinitio::HedgeArchive::incoming_structures_
BatchList protocols::abinitio::HedgeArchive::old_batches_
core::Real protocols::abinitio::HedgeArchive::score_cut_per_batch_

Referenced by incorporate_batch().

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