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Rosetta 3.5
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Rosetta 3.5
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#include <VarianceStatisticsArchive.hh>
Public Member Functions | |
| VarianceStatisticsArchive (std::string name) | |
| virtual bool | add_evaluated_structure (core::io::silent::SilentStructOP, Batch const &) |
| add an evaluated decoy to Archive (i.e, evaluated_decoy = evaluate( some_decoy ) ); More... | |
| virtual void | generate_batch () |
| create a new batch with manager().start_new_batch() and manager().finalize_batch(); More... | |
| virtual void | init_from_decoy_set (core::io::silent::SilentFileData const &) |
| overloaded to make input decoys appear the same as decoys coming from batches More... | |
| void | set_insertion_prob (core::Real setting) |
 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 from_batch, Batch const &) |
| 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... | |
| virtual bool | restore_from_file () |
| overloaded that we can sort the pool after reading More... | |
| virtual void | read_structures (core::io::silent::SilentFileData &, Batch const &batch) |
| 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) |
| virtual void | rescore () |
| recompute all score-values of all decoys and re-order the archive by (new) select_score More... | |
| 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 |
| 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 &) |
| virtual void | save_to_file (std::string suffix="") |
| overloaded to save / restore the variance_archive_ More... | |
| Public Member Functions inherited from protocols::jd2::archive::ArchiveBase | |
| ArchiveBase (ArchiveManagerAP ptr=NULL) | |
| ~ArchiveBase () | |
| virtual bool | finished () const |
| is archive converged ? More... | |
| virtual void | initialize () |
| 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... | |
| 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 (ArchiveManagerAP 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... | |
| 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) |
Private Types | |
| typedef EvaluatedArchive | Parent |
| typedef utility::vector1 < core::io::silent::SilentStructOP > | SilentStructVector |
Private Attributes | |
| core::Real | insertion_prob_ |
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 |
| Static Public Member Functions inherited from protocols::jd2::archive::EvaluatedArchive | |
| static void | register_options () |
| Archive specific options. More... | |
| 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 |
| 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 () |
| Static Protected Attributes inherited from protocols::jd2::archive::ArchiveBase | |
| static std::string const | TAG_IN_FILE |
| static std::string const | SOURCE_FILE |
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private |
| protocols::jd2::archive::VarianceStatisticsArchive::VarianceStatisticsArchive | ( | std::string | name) |
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virtual |
add an evaluated decoy to Archive (i.e, evaluated_decoy = evaluate( some_decoy ) );
Reimplemented from protocols::jd2::archive::EvaluatedArchive.
References protocols::jd2::archive::ArchiveBase::decoys(), core::sequence::end, insertion_prob_, protocols::jd2::archive::EvaluatedArchive::invalidate_score_variations(), protocols::jd2::archive::AbstractArchiveBase::name(), protocols::jd2::archive::ArchiveBase::nstruct(), protocols::RG(), core::io::serialization::size(), and protocols::jd2::tr().
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inlinevirtual |
create a new batch with manager().start_new_batch() and manager().finalize_batch();
Implements protocols::jd2::archive::ArchiveBase.
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inlinevirtual |
overloaded to make input decoys appear the same as decoys coming from batches
Implements protocols::jd2::archive::EvaluatedArchive.
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inline |
References insertion_prob_.
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private |
Referenced by add_evaluated_structure(), and set_insertion_prob().
1.8.4