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protocols::abinitio::IterativeFullatom Class Reference

#include <IterativeFullatom.hh>

Inheritance diagram for protocols::abinitio::IterativeFullatom:
Inheritance graph
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Public Member Functions

 IterativeFullatom ()
 
void initialize () override
 do initializing work that requires fully setup object here More...
 
bool ready_for_batch () const override
 we are always ready to generate a new batch More...
 
void generate_batch () override
 generate a new batch, use different recipe according to current stage More...
 
core::Size generate_batch (jd2::archive::Batch &, core::Size repeat_id) override
 
- Public Member Functions inherited from protocols::abinitio::IterativeBase
 IterativeBase (std::string name)
 
 ~IterativeBase () override
 
bool finished () const override
 archive is finished when at last stage More...
 
void set_finish_stage (IterationStage setting)
 where to stop ? More...
 
void test_for_stage_end ()
 calls increment_stage() if appropriate More...
 
void init_from_decoy_set (core::io::silent::SilentFileData const &sfd) override
 overloaded to make input decoys appear the same as decoys coming from batches More...
 
bool still_interested (jd2::archive::Batch const &batch) const override
 we are not interested in batches that were generated in old stages More...
 
void idle () override
 while waiting for jobs to finish More...
 
void rescore () override
 
void save_status (std::ostream &) const override
 
void restore_status (std::istream &) override
 
bool add_structure (core::io::silent::SilentStructOP new_decoy, core::io::silent::SilentStructOP alternative_decoy, jd2::archive::Batch const &) override
 overloaded to handel special convergence check 'pool_converged_rmsd' More...
 
void setup_default_evaluators ()
 setup JumpNrEvaluator More...
 
void read_structures (core::io::silent::SilentFileData &sfd, core::io::silent::SilentFileData &alternative_decoys, jd2::archive::Batch const &batch) override
 overloaded so we can test for end of IterationStage after reading More...
 
virtual void gen_evaluation_output (jd2::archive::Batch &batch, bool fullatom=false)
 generate flags and stuff for the out-sourced evaluation —> such that score_final column is returned for each decoy note needs to be public, since IterativeCentroid calls this from IterativeFullatom to prepare evaluation for soon to be full-atom decoys More...
 
virtual void gen_diversity_pool (jd2::archive::Batch &, bool fullatom=false)
 
virtual void gen_dynamic_patches (jd2::archive::Batch &batch)
 
virtual void update_noesy_filter_files (std::string const &current, bool fullatom)
 
- Public Member Functions inherited from protocols::jd2::archive::NormalizedEvaluatedArchive
 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 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...
 
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 ()
 
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 ()
 
- Static Public Member Functions inherited from protocols::abinitio::IterativeBase
static void register_options ()
 
- Static Public Member Functions inherited from protocols::jd2::archive::NormalizedEvaluatedArchive
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 gen_resample_core (jd2::archive::Batch &batch, bool flex)
 
- Protected Member Functions inherited from protocols::abinitio::IterativeBase
void set_noesy_assign_float_cycle (core::Real setting)
 
bool super_quick_relax_of_centroids () const
 
void gen_resample_topologies (jd2::archive::Batch &batch)
 ----------— helper functions to be used from generate_batch() -----------------— More...
 
void gen_start_structures (jd2::archive::Batch &batch)
 in the comp. modelling protocol the topo-resampling stage might also contain a RigidChunkClaimer... provide start-structures for this as -in:file:silent More...
 
void gen_enumerate_pairings (jd2::archive::Batch &batch)
 
void gen_resample_stage2 (jd2::archive::Batch &batch)
 restart runs from stage2-structures that correspond to those in the pool More...
 
void gen_resample_fragments (jd2::archive::Batch &batch)
 
void gen_cen2fullatom (jd2::archive::Batch &batch)
 
void gen_cen2fullatom_non_pool_decoys (jd2::archive::Batch &batch)
 
void collect_hedgeing_decoys_from_batches (jd2::archive::Batch const &batch, core::io::silent::SilentStructOPs &start_decoys, core::Real score_cut_per_batch)
 
void add_fullatom_flags (jd2::archive::Batch &batch)
 
void reassign_noesy_data (jd2::archive::Batch &batch)
 actually run the assignment machinery (only after batch is started to keep archive from hogging the queue... ) More...
 
void gen_noe_assignments (jd2::archive::Batch &batch)
 generate cst-input from current assigned noesy data More...
 
PairingStatisticsOP compute_beta_topology ()
 some helpers for the helpers More...
 
void guess_pairings_from_secondary_structure (core::fragment::FragSet const &frags, std::string const &out_pairings_file, std::string const &out_frag_ss_file) const
 
void compute_cores ()
 
std::string const & fa_score () const
 these are set by the cmd-line options iterative::fa_score and iterative::fa_score_patch More...
 
std::string const & fa_score_patch () const
 
std::string const & cen_score () const
 these are set by the cmd-line options iterative::cen_score and iterative::cen_score_patch More...
 
std::string const & cen_score_patch () const
 
core::Real overall_cstfilter_weight () const
 this is set from score::atom_pair_constraint of the pool-scorefunction More...
 
void set_overall_cstfilter_weight (core::Real setting)
 this is set from score::atom_pair_constraint of the pool-scorefunction More...
 
loops::Loops const & core (core::Size i)
 OBSOLET cores are computed by compute_cores() in idle() More...
 
IterationStage stage () const
 current stage? More...
 
std::string const & target_sequence () const
 needed for writing of psi-pred fiels (guess_pairings_from_secondary_structure) More...
 
void set_stage (IterationStage setting)
 
void cluster ()
 cluster structures with min_diversity_list_[ stage_ ] as cluster:radius More...
 
std::string const & chemshift_column () const
 
void test_broker_settings (jd2::archive::Batch const &batch)
 Helper functions. More...
 
void setup_filter_cst (core::Real weight)
 
virtual void collect_alternative_decoys (SilentStructs, std::string, SilentStructVector &)
 
- Protected Member Functions inherited from protocols::jd2::archive::NormalizedEvaluatedArchive
void invalidate_score_variations () override
 
- Protected Member Functions inherited from protocols::jd2::archive::EvaluatedArchive
core::scoring::ScoreFunctionOP scorefxn_non_const ()
 
- 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 IterativeBase Parent
 

Private Attributes

core::Real perturb_start_structures_
 

Static Private Attributes

static bool options_registered_
 

Additional Inherited Members

- Public Types inherited from protocols::abinitio::IterativeBase
enum  IterationStage {
  ENUMERATION = 1, TOPO_RESAMPLING, PURE_TOPO_RESAMPLING, STAGE2_RESAMPLING,
  NOESY_PHASEII_TOPO, NOESY_PHASEII_S2_RESAMPLING, CEN2FULLATOM, LAST_CENTROID_START = CEN2FULLATOM,
  RIGID_CORE_RESAMPLING, FINISHED
}
 
- 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::abinitio::IterativeBase
typedef utility::vector1
< core::io::silent::SilentStructOP
SilentStructVector
 
- 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 Attributes inherited from protocols::abinitio::IterativeBase
bool never_switched_noe_filter_
 
loops::Loops scored_core_
 
- 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::IterativeFullatom::IterativeFullatom ( )

Member Function Documentation

void protocols::abinitio::IterativeFullatom::gen_resample_core ( jd2::archive::Batch batch,
bool  flex 
)
protected
void protocols::abinitio::IterativeFullatom::generate_batch ( )
inlineoverridevirtual

generate a new batch, use different recipe according to current stage

generate a new batch, use different recipe according to current stage

Reimplemented from protocols::abinitio::IterativeBase.

References protocols::abinitio::IterativeBase::generate_batch().

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

core::Size protocols::abinitio::IterativeFullatom::generate_batch ( jd2::archive::Batch batch,
core::Size  repeat_id 
)
overridevirtual

generate new batch... type of batch depends on stage_. we switch to next stage based on some convergence criteria: right now it is how many decoys were accepted from last batch.. if this number drops sufficiently —> next stage... (maybe need to put a safeguard in here: ratio small but at least XXX decoys proposed since last batch... )

Reimplemented from protocols::abinitio::IterativeBase.

References protocols::abinitio::IterativeBase::cluster(), protocols::abinitio::IterativeBase::gen_evaluation_output(), protocols::abinitio::IterativeBase::gen_noe_assignments(), gen_resample_core(), protocols::abinitio::IterativeBase::gen_resample_fragments(), protocols::abinitio::IterativeBase::RIGID_CORE_RESAMPLING, protocols::jd2::archive::Batch::set_intermediate_structs(), and protocols::abinitio::IterativeBase::stage().

void protocols::abinitio::IterativeFullatom::initialize ( )
overridevirtual
bool protocols::abinitio::IterativeFullatom::ready_for_batch ( ) const
overridevirtual
void protocols::abinitio::IterativeFullatom::register_options ( )
static

Member Data Documentation

bool protocols::abinitio::IterativeFullatom::options_registered_
staticprivate
core::Real protocols::abinitio::IterativeFullatom::perturb_start_structures_
private

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