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protocols::abinitio::IterativeCentroid Class Reference

#include <IterativeCentroid.hh>

Inheritance diagram for protocols::abinitio::IterativeCentroid:
Inheritance graph
Collaboration diagram for protocols::abinitio::IterativeCentroid:
Collaboration graph

Public Member Functions

 IterativeCentroid (IterativeFullatom *fullatom_pool_ptr)
virtual void gen_diversity_pool (jd2::archive::Batch &batch, bool fullatom=false)
virtual void update_noesy_filter_files (std::string const &current, bool fullatom)
- Public Member Functions inherited from protocols::abinitio::IterativeBase
 IterativeBase (std::string name)
 ~IterativeBase ()
virtual bool finished () const
 archive is finished when at last stage More...
virtual void initialize ()
 do initializing work that requires fully setup object here More...
void set_finish_stage (IterationStage setting)
 where to stop ? More...
void test_for_stage_end ()
 calls increment_stage() if appropriate More...
virtual void init_from_decoy_set (core::io::silent::SilentFileData const &sfd)
 overloaded to make input decoys appear the same as decoys coming from batches More...
virtual bool ready_for_batch () const
 we are always ready to generate a new batch More...
virtual bool still_interested (jd2::archive::Batch const &batch) const
 we are not interested in batches that were generated in old stages More...
virtual void generate_batch ()
virtual void idle ()
 while waiting for jobs to finish More...
virtual void rescore ()
virtual void save_status (std::ostream &) const
 save and restore status of archive to file-system More...
virtual void restore_status (std::istream &)
virtual bool add_structure (core::io::silent::SilentStructOP, jd2::archive::Batch const &)
 overloaded to handel special convergence check 'pool_converged_rmsd' More...
void setup_default_evaluators ()
 setup JumpNrEvaluator More...
virtual void read_structures (core::io::silent::SilentFileData &returned_decoys, jd2::archive::Batch const &batch)
 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_dynamic_patches (jd2::archive::Batch &batch)
- Public Member Functions inherited from protocols::jd2::archive::NormalizedEvaluatedArchive
 NormalizedEvaluatedArchive (ArchiveManagerAP ptr)
 Constructor and Destructor. More...
 NormalizedEvaluatedArchive ()
 ~NormalizedEvaluatedArchive ()
void init_from_options ()
virtual bool add_evaluated_structure (core::io::silent::SilentStructOP from_batch, Batch const &)
 add decoy to Archive evaluate decoy and call add_evaluated_structure 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 ()
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 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
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 ()
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...
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
virtual ~AbstractArchiveBase ()
 Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
 AbstractArchiveBase (ArchiveManagerAP 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
ArchiveManagermanager ()
 access to the ArchiveManager (control of batches) More...
virtual void set_manager (ArchiveManagerAP manager)

Private Types

typedef IterativeBase Parent

Private Attributes


Additional Inherited Members

- Public Types inherited from protocols::abinitio::IterativeBase
enum  IterationStage {
- Static Public Member Functions inherited from protocols::abinitio::IterativeBase
static void register_options ()
- Protected Types inherited from protocols::jd2::archive::ArchiveBase
typedef std::list
< core::io::silent::SilentStructOP
- 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)
void setup_filter_cst (core::Real weight)
- 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::IterativeCentroid::IterativeCentroid ( IterativeFullatom fullatom_pool_ptr)

Member Function Documentation

void protocols::abinitio::IterativeCentroid::gen_diversity_pool ( jd2::archive::Batch batch,
bool  fullatom = false 
void protocols::abinitio::IterativeCentroid::update_noesy_filter_files ( std::string const &  current,
bool  fullatom 

Member Data Documentation

IterativeFullatom* protocols::abinitio::IterativeCentroid::fullatom_pool_ptr_

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