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protocols::abinitio::IterativeBase Class Reference

#include <IterativeBase.hh>

Inheritance diagram for protocols::abinitio::IterativeBase:
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Public Types

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
 

Public Member Functions

 IterativeBase (std::string name)
 
 ~IterativeBase () override
 
bool finished () const override
 archive is finished when at last stage More...
 
void initialize () override
 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...
 
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...
 
virtual bool ready_for_batch () const
 we are always ready to generate a new batch 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 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
 
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::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 Types

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 Member Functions

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 ()
 

Protected Attributes

bool never_switched_noe_filter_
 
loops::Loops scored_core_
 

Private Types

typedef
jd2::archive::NormalizedEvaluatedArchive 
Parent
 

Private Member Functions

void collect_hedge_structures (core::io::silent::SilentStructOP evaluated_decoy, jd2::archive::Batch const &batch)
 
void score (core::pose::Pose &pose) const override
 score a pose with Pool-Scoring function (adds necessary data to pose (RDC, constraints, etc ) ) More...
 
core::Real target_accept_ratio () const
 what is the expected lowest acceptance ratio at the current stage ? More...
 
void add_core_evaluator (loops::Loops const &core, std::string const &core_tag)
 [OBSOLET] add score_coreX and rms_coreX evaluators (and columns) with 0.0 weight More...
 
void increment_stage ()
 necessary steps to go to next stage... e.g., saving snapshot of archive More...
 
void replace_noesy_filter_constraints ()
 
void rescore_nonlocal_archive ()
 
void setup_autoNOE ()
 
void do_dynamic_patching (jd2::archive::Batch &batch, utility::io::ozstream &flags, std::string score, utility::options::FileVectorOptionKey const &key) const
 

Private Attributes

IterationStage stage_
 -----------—— – private data members – --------------—— More...
 
IterationStage finish_stage_
 end-condition More...
 
core::Size first_batch_this_stage_
 indices of prominent batches ( STATUS file ) More...
 
core::Size first_fullatom_batch_
 
bool bEnumeratedLastTime_
 toggle to keep track of the enumerate-pairings mode .. want to run this only every 2nd batch More...
 
core::Size last_accepted_decoys_in_idle_
 [OBSOLET?] keep track when idle() has been run ... More...
 
loops::Loops core15_
 core-regions — used in IterativeFullatom for the "rigid-core" sampling step... More...
 
loops::Loops core2_
 
loops::Loops core3_
 
loops::Loops core4_
 
utility::vector1< int > max_nstruct_list_
 -----—— some cmd-line controlled settings -----------—— More...
 
utility::vector1< core::Realmin_diversity_list_
 cluster:radius for minimum diversity in stage X More...
 
utility::vector1< core::Realtarget_accept_ratio_
 minimum acceptance ratio .. current_accept_ratio < target_accept_ratio[ stage_ ] –> increment_stage More...
 
core::pose::PoseCOP reference_pose_
 for RMSD ... e.g., in:file:native More...
 
std::string cen_score_
 from cmd-line cen-score and patch names More...
 
std::string cen_score_patch_
 
std::string fa_score_
 from cmd-line fa-score and patch names More...
 
std::string fa_score_patch_
 
core::Real overall_cstfilter_weight_
 this is set from score::atom_pair_constraint of the pool-scorefunction More...
 
std::string target_sequence_
 
protocols::noesy_assign::NoesyModuleOP noesy_module_
 
core::Real noesy_assign_float_cycle_
 
std::string first_noesy_cst_file_
 
std::string first_noesy_fa_cst_file_
 
std::string current_noesy_sampling_file_
 
bool bCombineNoesyCst_
 
size_t noesy_assign_hash_
 
boost::hash< std::string > hasher
 
std::string chemshift_column_
 even in centroid mode the end of abinitio will have a fast relax... enables cs-score and noe-assignment More...
 
bool bDoBetaJumping_
 
bool super_quick_relax_of_centroids_
 even in centroid mode the end of abinitio will have a fast relax... enables cs-score and noe-assignment More...
 
bool use_dynamic_weights_for_sampling_
 use the score_variations from EvaluatedArchive to determine new sampling weights More...
 
core::Size delay_noesy_reassign_
 
HedgeArchiveOP hedge_archive_
 
core::scoring::ResidualDipolarCouplingOP rdc_data_
 cache some of the experimental data so we don't reload from file for each evaluation More...
 
core::scoring::constraints::ConstraintSetOP cst_data_
 
core::scoring::constraints::ConstraintSetOP cst_fa_data_
 
utility::options::OptionCollection
const 
vanilla_options_
 ---------------— register cmdline options ------------------------— More...
 

Static Private Attributes

static bool options_registered_
 

Additional Inherited Members

- 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

Member Enumeration Documentation

Enumerator
ENUMERATION 
TOPO_RESAMPLING 
PURE_TOPO_RESAMPLING 
STAGE2_RESAMPLING 
NOESY_PHASEII_TOPO 
NOESY_PHASEII_S2_RESAMPLING 
CEN2FULLATOM 
LAST_CENTROID_START 
RIGID_CORE_RESAMPLING 
FINISHED 

Constructor & Destructor Documentation

protocols::abinitio::IterativeBase::IterativeBase ( std::string  name)
protocols::abinitio::IterativeBase::~IterativeBase ( )
overridedefault

Member Function Documentation

void protocols::abinitio::IterativeBase::add_core_evaluator ( loops::Loops const &  core,
std::string const &  core_tag 
)
private
void protocols::abinitio::IterativeBase::add_fullatom_flags ( jd2::archive::Batch batch)
protected
bool protocols::abinitio::IterativeBase::add_structure ( core::io::silent::SilentStructOP  new_decoy,
core::io::silent::SilentStructOP  alternative_decoy,
jd2::archive::Batch const &  batch 
)
overridevirtual
std::string const& protocols::abinitio::IterativeBase::cen_score ( ) const
inlineprotected

these are set by the cmd-line options iterative::cen_score and iterative::cen_score_patch

References cen_score_.

Referenced by initialize().

std::string const& protocols::abinitio::IterativeBase::cen_score_patch ( ) const
inlineprotected

References cen_score_patch_.

Referenced by initialize().

std::string const& protocols::abinitio::IterativeBase::chemshift_column ( ) const
inlineprotected
void protocols::abinitio::IterativeBase::cluster ( )
protected

cluster structures with min_diversity_list_[ stage_ ] as cluster:radius

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

virtual void protocols::abinitio::IterativeBase::collect_alternative_decoys ( SilentStructs  ,
std::string  ,
SilentStructVector  
)
inlineprotectedvirtual
void protocols::abinitio::IterativeBase::collect_hedge_structures ( core::io::silent::SilentStructOP  evaluated_decoy,
jd2::archive::Batch const &  batch 
)
private
void protocols::abinitio::IterativeBase::collect_hedgeing_decoys_from_batches ( jd2::archive::Batch const &  batch,
core::io::silent::SilentStructOPs start_decoys,
core::Real  score_cut_per_batch 
)
protected
PairingStatisticsOP protocols::abinitio::IterativeBase::compute_beta_topology ( )
protected

some helpers for the helpers

============================================================================ --------— methods to compute stuff from archive ---------—

--------— these may be called from idle() ---------—

References protocols::jd2::archive::ArchiveBase::decoys().

Referenced by gen_resample_topologies().

void protocols::abinitio::IterativeBase::compute_cores ( )
protected
loops::Loops const& protocols::abinitio::IterativeBase::core ( core::Size  i)
inlineprotected

OBSOLET cores are computed by compute_cores() in idle()

References core15_, core2_, core3_, and core4_.

Referenced by protocols::abinitio::IterativeFullatom::gen_resample_core().

void protocols::abinitio::IterativeBase::do_dynamic_patching ( jd2::archive::Batch batch,
utility::io::ozstream &  flags,
std::string  score,
utility::options::FileVectorOptionKey const &  key 
) const
private

============================================================================ --------— methods to make new batches ---------—

--— each method should only "append" to broker and flags --—

References core::scoring::atom_pair_constraint, protocols::jd2::archive::Batch::dir(), protocols::jd2::archive::EvaluatedArchive::get_weight(), core::scoring::rdc, protocols::jd2::archive::NormalizedEvaluatedArchive::score_variation(), protocols::jd2::archive::NormalizedEvaluatedArchive::score_variations(), protocols::jd2::archive::EvaluatedArchive::scorefxn(), and tr().

Referenced by gen_dynamic_patches().

std::string const& protocols::abinitio::IterativeBase::fa_score ( ) const
inlineprotected

these are set by the cmd-line options iterative::fa_score and iterative::fa_score_patch

References fa_score_.

Referenced by protocols::abinitio::IterativeFullatom::initialize(), and rescore_nonlocal_archive().

std::string const& protocols::abinitio::IterativeBase::fa_score_patch ( ) const
inlineprotected
bool protocols::abinitio::IterativeBase::finished ( ) const
inlineoverridevirtual

archive is finished when at last stage

Implements protocols::jd2::archive::AbstractArchiveBase.

References finish_stage_, and stage_.

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

void protocols::abinitio::IterativeBase::gen_cen2fullatom ( jd2::archive::Batch batch)
protected
void protocols::abinitio::IterativeBase::gen_cen2fullatom_non_pool_decoys ( jd2::archive::Batch batch)
protected
void protocols::abinitio::IterativeBase::gen_diversity_pool ( jd2::archive::Batch batch,
bool  fullatom = false 
)
virtual
void protocols::abinitio::IterativeBase::gen_dynamic_patches ( jd2::archive::Batch batch)
virtual
void protocols::abinitio::IterativeBase::gen_enumerate_pairings ( jd2::archive::Batch batch)
protected
void protocols::abinitio::IterativeBase::gen_evaluation_output ( jd2::archive::Batch batch,
bool  fullatom = false 
)
virtual
void protocols::abinitio::IterativeBase::gen_noe_assignments ( jd2::archive::Batch batch)
protected
void protocols::abinitio::IterativeBase::gen_resample_fragments ( jd2::archive::Batch batch)
protected
void protocols::abinitio::IterativeBase::gen_resample_stage2 ( jd2::archive::Batch batch)
protected
void protocols::abinitio::IterativeBase::gen_resample_topologies ( jd2::archive::Batch batch)
protected

----------— helper functions to be used from generate_batch() -----------------—

figure out beta-sheet topologies from pooled decoys and run with jumping

References bDoBetaJumping_, protocols::jd2::archive::Batch::broker_file(), compute_beta_topology(), protocols::jd2::archive::Batch::dir(), protocols::jd2::archive::ArchiveBase::total_accepts(), and tr().

Referenced by generate_batch().

void protocols::abinitio::IterativeBase::gen_start_structures ( jd2::archive::Batch batch)
protected

in the comp. modelling protocol the topo-resampling stage might also contain a RigidChunkClaimer... provide start-structures for this as -in:file:silent

void protocols::abinitio::IterativeBase::generate_batch ( )
overridevirtual
core::Size protocols::abinitio::IterativeBase::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::jd2::archive::AbstractArchiveBase.

Reimplemented in protocols::abinitio::IterativeFullatom.

References protocols::jd2::archive::Batch::batch(), CEN2FULLATOM, gen_cen2fullatom(), gen_cen2fullatom_non_pool_decoys(), gen_dynamic_patches(), gen_enumerate_pairings(), gen_evaluation_output(), gen_noe_assignments(), gen_resample_fragments(), gen_resample_stage2(), gen_resample_topologies(), mem_tr, protocols::jd2::archive::AbstractArchiveBase::name(), NOESY_PHASEII_S2_RESAMPLING, NOESY_PHASEII_TOPO, PURE_TOPO_RESAMPLING, protocols::jd2::archive::Batch::set_intermediate_structs(), STAGE2_RESAMPLING, stage_, test_broker_settings(), TOPO_RESAMPLING, and tr().

void protocols::abinitio::IterativeBase::guess_pairings_from_secondary_structure ( core::fragment::FragSet const &  frags,
std::string const &  out_pairings_file,
std::string const &  out_frag_ss_file 
) const
protected
void protocols::abinitio::IterativeBase::idle ( )
overridevirtual

while waiting for jobs to finish

ready for new batch .... if queue is empty batch will be generated any way, but otherwise we only generate if this yields true. logic here: new batch at beginning, but only if we are in startup phase ( not a reload of a full archive ) otherwise make new batch if sufficiently many structures have been accepted since last batch

Implements protocols::jd2::archive::AbstractArchiveBase.

References protocols::jd2::archive::ArchiveBase::accepts_since_last_batch(), protocols::noesy_assign::NoesyModule::cmdline_options_activated(), compute_cores(), protocols::jd2::archive::ArchiveBase::decoys(), core::sequence::end, protocols::jd2::archive::EvaluatedArchive::evaluate_local(), last_accepted_decoys_in_idle_, never_switched_noe_filter_, replace_noesy_filter_constraints(), rescore(), STAGE2_RESAMPLING, stage_, protocols::jd2::archive::ArchiveBase::total_accepts(), and tr().

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

void protocols::abinitio::IterativeBase::increment_stage ( )
private
void protocols::abinitio::IterativeBase::init_from_decoy_set ( core::io::silent::SilentFileData const &  sfd)
overridevirtual
void protocols::abinitio::IterativeBase::initialize ( )
overridevirtual
core::Real protocols::abinitio::IterativeBase::overall_cstfilter_weight ( ) const
inlineprotected

this is set from score::atom_pair_constraint of the pool-scorefunction

References overall_cstfilter_weight_.

Referenced by protocols::abinitio::IterativeFullatom::initialize(), and initialize().

void protocols::abinitio::IterativeBase::read_structures ( core::io::silent::SilentFileData sfd,
core::io::silent::SilentFileData alternative_decoys,
jd2::archive::Batch const &  batch 
)
overridevirtual
virtual bool protocols::abinitio::IterativeBase::ready_for_batch ( ) const
inlinevirtual

we are always ready to generate a new batch

Reimplemented in protocols::abinitio::IterativeFullatom.

void protocols::abinitio::IterativeBase::reassign_noesy_data ( jd2::archive::Batch batch)
protected

actually run the assignment machinery (only after batch is started to keep archive from hogging the queue... )


END gen_xxx ( batch ) methods

References protocols::jd2::archive::EvaluatedArchive::add_evaluation(), bCombineNoesyCst_, CEN2FULLATOM, protocols::noesy_assign::NoesyModule::cmdline_options_activated(), current_noesy_sampling_file_, protocols::noesy_assign::PeakAssignmentParameters::dcut_, protocols::jd2::archive::ArchiveBase::decoys(), delay_noesy_reassign_, protocols::jd2::archive::Batch::dir(), protocols::jd2::archive::EvaluatedArchive::evaluate_local(), core::chemical::FA_STANDARD, protocols::noesy_assign::PeakAssignmentParameters::get_nonconst_instance(), protocols::jd2::archive::EvaluatedArchive::get_weight(), hasher, protocols::jd2::archive::Batch::id(), core::pose::make_pose_from_sequence(), protocols::jd2::archive::AbstractArchiveBase::manager(), mem_tr, noesy_assign_hash_, NOESY_CST_FILE_NAME(), noesy_module_, protocols::jd2::archive::ArchiveBase::nstruct(), overall_cstfilter_weight_, reference_pose_, rescore(), protocols::noesy_assign::PeakAssignmentParameters::reset(), protocols::jd2::archive::BaseArchiveManager::save_archive(), protocols::noesy_assign::PeakAssignmentParameters::set_cycle(), protocols::noesy_assign::PeakAssignmentParameters::show(), protocols::noesy_assign::PeakAssignmentParameters::show_on_tracer(), core::scoring::constraints::skip_redundant_constraints(), stage(), STAGE2_RESAMPLING, target_sequence_, protocols::jd2::archive::ArchiveBase::total_proposed(), tr(), protocols::noesy_assign::PeakAssignmentParameters::use_local_distviol_, and vanilla_options_.

Referenced by generate_batch().

void protocols::abinitio::IterativeBase::register_options ( )
static
void protocols::abinitio::IterativeBase::replace_noesy_filter_constraints ( )
private
void protocols::abinitio::IterativeBase::rescore ( )
overridevirtual
void protocols::abinitio::IterativeBase::rescore_nonlocal_archive ( )
private
void protocols::abinitio::IterativeBase::restore_status ( std::istream &  is)
overridevirtual
void protocols::abinitio::IterativeBase::save_status ( std::ostream &  os) const
overridevirtual
void protocols::abinitio::IterativeBase::score ( core::pose::Pose pose) const
overrideprivatevirtual

score a pose with Pool-Scoring function (adds necessary data to pose (RDC, constraints, etc ) )

before we can apply score-fxn we have to add extra data: RDC, NOES, (not supported yet: PCS, ... )

Reimplemented from protocols::jd2::archive::EvaluatedArchive.

References core::scoring::rdc, rdc_data_, protocols::jd2::archive::EvaluatedArchive::score(), and core::scoring::store_RDC_in_pose().

void protocols::abinitio::IterativeBase::set_finish_stage ( IterationStage  setting)
inline
void protocols::abinitio::IterativeBase::set_noesy_assign_float_cycle ( core::Real  setting)
inlineprotected
void protocols::abinitio::IterativeBase::set_overall_cstfilter_weight ( core::Real  setting)
inlineprotected

this is set from score::atom_pair_constraint of the pool-scorefunction

References overall_cstfilter_weight_.

Referenced by protocols::abinitio::IterativeFullatom::initialize(), and initialize().

void protocols::abinitio::IterativeBase::set_stage ( IterationStage  setting)
inlineprotected
void protocols::abinitio::IterativeBase::setup_autoNOE ( )
private
void protocols::abinitio::IterativeBase::setup_default_evaluators ( )
void protocols::abinitio::IterativeBase::setup_filter_cst ( core::Real  weight)
protected
IterationStage protocols::abinitio::IterativeBase::stage ( ) const
inlineprotected
bool protocols::abinitio::IterativeBase::still_interested ( jd2::archive::Batch const &  batch) const
overridevirtual

we are not interested in batches that were generated in old stages

-----------—— stage control ----------------——

batch is expired ?

Reimplemented from protocols::jd2::archive::AbstractArchiveBase.

References first_batch_this_stage_, protocols::jd2::archive::Batch::id(), and protocols::jd2::archive::AbstractArchiveBase::still_interested().

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

bool protocols::abinitio::IterativeBase::super_quick_relax_of_centroids ( ) const
inlineprotected
core::Real protocols::abinitio::IterativeBase::target_accept_ratio ( ) const
inlineprivate

what is the expected lowest acceptance ratio at the current stage ?

References stage_, and target_accept_ratio_.

Referenced by test_for_stage_end().

std::string const& protocols::abinitio::IterativeBase::target_sequence ( ) const
inlineprotected

needed for writing of psi-pred fiels (guess_pairings_from_secondary_structure)

References target_sequence_.

Referenced by guess_pairings_from_secondary_structure().

void protocols::abinitio::IterativeBase::test_broker_settings ( jd2::archive::Batch const &  batch)
protected
void protocols::abinitio::IterativeBase::test_for_stage_end ( )
void protocols::abinitio::IterativeBase::update_noesy_filter_files ( std::string const &  current,
bool  fullatom 
)
virtual

Member Data Documentation

bool protocols::abinitio::IterativeBase::bCombineNoesyCst_
private
bool protocols::abinitio::IterativeBase::bDoBetaJumping_
private
bool protocols::abinitio::IterativeBase::bEnumeratedLastTime_
private

toggle to keep track of the enumerate-pairings mode .. want to run this only every 2nd batch

------------------------------— other ---------------------------------—

Referenced by gen_enumerate_pairings().

std::string protocols::abinitio::IterativeBase::cen_score_
private

from cmd-line cen-score and patch names

Referenced by cen_score().

std::string protocols::abinitio::IterativeBase::cen_score_patch_
private

Referenced by cen_score_patch().

std::string protocols::abinitio::IterativeBase::chemshift_column_
private

even in centroid mode the end of abinitio will have a fast relax... enables cs-score and noe-assignment

Referenced by chemshift_column(), and initialize().

loops::Loops protocols::abinitio::IterativeBase::core15_
private

core-regions — used in IterativeFullatom for the "rigid-core" sampling step...

Referenced by compute_cores(), and core().

loops::Loops protocols::abinitio::IterativeBase::core2_
private

Referenced by compute_cores(), and core().

loops::Loops protocols::abinitio::IterativeBase::core3_
private

Referenced by compute_cores(), and core().

loops::Loops protocols::abinitio::IterativeBase::core4_
private

Referenced by compute_cores(), and core().

core::scoring::constraints::ConstraintSetOP protocols::abinitio::IterativeBase::cst_data_
mutableprivate
core::scoring::constraints::ConstraintSetOP protocols::abinitio::IterativeBase::cst_fa_data_
mutableprivate
std::string protocols::abinitio::IterativeBase::current_noesy_sampling_file_
private
core::Size protocols::abinitio::IterativeBase::delay_noesy_reassign_
private
std::string protocols::abinitio::IterativeBase::fa_score_
private

from cmd-line fa-score and patch names

Referenced by fa_score().

std::string protocols::abinitio::IterativeBase::fa_score_patch_
private

Referenced by fa_score_patch().

IterationStage protocols::abinitio::IterativeBase::finish_stage_
private

end-condition

Referenced by finished(), increment_stage(), and set_finish_stage().

core::Size protocols::abinitio::IterativeBase::first_batch_this_stage_
private

indices of prominent batches ( STATUS file )

Referenced by add_structure(), increment_stage(), restore_status(), save_status(), and still_interested().

core::Size protocols::abinitio::IterativeBase::first_fullatom_batch_
private
std::string protocols::abinitio::IterativeBase::first_noesy_cst_file_
private
std::string protocols::abinitio::IterativeBase::first_noesy_fa_cst_file_
private
boost::hash<std::string> protocols::abinitio::IterativeBase::hasher
private
HedgeArchiveOP protocols::abinitio::IterativeBase::hedge_archive_
private
core::Size protocols::abinitio::IterativeBase::last_accepted_decoys_in_idle_
private

[OBSOLET?] keep track when idle() has been run ...

Referenced by idle().

utility::vector1< int > protocols::abinitio::IterativeBase::max_nstruct_list_
private

-----—— some cmd-line controlled settings -----------——

how many structures are maximally produced in stage X

Referenced by increment_stage(), IterativeBase(), and test_for_stage_end().

utility::vector1< core::Real > protocols::abinitio::IterativeBase::min_diversity_list_
private

cluster:radius for minimum diversity in stage X

Referenced by add_structure(), gen_diversity_pool(), gen_evaluation_output(), and IterativeBase().

bool protocols::abinitio::IterativeBase::never_switched_noe_filter_
protected

Referenced by idle(), and IterativeBase().

core::Real protocols::abinitio::IterativeBase::noesy_assign_float_cycle_
private
size_t protocols::abinitio::IterativeBase::noesy_assign_hash_
private
protocols::noesy_assign::NoesyModuleOP protocols::abinitio::IterativeBase::noesy_module_
private

Referenced by reassign_noesy_data().

bool protocols::abinitio::IterativeBase::options_registered_
staticprivate
core::Real protocols::abinitio::IterativeBase::overall_cstfilter_weight_
private

this is set from score::atom_pair_constraint of the pool-scorefunction

Referenced by overall_cstfilter_weight(), reassign_noesy_data(), replace_noesy_filter_constraints(), restore_status(), set_overall_cstfilter_weight(), and setup_autoNOE().

core::scoring::ResidualDipolarCouplingOP protocols::abinitio::IterativeBase::rdc_data_
mutableprivate

cache some of the experimental data so we don't reload from file for each evaluation

Referenced by score().

core::pose::PoseCOP protocols::abinitio::IterativeBase::reference_pose_
private

for RMSD ... e.g., in:file:native

Referenced by add_core_evaluator(), IterativeBase(), and reassign_noesy_data().

loops::Loops protocols::abinitio::IterativeBase::scored_core_
protected
IterationStage protocols::abinitio::IterativeBase::stage_
private

-----------—— – private data members – --------------——

---------------------------— stage - control -----------------------— current stage

Referenced by add_structure(), finished(), generate_batch(), idle(), increment_stage(), initialize(), rescore_nonlocal_archive(), restore_status(), save_status(), set_stage(), stage(), target_accept_ratio(), and test_for_stage_end().

bool protocols::abinitio::IterativeBase::super_quick_relax_of_centroids_
private

even in centroid mode the end of abinitio will have a fast relax... enables cs-score and noe-assignment

Referenced by gen_evaluation_output(), initialize(), rescore_nonlocal_archive(), setup_autoNOE(), super_quick_relax_of_centroids(), and update_noesy_filter_files().

utility::vector1< core::Real > protocols::abinitio::IterativeBase::target_accept_ratio_
private

minimum acceptance ratio .. current_accept_ratio < target_accept_ratio[ stage_ ] –> increment_stage

Referenced by IterativeBase(), and target_accept_ratio().

std::string protocols::abinitio::IterativeBase::target_sequence_
private
bool protocols::abinitio::IterativeBase::use_dynamic_weights_for_sampling_
private

use the score_variations from EvaluatedArchive to determine new sampling weights

Referenced by gen_dynamic_patches().

utility::options::OptionCollection const protocols::abinitio::IterativeBase::vanilla_options_
private

---------------— register cmdline options ------------------------—

Referenced by reassign_noesy_data().


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