Rosetta 3.4
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes
protocols::abinitio::IterativeBase Class Reference

#include <IterativeBase.hh>

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List of all members.

Public Types

enum  IterationStage {
  ENUMERATION = 1, TOPO_RESAMPLING, PURE_TOPO_RESAMPLING, STAGE2_RESAMPLING,
  CEN2FULLATOM, LAST_CENTROID_START = CEN2FULLATOM, RIGID_CORE_RESAMPLING, FINISHED
}

Public Member Functions

 IterativeBase (std::string name)
 ~IterativeBase ()
virtual bool finished () const
 archive is finished when at last stage
void set_finish_stage (IterationStage setting)
 where to stop ?
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
virtual bool ready_for_batch () const
 we are always ready to generate a new batch
virtual bool still_interested (jd2::archive::Batch const &batch) const
 we are not interested in batches that were generated in old stages
virtual void generate_batch ()
virtual void idle ()
 while waiting for jobs to finish
virtual void save_status (std::ostream &) const
 save and restore status of archive to file-system
virtual void restore_status (std::istream &)
virtual bool add_structure (core::io::silent::SilentStructOP)
 overloaded to handel special convergence check 'pool_converged_rmsd'
void setup_default_evaluators ()
 setup JumpNrEvaluator
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
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

Static Public Member Functions

static void register_options ()
 Archive specific options.

Protected Member Functions

void set_noesy_assign_float_cycle (core::Real setting)
void gen_resample_topologies (jd2::archive::Batch &batch)
 figure out beta-sheet topologies from pooled decoys and run with jumping
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
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
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 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... )
void gen_noe_assignments (jd2::archive::Batch &batch)
 generate cst-input from current assigned noesy data
PairingStatisticsOP compute_beta_topology ()
 some helpers for the helpers
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
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
std::string const & cen_score_patch () const
loops::Loops const & core (core::Size i)
 OBSOLET cores are computed by compute_cores() in idle()
IterationStage stage () const
 current stage?
std::string const & target_sequence () const
 needed for writing of psi-pred fiels (guess_pairings_from_secondary_structure)
void set_stage (IterationStage setting)
void cluster ()
 cluster structures with min_diversity_list_[ stage_ ] as cluster:radius
std::string const & chemshift_column () const
void test_broker_settings (jd2::archive::Batch const &batch)

Protected Attributes

bool scored_core_initialized_
loops::Loops scored_core_
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

Member Enumeration Documentation

Enumerator:
ENUMERATION 
TOPO_RESAMPLING 
PURE_TOPO_RESAMPLING 
STAGE2_RESAMPLING 
CEN2FULLATOM 
LAST_CENTROID_START 
RIGID_CORE_RESAMPLING 
FINISHED 

Constructor & Destructor Documentation

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

Member Function Documentation

void protocols::abinitio::IterativeBase::add_fullatom_flags ( jd2::archive::Batch batch) [protected]
bool protocols::abinitio::IterativeBase::add_structure ( core::io::silent::SilentStructOP  from_batch) [virtual]

overloaded to handel special convergence check 'pool_converged_rmsd'

overload to check for pool_convergence data in incoming decoys

------------------------ end stage control

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

References protocols::jd2::archive::EvaluatedArchive::add_evaluated_structure(), protocols::jd2::archive::ArchiveBase::decoys(), core::sequence::end, protocols::jd2::archive::EvaluatedArchive::evaluate_silent_struct(), protocols::jd2::archive::EvaluatedArchive::select_score(), stage(), and tr().

std::string const& protocols::abinitio::IterativeBase::cen_score ( ) const [inline, protected]

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

Referenced by gen_evaluation_output(), and IterativeBase().

std::string const& protocols::abinitio::IterativeBase::cen_score_patch ( ) const [inline, protected]
std::string const& protocols::abinitio::IterativeBase::chemshift_column ( ) const [inline, protected]
void protocols::abinitio::IterativeBase::cluster ( ) [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 make_table_of_pilot_apps::begin, and 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) [inline, protected]
std::string const& protocols::abinitio::IterativeBase::fa_score ( ) const [inline, protected]

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

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

std::string const& protocols::abinitio::IterativeBase::fa_score_patch ( ) const [inline, protected]
virtual bool protocols::abinitio::IterativeBase::finished ( ) const [inline, virtual]

archive is finished when at last stage

Reimplemented from protocols::jd2::archive::ArchiveBase.

Reimplemented in protocols::abinitio::IterativeAbrelax.

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_enumerate_pairings ( jd2::archive::Batch batch) [protected]
void protocols::abinitio::IterativeBase::gen_evaluation_output ( jd2::archive::Batch batch,
bool  fullatom = false 
) [virtual]

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

============================================================================ ----------- methods to make new batches ------------ ----- each method should only "append" to broker and flags ----- ============================================================================

Reimplemented in protocols::abinitio::IterativeCentroid.

References core::io::silent::SilentFileData::add_structure(), cen_score(), cen_score_patch(), protocols::noesy_assign::NoesyModule::cmdline_options_activated(), protocols::jd2::archive::ArchiveBase::decoys(), protocols::jd2::archive::Batch::dir(), fa_score(), fa_score_patch(), protocols::jd2::archive::Batch::flag_file(), protocols::jd2::archive::AbstractArchiveBase::name(), protocols::loops::Loops::nr_residues(), scored_core_, scored_core_initialized_, core::io::silent::SilentFileData::size(), stage(), super_quick_relax_of_centroids_, core::io::silent::SilentFileData::write_all(), and protocols::loops::Loops::write_loops_to_file().

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

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]

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

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

References 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]
void protocols::abinitio::IterativeBase::generate_batch ( ) [virtual]

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

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... )

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

Reimplemented in protocols::abinitio::IterativeAbrelax, and protocols::abinitio::IterativeFullatom.

References protocols::jd2::archive::Batch::batch(), CEN2FULLATOM, cluster(), protocols::jd2::archive::ArchiveManager::finalize_batch(), gen_cen2fullatom(), gen_cen2fullatom_non_pool_decoys(), gen_enumerate_pairings(), gen_evaluation_output(), gen_noe_assignments(), gen_resample_fragments(), gen_resample_stage2(), gen_resample_topologies(), gen_start_structures(), protocols::jd2::archive::AbstractArchiveBase::manager(), protocols::jd2::archive::AbstractArchiveBase::name(), PURE_TOPO_RESAMPLING, reassign_noesy_data(), protocols::jd2::archive::Batch::set_intermediate_structs(), STAGE2_RESAMPLING, test_broker_settings(), TOPO_RESAMPLING, and tr().

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

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 ( ) [virtual]
void protocols::abinitio::IterativeBase::init_from_decoy_set ( core::io::silent::SilentFileData const &  sfd) [virtual]
void protocols::abinitio::IterativeBase::read_structures ( core::io::silent::SilentFileData returned_decoys,
jd2::archive::Batch const &  batch 
) [virtual]

overloaded so we can test for end of IterationStage after reading

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

Reimplemented in protocols::abinitio::IterativeAbrelax.

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

virtual bool protocols::abinitio::IterativeBase::ready_for_batch ( ) const [inline, virtual]

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]
void protocols::abinitio::IterativeBase::register_options ( ) [static]
void protocols::abinitio::IterativeBase::restore_status ( std::istream &  is) [virtual]
void protocols::abinitio::IterativeBase::save_status ( std::ostream &  os) const [virtual]
void protocols::abinitio::IterativeBase::set_finish_stage ( IterationStage  setting) [inline]
void protocols::abinitio::IterativeBase::set_noesy_assign_float_cycle ( core::Real  setting) [inline, protected]
void protocols::abinitio::IterativeBase::set_stage ( IterationStage  setting) [inline, protected]
void protocols::abinitio::IterativeBase::setup_default_evaluators ( )
IterationStage protocols::abinitio::IterativeBase::stage ( ) const [inline, protected]
bool protocols::abinitio::IterativeBase::still_interested ( jd2::archive::Batch const &  batch) const [virtual]

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

batch is expired ?

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 ----------------- stage control ----------------------

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

Reimplemented in protocols::abinitio::IterativeAbrelax.

References protocols::jd2::archive::Batch::id().

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

std::string const& protocols::abinitio::IterativeBase::target_sequence ( ) const [inline, protected]

needed for writing of psi-pred fiels (guess_pairings_from_secondary_structure)

Referenced by guess_pairings_from_secondary_structure().

void protocols::abinitio::IterativeBase::test_broker_settings ( jd2::archive::Batch const &  batch) [protected]

Member Data Documentation

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

Referenced by gen_evaluation_output(), gen_resample_fragments(), IterativeBase(), and protocols::abinitio::IterativeFullatom::IterativeFullatom().


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