#include <IterativeBase.hh>

Inheritance diagram for protocols::abinitio::IterativeBase:

Collaboration diagram for protocols::abinitio::IterativeBase:

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

enum protocols::abinitio::IterativeBase::IterationStage

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 )

References cen_score(), cen_score_patch(), core::scoring::chainbreak, protocols::noesy_assign::NoesyModule::cmdline_options_activated(), core::scoring::ScoreFunctionFactory::create_score_function(), protocols::jd2::archive::EvaluatedArchive::evaluate_local(), protocols::swa::rna::file_exists(), FINISHED, core::scoring::ScoreFunction::get_weight(), core::scoring::linear_chainbreak, protocols::jd2::archive::AbstractArchiveBase::name(), core::scoring::overlap_chainbreak, core::import_pose::pose_from_pdb(), PURE_TOPO_RESAMPLING, core::fragment::FragmentIO::read_data(), core::sequence::read_fasta_file(), scored_core_, protocols::jd2::archive::EvaluatedArchive::scorefxn(), protocols::jd2::archive::AbstractArchiveBase::set_name(), protocols::jd2::archive::EvaluatedArchive::set_scorefxn(), protocols::jd2::archive::EvaluatedArchive::set_weight(), core::scoring::ScoreFunction::set_weight(), core::scoring::ScoreFunction::show(), core::fragment::SecondaryStructure::strand_fraction(), super_quick_relax_of_centroids_, core::fragment::SecondaryStructure::total_residue(), tr(), and protocols::loops::LoopsFileIO::use_custom_legacy_file_format().

protocols::abinitio::IterativeBase::~IterativeBase ( )

Member Function Documentation

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

References protocols::jd2::archive::Batch::broker_file(), protocols::jd2::archive::Batch::flag_file(), and protocols::jd2::archive::Batch::id().

Referenced by gen_cen2fullatom(), gen_cen2fullatom_non_pool_decoys(), and protocols::abinitio::IterativeFullatom::gen_resample_core().

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]

Referenced by gen_evaluation_output(), and IterativeBase().

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

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

void protocols::abinitio::IterativeBase::cluster ( ) [protected]

cluster structures with min_diversity_list_[ stage_ ] as cluster:radius

References make_table_of_pilot_apps::begin, protocols::toolbox::ClusterOptions::cluster_radius, protocols::toolbox::cluster_silent_structs(), protocols::jd2::archive::ArchiveBase::count_removed_structures(), protocols::jd2::archive::ArchiveBase::decoys(), core::sequence::end, protocols::toolbox::ClusterOptions::keep_center, protocols::jd2::archive::EvaluatedArchive::select_score(), stage(), and tr().

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

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]

References make_table_of_pilot_apps::begin, protocols::jd2::archive::ArchiveBase::decoys(), protocols::jd2::archive::EvaluatedArchive::evaluate_local(), protocols::abinitio::get_core(), protocols::jd2::archive::ArchiveBase::nstruct(), protocols::toolbox::DecoySetEvaluation::push_back(), protocols::toolbox::DecoySetEvaluation::reserve(), protocols::jd2::archive::EvaluatedArchive::set_weight(), core::pose::Pose::total_residue(), and tr().

Referenced by idle(), and restore_status().

loops::Loops const& protocols::abinitio::IterativeBase::core ( core::Size i ) [inline, protected]

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

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

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]

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

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]

References add_fullatom_flags(), core::io::silent::SilentFileData::add_structure(), make_table_of_pilot_apps::begin, protocols::jd2::archive::Batch::broker_file(), protocols::jd2::archive::ArchiveBase::decoys(), core::sequence::end, protocols::jd2::archive::Batch::flag_file(), protocols::jd2::archive::Batch::nstruct(), protocols::jd2::archive::Batch::set_has_silent_in(), protocols::jd2::archive::Batch::silent_in(), and core::io::silent::SilentFileData::write_all().

Referenced by generate_batch().

void protocols::abinitio::IterativeBase::gen_cen2fullatom_non_pool_decoys ( jd2::archive::Batch & batch ) [protected]

Referenced by generate_batch().

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

References protocols::jd2::archive::Batch::broker_file(), protocols::jd2::archive::Batch::dir(), guess_pairings_from_secondary_structure(), core::fragment::FragmentIO::read_data(), protocols::jd2::archive::ArchiveBase::total_accepts(), and tr().

Referenced by generate_batch().

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]

generate cst-input from current assigned noesy data

References protocols::jd2::archive::Batch::broker_file(), CEN2FULLATOM, protocols::noesy_assign::NoesyModule::cmdline_options_activated(), protocols::jd2::archive::Batch::dir(), protocols::swa::rna::file_exists(), protocols::jd2::archive::Batch::id(), NOESY_CST_FILE_NAME(), core::scoring::constraints::skip_redundant_constraints(), and stage().

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

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

References core::fragment::FragSet::add(), protocols::loops::Loops::add_loop(), make_table_of_pilot_apps::begin, protocols::noesy_assign::NoesyModule::cmdline_options_activated(), protocols::jd2::archive::ArchiveBase::decoys(), protocols::loops::define_scorable_core_from_secondary_structure(), protocols::jd2::archive::Batch::dir(), core::sequence::end, protocols::jd2::archive::Batch::flag_file(), protocols::jd2::archive::Batch::id(), core::pose::Pose::is_fullatom(), protocols::jd2::archive::AbstractArchiveBase::name(), core::fragment::FragmentIO::read_data(), protocols::jd2::archive::EvaluatedArchive::rescore(), scored_core_, scored_core_initialized_, protocols::loops::Loops::size(), STAGE2_RESAMPLING, core::fragment::steal_constant_length_frag_set_from_pose(), super_quick_relax_of_centroids_, core::pose::Pose::total_residue(), tr(), protocols::loops::LoopsFileIO::use_custom_legacy_file_format(), and core::fragment::FragmentIO::write_data().

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

void protocols::abinitio::IterativeBase::gen_resample_stage2 ( jd2::archive::Batch & batch ) [protected]

restart runs from stage2-structures that correspond to those in the pool

References core::io::silent::SilentFileData::add_structure(), protocols::jd2::archive::Batch::broker_file(), protocols::jd2::archive::ArchiveBase::decoys(), protocols::jd2::archive::Batch::flag_file(), protocols::jd2::archive::Batch::nstruct(), protocols::abinitio::RG(), protocols::jd2::archive::Batch::set_has_silent_in(), protocols::jd2::archive::Batch::silent_in(), tr(), and core::io::silent::SilentFileData::write_all().

Referenced by generate_batch().

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]

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

References core::io::silent::SilentFileData::add_structure(), make_table_of_pilot_apps::begin, protocols::jd2::archive::Batch::broker_file(), protocols::jd2::archive::ArchiveBase::decoys(), protocols::jd2::archive::Batch::nstruct(), protocols::jd2::archive::Batch::set_has_silent_in(), protocols::jd2::archive::Batch::silent_in(), and core::io::silent::SilentFileData::write_all().

Referenced by generate_batch().

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]`

References protocols::loops::Loops::push_back(), core::fragment::SecondaryStructure::sheet_fraction(), target_sequence(), core::fragment::SecondaryStructure::total_residue(), tr(), and core::fragment::SecondaryStructure::write_psipred_ss2().

Referenced by gen_enumerate_pairings().

void protocols::abinitio::IterativeBase::idle ( ) [virtual]

while waiting for jobs to finish

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

Reimplemented in protocols::abinitio::IterativeAbrelax.

References protocols::jd2::archive::ArchiveBase::accepts_since_last_batch(), compute_cores(), and protocols::jd2::archive::ArchiveBase::total_accepts().

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

void protocols::abinitio::IterativeBase::init_from_decoy_set ( core::io::silent::SilentFileData const & sfd ) [virtual]

overloaded to make input decoys appear the same as decoys coming from batches

load decoys into archive from -archive:input_pool or so

Implements protocols::jd2::archive::EvaluatedArchive.

Reimplemented in protocols::abinitio::IterativeAbrelax.

References protocols::jd2::archive::EvaluatedArchive::add_evaluation(), protocols::jd2::archive::EvaluatedArchive::evaluate_local(), protocols::jd2::archive::EvaluatedArchive::remove_evaluation(), protocols::jd2::archive::EvaluatedArchive::scorefxn_non_const(), protocols::jd2::archive::EvaluatedArchive::set_evaluate_local(), protocols::jd2::archive::EvaluatedArchive::set_weight(), and tr().

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

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]

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

References make_table_of_pilot_apps::begin, protocols::noesy_assign::NoesyModule::cmdline_options_activated(), protocols::noesy_assign::PeakAssignmentParameters::dcut_, protocols::jd2::archive::ArchiveBase::decoys(), protocols::jd2::archive::Batch::dir(), core::chemical::FA_STANDARD, protocols::noesy_assign::PeakAssignmentParameters::get_nonconst_instance(), protocols::jd2::archive::Batch::id(), core::pose::make_pose_from_sequence(), protocols::jd2::archive::AbstractArchiveBase::manager(), NOESY_CST_FILE_NAME(), protocols::jd2::archive::ArchiveBase::nstruct(), protocols::jd2::archive::ArchiveManager::save_archive(), protocols::noesy_assign::PeakAssignmentParameters::show(), protocols::noesy_assign::PeakAssignmentParameters::show_on_tracer(), stage(), STAGE2_RESAMPLING, protocols::jd2::archive::ArchiveBase::total_proposed(), and tr().

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

void protocols::abinitio::IterativeBase::register_options ( ) [static]

Archive specific options.

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

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

References protocols::evaluation::options_registered_, protocols::evaluation::register_options(), and core::scoring::constraints::skip_redundant_constraints().

void protocols::abinitio::IterativeBase::restore_status ( std::istream & is ) [virtual]

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

References compute_cores(), protocols::jd2::archive::AbstractArchiveBase::name(), scored_core_, scored_core_initialized_, stage(), STAGE2_RESAMPLING, tr(), and protocols::loops::LoopsFileIO::use_custom_legacy_file_format().

void protocols::abinitio::IterativeBase::save_status ( std::ostream & os ) const [virtual]

save and restore status of archive to file-system

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

Reimplemented in protocols::abinitio::IterativeAbrelax.

References scored_core_, scored_core_initialized_, and protocols::loops::Loops::write_loops_to_stream().

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

void protocols::abinitio::IterativeBase::set_finish_stage ( IterationStage setting ) [inline]

where to stop ?

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

void protocols::abinitio::IterativeBase::set_noesy_assign_float_cycle ( core::Real setting ) [inline, protected]

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

void protocols::abinitio::IterativeBase::set_stage ( IterationStage setting ) [inline, protected]

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

void protocols::abinitio::IterativeBase::setup_default_evaluators ( )

setup JumpNrEvaluator

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

References protocols::jd2::archive::EvaluatedArchive::add_evaluation().

IterationStage protocols::abinitio::IterativeBase::stage ( ) const [inline, protected]

current stage?

Referenced by add_structure(), cluster(), gen_evaluation_output(), gen_noe_assignments(), protocols::abinitio::IterativeFullatom::generate_batch(), protocols::abinitio::IterativeFullatom::ready_for_batch(), reassign_noesy_data(), and restore_status().

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]

References protocols::topology_broker::add_cmdline_claims(), protocols::jd2::archive::Batch::all_broker_files(), protocols::jd2::archive::Batch::flag_file(), and tr().

Referenced by generate_batch().