protocols::jd2 Namespace Reference

Namespaces
	archive
	JobInputterInputSource

Classes
class	AtomTreeDiffJobInputter
class	AtomTreeDiffJobInputterCreator
class	AtomTreeDiffJobOutputter
class	AtomTreeDiffJobOutputterCreator
class	BatchJobInputter
class	BOINCJobDistributor
class	EmptyPoseJobInputter
class	EmptyPoseJobInputterCreator
class	EnsembleJobInputter
	A Job Inputter for distributing a job based on a set of input structures that make up an ensemble Two modes. Seed Ensemble and Grid Ensemble. More...
class	EnsembleJobInputterCreator
class	FileJobOutputter
class	FileSystemJobDistributor
class	InnerJob
class	InnerMultiThreadingJob
class	Job
class	JD2Failure
	A catchable exception which represents that some issue has occured during the JD2 run. This isn't an error in itself, but represents that JD2 caught another error and then continued, raising this exception after the remaining jobs had a chance to continue. More...
class	JobDistributor
class	JobDistributorFactory
class	JobInputter
	The JobInputter class is responsible for. More...
class	JobInputterCreator
	Abstract base class for a JobInputter factory; the Creator class is responsible for creating a particular mover class. More...
class	JobInputterRegistrator
	This templated class will register an instance of an JobInputterCreator (class T) with the JobInputterFactory. It will ensure that no JobInputterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
class	JobInputterFactory
class	JobOutputter
class	JobOutputterCreator
	Abstract base class for a JobOutputter factory; the Creator class is responsible for creating a particular mover class. More...
class	JobOutputterRegistrator
	This templated class will register an instance of an JobOutputterCreator (class T) with the JobOutputterFactory. It will ensure that no JobOutputterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
class	JobOutputterFactory
class	JobOutputterObserver
class	JobsContainer
class	LargeNstructJobInputter
class	LargeNstructJobInputterCreator
class	LazySilentFileJobInputter
class	LazySilentFileJobInputterCreator
class	mmCIFJobOutputter
class	mmCIFJobOutputterCreator
class	mmtfJobOutputter
class	mmtfJobOutputterCreator
class	MpiFileBuffer
class	WriteOut_MpiFileBuffer
class	DebugOut_MpiFileBuffer
class	MPIFileBufJobDistributor
class	MPIMultiCommJobDistributor
class	MPIWorkPartitionJobDistributor
class	MPIWorkPoolJobDistributor
class	MultiThreadingJob
class	NoOutputJobOutputter
class	NoOutputJobOutputterCreator
class	PDBJobInputter
class	PDBJobInputterCreator
class	PDBJobOutputter
class	PDBJobOutputterCreator
class	PoseInputStreamJobInputter
class	PoseInputStreamJobInputterCreator
class	RNA_DeNovoJobOutputter
class	RNA_DeNovoJobOutputterCreator
class	ScoreOnlyJobOutputter
class	ScoreOnlyJobOutputterCreator
class	ScreeningJobInputter
class	ScreeningJobInputterCreator
class	SerializedPoseJobInputter
class	SerializedPoseJobInputterCreator
class	SerializedPoseJobOutputter
class	SerializedPoseJobOutputterCreator
class	ShuffleFileSystemJobDistributor
class	SilentFileJobInputter
class	SilentFileJobInputterCreator
class	SilentFileJobOutputter
class	CompareTags
class	SilentFileJobOutputterCreator
class	SingleFileBuffer
class	WriteFileSFB
class	VectorPoseJobDistributor
	Job distributor subclass for running RECON multistate design Takes in all input poses from the command line and passes them to any mover or filter that derives from VectorPoseMover or VectorPoseFilter, meaning that it is able to receive and operate on multiple poses simultaneously. Only accessible through recon application. More...
class	wwPDBJobOutputter

Typedefs
typedef utility::pointer::shared_ptr< GenericJobInputter >	GenericJobInputterOP
typedef utility::pointer::shared_ptr< AtomTreeDiffJobInputter >	AtomTreeDiffJobInputterOP
typedef utility::pointer::shared_ptr< AtomTreeDiffJobOutputter >	AtomTreeDiffJobOutputterOP
typedef utility::pointer::shared_ptr< AtomTreeDiffJobOutputter const >	AtomTreeDiffJobOutputterCOP
typedef utility::pointer::shared_ptr< BatchJobInputter >	BatchJobInputterOP
typedef utility::pointer::shared_ptr< EmptyPoseJobInputter >	EmptyPoseJobInputterOP
typedef utility::pointer::shared_ptr< EnsembleJobInputter >	EnsembleJobInputterOP
typedef utility::pointer::shared_ptr< EnsembleJobInputter const >	EnsembleJobInputterCOP
typedef utility::pointer::shared_ptr< FileJobOutputter >	FileJobOutputterOP
typedef utility::pointer::shared_ptr< InnerJob >	InnerJobOP
typedef utility::pointer::shared_ptr< InnerJob const >	InnerJobCOP
typedef utility::pointer::shared_ptr< InnerMultiThreadingJob >	InnerMultiThreadingJobOP
typedef utility::pointer::shared_ptr< InnerMultiThreadingJob const >	InnerMultiThreadingJobCOP
typedef utility::pointer::shared_ptr< Job >	JobOP
typedef utility::pointer::shared_ptr< Job const >	JobCOP
typedef utility::vector1< JobOP >	Jobs
typedef utility::pointer::weak_ptr< JobInputter >	JobInputterAP
typedef utility::pointer::weak_ptr< JobInputter const >	JobInputterCAP
typedef utility::pointer::shared_ptr< JobInputter >	JobInputterOP
typedef utility::pointer::shared_ptr< JobInputter const >	JobInputterCOP
typedef utility::pointer::shared_ptr< JobInputterCreator >	JobInputterCreatorOP
typedef utility::pointer::shared_ptr< JobInputterCreator const >	JobInputterCreatorCOP
typedef utility::pointer::shared_ptr< JobInputterFactory >	JobInputterFactoryOP
typedef utility::pointer::shared_ptr< JobInputterFactory const >	JobInputterFactoryCOP
typedef utility::pointer::shared_ptr< JobOutputter >	JobOutputterOP
typedef utility::pointer::shared_ptr< JobOutputter const >	JobOutputterCOP
typedef utility::pointer::shared_ptr< JobOutputterCreator >	JobOutputterCreatorOP
typedef utility::pointer::shared_ptr< JobOutputterCreator const >	JobOutputterCreatorCOP
typedef utility::pointer::shared_ptr< JobOutputterFactory >	JobOutputterFactoryOP
typedef utility::pointer::shared_ptr< JobOutputterFactory const >	JobOutputterFactoryCOP
typedef utility::pointer::weak_ptr< JobOutputterObserver const >	JobOutputterObserverAP
typedef utility::pointer::shared_ptr< JobOutputterObserver const >	JobOutputterObserverOP
typedef utility::pointer::shared_ptr< JobsContainer >	JobsContainerOP
typedef utility::pointer::shared_ptr< JobsContainer const >	JobsContainerCOP
typedef utility::pointer::weak_ptr< LargeNstructJobInputter >	LargeNstructJobInputterAP
typedef utility::pointer::weak_ptr< LargeNstructJobInputter const >	LargeNstructJobInputterCAP
typedef utility::pointer::shared_ptr< LargeNstructJobInputter >	LargeNstructJobInputterOP
typedef utility::pointer::shared_ptr< LargeNstructJobInputter const >	LargeNstructJobInputterCOP
typedef utility::pointer::shared_ptr< LazySilentFileJobInputter >	LazySilentFileJobInputterOP
typedef utility::pointer::shared_ptr< mmCIFJobOutputter >	mmCIFJobOutputterOP
typedef utility::pointer::shared_ptr< mmtfJobOutputter >	mmtfJobOutputterOP
typedef utility::pointer::shared_ptr< MpiFileBuffer >	MpiFileBufferOP
typedef utility::pointer::shared_ptr< MpiFileBuffer const >	MpiFileBufferCOP
typedef utility::pointer::shared_ptr< MultiThreadingJob >	MultiThreadingJobOP
typedef utility::pointer::shared_ptr< MultiThreadingJob const >	MultiThreadingJobCOP
typedef utility::pointer::shared_ptr< PDBJobInputter >	PDBJobInputterOP
typedef utility::pointer::shared_ptr< PDBJobOutputter >	PDBJobOutputterOP
typedef utility::pointer::shared_ptr< PoseInputStreamJobInputter >	PoseInputStreamJobInputterOP
typedef utility::pointer::shared_ptr< RNA_DeNovoJobOutputter >	RNA_DeNovoJobOutputterOP
typedef utility::pointer::shared_ptr< ScreeningJobInputter >	ScreeningJobInputterOP
typedef utility::pointer::shared_ptr< SerializedPoseJobInputter >	SerializedPoseJobInputterOP
typedef utility::pointer::shared_ptr< SerializedPoseJobOutputter >	SerializedPoseJobOutputterOP
typedef utility::pointer::shared_ptr< SilentFileJobInputter >	SilentFileJobInputterOP
typedef utility::pointer::shared_ptr< SilentFileJobOutputter >	SilentFileJobOutputterOP
typedef utility::pointer::shared_ptr< SingleFileBuffer >	SingleFileBufferOP
typedef utility::pointer::shared_ptr< SingleFileBuffer const >	SingleFileBufferCOP
typedef utility::pointer::shared_ptr< VectorPoseJobDistributor >	VectorPoseJobDistributorOP
typedef utility::pointer::shared_ptr< VectorPoseJobDistributor const >	VectorPoseJobDistributorCOP
typedef utility::pointer::shared_ptr< wwPDBJobOutputter >	wwPDBJobOutputterOP

Functions
core::Size	get_min_nstruct_index_checkpoint_file ()
std::ostream &	operator<< (std::ostream &out, const InnerJob &inner_job)
static basic::Tracer	TR ("protocols.jd2.internal_util")
void	add_job_data_to_ss (core::io::silent::SilentStructOP ss, JobCOP job_op)
void	register_options ()
JobOP	get_current_job ()
JobCOP const	JD2_BOGUS_JOB (utility::pointer::make_shared< Job >(utility::pointer::make_shared< InnerJob >("EMPTY_JOB_use_jd2", 0), 0))
bool	operator== (Job const &a, Job const &b)
bool	operator!= (Job const &a, Job const &b)
std::ostream &	operator<< (std::ostream &out, const Job &job)
static basic::Tracer	tr ("protocols.jd2.JobDistributor")
static basic::Tracer	TR ("protocols.jd2.JobInputterFactory")
static basic::Tracer	TR ("protocols.jd2.JobOutputterFactory")
static basic::Tracer	tr ("protocols.jd2.MpiFileBuffer")
Size const	MPI_CLOSE_FILE (1004)
core::Size const	MPI_JOB_DIST_TAG (1542)
	this tag is used for all communication with JobDistributor ( use this tag to be received in the main MSG-loop of jd2 cf. process_message() ) More...
static basic::Tracer	TR ("protocols.jd2.ScoreOnlyJobOutputter")
static basic::Tracer	TR ("protocols.jd2.ScreeningJobInputter")
utility::vector1< core::Size >	get_spanning_jobs (JobsContainer const &jobs)
static basic::Tracer	tr ("protocols.jd2.MpiFileBuffer")
std::string const	START_BLOCK ("MPI_FILE_BUFFER_BLOCK_START")
std::string const	END_BLOCK ("MPI_FILE_BUFFER_BLOCK_END")
static basic::Tracer	TR ("protocols.jd2.util")
static basic::Tracer	tr_score ("protocols.jd2.score", basic::t_info, true)
bool	jd2_used ()
	is this application running with JD2? Useful for code that might not be running under JD2. More...
std::string	current_input_tag ()
	What is the tag of the current input structure? More...
core::Size	current_nstruct_index ()
	What 'nstruct' value are we currently processing? More...
core::Size	max_nstruct_index ()
	What's the maximum nstruct we're processing? More...
std::string	current_output_name ()
	gets used output name of pose ask jd for current-job —> ask jobOutputter for name of this job More...
std::string	current_output_filename ()
	call the 'filename' accessor of the current job-distributor with the current job More...
std::string	current_batch ()
core::Size	current_batch_id ()
core::Size	current_replica ()
	returns 0 if no replicas (i.e., multiple processes per job ) otherwise it returns the sub-rank of the process within the job starting at 1 More...
core::pose::PoseCOP	get_current_jobs_starting_pose ()
	Get the starting structure for the current run. Will return a null pointer if that is not possible. More...
void	output_intermediate_pose (core::pose::Pose const &pose, std::string const &stage_tag, int copy_count, bool score_only)
	end parser interface, start Job Distributor interface///////////// More...
void	add_string_to_current_job (std::string const &string_in)
	add output string More...
void	add_strings_to_current_job (std::list< std::string > const &strings)
	add output strings More...
void	add_string_string_pair_to_current_job (std::string const &string1, std::string const &string2)
	add a string/string pair More...
void	add_string_real_pair_to_current_job (std::string const &string_in, core::Real const real_in)
	add a string/real pair More...
std::list< std::string >	get_strings_from_current_job ()
std::map< std::string, std::string >	get_string_string_pairs_from_current_job ()
std::map< std::string, core::Real >	get_string_real_pairs_from_current_job ()
void	add_current_job_data_to_ss (core::io::silent::SilentStructOP ss)
void	write_score_tracer (core::pose::Pose const &pose_in, std::string tracer_point)
utility::vector1< utility::file::FileName >	input_pdb_files_from_command_line ()
	Read the -s and -l flags to get a list of PDB files that should be read in and operated upon. More...
void	set_native_in_mover (protocols::moves::Mover &mover)
	Set the "native" for the Mover by reading from the global option collection. More...
void	set_native_in_mover (protocols::moves::Mover &mover, utility::options::OptionCollection const &options)
	Set the "native" for the Mover by reading from a possibly-local option collection. More...
void	options_for_set_native_in_mover (utility::options::OptionKeyList &opts)
	Companion function for set_native_in_mover that reports on the options that are read out of the (possibly-local) option collection. More...
static basic::Tracer	TR ("protocols.jd2.VectorPoseJobDistributor")

Variables
JobCOP const	JD2_BOGUS_JOB
static basic::MemTracer	mem_tr
static basic::MemTracer	mem_tr
core::Size const	NEW_JOB_ID = 1
	Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input. More...
core::Size const	BAD_INPUT = 2
core::Size const	JOB_SUCCESS = 3
core::Size const	JOB_FAILED_NO_RETRY = 4

Typedef Documentation

AtomTreeDiffJobInputterOP

typedef utility::pointer::shared_ptr< AtomTreeDiffJobInputter > protocols::jd2::AtomTreeDiffJobInputterOP

AtomTreeDiffJobOutputterCOP

typedef utility::pointer::shared_ptr< AtomTreeDiffJobOutputter const > protocols::jd2::AtomTreeDiffJobOutputterCOP

AtomTreeDiffJobOutputterOP

typedef utility::pointer::shared_ptr< AtomTreeDiffJobOutputter > protocols::jd2::AtomTreeDiffJobOutputterOP

BatchJobInputterOP

typedef utility::pointer::shared_ptr< BatchJobInputter > protocols::jd2::BatchJobInputterOP

EmptyPoseJobInputterOP

typedef utility::pointer::shared_ptr< EmptyPoseJobInputter > protocols::jd2::EmptyPoseJobInputterOP

EnsembleJobInputterCOP

typedef utility::pointer::shared_ptr< EnsembleJobInputter const > protocols::jd2::EnsembleJobInputterCOP

EnsembleJobInputterOP

typedef utility::pointer::shared_ptr< EnsembleJobInputter > protocols::jd2::EnsembleJobInputterOP

FileJobOutputterOP

typedef utility::pointer::shared_ptr< FileJobOutputter > protocols::jd2::FileJobOutputterOP

GenericJobInputterOP

typedef utility::pointer::shared_ptr< GenericJobInputter > protocols::jd2::GenericJobInputterOP

InnerJobCOP

typedef utility::pointer::shared_ptr< InnerJob const > protocols::jd2::InnerJobCOP

InnerJobOP

typedef utility::pointer::shared_ptr< InnerJob > protocols::jd2::InnerJobOP

InnerMultiThreadingJobCOP

typedef utility::pointer::shared_ptr< InnerMultiThreadingJob const > protocols::jd2::InnerMultiThreadingJobCOP

InnerMultiThreadingJobOP

typedef utility::pointer::shared_ptr< InnerMultiThreadingJob > protocols::jd2::InnerMultiThreadingJobOP

JobCOP

typedef utility::pointer::shared_ptr< Job const > protocols::jd2::JobCOP

JobInputterAP

typedef utility::pointer::weak_ptr< JobInputter > protocols::jd2::JobInputterAP

JobInputterCAP

typedef utility::pointer::weak_ptr< JobInputter const > protocols::jd2::JobInputterCAP

JobInputterCOP

typedef utility::pointer::shared_ptr< JobInputter const > protocols::jd2::JobInputterCOP

JobInputterCreatorCOP

typedef utility::pointer::shared_ptr< JobInputterCreator const > protocols::jd2::JobInputterCreatorCOP

JobInputterCreatorOP

typedef utility::pointer::shared_ptr< JobInputterCreator > protocols::jd2::JobInputterCreatorOP

JobInputterFactoryCOP

typedef utility::pointer::shared_ptr< JobInputterFactory const > protocols::jd2::JobInputterFactoryCOP

JobInputterFactoryOP

typedef utility::pointer::shared_ptr< JobInputterFactory > protocols::jd2::JobInputterFactoryOP

JobInputterOP

typedef utility::pointer::shared_ptr< JobInputter > protocols::jd2::JobInputterOP

JobOP

typedef utility::pointer::shared_ptr< Job > protocols::jd2::JobOP

JobOutputterCOP

typedef utility::pointer::shared_ptr< JobOutputter const > protocols::jd2::JobOutputterCOP

JobOutputterCreatorCOP

typedef utility::pointer::shared_ptr< JobOutputterCreator const > protocols::jd2::JobOutputterCreatorCOP

JobOutputterCreatorOP

typedef utility::pointer::shared_ptr< JobOutputterCreator > protocols::jd2::JobOutputterCreatorOP

JobOutputterFactoryCOP

typedef utility::pointer::shared_ptr< JobOutputterFactory const > protocols::jd2::JobOutputterFactoryCOP

JobOutputterFactoryOP

typedef utility::pointer::shared_ptr< JobOutputterFactory > protocols::jd2::JobOutputterFactoryOP

JobOutputterObserverAP

typedef utility::pointer::weak_ptr< JobOutputterObserver const > protocols::jd2::JobOutputterObserverAP

JobOutputterObserverOP

typedef utility::pointer::shared_ptr< JobOutputterObserver const > protocols::jd2::JobOutputterObserverOP

JobOutputterOP

typedef utility::pointer::shared_ptr< JobOutputter > protocols::jd2::JobOutputterOP

Jobs

typedef utility::vector1< JobOP > protocols::jd2::Jobs

JobsContainerCOP

typedef utility::pointer::shared_ptr< JobsContainer const > protocols::jd2::JobsContainerCOP

JobsContainerOP

typedef utility::pointer::shared_ptr< JobsContainer > protocols::jd2::JobsContainerOP

LargeNstructJobInputterAP

typedef utility::pointer::weak_ptr< LargeNstructJobInputter > protocols::jd2::LargeNstructJobInputterAP

LargeNstructJobInputterCAP

typedef utility::pointer::weak_ptr< LargeNstructJobInputter const > protocols::jd2::LargeNstructJobInputterCAP

LargeNstructJobInputterCOP

typedef utility::pointer::shared_ptr< LargeNstructJobInputter const > protocols::jd2::LargeNstructJobInputterCOP

LargeNstructJobInputterOP

typedef utility::pointer::shared_ptr< LargeNstructJobInputter > protocols::jd2::LargeNstructJobInputterOP

LazySilentFileJobInputterOP

typedef utility::pointer::shared_ptr< LazySilentFileJobInputter > protocols::jd2::LazySilentFileJobInputterOP

mmCIFJobOutputterOP

typedef utility::pointer::shared_ptr< mmCIFJobOutputter > protocols::jd2::mmCIFJobOutputterOP

mmtfJobOutputterOP

typedef utility::pointer::shared_ptr< mmtfJobOutputter > protocols::jd2::mmtfJobOutputterOP

MpiFileBufferCOP

typedef utility::pointer::shared_ptr< MpiFileBuffer const > protocols::jd2::MpiFileBufferCOP

MpiFileBufferOP

typedef utility::pointer::shared_ptr< MpiFileBuffer > protocols::jd2::MpiFileBufferOP

MultiThreadingJobCOP

typedef utility::pointer::shared_ptr< MultiThreadingJob const > protocols::jd2::MultiThreadingJobCOP

MultiThreadingJobOP

typedef utility::pointer::shared_ptr< MultiThreadingJob > protocols::jd2::MultiThreadingJobOP

PDBJobInputterOP

typedef utility::pointer::shared_ptr< PDBJobInputter > protocols::jd2::PDBJobInputterOP

PDBJobOutputterOP

typedef utility::pointer::shared_ptr< PDBJobOutputter > protocols::jd2::PDBJobOutputterOP

PoseInputStreamJobInputterOP

typedef utility::pointer::shared_ptr< PoseInputStreamJobInputter > protocols::jd2::PoseInputStreamJobInputterOP

RNA_DeNovoJobOutputterOP

typedef utility::pointer::shared_ptr< RNA_DeNovoJobOutputter > protocols::jd2::RNA_DeNovoJobOutputterOP

ScreeningJobInputterOP

typedef utility::pointer::shared_ptr< ScreeningJobInputter > protocols::jd2::ScreeningJobInputterOP

SerializedPoseJobInputterOP

typedef utility::pointer::shared_ptr< SerializedPoseJobInputter > protocols::jd2::SerializedPoseJobInputterOP

SerializedPoseJobOutputterOP

typedef utility::pointer::shared_ptr< SerializedPoseJobOutputter > protocols::jd2::SerializedPoseJobOutputterOP

SilentFileJobInputterOP

typedef utility::pointer::shared_ptr< SilentFileJobInputter > protocols::jd2::SilentFileJobInputterOP

SilentFileJobOutputterOP

typedef utility::pointer::shared_ptr< SilentFileJobOutputter > protocols::jd2::SilentFileJobOutputterOP

SingleFileBufferCOP

typedef utility::pointer::shared_ptr< SingleFileBuffer const > protocols::jd2::SingleFileBufferCOP

SingleFileBufferOP

typedef utility::pointer::shared_ptr< SingleFileBuffer > protocols::jd2::SingleFileBufferOP

VectorPoseJobDistributorCOP

typedef utility::pointer::shared_ptr< VectorPoseJobDistributor const > protocols::jd2::VectorPoseJobDistributorCOP

VectorPoseJobDistributorOP

typedef utility::pointer::shared_ptr< VectorPoseJobDistributor > protocols::jd2::VectorPoseJobDistributorOP

wwPDBJobOutputterOP

typedef utility::pointer::shared_ptr< wwPDBJobOutputter > protocols::jd2::wwPDBJobOutputterOP

Function Documentation

add_current_job_data_to_ss()

void protocols::jd2::add_current_job_data_to_ss

(

core::io::silent::SilentStructOP

ss

)

References add_job_data_to_ss(), protocols::jd2::JobDistributor::current_job(), and protocols::jd2::JobDistributor::get_instance().

Referenced by protocols::canonical_sampling::MetropolisHastingsMover::write_checkpoint(), and write_score_tracer().

add_job_data_to_ss()

void protocols::jd2::add_job_data_to_ss	(	core::io::silent::SilentStructOP	ss,
		JobCOP	job_op
	)

References core::sequence::end.

Referenced by add_current_job_data_to_ss(), protocols::jd2::RNA_DeNovoJobOutputter::dump_pose(), and protocols::jd2::SilentFileJobOutputter::dump_pose().

add_string_real_pair_to_current_job()

void protocols::jd2::add_string_real_pair_to_current_job	(	std::string const &	string_in,
		core::Real const	real_in
	)

add a string/real pair

References protocols::jd2::JobDistributor::current_job(), and protocols::jd2::JobDistributor::get_instance().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::anchored_design::AnchoredDesignMover::apply(), protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), protocols::docking::DockingProtocol::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::ligand_docking::HighResEnsemble::apply(), protocols::ligand_docking::InterfaceScoreCalculator::apply(), protocols::ligand_docking::ProtLigEnsemble::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::TransformEnsemble::apply(), protocols::loop_build::LoopBuildMover::apply(), protocols::membrane::MPQuickRelaxMover::apply(), protocols::ncbb::NcbbDockDesignProtocol::apply(), protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::qsar::qsarMover::apply(), protocols::surface_docking::SurfaceDockingProtocol::apply(), protocols::constraint_filters::ConstraintScoreCutoffFilter::apply(), protocols::simple_moves::AddJobPairData::apply(), protocols::docking::membrane::QuickRelaxPartnersSeparately::apply(), protocols::relax::RangeRelaxMover::apply(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::ncbb::calculate_statistics(), protocols::floppy_tail::create_extra_output(), protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_output(), protocols::canonical_sampling::TemperingBase::initialize_simulation(), protocols::features::JobDataFeatures::load_string_real_data(), protocols::canonical_sampling::mc_convergence_checks::Pool_ConvergenceCheck::operator()(), protocols::legacy_sewing::LegacyRepeatAssemblyMover::output_base_stats(), protocols::surface_docking::FullatomRelaxMover::output_solution_state(), protocols::legacy_sewing::LegacyAssemblyMover::output_stats(), protocols::analysis::InterfaceAnalyzerMover::report_data(), protocols::calc_taskop_filters::Operator::report_sm(), protocols::docking::DockingPrepackProtocol::score_and_output(), protocols::canonical_sampling::TemperingBase::set_current_temp(), protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics(), protocols::simple_filters::ShapeComplementarityFilter::write_area(), protocols::simple_filters::Worst9merFilter::write_mean_median(), and protocols::simple_filters::ShapeComplementarityFilter::write_median_distance().

add_string_string_pair_to_current_job()

void protocols::jd2::add_string_string_pair_to_current_job	(	std::string const &	string1,
		std::string const &	string2
	)

add a string/string pair

References protocols::jd2::JobDistributor::current_job(), and protocols::jd2::JobDistributor::get_instance().

Referenced by protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), protocols::ligand_docking::ComputeLigandRDF::apply(), protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::surface_docking::SurfaceDockingProtocol::apply(), protocols::simple_moves::AddJobPairData::apply(), protocols::hotspot_hashing::movers::PlaceProbeMover::execute_one_search(), protocols::features::JobDataFeatures::load_string_string_data(), protocols::canonical_sampling::mc_convergence_checks::Pool_ConvergenceCheck::operator()(), protocols::surface_docking::FullatomRelaxMover::output_solution_state(), and protocols::legacy_sewing::LegacyAssemblyMover::output_stats().

add_string_to_current_job()

void protocols::jd2::add_string_to_current_job

(

std::string const &

string_in

)

add output string

References protocols::jd2::JobDistributor::current_job(), and protocols::jd2::JobDistributor::get_instance().

Referenced by protocols::simple_moves::ReportEffectivePKA::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::anchored_design::AnchoredDesignMover::apply(), protocols::floppy_tail::create_extra_output(), protocols::features::JobDataFeatures::load_string_data(), protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_hbond_unsat(), protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_interface_residues(), protocols::matdes::ClashCheckFilter::write_pymol_string_to_pdb(), protocols::matdes::SymUnsatHbondFilter::write_pymol_string_to_pdb(), protocols::simple_ddg::DdGScan::write_to_pdb(), protocols::simple_filters::TaskAwareScoreTypeFilter::write_to_pdb(), protocols::matdes::OligomericAverageDegreeFilter::write_to_pdb(), protocols::simple_filters::MutationsFilter::write_to_pdb(), protocols::matdes::ClashCheckFilter::write_to_pdb(), protocols::matdes::SymUnsatHbondFilter::write_to_pdb(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::write_to_pdb(), and protocols::protein_interface_design::filters::SequenceRecoveryFilter::write_to_pdb().

add_strings_to_current_job()

void protocols::jd2::add_strings_to_current_job

(

std::list< std::string > const &

strings

)

add output strings

References protocols::jd2::JobDistributor::current_job(), and protocols::jd2::JobDistributor::get_instance().

Referenced by protocols::RotamerDump::RotamerDumpMover::apply().

current_batch()

std::string protocols::jd2::current_batch

(

)

References protocols::jd2::JobDistributor::get_current_batch(), and protocols::jd2::JobDistributor::get_instance().

Referenced by protocols::abinitio::AbrelaxMover::apply(), and protocols::simple_filters::BatchEvaluator::apply().

current_batch_id()

core::Size protocols::jd2::current_batch_id

(

)

References protocols::jd2::JobDistributor::current_batch_id(), and protocols::jd2::JobDistributor::get_instance().

Referenced by protocols::simple_filters::BatchNrEvaluator::apply(), and protocols::jd2::MPIMultiCommJobDistributor::get_new_job_id().

current_input_tag()

std::string protocols::jd2::current_input_tag

(

)

What is the tag of the current input structure?

References protocols::jd2::JobDistributor::current_job(), and protocols::jd2::JobDistributor::get_instance().

Referenced by protocols::backrub::BackrubProtocol::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::ligand_docking::StartFrom::apply(), protocols::loop_build::LoopBuildMover::apply(), protocols::protein_interface_design::movers::DockWithHotspotMover::apply(), protocols::protein_interface_design::movers::InterfaceRecapitulationMover::apply(), protocols::loops::loops_definers::LoopsDatabaseDefiner::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::task_operations::ReadResfileFromDB::apply(), protocols::contact_map::ContactMap::apply(), protocols::pose_length_moves::AnalyzeLoopModeling::apply(), protocols::electron_density::DockFragmentsIntoDensityMover::apply_multi(), protocols::pose_length_moves::NearNativeLoopCloser::close_loop(), protocols::features::ReportToDB::ensure_structure_tags_are_ready(), protocols::features::TopCountOfEachInput::operator()(), protocols::simple_moves::SequenceProfileMover::parse_my_tag(), protocols::moves::StructureRestrictor::pose_name(), protocols::jd2::MPIWorkPartitionJobDistributor::remove_bad_inputs_from_job_list(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), and protocols::features::ProteinSilentReport::write_full_report().

current_nstruct_index()

core::Size protocols::jd2::current_nstruct_index

(

)

What 'nstruct' value are we currently processing?

References protocols::jd2::JobDistributor::current_job(), and protocols::jd2::JobDistributor::get_instance().

Referenced by protocols::helical_bundle::BackboneGridSampler::apply(), protocols::helical_bundle::BundleGridSampler::apply(), protocols::indel::IndelOptimizationMover::apply(), protocols::ligand_docking::HighResEnsemble::apply(), protocols::ligand_docking::ProtLigEnsemble::apply(), protocols::loop_build::LoopBuildMover::apply(), protocols::helical_bundle::BundleReporterFilter::apply(), protocols::hotspot_hashing::movers::PlaceProbeMover::apply(), protocols::rosetta_scripts::RosettaScriptsParser::initialize_data_map(), and protocols::canonical_sampling::MetricRecorder::update_after_boltzmann().

current_output_filename()

std::string protocols::jd2::current_output_filename

(

)

call the 'filename' accessor of the current job-distributor with the current job

References protocols::jd2::JobDistributor::current_job(), protocols::jd2::JobDistributor::get_instance(), and protocols::jd2::JobDistributor::job_outputter().

Referenced by protocols::fold_from_loops::NubInitioMover::dump_centroid(), protocols::canonical_sampling::MetropolisHastingsMover::get_checkpoints(), and protocols::canonical_sampling::MetropolisHastingsMover::write_checkpoint().

current_output_name()

std::string protocols::jd2::current_output_name

(

)

gets used output name of pose ask jd for current-job —> ask jobOutputter for name of this job

References protocols::jd2::JobDistributor::current_job(), protocols::jd2::JobDistributor::get_instance(), and protocols::jd2::JobDistributor::job_outputter().

Referenced by protocols::abinitio::AbrelaxMover::apply(), protocols::backrub::BackrubProtocol::apply(), protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::coupled_moves::CoupledMovesProtocol::apply(), protocols::cryst::TagPoseWithRefinementStatsMover::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::matdes::ExtractSubposeMover::apply(), protocols::protein_interface_design::movers::SecretionOptimizationMover::apply(), protocols::contact_map::ContactMap::apply(), protocols::design_opt::GreedyOptMutationMover::apply(), protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::apply(), protocols::matdes::MatDesGreedyOptMutationMover::apply(), protocols::simple_ddg::ddG::calculate(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), protocols::matdes::ClashCheckFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::matdes::GetRBDOFValues::compute(), protocols::simple_ddg::DdGScan::ddG_for_single_residue(), protocols::fold_from_loops::NubInitioMover::dump_centroid(), protocols::features::ReportToDB::ensure_structure_tags_are_ready(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::evaluate_and_add(), protocols::protein_interface_design::filters::FilterScanFilter::FilterScanFilter(), protocols::canonical_sampling::BiasEnergy::finalize_simulation(), protocols::features::FeaturesReporter::find_tag(), protocols::rosetta_scripts::ParsedProtocol::finish_protocol(), protocols::rosetta_scripts::RosettaScriptsParser::generate_mover(), protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol(), protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_xml_string(), protocols::canonical_sampling::MetropolisHastingsMover::get_checkpoints(), protocols::hbnet::HBNet::get_file_name(), protocols::relax::RelaxProtocolBase::output_debug_structure(), protocols::legacy_sewing::LegacyAssemblyMover::output_stats(), protocols::canonical_sampling::MetropolisHastingsMover::prepare_simulation(), protocols::simple_filters::print_nmer_svm_energy_data(), protocols::peptide_deriver::PeptideDeriverFilter::report(), protocols::simple_filters::ReportFilter::report(), protocols::rotamer_recovery::RRReporterSQLite::report_predicted_features(), protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), protocols::analysis::InterfaceAnalyzerMover::set_pose_info(), protocols::matdes::SymDofMoverSampler::step(), protocols::canonical_sampling::SimulatedTempering::temperature_move(), protocols::canonical_sampling::MetricRecorder::update_after_boltzmann(), protocols::canonical_sampling::MetropolisHastingsMover::write_checkpoint(), protocols::hbnet::HBNet::write_network_pdb(), protocols::matdes::ClashCheckFilter::write_pymol_string_to_pdb(), protocols::matdes::SymUnsatHbondFilter::write_pymol_string_to_pdb(), protocols::simple_filters::SaveResfileToDiskFilter::write_resfile(), and write_score_tracer().

current_replica()

core::Size protocols::jd2::current_replica

(

)

returns 0 if no replicas (i.e., multiple processes per job ) otherwise it returns the sub-rank of the process within the job starting at 1

References protocols::jd2::JobDistributor::get_instance(), and protocols::jd2::MPIMultiCommJobDistributor::sub_rank().

Referenced by protocols::jd2::RNA_DeNovoJobOutputter::dump_pose(), protocols::jd2::SilentFileJobOutputter::dump_pose(), protocols::canonical_sampling::MetropolisHastingsMover::get_checkpoints(), protocols::canonical_sampling::MetropolisHastingsMover::output_file_name(), protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), protocols::canonical_sampling::MetricRecorder::update_after_boltzmann(), protocols::canonical_sampling::MetropolisHastingsMover::write_checkpoint(), and protocols::canonical_sampling::PDBTrajectoryRecorder::write_model().

END_BLOCK()

std::string const protocols::jd2::END_BLOCK

(

"MPI_FILE_BUFFER_BLOCK_END"

)

get_current_job()

JobOP protocols::jd2::get_current_job

(

)

References protocols::jd2::JobDistributor::current_job(), protocols::jd2::JobDistributor::get_instance(), and protocols::jd2::JobDistributor::job_inputter().

Referenced by protocols::abinitio::KinematicTaskControl::apply(), protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::apply(), and protocols::canonical_sampling::SilentTrajectoryRecorder::write_model().

get_current_jobs_starting_pose()

core::pose::PoseCOP protocols::jd2::get_current_jobs_starting_pose

(

)

Get the starting structure for the current run. Will return a null pointer if that is not possible.

References protocols::jd2::JobDistributor::current_job(), protocols::jd2::JobDistributor::get_instance(), protocols::jd2::JobDistributor::job_inputter(), and protocols::jd2::JobDistributor::job_outputter().

Referenced by protocols::simple_filters::ChiWellRmsdEvaluator::apply(), protocols::simple_filters::SelectRmsdEvaluator::apply(), protocols::simple_filters::SelectGdtEvaluator::apply(), protocols::simple_filters::LoopRmsdEvaluator::apply(), protocols::rosetta_scripts::legacy_saved_pose_or_input(), protocols::splice::SampleRotamersFromPDB::parse_tag(), and protocols::task_operations::JointSequenceOperation::parse_tag().

get_min_nstruct_index_checkpoint_file()

core::Size protocols::jd2::get_min_nstruct_index_checkpoint_file

(

)

References core::sequence::end, and core::conformation::membrane::in.

Referenced by protocols::jd2::FileSystemJobDistributor::get_new_job_id().

get_spanning_jobs()

utility::vector1<core::Size> protocols::jd2::get_spanning_jobs

(

JobsContainer const &

jobs

)

References protocols::jd2::JobsContainer::size().

Referenced by protocols::jd2::ShuffleFileSystemJobDistributor::scramble_job_order().

get_string_real_pairs_from_current_job()

std::map< std::string, core::Real > protocols::jd2::get_string_real_pairs_from_current_job

(

)

References protocols::jd2::JobDistributor::current_job(), and protocols::jd2::JobDistributor::get_instance().

Referenced by protocols::ligand_docking::HighResEnsemble::apply(), protocols::ligand_docking::StartFrom::apply(), protocols::ligand_docking::WriteLigandMolFile::apply(), protocols::features::ScreeningFeatures::get_desriptor_data(), protocols::features::get_write_delete_pair(), protocols::features::JobDataFeatures::insert_string_real_rows(), and protocols::canonical_sampling::SilentTrajectoryRecorder::observe_after_metropolis().

get_string_string_pairs_from_current_job()

std::map< std::string, std::string > protocols::jd2::get_string_string_pairs_from_current_job

(

)

References protocols::jd2::JobDistributor::current_job(), and protocols::jd2::JobDistributor::get_instance().

Referenced by protocols::ligand_docking::InterfaceScoreCalculator::apply(), protocols::ligand_docking::WriteLigandMolFile::apply(), protocols::features::ScreeningFeatures::get_desriptor_data(), protocols::features::JobDataFeatures::insert_string_string_rows(), and protocols::features::ScreeningFeatures::report_features().

get_strings_from_current_job()

std::list< std::string > protocols::jd2::get_strings_from_current_job

(

)

References protocols::jd2::JobDistributor::current_job(), and protocols::jd2::JobDistributor::get_instance().

Referenced by protocols::features::JobDataFeatures::insert_string_rows().

input_pdb_files_from_command_line()

utility::vector1< utility::file::FileName > protocols::jd2::input_pdb_files_from_command_line

(

)

Read the -s and -l flags to get a list of PDB files that should be read in and operated upon.

References protocols::abinitio::filename().

Referenced by protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter::chunk_library_input_sources_from_command_line(), protocols::jd3::full_model_inputters::PDBFullModelInputter::full_model_input_sources_from_command_line(), protocols::stepwise::sampler::protein::generate_beta_database_test(), protocols::jobdist::load_s_and_l(), and protocols::jd3::pose_inputters::PDBPoseInputter::pose_input_sources_from_command_line().

JD2_BOGUS_JOB()

JobCOP const protocols::jd2::JD2_BOGUS_JOB

(

utility::pointer::make_shared< Job >

utility::pointer::make_shared< InnerJob >("EMPTY_JOB_use_jd2", 0), 0

)

jd2_used()

bool protocols::jd2::jd2_used

(

)

is this application running with JD2? Useful for code that might not be running under JD2.

This works by checking whether the JD2 job distributor has been instantiated. If it has not, then it returns false. If it has, then it interrogates the job distributor for information about whether it's a dummy job distributor (in which case it returns false). If it is not a dummy job distributor, it returns true.

Note

Can return a false negative if the job distributor has not yet been instantiated!

References protocols::jd2::JobDistributor::current_job(), protocols::jd2::JobDistributor::get_instance(), protocols::jd2::JobDistributor::has_been_instantiated(), JD2_BOGUS_JOB, and protocols::jd2::JobDistributor::job_outputter().

Referenced by protocols::helical_bundle::BackboneGridSampler::apply(), protocols::helical_bundle::BundleGridSampler::apply(), protocols::constraint_filters::ConstraintScoreCutoffFilter::apply(), protocols::design_opt::GreedyOptMutationMover::apply(), protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::apply(), protocols::matdes::MatDesGreedyOptMutationMover::apply(), protocols::rosetta_scripts::ParsedProtocol::apply(), protocols::fold_from_loops::NubInitioMover::dump_centroid(), protocols::rosetta_scripts::ParsedProtocol::finish_protocol(), protocols::rosetta_scripts::RosettaScriptsParser::initialize_data_map(), protocols::canonical_sampling::BiasEnergy::initialize_simulation(), protocols::rosetta_scripts::legacy_saved_pose_or_input(), protocols::peptide_deriver::PeptideDeriverPoseOutputter::output_pose(), protocols::simple_moves::SixDoFGridDockMover::parse_my_tag(), protocols::simple_filters::print_nmer_svm_energy_data(), protocols::peptide_deriver::PeptideDeriverFilter::report(), protocols::features::RuntimeFeatures::report_features(), protocols::features::TopPercentOfAllInputs::TopPercentOfAllInputs(), protocols::canonical_sampling::MetricRecorder::update_after_boltzmann(), write_score_tracer(), and protocols::canonical_sampling::BiasEnergy::~BiasEnergy().

max_nstruct_index()

core::Size protocols::jd2::max_nstruct_index

(

)

What's the maximum nstruct we're processing?

References protocols::jd2::JobDistributor::current_job(), and protocols::jd2::JobDistributor::get_instance().

Referenced by protocols::helical_bundle::BackboneGridSampler::apply(), protocols::helical_bundle::BundleGridSampler::apply(), and protocols::hotspot_hashing::movers::PlaceProbeMover::check_and_initialize().

MPI_CLOSE_FILE()

Size const protocols::jd2::MPI_CLOSE_FILE

(

1004

)

Referenced by protocols::jd2::MpiFileBuffer::remote_close_file(), and protocols::jd2::MpiFileBuffer::run().

MPI_JOB_DIST_TAG()

core::Size const protocols::jd2::MPI_JOB_DIST_TAG

(

1542

)

this tag is used for all communication with JobDistributor ( use this tag to be received in the main MSG-loop of jd2 cf. process_message() )

Referenced by protocols::jd2::archive::ArchiveManager::cancel_batch(), protocols::jd2::MPIFileBufJobDistributor::eat_signal(), protocols::jd2::MPIFileBufJobDistributor::master_go(), protocols::jd2::archive::ArchiveManager::queue_batch(), protocols::jd2::archive::MPIArchiveJobDistributor::receive_batch(), protocols::jd2::MPIFileBufJobDistributor::send_job_to_slave(), protocols::jd2::MPIFileBufJobDistributor::slave_to_master(), and protocols::jd2::archive::MPIArchiveJobDistributor::sync_batches().

operator!=()

bool protocols::jd2::operator!=	(	Job const &	a,
		Job const &	b
	)

operator<<() [1/2]

std::ostream& protocols::jd2::operator<<	(	std::ostream &	out,
		const InnerJob &	inner_job
	)

operator<<() [2/2]

std::ostream& protocols::jd2::operator<<	(	std::ostream &	out,
		const Job &	job
	)

operator==()

bool protocols::jd2::operator==	(	Job const &	a,
		Job const &	b
	)

options_for_set_native_in_mover()

void protocols::jd2::options_for_set_native_in_mover

(

utility::options::OptionKeyList &

opts

)

Companion function for set_native_in_mover that reports on the options that are read out of the (possibly-local) option collection.

output_intermediate_pose()

void protocols::jd2::output_intermediate_pose	(	core::pose::Pose const &	pose,
		std::string const &	stage_tag,
		int	copy_count = -1,
		bool	score_only = false
	)

end parser interface, start Job Distributor interface/////////////

writes pose to intermediate-scorefile using current Job and JobOutputter ..

copy count is used if multiple poses with same job-tag are written as for instance into a trajectory. -1 indicates no copy count >=0 copy_count will be attached as zerofilled postfix to job-tag

References protocols::jd2::JobDistributor::current_job(), protocols::jd2::JobDistributor::get_instance(), protocols::jd2::JobDistributor::job_outputter(), and TR().

Referenced by protocols::abinitio::AbrelaxMover::apply(), protocols::abinitio::FragmentSampler::apply(), protocols::anchored_design::AnchoredDesignMover::apply(), protocols::anchored_design::AnchoredPerturbMover::apply(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::apply(), protocols::surface_docking::SurfaceDockingProtocol::apply(), protocols::antibody::design::AntibodyDesignMover::apply_to_cdr(), protocols::abinitio::abscript::AbscriptMover::StageTracker::begin_stage(), protocols::abinitio::FragmentSampler::checkpointed_cycle_block(), protocols::anchored_design::debug_dump_pose(), protocols::abinitio::FragmentSampler::do_stage1_cycles(), protocols::abinitio::FragmentSampler::do_stage2_cycles(), protocols::abinitio::FragmentSampler::do_stage3_cycles(), protocols::abinitio::FragmentSampler::do_stage4_cycles(), protocols::abinitio::abscript::AbscriptMover::StageTracker::end_stage(), protocols::floppy_tail::FloppyTailMover::low_res(), protocols::peptide_deriver::PeptideDeriverPoseOutputter::output_pose(), protocols::surface_docking::FullatomRelaxMover::output_solution_state(), protocols::docking::DockingPrepackProtocol::score_and_output(), and protocols::canonical_sampling::SilentTrajectoryRecorder::write_model().

register_options()

void protocols::jd2::register_options

(

)

References protocols::evaluation::register_options().

set_native_in_mover() [1/2]

void protocols::jd2::set_native_in_mover

(

protocols::moves::Mover &

mover

)

Set the "native" for the Mover by reading from the global option collection.

Referenced by protocols::cryst::TagPoseWithRefinementStatsMover::apply(), and protocols::relax::Relax_main().

set_native_in_mover() [2/2]

void protocols::jd2::set_native_in_mover	(	protocols::moves::Mover &	mover,
		utility::options::OptionCollection const &	options
	)

Set the "native" for the Mover by reading from a possibly-local option collection.

References core::import_pose::PDB_file, core::import_pose::pose_from_file(), and protocols::moves::Mover::set_native_pose().

START_BLOCK()

std::string const protocols::jd2::START_BLOCK

(

"MPI_FILE_BUFFER_BLOCK_START"

)

this is a implementation of Buffer for silent-file-based output.

TR() [1/7]

static basic::Tracer protocols::jd2::TR ( "protocols.jd2.internal_util"  )

static

Referenced by protocols::jd2::VectorPoseJobDistributor::apply_parsed_protocol_mpi(), protocols::jd2::VectorPoseJobDistributor::apply_parsed_protocol_serial(), protocols::jd2::AtomTreeDiffJobOutputter::dump_pose(), protocols::jd2::EnsembleJobInputter::EnsembleJobInputter(), protocols::jd2::FileJobOutputter::file(), protocols::jd2::EnsembleJobInputter::fill_jobs(), protocols::jd2::PDBJobInputter::fill_jobs(), protocols::jd2::ScreeningJobInputter::fill_jobs(), protocols::jd2::SerializedPoseJobInputter::fill_jobs(), protocols::jd2::wwPDBJobOutputter::final_pose(), protocols::jd2::JobInputterFactory::get_JobInputter_from_string(), protocols::jd2::JobOutputterFactory::get_JobOutputter_from_string(), protocols::jd2::FileSystemJobDistributor::get_new_job_id(), protocols::jd2::ShuffleFileSystemJobDistributor::get_new_job_id(), protocols::jd2::VectorPoseJobDistributor::go_mpi(), protocols::jd2::VectorPoseJobDistributor::go_serial(), protocols::jd2::MPIWorkPoolJobDistributor::job_failed(), protocols::jd2::ScoreOnlyJobOutputter::job_has_completed(), protocols::jd2::FileSystemJobDistributor::mark_current_job_id_for_repetition(), protocols::jd2::MPIWorkPoolJobDistributor::master_get_new_job_id(), protocols::jd2::MPIWorkPoolJobDistributor::master_go(), protocols::jd2::MPIWorkPoolJobDistributor::master_job_succeeded(), protocols::jd2::MPIWorkPoolJobDistributor::master_mark_current_job_id_for_repetition(), protocols::jd2::MPIWorkPoolJobDistributor::master_mark_job_as_completed(), protocols::jd2::MPIWorkPoolJobDistributor::master_mark_job_as_failed(), protocols::jd2::MPIWorkPoolJobDistributor::master_remove_bad_inputs_from_job_list(), protocols::jd2::mmCIFJobOutputter::mmCIFJobOutputter(), protocols::jd2::mmtfJobOutputter::mmtfJobOutputter(), protocols::jd2::MPIWorkPartitionJobDistributor::MPIWorkPartitionJobDistributor(), protocols::jd2::JobsContainer::operator[](), protocols::jd2::wwPDBJobOutputter::other_pose(), output_intermediate_pose(), protocols::jd2::PDBJobInputter::PDBJobInputter(), protocols::jd2::PDBJobOutputter::PDBJobOutputter(), protocols::jd2::PDBJobInputter::pose_from_job(), protocols::jd2::ScreeningJobInputter::pose_from_job(), protocols::jd2::SerializedPoseJobInputter::pose_from_job(), protocols::jd2::EnsembleJobInputter::read_get_weights(), protocols::jd2::FileSystemJobDistributor::remove_bad_inputs_from_job_list(), protocols::jd2::MPIWorkPartitionJobDistributor::remove_bad_inputs_from_job_list(), protocols::jd2::FileJobOutputter::scorefile(), protocols::jd2::SerializedPoseJobInputter::SerializedPoseJobInputter(), protocols::jd2::SerializedPoseJobOutputter::SerializedPoseJobOutputter(), protocols::jd2::FileJobOutputter::set_defaults(), protocols::jd2::MPIWorkPoolJobDistributor::slave_get_new_job_id(), protocols::jd2::MPIWorkPoolJobDistributor::slave_job_succeeded(), and protocols::jd2::MPIWorkPoolJobDistributor::slave_mark_current_job_id_for_repetition().

tr() [1/3]

static basic::Tracer protocols::jd2::tr ( "protocols.jd2.JobDistributor"  )

static

Referenced by protocols::jd2::archive::MPIArchiveJobDistributor::_notify_archive(), protocols::jd2::archive::EvaluatedArchive::add_evaluated_structure(), protocols::jd2::archive::NormalizedEvaluatedArchive::add_evaluated_structure(), protocols::jd2::archive::VarianceStatisticsArchive::add_evaluated_structure(), protocols::jd2::archive::EvaluatedArchive::add_evaluation(), protocols::jd2::archive::EvaluatedArchive::add_structure(), protocols::jd2::AtomTreeDiffJobInputter::AtomTreeDiffJobInputter(), protocols::jd2::archive::MPIArchiveJobDistributor::batch_underflow(), protocols::jd2::BatchJobInputter::BatchJobInputter(), protocols::jd2::SingleFileBuffer::block(), protocols::jd2::WriteFileSFB::block(), protocols::jd2::MpiFileBuffer::block_file(), protocols::jd2::archive::ArchiveManager::cancel_batch(), protocols::jd2::MpiFileBuffer::clear_channel_from_garbage_collector(), protocols::jd2::SingleFileBuffer::close(), protocols::jd2::MpiFileBuffer::close_channel(), protocols::jd2::MpiFileBuffer::close_file(), protocols::jd2::archive::NormalizedEvaluatedArchive::determine_score_variations(), protocols::jd2::RNA_DeNovoJobOutputter::dump_pose(), protocols::jd2::SilentFileJobOutputter::dump_pose(), protocols::jd2::MPIFileBufJobDistributor::eat_signal(), protocols::jd2::EmptyPoseJobInputter::EmptyPoseJobInputter(), protocols::jd2::archive::EvaluatedArchive::evaluate_pose(), protocols::jd2::archive::EvaluatedArchive::evaluate_silent_struct(), protocols::jd2::AtomTreeDiffJobInputter::fill_jobs(), protocols::jd2::LazySilentFileJobInputter::fill_jobs(), protocols::jd2::PoseInputStreamJobInputter::fill_jobs(), protocols::jd2::SilentFileJobInputter::fill_jobs(), protocols::jd2::EmptyPoseJobInputter::fill_jobs(), protocols::jd2::LargeNstructJobInputter::fill_jobs(), protocols::jd2::archive::BaseArchiveManager::finalize_batch(), protocols::jd2::MpiFileBuffer::flush_channel(), protocols::jd2::MpiFileBuffer::garbage_collection(), protocols::jd2::JobDistributor::get_job_time_estimate(), protocols::jd2::archive::ArchiveManager::go(), protocols::jd2::archive::MPIArchiveJobDistributor::go(), protocols::jd2::MPIFileBufJobDistributor::go(), protocols::jd2::JobDistributor::go_main(), protocols::jd2::archive::ArchiveManager::idle(), protocols::jd2::archive::ArchiveBase::init_from_decoy_set(), protocols::jd2::JobDistributor::init_jd(), protocols::jd2::RNA_DeNovoJobOutputter::job_has_completed(), protocols::jd2::SilentFileJobOutputter::job_has_completed(), protocols::jd2::archive::ArchiveManager::jobs_completed(), protocols::jd2::LargeNstructJobInputter::LargeNstructJobInputter(), protocols::jd2::LazySilentFileJobInputter::LazySilentFileJobInputter(), protocols::jd2::JobDistributor::load_new_batch(), protocols::jd2::JobDistributor::mark_job_as_completed(), protocols::jd2::archive::MPIArchiveJobDistributor::mark_job_as_completed(), protocols::jd2::MPIFileBufJobDistributor::master_get_new_job_id(), protocols::jd2::MPIFileBufJobDistributor::master_go(), protocols::jd2::MPIFileBufJobDistributor::master_job_succeeded(), protocols::jd2::MPIFileBufJobDistributor::master_mark_current_job_id_for_repetition(), protocols::jd2::MPIFileBufJobDistributor::master_remove_bad_inputs_from_job_list(), protocols::jd2::JobDistributor::next_batch(), protocols::jd2::archive::MPIArchiveJobDistributor::notify_archive(), protocols::jd2::AtomTreeDiffJobInputter::pose_from_job(), protocols::jd2::LazySilentFileJobInputter::pose_from_job(), protocols::jd2::PoseInputStreamJobInputter::pose_from_job(), protocols::jd2::SilentFileJobInputter::pose_from_job(), protocols::jd2::EmptyPoseJobInputter::pose_from_job(), protocols::jd2::LargeNstructJobInputter::pose_from_job(), protocols::jd2::PoseInputStreamJobInputter::PoseInputStreamJobInputter(), protocols::jd2::archive::MPIArchiveJobDistributor::process_message(), protocols::jd2::MPIFileBufJobDistributor::process_message(), protocols::jd2::archive::ArchiveManager::queue_batch(), protocols::jd2::archive::ArchiveManager::read_existing_batches(), protocols::jd2::archive::BaseArchiveManager::read_returning_decoys(), protocols::jd2::archive::ArchiveBase::read_structures(), protocols::jd2::archive::EvaluatedArchive::read_structures(), protocols::jd2::archive::MPIArchiveJobDistributor::receive_batch(), protocols::jd2::MpiFileBuffer::release_file(), protocols::jd2::MpiFileBuffer::remote_close_file(), protocols::jd2::archive::EvaluatedArchive::remove_evaluation(), protocols::jd2::archive::EvaluatedArchive::rescore(), protocols::jd2::archive::ArchiveBase::restore_from_file(), protocols::jd2::MpiFileBuffer::run(), protocols::jd2::JobDistributor::run_one_job(), protocols::jd2::archive::ArchiveBase::save_to_file(), protocols::jd2::archive::NormalizedEvaluatedArchive::score_variation(), protocols::jd2::archive::NormalizedEvaluatedArchive::score_variations(), protocols::jd2::archive::EvaluatedArchive::select_score(), protocols::jd2::MPIFileBufJobDistributor::send_job_to_slave(), protocols::jd2::archive::ArchiveManager::send_stop_to_jobdistributor(), protocols::jd2::JobDistributor::set_batch_id(), protocols::jd2::RNA_DeNovoJobOutputter::set_defaults(), protocols::jd2::SilentFileJobOutputter::set_defaults(), protocols::jd2::archive::EvaluatedArchive::set_weight(), protocols::jd2::JobDistributor::setup_pymol_observer(), protocols::jd2::MPIMultiCommJobDistributor::setup_sub_communicators(), protocols::jd2::SilentFileJobInputter::SilentFileJobInputter(), protocols::jd2::MPIFileBufJobDistributor::slave_get_new_job_id(), protocols::jd2::MPIFileBufJobDistributor::slave_mark_current_job_id_for_repetition(), protocols::jd2::archive::EvaluatedArchive::start_evaluation_timer(), protocols::jd2::archive::BaseArchiveManager::start_new_batch(), protocols::jd2::MpiFileBuffer::store_to_channel(), protocols::jd2::archive::MPIArchiveJobDistributor::sync_batches(), protocols::jd2::archive::ArchiveManager::unlock_file(), protocols::jd2::LargeNstructJobInputter::update_jobs_list(), protocols::jd2::RNA_DeNovoJobOutputter::write_all_structs(), protocols::jd2::SilentFileJobOutputter::write_all_structs(), protocols::jd2::archive::Batch::write_info_file(), protocols::jd2::WriteFileSFB::write_lines(), protocols::jd2::JobDistributor::write_output_from_job(), protocols::jd2::WriteFileSFB::WriteFileSFB(), and protocols::jd2::WriteFileSFB::~WriteFileSFB().

TR() [2/7]

static basic::Tracer protocols::jd2::TR ( "protocols.jd2.JobInputterFactory"  )

static

TR() [3/7]

static basic::Tracer protocols::jd2::TR ( "protocols.jd2.JobOutputterFactory"  )

static

tr() [2/3]

static basic::Tracer protocols::jd2::tr ( "protocols.jd2.MpiFileBuffer"  )

static

tr() [3/3]

static basic::Tracer protocols::jd2::tr ( "protocols.jd2.MpiFileBuffer"  )

static

TR() [4/7]

static basic::Tracer protocols::jd2::TR ( "protocols.jd2.ScoreOnlyJobOutputter"  )

static

TR() [5/7]

static basic::Tracer protocols::jd2::TR ( "protocols.jd2.ScreeningJobInputter"  )

static

TR() [6/7]

static basic::Tracer protocols::jd2::TR ( "protocols.jd2.util"  )

static

TR() [7/7]

static basic::Tracer protocols::jd2::TR ( "protocols.jd2.VectorPoseJobDistributor"  )

static

tr_score()

static basic::Tracer protocols::jd2::tr_score ( "protocols.jd2.score"  , basic::t_info  , true    )

static

Referenced by write_score_tracer().

write_score_tracer()

void protocols::jd2::write_score_tracer	(	core::pose::Pose const &	pose_in,
		std::string	tracer_point
	)

References add_current_job_data_to_ss(), current_output_name(), protocols::jd2::JobDistributor::get_instance(), jd2_used(), protocols::jd2::JobDistributor::job_outputter(), tr_score(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by protocols::docking::DockingProtocol::apply(), and protocols::docking::DockMCMProtocol::apply().

Variable Documentation

BAD_INPUT

core::Size const protocols::jd2::BAD_INPUT = 2

Referenced by protocols::jd2::MPIFileBufJobDistributor::process_message(), and protocols::jd2::MPIFileBufJobDistributor::slave_remove_bad_inputs_from_job_list().

JD2_BOGUS_JOB

JobCOP const protocols::jd2::JD2_BOGUS_JOB

extern

Referenced by jd2_used(), protocols::jd2::JobDistributor::load_new_batch(), and protocols::jd2::JobDistributor::reset_job_state().

JOB_FAILED_NO_RETRY

core::Size const protocols::jd2::JOB_FAILED_NO_RETRY = 4

Referenced by protocols::jd2::MPIFileBufJobDistributor::job_failed(), and protocols::jd2::MPIFileBufJobDistributor::process_message().

JOB_SUCCESS

core::Size const protocols::jd2::JOB_SUCCESS = 3

Referenced by protocols::jd2::MPIFileBufJobDistributor::process_message(), and protocols::jd2::MPIFileBufJobDistributor::slave_job_succeeded().

mem_tr [1/2]

basic::MemTracer protocols::jd2::mem_tr

static

Referenced by protocols::jd2::MpiFileBuffer::close_channel(), protocols::jd2::MpiFileBuffer::garbage_collection(), protocols::jd2::archive::ArchiveManager::go(), protocols::jd2::archive::MPIArchiveJobDistributor::go(), protocols::jd2::JobOutputter::JobOutputter(), protocols::jd2::archive::ArchiveBase::load_decoys(), protocols::jd2::archive::MPIArchiveJobDistributor::load_new_batch(), protocols::jd2::archive::ArchiveBase::read_structures(), protocols::jd2::archive::ArchiveBase::restore_from_file(), and protocols::jd2::archive::ArchiveBase::restore_status().

mem_tr [2/2]

basic::MemTracer protocols::jd2::mem_tr

static

NEW_JOB_ID

core::Size const protocols::jd2::NEW_JOB_ID = 1

Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input.

Referenced by protocols::jd2::MPIFileBufJobDistributor::process_message(), and protocols::jd2::MPIFileBufJobDistributor::slave_get_new_job_id().