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protocols::jd2 Namespace Reference

Namespaces

 archive
 
 JobInputterInputSource
 

Classes

class  AtomTreeDiffJobInputter
 
class  AtomTreeDiffJobInputterCreator
 
class  AtomTreeDiffJobOutputter
 
class  AtomTreeDiffJobOutputterCreator
 
class  BatchJobInputter
 
class  BOINCJobDistributor
 
class  CompareTags
 
class  DebugOut_MpiFileBuffer
 
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  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  JobInputterFactory
 
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  JobOutputter
 
class  JobOutputterCreator
 Abstract base class for a JobOutputter factory; the Creator class is responsible for creating a particular mover class. More...
 
class  JobOutputterFactory
 
class  JobOutputterObserver
 
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  JobsContainer
 
class  LargeNstructJobInputter
 
class  LargeNstructJobInputterCreator
 
class  LazySilentFileJobInputter
 
class  LazySilentFileJobInputterCreator
 
class  mmCIFJobOutputter
 
class  mmCIFJobOutputterCreator
 
class  MpiFileBuffer
 
class  MPIFileBufJobDistributor
 
class  MPIMultiCommJobDistributor
 
class  MPIWorkPartitionJobDistributor
 
class  MPIWorkPoolJobDistributor
 
class  MSDJobDistributor
 
class  MultiThreadingJob
 
class  NoOutputJobOutputter
 
class  NoOutputJobOutputterCreator
 
class  PDBJobInputter
 
class  PDBJobInputterCreator
 
class  PDBJobOutputter
 
class  PDBJobOutputterCreator
 
class  PoseInputStreamJobInputter
 
class  PoseInputStreamJobInputterCreator
 
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  SilentFileJobOutputterCreator
 
class  SingleFileBuffer
 
class  WriteFileSFB
 
class  WriteOut_MpiFileBuffer
 
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
< 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< JobOPJobs
 
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
< MpiFileBuffer
MpiFileBufferOP
 
typedef
utility::pointer::shared_ptr
< MpiFileBuffer const > 
MpiFileBufferCOP
 
typedef
utility::pointer::shared_ptr
< MSDJobDistributor
MSDJobDistributorOP
 
typedef
utility::pointer::shared_ptr
< MSDJobDistributor const > 
MSDJobDistributorCOP
 
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
< 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
< 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 ()
 
static basic::Tracer TR ("protocols.resource_manager.planner.JD2ResourceManager")
 
static basic::Tracer tr ("protocols.jd2.JD2ResourceManagerJobInputter")
 
JobCOP const JD2_BOGUS_JOB (JobOP(new Job(InnerJobOP(new 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.MSDJobDistributor")
 
static basic::Tracer TR ("protocols.jd2.ScoreOnlyJobOutputter")
 
static basic::Tracer TR ("protocols.jd2.ScreeningJobInputter")
 
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::Realget_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...
 

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

typedef utility::pointer::shared_ptr< AtomTreeDiffJobInputter > protocols::jd2::AtomTreeDiffJobInputterOP
typedef utility::pointer::shared_ptr< AtomTreeDiffJobOutputter const > protocols::jd2::AtomTreeDiffJobOutputterCOP
typedef utility::pointer::shared_ptr< BatchJobInputter > protocols::jd2::BatchJobInputterOP
typedef utility::pointer::shared_ptr< EnsembleJobInputter const > protocols::jd2::EnsembleJobInputterCOP
typedef utility::pointer::shared_ptr< EnsembleJobInputter > protocols::jd2::EnsembleJobInputterOP
typedef utility::pointer::shared_ptr< FileJobOutputter > protocols::jd2::FileJobOutputterOP
typedef utility::pointer::shared_ptr< GenericJobInputter > protocols::jd2::GenericJobInputterOP
typedef utility::pointer::shared_ptr< InnerJob const > protocols::jd2::InnerJobCOP
typedef utility::pointer::shared_ptr< InnerJob > protocols::jd2::InnerJobOP
typedef utility::pointer::shared_ptr< InnerMultiThreadingJob const > protocols::jd2::InnerMultiThreadingJobCOP
typedef utility::pointer::shared_ptr< InnerMultiThreadingJob > protocols::jd2::InnerMultiThreadingJobOP
typedef utility::pointer::shared_ptr< Job const > protocols::jd2::JobCOP
typedef utility::pointer::weak_ptr< JobInputter > protocols::jd2::JobInputterAP
typedef utility::pointer::weak_ptr< JobInputter const > protocols::jd2::JobInputterCAP
typedef utility::pointer::shared_ptr< JobInputter const > protocols::jd2::JobInputterCOP
typedef utility::pointer::shared_ptr< JobInputterCreator const > protocols::jd2::JobInputterCreatorCOP
typedef utility::pointer::shared_ptr< JobInputterCreator > protocols::jd2::JobInputterCreatorOP
typedef utility::pointer::shared_ptr< JobInputterFactory const > protocols::jd2::JobInputterFactoryCOP
typedef utility::pointer::shared_ptr< JobInputterFactory > protocols::jd2::JobInputterFactoryOP
typedef utility::pointer::shared_ptr< JobInputter > protocols::jd2::JobInputterOP
typedef utility::pointer::shared_ptr< Job > protocols::jd2::JobOP
typedef utility::pointer::shared_ptr< JobOutputter const > protocols::jd2::JobOutputterCOP
typedef utility::pointer::shared_ptr< JobOutputterCreator const > protocols::jd2::JobOutputterCreatorCOP
typedef utility::pointer::shared_ptr< JobOutputterCreator > protocols::jd2::JobOutputterCreatorOP
typedef utility::pointer::shared_ptr< JobOutputterFactory const > protocols::jd2::JobOutputterFactoryCOP
typedef utility::pointer::shared_ptr< JobOutputterFactory > protocols::jd2::JobOutputterFactoryOP
typedef utility::pointer::weak_ptr< JobOutputterObserver const > protocols::jd2::JobOutputterObserverAP
typedef utility::pointer::shared_ptr< JobOutputterObserver const > protocols::jd2::JobOutputterObserverOP
typedef utility::pointer::shared_ptr< JobOutputter > protocols::jd2::JobOutputterOP
typedef utility::vector1< JobOP > protocols::jd2::Jobs
typedef utility::pointer::shared_ptr< JobsContainer const > protocols::jd2::JobsContainerCOP
typedef utility::pointer::shared_ptr< JobsContainer > protocols::jd2::JobsContainerOP
typedef utility::pointer::weak_ptr< LargeNstructJobInputter const > protocols::jd2::LargeNstructJobInputterCAP
typedef utility::pointer::shared_ptr< LargeNstructJobInputter const > protocols::jd2::LargeNstructJobInputterCOP
typedef utility::pointer::shared_ptr< LargeNstructJobInputter > protocols::jd2::LargeNstructJobInputterOP
typedef utility::pointer::shared_ptr< mmCIFJobOutputter > protocols::jd2::mmCIFJobOutputterOP
typedef utility::pointer::shared_ptr< MpiFileBuffer const > protocols::jd2::MpiFileBufferCOP
typedef utility::pointer::shared_ptr< MpiFileBuffer > protocols::jd2::MpiFileBufferOP
typedef utility::pointer::shared_ptr< MSDJobDistributor const > protocols::jd2::MSDJobDistributorCOP
typedef utility::pointer::shared_ptr< MSDJobDistributor > protocols::jd2::MSDJobDistributorOP
typedef utility::pointer::shared_ptr< MultiThreadingJob const > protocols::jd2::MultiThreadingJobCOP
typedef utility::pointer::shared_ptr< MultiThreadingJob > protocols::jd2::MultiThreadingJobOP
typedef utility::pointer::shared_ptr< PDBJobInputter > protocols::jd2::PDBJobInputterOP
typedef utility::pointer::shared_ptr< PDBJobOutputter > protocols::jd2::PDBJobOutputterOP
typedef utility::pointer::shared_ptr< ScreeningJobInputter > protocols::jd2::ScreeningJobInputterOP
typedef utility::pointer::shared_ptr< SilentFileJobInputter > protocols::jd2::SilentFileJobInputterOP
typedef utility::pointer::shared_ptr< SilentFileJobOutputter > protocols::jd2::SilentFileJobOutputterOP
typedef utility::pointer::shared_ptr< SingleFileBuffer const > protocols::jd2::SingleFileBufferCOP
typedef utility::pointer::shared_ptr< SingleFileBuffer > protocols::jd2::SingleFileBufferOP
typedef utility::pointer::shared_ptr< wwPDBJobOutputter > protocols::jd2::wwPDBJobOutputterOP

Function Documentation

void protocols::jd2::add_current_job_data_to_ss ( core::io::silent::SilentStructOP  ss)
void protocols::jd2::add_job_data_to_ss ( core::io::silent::SilentStructOP  ss,
JobCOP  job_op 
)
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::loop_build::LoopBuildMover::apply(), protocols::simple_moves::AddJobPairData::apply(), protocols::qsar::qsarMover::apply(), protocols::anchored_design::AnchoredDesignMover::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::ligand_docking::InterfaceScoreCalculator::apply(), protocols::constraint_filters::ConstraintScoreCutoffFilter::apply(), protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::TransformEnsemble::apply(), protocols::ncbb::NcbbDockDesignProtocol::apply(), protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::surface_docking::SurfaceDockingProtocol::apply(), protocols::docking::membrane::QuickRelaxPartnersSeparately::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::ligand_docking::HighResEnsemble::apply(), protocols::relax::RangeRelaxMover::apply(), protocols::membrane::MPQuickRelaxMover::apply(), protocols::ligand_docking::ProtLigEnsemble::apply(), protocols::docking::DockingProtocol::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(), and protocols::simple_filters::ShapeComplementarityFilter::write_median_distance().

void protocols::jd2::add_string_string_pair_to_current_job ( std::string const &  string1,
std::string const &  string2 
)
void protocols::jd2::add_string_to_current_job ( std::string const &  string_in)
void protocols::jd2::add_strings_to_current_job ( std::list< std::string > const &  strings)
std::string protocols::jd2::current_batch ( )
core::Size protocols::jd2::current_batch_id ( )
std::string protocols::jd2::current_input_tag ( )
core::Size protocols::jd2::current_nstruct_index ( )
std::string protocols::jd2::current_output_filename ( )
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::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::matdes::ExtractSubposeMover::apply(), protocols::backrub::BackrubProtocol::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::contact_map::ContactMap::apply(), protocols::design_opt::GreedyOptMutationMover::apply(), protocols::coupled_moves::CoupledMovesProtocol::apply(), protocols::matdes::MatDesGreedyOptMutationMover::apply(), protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::apply(), protocols::cryst::TagPoseWithRefinementStatsMover::apply(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::matdes::ClashCheckFilter::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_for_protocol(), 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::simple_filters::ReportFilter::report(), protocols::peptide_deriver::PeptideDeriverFilter::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::SymUnsatHbondFilter::write_pymol_string_to_pdb(), protocols::matdes::ClashCheckFilter::write_pymol_string_to_pdb(), protocols::simple_filters::SaveResfileToDiskFilter::write_resfile(), and write_score_tracer().

core::Size protocols::jd2::current_replica ( )
std::string const protocols::jd2::END_BLOCK ( "MPI_FILE_BUFFER_BLOCK_END"  )
JobOP protocols::jd2::get_current_job ( )
core::pose::PoseCOP protocols::jd2::get_current_jobs_starting_pose ( )
core::Size protocols::jd2::get_min_nstruct_index_checkpoint_file ( )
std::map< std::string, core::Real > protocols::jd2::get_string_real_pairs_from_current_job ( )
std::map< std::string, std::string > protocols::jd2::get_string_string_pairs_from_current_job ( )
std::list< std::string > protocols::jd2::get_strings_from_current_job ( )
utility::vector1< utility::file::FileName > protocols::jd2::input_pdb_files_from_command_line ( )
JobCOP const protocols::jd2::JD2_BOGUS_JOB ( JobOP(new Job(InnerJobOP(new InnerJob("EMPTY_JOB_use_jd2", 0)), 0))  )
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::design_opt::GreedyOptMutationMover::apply(), protocols::matdes::MatDesGreedyOptMutationMover::apply(), protocols::constraint_filters::ConstraintScoreCutoffFilter::apply(), protocols::helical_bundle::BackboneGridSampler::apply(), protocols::rosetta_scripts::ParsedProtocol::apply(), protocols::helical_bundle::BundleGridSampler::apply(), protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::apply(), protocols::fold_from_loops::NubInitioMover::dump_centroid(), protocols::rosetta_scripts::ParsedProtocol::finish_protocol(), protocols::canonical_sampling::BiasEnergy::initialize_simulation(), protocols::peptide_deriver::PeptideDeriverPoseOutputter::output_pose(), 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().

core::Size protocols::jd2::max_nstruct_index ( )
Size const protocols::jd2::MPI_CLOSE_FILE ( 1004  )
core::Size const protocols::jd2::MPI_JOB_DIST_TAG ( 1542  )
bool protocols::jd2::operator!= ( Job const &  a,
Job const &  b 
)
std::ostream& protocols::jd2::operator<< ( std::ostream &  out,
const InnerJob &  inner_job 
)
std::ostream& protocols::jd2::operator<< ( std::ostream &  out,
const Job &  job 
)
bool protocols::jd2::operator== ( Job const &  a,
Job const &  b 
)
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.

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::anchored_design::AnchoredDesignMover::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::surface_docking::SurfaceDockingProtocol::apply(), protocols::abinitio::FragmentSampler::apply(), protocols::anchored_design::AnchoredPerturbMover::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::antibody::design::AntibodyDesignProtocol::output_ensemble(), 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().

void protocols::jd2::register_options ( )
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().

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().

std::string const protocols::jd2::START_BLOCK ( "MPI_FILE_BUFFER_BLOCK_START"  )

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

static basic::Tracer protocols::jd2::TR ( "protocols.jd2.ScoreOnlyJobOutputter"  )
static
static basic::Tracer protocols::jd2::tr ( "protocols.jd2.MpiFileBuffer"  )
static
static basic::Tracer protocols::jd2::TR ( "protocols.jd2.JobOutputterFactory"  )
static
static basic::Tracer protocols::jd2::TR ( "protocols.jd2.JobInputterFactory"  )
static
static basic::Tracer protocols::jd2::tr ( "protocols.jd2.MpiFileBuffer"  )
static
static basic::Tracer protocols::jd2::TR ( "protocols.jd2.MSDJobDistributor"  )
static
static basic::Tracer protocols::jd2::TR ( "protocols.jd2.ScreeningJobInputter"  )
static
static basic::Tracer protocols::jd2::TR ( "protocols.jd2.util"  )
static
static basic::Tracer protocols::jd2::TR ( "protocols.jd2.internal_util"  )
static

Referenced by protocols::jd2::MSDJobDistributor::apply_parsed_protocol(), protocols::jd2::AtomTreeDiffJobOutputter::dump_pose(), protocols::jd2::EnsembleJobInputter::EnsembleJobInputter(), protocols::jd2::FileJobOutputter::file(), protocols::jd2::ScreeningJobInputter::fill_jobs(), protocols::jd2::SerializedPoseJobInputter::fill_jobs(), protocols::jd2::PDBJobInputter::fill_jobs(), protocols::jd2::EnsembleJobInputter::fill_jobs(), protocols::jd2::wwPDBJobOutputter::final_pose(), protocols::jd2::JobInputterFactory::get_JobInputter_from_string(), protocols::jd2::JobOutputterFactory::get_JobOutputter_from_string(), protocols::jd2::ShuffleFileSystemJobDistributor::get_new_job_id(), protocols::jd2::FileSystemJobDistributor::get_new_job_id(), protocols::jd2::MSDJobDistributor::go(), 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::MPIWorkPartitionJobDistributor::MPIWorkPartitionJobDistributor(), protocols::jd2::JobsContainer::operator[](), protocols::jd2::wwPDBJobOutputter::other_pose(), output_intermediate_pose(), protocols::jd2::PDBJobInputter::PDBJobInputter(), protocols::jd2::PDBJobOutputter::PDBJobOutputter(), protocols::jd2::ScreeningJobInputter::pose_from_job(), protocols::jd2::SerializedPoseJobInputter::pose_from_job(), protocols::jd2::PDBJobInputter::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().

static basic::Tracer protocols::jd2::tr ( "protocols.jd2.JobDistributor"  )
static
static basic::Tracer protocols::jd2::TR ( "protocols.resource_manager.planner.JD2ResourceManager"  )
static
static basic::Tracer protocols::jd2::tr ( "protocols.jd2.JD2ResourceManagerJobInputter"  )
static

Referenced by protocols::jd2::archive::MPIArchiveJobDistributor::_notify_archive(), protocols::jd2::archive::VarianceStatisticsArchive::add_evaluated_structure(), protocols::jd2::archive::NormalizedEvaluatedArchive::add_evaluated_structure(), protocols::jd2::archive::EvaluatedArchive::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::SilentFileJobOutputter::dump_pose(), protocols::jd2::MPIFileBufJobDistributor::eat_signal(), protocols::jd2::archive::EvaluatedArchive::evaluate_pose(), protocols::jd2::archive::EvaluatedArchive::evaluate_silent_struct(), protocols::jd2::LazySilentFileJobInputter::fill_jobs(), protocols::jd2::PoseInputStreamJobInputter::fill_jobs(), protocols::jd2::LargeNstructJobInputter::fill_jobs(), protocols::jd2::AtomTreeDiffJobInputter::fill_jobs(), protocols::jd2::SilentFileJobInputter::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::MPIFileBufJobDistributor::go(), protocols::jd2::archive::MPIArchiveJobDistributor::go(), protocols::jd2::archive::ArchiveManager::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::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::archive::MPIArchiveJobDistributor::mark_job_as_completed(), protocols::jd2::JobDistributor::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::LazySilentFileJobInputter::pose_from_job(), protocols::jd2::PoseInputStreamJobInputter::pose_from_job(), protocols::jd2::LargeNstructJobInputter::pose_from_job(), protocols::jd2::AtomTreeDiffJobInputter::pose_from_job(), protocols::jd2::SilentFileJobInputter::pose_from_job(), protocols::jd2::PoseInputStreamJobInputter::PoseInputStreamJobInputter(), protocols::jd2::MPIFileBufJobDistributor::process_message(), protocols::jd2::archive::MPIArchiveJobDistributor::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::EvaluatedArchive::read_structures(), protocols::jd2::archive::ArchiveBase::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::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::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().

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

Referenced by write_score_tracer().

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

Variable Documentation

core::Size const protocols::jd2::BAD_INPUT = 2
JobCOP const protocols::jd2::JD2_BOGUS_JOB
core::Size const protocols::jd2::JOB_FAILED_NO_RETRY = 4
core::Size const protocols::jd2::JOB_SUCCESS = 3
basic::MemTracer protocols::jd2::mem_tr
static
basic::MemTracer protocols::jd2::mem_tr
static
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().