Rosetta 3.4
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protocols::jd2 Namespace Reference

Namespaces

namespace  archive
namespace  JobInputterInputSource
namespace  parser

Classes

class  AtomTreeDiffJobInputter
class  AtomTreeDiffJobInputterCreator
class  AtomTreeDiffJobOutputter
class  AtomTreeDiffJobOutputterCreator
class  BatchJobInputter
class  BOINCJobDistributor
class  DockDesignParser
 Reading the xml file and generating the mover. More...
class  FileJobOutputter
class  FileSystemJobDistributor
class  InnerJob
class  InnerMultiThreadingJob
class  Job
class  JobDistributor
class  JobDistributorFactory
class  JobInputter
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  LazySilentFileJobInputter
class  LazySilentFileJobInputterCreator
class  MpiFileBuffer
class  WriteOut_MpiFileBuffer
class  DebugOut_MpiFileBuffer
class  MPIFileBufJobDistributor
class  MPIMultiCommJobDistributor
class  MPIWorkPartitionJobDistributor
class  MPIWorkPoolJobDistributor
class  MultiThreadingJob
class  NoOutputJobOutputter
class  NoOutputJobOutputterCreator
class  Parser
class  PDBJobInputter
class  PDBJobInputterCreator
class  PDBJobOutputter
class  PDBJobOutputterCreator
class  PoseInputStreamJobInputter
class  PoseInputStreamJobInputterCreator
class  ScoreMap
class  ScoreOnlyJobOutputter
class  ScoreOnlyJobOutputterCreator
class  ShuffleFileSystemJobDistributor
class  SilentFileJobInputter
class  SilentFileJobInputterCreator
class  SilentFileJobOutputter
class  CompareTags
class  SilentFileJobOutputterCreator
class  SingleFileBuffer
class  WriteFileSFB

Typedefs

typedef
utility::pointer::owning_ptr
< GenericJobInputter > 
GenericJobInputterOP
typedef
utility::pointer::owning_ptr
< AtomTreeDiffJobInputter
AtomTreeDiffJobInputterOP
typedef
utility::pointer::owning_ptr
< AtomTreeDiffJobOutputter
AtomTreeDiffJobOutputterOP
typedef
utility::pointer::owning_ptr
< AtomTreeDiffJobOutputter
const > 
AtomTreeDiffJobOutputterCOP
typedef
utility::pointer::owning_ptr
< BatchJobInputter
BatchJobInputterOP
typedef utility::tag::TagPtr TagPtr
typedef utility::vector0< TagPtrTagPtrs
typedef
utility::pointer::owning_ptr
< FileJobOutputter
FileJobOutputterOP
typedef
utility::pointer::owning_ptr
< InnerJob
InnerJobOP
typedef
utility::pointer::owning_ptr
< InnerJob const > 
InnerJobCOP
typedef
utility::pointer::owning_ptr
< InnerMultiThreadingJob
InnerMultiThreadingJobOP
typedef
utility::pointer::owning_ptr
< InnerMultiThreadingJob const > 
InnerMultiThreadingJobCOP
typedef
utility::pointer::owning_ptr
< Job
JobOP
typedef
utility::pointer::owning_ptr
< Job const > 
JobCOP
typedef utility::vector1< JobOPJobs
typedef
utility::pointer::access_ptr
< JobInputter
JobInputterAP
typedef
utility::pointer::access_ptr
< JobInputter const > 
JobInputterCAP
typedef
utility::pointer::owning_ptr
< JobInputter
JobInputterOP
typedef
utility::pointer::owning_ptr
< JobInputter const > 
JobInputterCOP
typedef
utility::pointer::owning_ptr
< JobInputterCreator
JobInputterCreatorOP
typedef
utility::pointer::owning_ptr
< JobInputterCreator const > 
JobInputterCreatorCOP
typedef
utility::pointer::owning_ptr
< JobInputterFactory
JobInputterFactoryOP
typedef
utility::pointer::owning_ptr
< JobInputterFactory const > 
JobInputterFactoryCOP
typedef
utility::pointer::owning_ptr
< JobOutputter
JobOutputterOP
typedef
utility::pointer::owning_ptr
< JobOutputter const > 
JobOutputterCOP
typedef
utility::pointer::owning_ptr
< JobOutputterCreator
JobOutputterCreatorOP
typedef
utility::pointer::owning_ptr
< JobOutputterCreator const > 
JobOutputterCreatorCOP
typedef
utility::pointer::owning_ptr
< JobOutputterFactory
JobOutputterFactoryOP
typedef
utility::pointer::owning_ptr
< JobOutputterFactory const > 
JobOutputterFactoryCOP
typedef
utility::pointer::owning_ptr
< LazySilentFileJobInputter
LazySilentFileJobInputterOP
typedef
utility::pointer::owning_ptr
< MpiFileBuffer
MpiFileBufferOP
typedef
utility::pointer::owning_ptr
< MpiFileBuffer const > 
MpiFileBufferCOP
typedef
utility::pointer::owning_ptr
< MultiThreadingJob
MultiThreadingJobOP
typedef
utility::pointer::owning_ptr
< MultiThreadingJob const > 
MultiThreadingJobCOP
typedef
utility::pointer::owning_ptr
< Parser
ParserOP
typedef
utility::pointer::owning_ptr
< Parser const > 
ParserCOP
typedef
utility::pointer::owning_ptr
< PDBJobInputter
PDBJobInputterOP
typedef
utility::pointer::owning_ptr
< PDBJobOutputter
PDBJobOutputterOP
typedef
utility::pointer::owning_ptr
< PoseInputStreamJobInputter
PoseInputStreamJobInputterOP
typedef
utility::pointer::owning_ptr
< SilentFileJobInputter
SilentFileJobInputterOP
typedef
utility::pointer::owning_ptr
< SilentFileJobOutputter
SilentFileJobOutputterOP
typedef
utility::pointer::owning_ptr
< SingleFileBuffer
SingleFileBufferOP
typedef
utility::pointer::owning_ptr
< SingleFileBuffer const > 
SingleFileBufferCOP

Enumerations

enum  mpi_tags { NEW_JOB_ID_TAG = 10, BAD_INPUT_TAG = 20, JOB_SUCCESS_TAG = 30 }
 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...

Functions

static basic::Tracer TR ("protocols.jd2.DockDesignParser")
JobOP const JD2_BOGUS_JOB (new Job((new InnerJob("EMPTY_JOB_use_jd2", 0)), 0))
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_WIND_DOWN (1001)
Size const MPI_BLOCK_FILE (1002)
Size const MPI_RELEASE_FILE (1003)
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() )
std::string const START_BLOCK ("MPI_FILE_BUFFER_BLOCK_START")
std::string const END_BLOCK ("MPI_FILE_BUFFER_BLOCK_END")
void register_options ()
static basic::Tracer TR ("protocols.jd2.JobDistributor")
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/////////////
std::string current_output_name ()
 gets used output name of pose ask jd for current-job ---> ask jobOutputter for name of this job
bool jd2_used ()
 is this application running with jd2 --- used for some code that yields backward compatability with old JobDistributor
std::string current_output_filename ()
 call the 'filename' accessor of the current job-distributor with the current job
void write_score_tracer (core::pose::Pose const &pose_in, std::string tracer_point)
JobOP get_current_job ()
core::pose::PoseCOP get_current_jobs_starting_pose ()
void add_job_data_to_ss (core::io::silent::SilentStructOP ss, JobCOP job_op)
void set_native_in_mover (protocols::moves::Mover &mover)
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

Variables

JobOP const JD2_BOGUS_JOB
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.
core::Size const BAD_INPUT = 2
core::Size const JOB_SUCCESS = 3
core::Size const JOB_FAILED_NO_RETRY = 4

Typedef Documentation

typedef utility::tag::TagPtr protocols::jd2::TagPtr

Enumeration Type Documentation

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.

Enumerator:
NEW_JOB_ID_TAG 
BAD_INPUT_TAG 
JOB_SUCCESS_TAG 

Function Documentation

void protocols::jd2::add_job_data_to_ss ( core::io::silent::SilentStructOP  ss,
JobCOP  job_op 
)
std::string protocols::jd2::current_output_filename ( )
std::string protocols::jd2::current_output_name ( )
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 ( )
JobOP const protocols::jd2::JD2_BOGUS_JOB ( new   Job(new InnerJob("EMPTY_JOB_use_jd2", 0)), 0)
bool protocols::jd2::jd2_used ( )
Size const protocols::jd2::MPI_BLOCK_FILE ( 1002  )
Size const protocols::jd2::MPI_CLOSE_FILE ( 1004  )
core::Size const protocols::jd2::MPI_JOB_DIST_TAG ( 1542  )
Size const protocols::jd2::MPI_RELEASE_FILE ( 1003  )
Size const protocols::jd2::MPI_WIND_DOWN ( 1001  )
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::FragmentSampler::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::abinitio::FragmentSampler::do_stage1_cycles(), and protocols::canonical_sampling::SilentTrajectoryRecorder::write_model().

void protocols::jd2::register_options ( )
void protocols::jd2::set_native_in_mover ( protocols::moves::Mover mover)
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.JobDistributor"  ) [static]
static basic::Tracer protocols::jd2::TR ( "protocols.jd2.JobOutputterFactory"  ) [static]
static basic::Tracer protocols::jd2::tr ( "protocols.jd2.MpiFileBuffer"  ) [static]
static basic::Tracer protocols::jd2::TR ( "protocols.jd2.JobInputterFactory"  ) [static]
static basic::Tracer protocols::jd2::tr ( "protocols.jd2.JobDistributor"  ) [static]

Referenced by protocols::jd2::AtomTreeDiffJobInputter::AtomTreeDiffJobInputter(), protocols::jd2::archive::MPIArchiveJobDistributor::batch_underflow(), protocols::jd2::BatchJobInputter::BatchJobInputter(), protocols::jd2::WriteFileSFB::block(), protocols::jd2::archive::ArchiveManager::cancel_batch(), protocols::jd2::SingleFileBuffer::close(), protocols::jd2::MpiFileBuffer::close_file(), protocols::jd2::SilentFileJobOutputter::dump_pose(), protocols::jd2::MPIFileBufJobDistributor::eat_signal(), protocols::jd2::archive::EvaluatedArchive::evaluate_silent_struct(), protocols::jd2::SilentFileJobInputter::fill_jobs(), protocols::jd2::PoseInputStreamJobInputter::fill_jobs(), protocols::jd2::LazySilentFileJobInputter::fill_jobs(), protocols::jd2::AtomTreeDiffJobInputter::fill_jobs(), protocols::jd2::archive::ArchiveManager::finalize_batch(), protocols::jd2::MpiFileBuffer::garbage_collection(), protocols::jd2::archive::DebugArchive::generate_batch(), 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::archive::ArchiveManager::jobs_completed(), 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::SilentFileJobInputter::pose_from_job(), protocols::jd2::PoseInputStreamJobInputter::pose_from_job(), protocols::jd2::LazySilentFileJobInputter::pose_from_job(), protocols::jd2::AtomTreeDiffJobInputter::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::EvaluatedArchive::read_structures(), protocols::jd2::archive::ArchiveBase::read_structures(), protocols::jd2::MpiFileBuffer::release_file(), protocols::jd2::archive::EvaluatedArchive::rescore(), protocols::jd2::archive::ArchiveBase::restore_from_file(), protocols::jd2::MpiFileBuffer::run(), 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::SilentFileJobInputter::SilentFileJobInputter(), protocols::jd2::MPIFileBufJobDistributor::slave_get_new_job_id(), protocols::jd2::MPIFileBufJobDistributor::slave_mark_current_job_id_for_repetition(), protocols::jd2::archive::ArchiveManager::start_new_batch(), protocols::jd2::archive::Batch::write_info_file(), protocols::jd2::WriteFileSFB::write_lines(), protocols::jd2::WriteFileSFB::WriteFileSFB(), and protocols::jd2::WriteFileSFB::~WriteFileSFB().

static basic::Tracer protocols::jd2::TR ( "protocols.jd2.DockDesignParser"  ) [static]
void protocols::jd2::write_score_tracer ( core::pose::Pose const &  pose_in,
std::string  tracer_point 
)

Variable Documentation

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().

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