Package rosetta :: Package protocols :: Package jd2 :: Module _protocols_jd2_
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Module _protocols_jd2_

Classes [hide private]
  AtomTreeDiffJobInputter
This is the simplest implementation of JobInputter, which reads from -s/-l and AtomTree files.
  AtomTreeDiffJobInputterAP
  AtomTreeDiffJobInputterCAP
  AtomTreeDiffJobInputterCreator
protocols/jd2/AtomTreeDiffJobInputterCreator.hh:22
  AtomTreeDiffJobInputterCreatorAP
  AtomTreeDiffJobInputterCreatorCAP
  AtomTreeDiffJobOutputter
this is a middle-layer implementation of JobOutputter for file-based output.
  AtomTreeDiffJobOutputterAP
  AtomTreeDiffJobOutputterCAP
  AtomTreeDiffJobOutputterCreator
protocols/jd2/AtomTreeDiffJobOutputterCreator.hh:22
  AtomTreeDiffJobOutputterCreatorAP
  AtomTreeDiffJobOutputterCreatorCAP
  BOINCJobDistributor
protocols/jd2/BOINCJobDistributor.hh:39
  BOINCJobDistributorAP
  BOINCJobDistributorCAP
  BatchJobInputter
This is the simplest implementation of JobInputter, which reads from -s/-l and Batch files.
  BatchJobInputterAP
  BatchJobInputterCAP
  CompareTags
protocols/jd2/SilentFileJobOutputter.hh:168
  CompareTagsAP
  CompareTagsCAP
  DebugOut_MpiFileBuffer
protocols/jd2/MpiFileBuffer.hh:109
  DebugOut_MpiFileBufferAP
  DebugOut_MpiFileBufferCAP
  FileJobOutputter
this is a middle-layer implementation of JobOutputter for file-based output.
  FileJobOutputterAP
  FileJobOutputterCAP
  FileSystemJobDistributor
protocols/jd2/FileSystemJobDistributor.hh:42
  FileSystemJobDistributorAP
  FileSystemJobDistributorCAP
  InnerJob
The InnerJob class is responsible for knowing input requirements for a given job - how many nstruct, and what the input is.
  InnerJobAP
  InnerJobCAP
  InnerMultiThreadingJob
protocols/jd2/InnerMultiThreadingJob.hh:31
  InnerMultiThreadingJobAP
  InnerMultiThreadingJobCAP
  JD2ResourceManager
The %JD2ResourceManager is the ResourceManager that should be used when running protocols under the jd2 JobDistributor.
  JD2ResourceManagerAP
  JD2ResourceManagerCAP
  JD2ResourceManagerCreator
The %JD2ResourceManagerCreator is responsible for instantiating the JD2ResourceManager for the ResourceManagerFactory
  JD2ResourceManagerCreatorAP
  JD2ResourceManagerCreatorCAP
  JD2ResourceManagerJobInputter
See the documentation in the JD2ResourceManager for a description of the file format for the ResourceLocators block (JD2ResourceManager::read_resource_locators_tags), the ResourceOptions block (JD2ResourceManager::read_resource_options_tags) and the Resources block (JD2ResourceManager::read_resources_tags).
  JD2ResourceManagerJobInputterAP
  JD2ResourceManagerJobInputterCAP
  JD2ResourceManagerJobInputterCreator
the %JD2ResourceManagerJobInputterCreator is responsible for instantiating the JD2ResourceManagerJobInputter for the JobDistributorFactory
  JD2ResourceManagerJobInputterCreatorAP
  JD2ResourceManagerJobInputterCreatorCAP
  Job
The Job class is directly used by the job distributor.
  JobAP
  JobCAP
  JobDistributor
protocols/jd2/JobDistributor.hh:61
  JobDistributorAP
  JobDistributorCAP
  JobDistributorFactory
protocols/jd2/JobDistributorFactory.hh:30
  JobDistributorFactoryAP
  JobDistributorFactoryCAP
  JobInputter
the JobInputter class is responsible for A) determining what jobs exist, and B) taking a job object and returning the starting pose associated with that job.
  JobInputterAP
  JobInputterCAP
  JobInputterCreator
Abstract base class for a JobInputter factory; the Creator class is responsible for creating a particular mover class.
  JobInputterCreatorAP
  JobInputterCreatorCAP
  JobInputterFactory
protocols/jd2/JobInputterFactory.hh:50
  JobInputterFactoryAP
  JobInputterFactoryCAP
  JobOutputter
the JobOutputter class is responsible for dealing with output, as well as determining what jobs have already been output and what sort of name is associated with a job.
  JobOutputterAP
  JobOutputterCAP
  JobOutputterCreator
Abstract base class for a JobOutputter factory; the Creator class is responsible for creating a particular mover class.
  JobOutputterCreatorAP
  JobOutputterCreatorCAP
  JobOutputterFactory
protocols/jd2/JobOutputterFactory.hh:52
  JobOutputterFactoryAP
  JobOutputterFactoryCAP
  JobOutputterObserver
protocols/jd2/JobOutputterObserver.hh:26
  JobOutputterObserverAP
  JobOutputterObserverCAP
  LazySilentFileJobInputter
protocols/jd2/LazySilentFileJobInputter.hh:26
  LazySilentFileJobInputterAP
  LazySilentFileJobInputterCAP
  LazySilentFileJobInputterCreator
protocols/jd2/LazySilentFileJobInputterCreator.hh:22
  LazySilentFileJobInputterCreatorAP
  LazySilentFileJobInputterCreatorCAP
  MPIFileBufJobDistributor
This JobDistributor is intended for machines where you have a large number of processors.
  MPIFileBufJobDistributorAP
  MPIFileBufJobDistributorCAP
  MPIMultiCommJobDistributor
This JobDistributor is intended for JD2 controlled runs of multiple parallel simulations that use multiple replicas: e.g., N trajectories of M replicas on N*M+2 processes.
  MPIMultiCommJobDistributorAP
  MPIMultiCommJobDistributorCAP
  MPIWorkPartitionJobDistributor
This job distributor is meant for running jobs where the number of jobs is equal to the number of processors (or, similarly, the jobs % processors calculation is very close to the number of processors and NOT a small number).
  MPIWorkPartitionJobDistributorAP
  MPIWorkPartitionJobDistributorCAP
  MPIWorkPoolJobDistributor
This job distributor is meant for running jobs where the machine you are using has a large number of processors, the number of jobs is much greater than the number of processors, or the runtimes of the individual jobs could vary greatly.
  MPIWorkPoolJobDistributorAP
  MPIWorkPoolJobDistributorCAP
  MSDJobDistributor
protocols/jd2/MSDJobDistributor.hh:31
  MSDJobDistributorAP
  MSDJobDistributorCAP
  MpiFileBuffer
protocols/jd2/MpiFileBuffer.hh:43
  MpiFileBufferAP
  MpiFileBufferCAP
  NoOutputJobOutputter
the NoOutputJobOutputter class is responsible for NOT dealing with output
  NoOutputJobOutputterAP
  NoOutputJobOutputterCAP
  NoOutputJobOutputterCreator
protocols/jd2/NoOutputJobOutputterCreator.hh:22
  NoOutputJobOutputterCreatorAP
  NoOutputJobOutputterCreatorCAP
  PDBJobInputter
This is the simplest implementation of JobInputter, which reads from -s/-l and PDB files.
  PDBJobInputterAP
  PDBJobInputterCAP
  PDBJobInputterCreator
protocols/jd2/PDBJobInputterCreator.hh:22
  PDBJobInputterCreatorAP
  PDBJobInputterCreatorCAP
  PDBJobOutputter
this simplest implementation of JobOutputter outputs raw PDBs and associated files, uncompressed.
  PDBJobOutputterAP
  PDBJobOutputterCAP
  PDBJobOutputterCreator
protocols/jd2/PDBJobOutputterCreator.hh:22
  PDBJobOutputterCreatorAP
  PDBJobOutputterCreatorCAP
  Parser
the Parser class can create a protocol (made of Movers) from an XML file.
  ParserAP
  ParserCAP
  PoseInputStreamJobInputter
This is the simplest implementation of JobInputter, which reads from -s/-l and SilentFile files.
  PoseInputStreamJobInputterAP
  PoseInputStreamJobInputterCAP
  PoseInputStreamJobInputterCreator
protocols/jd2/PoseInputStreamJobInputterCreator.hh:22
  PoseInputStreamJobInputterCreatorAP
  PoseInputStreamJobInputterCreatorCAP
  ScoreMap
protocols/jd2/ScoreMap.hh:31
  ScoreMapAP
  ScoreMapCAP
  ScoreOnlyJobOutputter
Joboutputter that only outputs score files, useful for screening protocols
  ScoreOnlyJobOutputterAP
  ScoreOnlyJobOutputterCAP
  ScoreOnlyJobOutputterCreator
protocols/jd2/ScoreOnlyJobOutputterCreator.hh:22
  ScoreOnlyJobOutputterCreatorAP
  ScoreOnlyJobOutputterCreatorCAP
  ScreeningJobInputter
protocols/jd2/ScreeningJobInputter.hh:30
  ScreeningJobInputterAP
  ScreeningJobInputterCAP
  ScreeningJobInputterCreator
protocols/jd2/ScreeningJobInputterCreator.hh:22
  ScreeningJobInputterCreatorAP
  ScreeningJobInputterCreatorCAP
  ShuffleFileSystemJobDistributor
protocols/jd2/ShuffleJobDistributor.hh:39
  ShuffleFileSystemJobDistributorAP
  ShuffleFileSystemJobDistributorCAP
  SilentFileJobInputter
This is the simplest implementation of JobInputter, which reads from -s/-l and SilentFile files.
  SilentFileJobInputterAP
  SilentFileJobInputterCAP
  SilentFileJobInputterCreator
protocols/jd2/SilentFileJobInputterCreator.hh:22
  SilentFileJobInputterCreatorAP
  SilentFileJobInputterCreatorCAP
  SilentFileJobOutputter
this is a implementation of JobOutputter for silent-file-based output.
  SilentFileJobOutputterAP
  SilentFileJobOutputterCAP
  SilentFileJobOutputterCreator
protocols/jd2/SilentFileJobOutputterCreator.hh:22
  SilentFileJobOutputterCreatorAP
  SilentFileJobOutputterCreatorCAP
  SingleFileBuffer
this is a implementation of Buffer for silent-file-based output.
  SingleFileBufferAP
  SingleFileBufferCAP
  SingletonBase_T_basic_resource_manager_ResourceManager_T
SingletonBase is meant to serve as a base class for singleton classes in Rosetta handling the initialization of the singleton in a thread-safe way.
  SingletonBase_T_basic_resource_manager_ResourceManager_TAP
  SingletonBase_T_basic_resource_manager_ResourceManager_TCAP
  SingletonBase_T_core_chemical_ChemicalManager_T
SingletonBase is meant to serve as a base class for singleton classes in Rosetta handling the initialization of the singleton in a thread-safe way.
  SingletonBase_T_core_chemical_ChemicalManager_TAP
  SingletonBase_T_core_chemical_ChemicalManager_TCAP
  SingletonBase_T_protocols_jd2_JobInputterFactory_T
SingletonBase is meant to serve as a base class for singleton classes in Rosetta handling the initialization of the singleton in a thread-safe way.
  SingletonBase_T_protocols_jd2_JobInputterFactory_TAP
  SingletonBase_T_protocols_jd2_JobInputterFactory_TCAP
  SingletonBase_T_protocols_jd2_JobOutputterFactory_T
SingletonBase is meant to serve as a base class for singleton classes in Rosetta handling the initialization of the singleton in a thread-safe way.
  SingletonBase_T_protocols_jd2_JobOutputterFactory_TAP
  SingletonBase_T_protocols_jd2_JobOutputterFactory_TCAP
  WriteFileSFB
protocols/jd2/SingleFileBuffer.hh:70
  WriteFileSFBAP
  WriteFileSFBCAP
  WriteOut_MpiFileBuffer
protocols/jd2/MpiFileBuffer.hh:102
  WriteOut_MpiFileBufferAP
  WriteOut_MpiFileBufferCAP
  __CPP_AtomTreeDiffJobInputterCreator__
  __CPP_AtomTreeDiffJobInputter__
  __CPP_AtomTreeDiffJobOutputterCreator__
  __CPP_AtomTreeDiffJobOutputter__
  __CPP_BatchJobInputter__
  __CPP_FileJobOutputter__
  __CPP_InnerJob__
  __CPP_JD2ResourceManagerJobInputterCreator__
  __CPP_JD2ResourceManagerJobInputter__
  __CPP_JobInputterCreator__
  __CPP_JobInputter__
  __CPP_JobOutputterCreator__
  __CPP_JobOutputterObserver__
  __CPP_JobOutputter__
  __CPP_Job__
  __CPP_LazySilentFileJobInputterCreator__
  __CPP_LazySilentFileJobInputter__
  __CPP_NoOutputJobOutputterCreator__
  __CPP_NoOutputJobOutputter__
  __CPP_PDBJobInputterCreator__
  __CPP_PDBJobInputter__
  __CPP_PDBJobOutputterCreator__
  __CPP_PDBJobOutputter__
  __CPP_Parser__
  __CPP_PoseInputStreamJobInputterCreator__
  __CPP_PoseInputStreamJobInputter__
  __CPP_ScoreOnlyJobOutputterCreator__
  __CPP_ScoreOnlyJobOutputter__
  __CPP_ScreeningJobInputterCreator__
  __CPP_ScreeningJobInputter__
  __CPP_SilentFileJobInputterCreator__
  __CPP_SilentFileJobInputter__
  __CPP_SilentFileJobOutputterCreator__
  __CPP_SilentFileJobOutputter__
  __CPP_SingleFileBuffer__
  __CPP_WriteFileSFB__
  mpi_tags
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
Functions [hide private]
 
add_job_data_to_ss(...)
add_job_data_to_ss( (__CPP_SilentStruct__)ss, (__CPP_Job__)job_op) -> None : protocols/jd2/util.hh:59
str :
current_batch()
protocols/jd2/util.hh:52
str :
current_output_filename()
call the 'filename' accessor of the current job-distributor with the current job
str :
current_output_name()
gets used output name of pose ask jd for current-job ---> ask jobOutputter for name of this job
int :
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
Job :
get_current_job()
protocols/jd2/util.hh:63
Pose :
get_current_jobs_starting_pose()
protocols/jd2/util.hh:57
bool :
jd2_used()
is this application running with jd2 --- used for some code that yields backward compatability with old JobDistributor
 
output_intermediate_pose(...)
output_intermediate_pose( (Pose)pose, (str)stage_tag [, (int)copy_count=-1 [, (bool)score_only=False]]) -> None : writes pose to intermediate-scorefile using current Job and JobOutputter ..
None :
register_options()
protocols/jd2/util.hh:61
 
set_native_in_mover(...)
set_native_in_mover( (Mover)mover) -> None : protocols/jd2/util.hh:66
 
write_score_tracer(...)
write_score_tracer( (Pose)pose_in, (str)tag) -> None : protocols/jd2/util.hh:69
Variables [hide private]
  BAD_INPUT_TAG = rosetta.protocols.jd2._protocols_jd2_.mpi_tags...
  JOB_GO_TAG = rosetta.protocols.jd2._protocols_jd2_.mpi_tags.JO...
  JOB_SUCCESS_TAG = rosetta.protocols.jd2._protocols_jd2_.mpi_ta...
  NEW_JOB_ID_TAG = rosetta.protocols.jd2._protocols_jd2_.mpi_tag...
  RECEIVE_MESSAGE_TAG = rosetta.protocols.jd2._protocols_jd2_.mp...
  REQUEST_MESSAGE_TAG = rosetta.protocols.jd2._protocols_jd2_.mp...
  __package__ = None
Function Details [hide private]

add_job_data_to_ss(...)

 

add_job_data_to_ss( (__CPP_SilentStruct__)ss, (__CPP_Job__)job_op) -> None :
    protocols/jd2/util.hh:59

    C++ signature :
        void add_job_data_to_ss(boost::shared_ptr<core::io::silent::SilentStruct>,boost::shared_ptr<protocols::jd2::Job const>)

current_batch()

 
    protocols/jd2/util.hh:52

    C++ signature :
        std::string current_batch()

Returns: str :

current_output_filename()

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

    C++ signature :
        std::string current_output_filename()

Returns: str :

current_output_name()

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

    C++ signature :
        std::string current_output_name()

Returns: str :

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
    

    C++ signature :
        unsigned long current_replica()

Returns: int :

get_current_job()

 
    protocols/jd2/util.hh:63

    C++ signature :
        boost::shared_ptr<protocols::jd2::Job> get_current_job()

Returns: Job :

get_current_jobs_starting_pose()

 
    protocols/jd2/util.hh:57

    C++ signature :
        boost::shared_ptr<core::pose::Pose const> get_current_jobs_starting_pose()

Returns: Pose :

jd2_used()

 
    is this application running with jd2 --- used for some code that yields backward compatability with old JobDistributor
    

    C++ signature :
        bool jd2_used()

Returns: bool :

output_intermediate_pose(...)

 

output_intermediate_pose( (Pose)pose, (str)stage_tag [, (int)copy_count=-1 [, (bool)score_only=False]]) -> None :
    writes pose to intermediate-scorefile using current Job and JobOutputter ..
    @detail 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
    

    C++ signature :
        void output_intermediate_pose(core::pose::Pose,std::string [,int=-1 [,bool=False]])

register_options()

 
    protocols/jd2/util.hh:61

    C++ signature :
        void register_options()

Returns: None :

set_native_in_mover(...)

 

set_native_in_mover( (Mover)mover) -> None :
    protocols/jd2/util.hh:66

    C++ signature :
        void set_native_in_mover(protocols::moves::Mover {lvalue})

write_score_tracer(...)

 

write_score_tracer( (Pose)pose_in, (str)tag) -> None :
    protocols/jd2/util.hh:69

    C++ signature :
        void write_score_tracer(core::pose::Pose,std::string)


Variables Details [hide private]

BAD_INPUT_TAG

Value:
rosetta.protocols.jd2._protocols_jd2_.mpi_tags.BAD_INPUT_TAG

JOB_GO_TAG

Value:
rosetta.protocols.jd2._protocols_jd2_.mpi_tags.JOB_GO_TAG

JOB_SUCCESS_TAG

Value:
rosetta.protocols.jd2._protocols_jd2_.mpi_tags.JOB_SUCCESS_TAG

NEW_JOB_ID_TAG

Value:
rosetta.protocols.jd2._protocols_jd2_.mpi_tags.NEW_JOB_ID_TAG

RECEIVE_MESSAGE_TAG

Value:
rosetta.protocols.jd2._protocols_jd2_.mpi_tags.RECEIVE_MESSAGE_TAG

REQUEST_MESSAGE_TAG

Value:
rosetta.protocols.jd2._protocols_jd2_.mpi_tags.REQUEST_MESSAGE_TAG