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AtomTreeDiffJobInputter
This is the simplest implementation of JobInputter, which reads
from -s/-l and AtomTree files.
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AtomTreeDiffJobInputterAP
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AtomTreeDiffJobInputterCAP
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AtomTreeDiffJobInputterCreator
protocols/jd2/AtomTreeDiffJobInputterCreator.hh:22
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AtomTreeDiffJobInputterCreatorAP
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AtomTreeDiffJobInputterCreatorCAP
|
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AtomTreeDiffJobOutputter
this is a middle-layer implementation of JobOutputter for
file-based output.
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AtomTreeDiffJobOutputterAP
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AtomTreeDiffJobOutputterCAP
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AtomTreeDiffJobOutputterCreator
protocols/jd2/AtomTreeDiffJobOutputterCreator.hh:22
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AtomTreeDiffJobOutputterCreatorAP
|
|
AtomTreeDiffJobOutputterCreatorCAP
|
|
BOINCJobDistributor
protocols/jd2/BOINCJobDistributor.hh:39
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BOINCJobDistributorAP
|
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BOINCJobDistributorCAP
|
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BatchJobInputter
This is the simplest implementation of JobInputter, which reads
from -s/-l and Batch files.
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|
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.
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|
FileJobOutputterAP
|
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FileJobOutputterCAP
|
|
FileSystemJobDistributor
protocols/jd2/FileSystemJobDistributor.hh:42
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FileSystemJobDistributorAP
|
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FileSystemJobDistributorCAP
|
|
InnerJob
The InnerJob class is responsible for knowing input requirements
for a given job - how many nstruct, and what the input is.
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InnerJobAP
|
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InnerJobCAP
|
|
InnerMultiThreadingJob
protocols/jd2/InnerMultiThreadingJob.hh:31
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InnerMultiThreadingJobAP
|
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InnerMultiThreadingJobCAP
|
|
JD2ResourceManager
The %JD2ResourceManager is the ResourceManager that should be used
when running protocols under the jd2 JobDistributor.
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JD2ResourceManagerAP
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JD2ResourceManagerCAP
|
|
JD2ResourceManagerCreator
The %JD2ResourceManagerCreator is responsible for instantiating the
JD2ResourceManager for the ResourceManagerFactory
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JD2ResourceManagerCreatorAP
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JD2ResourceManagerCreatorCAP
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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).
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|
JD2ResourceManagerJobInputterAP
|
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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
|