Bindings for protocols::jd2 namespace

Modules
		rosetta.protocols.jd2.JobInputterInputSource rosetta.protocols.jd2.archive rosetta.protocols.jd2.parser

Classes
		builtins.object InnerJob InnerMultiThreadingJob Job MultiThreadingJob JobDistributor FileSystemJobDistributor ShuffleFileSystemJobDistributor BOINCJobDistributor MPIFileBufJobDistributor MPIMultiCommJobDistributor MPIWorkPartitionJobDistributor MPIWorkPoolJobDistributor MSDJobDistributor JobDistributorFactory JobInputter AtomTreeDiffJobInputter BatchJobInputter JD2ResourceManagerJobInputter LargeNstructJobInputter LazySilentFileJobInputter PDBJobInputter EnsembleJobInputter PoseInputStreamJobInputter ScreeningJobInputter SilentFileJobInputter JobInputterCreator AtomTreeDiffJobInputterCreator EnsembleJobInputterCreator JD2ResourceManagerJobInputterCreator LargeNstructJobInputterCreator LazySilentFileJobInputterCreator PDBJobInputterCreator PoseInputStreamJobInputterCreator ScreeningJobInputterCreator SilentFileJobInputterCreator JobOutputter FileJobOutputter AtomTreeDiffJobOutputter PDBJobOutputter ScoreOnlyJobOutputter SilentFileJobOutputter NoOutputJobOutputter JobOutputterCreator AtomTreeDiffJobOutputterCreator NoOutputJobOutputterCreator PDBJobOutputterCreator ScoreOnlyJobOutputterCreator SilentFileJobOutputterCreator JobOutputterObserver JobsContainer MpiFileBuffer DebugOut_MpiFileBuffer WriteOut_MpiFileBuffer Parser ScoreMap SingleFileBuffer WriteFileSFB rosetta.basic.resource_manager.LazyResourceManager(rosetta.basic.resource_manager.ResourceManager) JD2ResourceManager rosetta.basic.resource_manager.ResourceManagerCreator(builtins.object) JD2ResourceManagerCreator rosetta.std.unary_function_std_string_bool_t(builtins.object) CompareTags rosetta.utility.SingletonBase_protocols_jd2_JobInputterFactory_t(builtins.object) JobInputterFactory rosetta.utility.SingletonBase_protocols_jd2_JobOutputterFactory_t(builtins.object) JobOutputterFactory   class AtomTreeDiffJobInputter(JobInputter)     This is the simplest implementation of JobInputter, which reads from -s/-l and AtomTree files.     Method resolution order: AtomTreeDiffJobInputter JobInputter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. all_ref_poses(...) from builtins.PyCapsule all_ref_poses(rosetta.protocols.jd2.AtomTreeDiffJobInputter) -> rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t   Utility function to allow mutatable (!) access to the reference  poses of the undelying AtomTreeDiff object. Use with caution.      This exists to allow setup on stored reference poses for properties that  don't get saved/restored in PDB format, like covalent constraints for enzyme design. fill_jobs(...) from builtins.PyCapsule fill_jobs(self : rosetta.protocols.jd2.AtomTreeDiffJobInputter, jobs : rosetta.protocols.jd2.JobsContainer) -> NoneType   this function determines what jobs exist from -in::file::silent and  -in::file::tags. input_source(...) from builtins.PyCapsule input_source(rosetta.protocols.jd2.AtomTreeDiffJobInputter) -> rosetta.protocols.jd2.JobInputterInputSource.Enum   Return the type of input source that the AtomTreeDiffJobInputter is currently   using.      Always ATOM_TREE_FILE. pose_from_job(...) from builtins.PyCapsule pose_from_job(self : rosetta.protocols.jd2.AtomTreeDiffJobInputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType   this function is responsible for filling the pose reference with  the pose indicated by the job.  The Job object (within its InnerJob)  contains a PoseCOP.  This function needs to either fill the pose  reference from the InnerJob or, on first demand of a pose from that  InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill  the reference.  This implementation uses pose_from_pdb Methods inherited from JobInputter: assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.JobInputter,  : rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self const owning pointers.   2. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self owning pointers. get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_const_protocols_jd2_JobInputter_t   Get self const weak pointers.   2. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_protocols_jd2_JobInputter_t   Get self weak pointers. job_inputter_input_source_to_string(...) from builtins.PyCapsule job_inputter_input_source_to_string(source : rosetta.protocols.jd2.JobInputterInputSource.Enum) -> str   call this with input_source() to get the input source of a  particular job inputter update_jobs_list(...) from builtins.PyCapsule update_jobs_list(self : rosetta.protocols.jd2.JobInputter, jobs : protocols::jd2::JobsContainer) -> NoneType   This function is only called by certain JobInputters to update the jobs list after it has already been created.      An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back. updates_jobs_list(...) from builtins.PyCapsule updates_jobs_list(rosetta.protocols.jd2.JobInputter) -> bool   Does this type of JobInputter update the jobs list?      False by default.  Override this function in derived classes to make it true.   class AtomTreeDiffJobInputterCreator(JobInputterCreator)       Method resolution order: AtomTreeDiffJobInputterCreator JobInputterCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.AtomTreeDiffJobInputterCreator,  : rosetta.protocols.jd2.AtomTreeDiffJobInputterCreator) -> rosetta.protocols.jd2.AtomTreeDiffJobInputterCreator create_JobInputter(...) from builtins.PyCapsule create_JobInputter(rosetta.protocols.jd2.AtomTreeDiffJobInputterCreator) -> rosetta.protocols.jd2.JobInputter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.AtomTreeDiffJobInputterCreator) -> str   class AtomTreeDiffJobOutputter(FileJobOutputter)     this is a middle-layer implementation of JobOutputter for file-based output.  It handles scorefile output, as scorefiles are common to file-outputting methods.     Method resolution order: AtomTreeDiffJobOutputter FileJobOutputter JobOutputter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. final_pose(...) from builtins.PyCapsule final_pose(self : rosetta.protocols.jd2.AtomTreeDiffJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   this function outputs the final result of a job. job_has_completed(...) from builtins.PyCapsule job_has_completed(self : rosetta.protocols.jd2.AtomTreeDiffJobOutputter, job : rosetta.protocols.jd2.Job) -> bool   this function is not used for output, but it belongs here since it needs to check the same output locations as the class normally writes to.  This class checks wherever output goes to see if the job's expected output already exists (on disk or whatever).  This is the most basic form of checkpointing.  The base implementation looks for a pdb with the job's name already in existence. other_pose(...) from builtins.PyCapsule other_pose(*args, **kwargs) Overloaded function.   1. other_pose(self : rosetta.protocols.jd2.AtomTreeDiffJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol.   2. other_pose(self : rosetta.protocols.jd2.AtomTreeDiffJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str, copy_count : int) -> NoneType   this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol.   3. other_pose(self : rosetta.protocols.jd2.AtomTreeDiffJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str, copy_count : int, score_only : bool) -> NoneType   this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. output_name(...) from builtins.PyCapsule output_name(self : rosetta.protocols.jd2.AtomTreeDiffJobOutputter, job : rosetta.protocols.jd2.Job) -> str   this is the master function for determining the unique output identifier for a job set_precision(...) from builtins.PyCapsule set_precision(self : rosetta.protocols.jd2.AtomTreeDiffJobOutputter, bb_precision : int, sc_precision : int, bondlen_precision : int) -> NoneType   what precision should the atom_tree_diff be ouput at? use_input_for_ref(...) from builtins.PyCapsule use_input_for_ref(*args, **kwargs) Overloaded function.   1. use_input_for_ref(rosetta.protocols.jd2.AtomTreeDiffJobOutputter) -> NoneType   use input as reference pose?   2. use_input_for_ref(self : rosetta.protocols.jd2.AtomTreeDiffJobOutputter, use_input : bool) -> NoneType   use input as reference pose? Methods inherited from FileJobOutputter: file(...) from builtins.PyCapsule file(self : rosetta.protocols.jd2.FileJobOutputter, job : rosetta.protocols.jd2.Job, data : str) -> NoneType   this function takes a string and writes it to disk (separately from Tracer output). scorefile_name(...) from builtins.PyCapsule scorefile_name(rosetta.protocols.jd2.FileJobOutputter) -> rosetta.utility.file.FileName set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.jd2.FileJobOutputter) -> NoneType write_scorefile(...) from builtins.PyCapsule write_scorefile(rosetta.protocols.jd2.FileJobOutputter) -> bool Methods inherited from JobOutputter: add_evaluation(...) from builtins.PyCapsule add_evaluation(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType   ////////////////////////////// evaluator interface //////////////////////////////////////////// call_output_observers(...) from builtins.PyCapsule call_output_observers(self : rosetta.protocols.jd2.JobOutputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType   call all output_observers clear_evaluators(...) from builtins.PyCapsule clear_evaluators(rosetta.protocols.jd2.JobOutputter) -> NoneType evaluate(...) from builtins.PyCapsule evaluate(self : rosetta.protocols.jd2.JobOutputter, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType evaluators(...) from builtins.PyCapsule evaluators(rosetta.protocols.jd2.JobOutputter) -> rosetta.protocols.evaluation.MetaPoseEvaluator filename(...) from builtins.PyCapsule filename(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.jd2.Job) -> str flush(...) from builtins.PyCapsule flush(rosetta.protocols.jd2.JobOutputter) -> NoneType   this function is meant to be redefined in child classes to allow for flushing of memory buffers.  Here's the long version: The SilentFileJobOutputter wanted to buffer output, but needed to guaruntee that  the output would be flushed at end of runtime.  The original implementation was to A) bend over backward to ensure  that the destructor was run (JobOutputter lives inside static JobDistributor, which was previously not destructed  because it's static) and B) flush the buffers in the destructor.  This caused a problem because the buffer-flushing  tried to use the Tracers, which had already been destructed...boom crash.    New solution: re-forbid use of destructors within the static JobDistributor system, and create a flush  function to force this stuff out.  So here it is: set_evaluators(...) from builtins.PyCapsule set_evaluators(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType starting_pose(...) from builtins.PyCapsule starting_pose(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.core.pose.Pose) -> NoneType   optionally pass a starting (reference) pose to a JobOutputter for later comparison  purposes and/or as interface for initializing evaluators   class AtomTreeDiffJobOutputterCreator(JobOutputterCreator)       Method resolution order: AtomTreeDiffJobOutputterCreator JobOutputterCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.AtomTreeDiffJobOutputterCreator,  : rosetta.protocols.jd2.AtomTreeDiffJobOutputterCreator) -> rosetta.protocols.jd2.AtomTreeDiffJobOutputterCreator create_JobOutputter(...) from builtins.PyCapsule create_JobOutputter(rosetta.protocols.jd2.AtomTreeDiffJobOutputterCreator) -> rosetta.protocols.jd2.JobOutputter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.AtomTreeDiffJobOutputterCreator) -> str   class BOINCJobDistributor(ShuffleFileSystemJobDistributor)       Method resolution order: BOINCJobDistributor ShuffleFileSystemJobDistributor FileSystemJobDistributor JobDistributor builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle, rosetta.protocols.jd2.BOINCJobDistributor) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.BOINCJobDistributor,  : rosetta.protocols.jd2.BOINCJobDistributor) -> rosetta.protocols.jd2.BOINCJobDistributor checkpoint_clear(...) from builtins.PyCapsule checkpoint_clear(rosetta.protocols.jd2.BOINCJobDistributor) -> NoneType checkpoint_read(...) from builtins.PyCapsule checkpoint_read(rosetta.protocols.jd2.BOINCJobDistributor) -> NoneType checkpoint_write(...) from builtins.PyCapsule checkpoint_write(rosetta.protocols.jd2.BOINCJobDistributor) -> NoneType get_new_job_id(...) from builtins.PyCapsule get_new_job_id(rosetta.protocols.jd2.BOINCJobDistributor) -> int go(...) from builtins.PyCapsule go(self : rosetta.protocols.jd2.BOINCJobDistributor, mover : rosetta.protocols.moves.Mover) -> NoneType Methods inherited from ShuffleFileSystemJobDistributor: mark_current_job_id_for_repetition(...) from builtins.PyCapsule mark_current_job_id_for_repetition(rosetta.protocols.jd2.ShuffleFileSystemJobDistributor) -> NoneType next_random_job(...) from builtins.PyCapsule next_random_job(rosetta.protocols.jd2.ShuffleFileSystemJobDistributor) -> int Methods inherited from FileSystemJobDistributor: current_job_finished(...) from builtins.PyCapsule current_job_finished(rosetta.protocols.jd2.FileSystemJobDistributor) -> NoneType remove_bad_inputs_from_job_list(...) from builtins.PyCapsule remove_bad_inputs_from_job_list(rosetta.protocols.jd2.FileSystemJobDistributor) -> NoneType restart(...) from builtins.PyCapsule restart(rosetta.protocols.jd2.FileSystemJobDistributor) -> NoneType Methods inherited from JobDistributor: add_batch(...) from builtins.PyCapsule add_batch(*args, **kwargs) Overloaded function.   1. add_batch(self : rosetta.protocols.jd2.JobDistributor,  : str) -> NoneType   add a new batch ( name will be interpreted as flag_file )   2. add_batch(self : rosetta.protocols.jd2.JobDistributor,  : str, id : int) -> NoneType   add a new batch ( name will be interpreted as flag_file ) current_batch_id(...) from builtins.PyCapsule current_batch_id(rosetta.protocols.jd2.JobDistributor) -> int   what is the current batch number ? --- refers to position in batches_ current_job(...) from builtins.PyCapsule current_job(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.Job   Movers may ask their controlling job distributor for information about the current job.  They may also write information to this job for later output, though this use is now discouraged  as the addition of the MultiplePoseMover now means that a single job may include several  separate trajectories. current_job_id(...) from builtins.PyCapsule current_job_id(rosetta.protocols.jd2.JobDistributor) -> int   integer access - which job are we on? current_output_name(...) from builtins.PyCapsule current_output_name(rosetta.protocols.jd2.JobDistributor) -> str   Movers may ask their controlling job distributor for the output name as defined by the Job and JobOutputter. get_current_batch(...) from builtins.PyCapsule get_current_batch(rosetta.protocols.jd2.JobDistributor) -> str   what is the current batch ? --- name refers to the flag-file used for this batch get_instance(...) from builtins.PyCapsule get_instance() -> rosetta.protocols.jd2.JobDistributor job_inputter(...) from builtins.PyCapsule job_inputter(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobInputter   JobInputter access job_inputter_input_source(...) from builtins.PyCapsule job_inputter_input_source(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobInputterInputSource.Enum   The input source for the current JobInputter. job_outputter(...) from builtins.PyCapsule job_outputter(rosetta.protocols.jd2.JobDistributor) -> protocols::jd2::JobOutputter   Movers (or derived classes) may ask for the JobOutputter mpi_finalize(...) from builtins.PyCapsule mpi_finalize(self : rosetta.protocols.jd2.JobDistributor, finalize : bool) -> NoneType   should the go() function call MPI_finalize()? It probably should, this is true by default. set_job_inputter(...) from builtins.PyCapsule set_job_inputter(self : rosetta.protocols.jd2.JobDistributor, new_job_inputter : rosetta.protocols.jd2.JobInputter) -> NoneType   Set the JobInputter and reset the Job list -- this is not something you want to do  after go() has been called, but before it has returned. set_job_outputter(...) from builtins.PyCapsule set_job_outputter(self : rosetta.protocols.jd2.JobDistributor, new_job_outputter : protocols::jd2::JobOutputter) -> NoneType   Movers (or derived classes) may ask for the JobOutputter total_nr_jobs(...) from builtins.PyCapsule total_nr_jobs(rosetta.protocols.jd2.JobDistributor) -> int   class BatchJobInputter(JobInputter)     This is the simplest implementation of JobInputter, which reads from -s/-l and Batch files.     Method resolution order: BatchJobInputter JobInputter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, batch : str) -> NoneType   2. __init__(handle, rosetta.protocols.jd2.BatchJobInputter) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. fill_jobs(...) from builtins.PyCapsule fill_jobs(self : rosetta.protocols.jd2.BatchJobInputter, jobs : rosetta.protocols.jd2.JobsContainer) -> NoneType   this function determines what jobs exist from -in::file::silent and  -in::file::tags. input_source(...) from builtins.PyCapsule input_source(rosetta.protocols.jd2.BatchJobInputter) -> rosetta.protocols.jd2.JobInputterInputSource.Enum   Return the type of input source that the BatchJobInputter is currently   using.      The input source for the current batch. pose_from_job(...) from builtins.PyCapsule pose_from_job(self : rosetta.protocols.jd2.BatchJobInputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType   this function is responsible for filling the pose reference with  the pose indicated by the job.  The Job object (within its InnerJob)  contains a PoseCOP.  This function needs to either fill the pose  reference from the InnerJob or, on first demand of a pose from that  InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill  the reference.  This implementation uses pose_from_pdb Methods inherited from JobInputter: assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.JobInputter,  : rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self const owning pointers.   2. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self owning pointers. get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_const_protocols_jd2_JobInputter_t   Get self const weak pointers.   2. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_protocols_jd2_JobInputter_t   Get self weak pointers. job_inputter_input_source_to_string(...) from builtins.PyCapsule job_inputter_input_source_to_string(source : rosetta.protocols.jd2.JobInputterInputSource.Enum) -> str   call this with input_source() to get the input source of a  particular job inputter update_jobs_list(...) from builtins.PyCapsule update_jobs_list(self : rosetta.protocols.jd2.JobInputter, jobs : protocols::jd2::JobsContainer) -> NoneType   This function is only called by certain JobInputters to update the jobs list after it has already been created.      An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back. updates_jobs_list(...) from builtins.PyCapsule updates_jobs_list(rosetta.protocols.jd2.JobInputter) -> bool   Does this type of JobInputter update the jobs list?      False by default.  Override this function in derived classes to make it true.   class CompareTags(rosetta.std.unary_function_std_string_bool_t)       Method resolution order: CompareTags rosetta.std.unary_function_std_string_bool_t builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.protocols.jd2.CompareTags, compare_tag : str) -> bool __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.jd2.CompareTags, querytag : str) -> NoneType   2. __init__(self : rosetta.protocols.jd2.CompareTags,  : rosetta.protocols.jd2.CompareTags) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Methods inherited from rosetta.std.unary_function_std_string_bool_t: assign(...) from builtins.PyCapsule assign(self : rosetta.std.unary_function_std_string_bool_t,  : rosetta.std.unary_function_std_string_bool_t) -> rosetta.std.unary_function_std_string_bool_t   class DebugOut_MpiFileBuffer(MpiFileBuffer)       Method resolution order: DebugOut_MpiFileBuffer MpiFileBuffer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, rank : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.DebugOut_MpiFileBuffer,  : rosetta.protocols.jd2.DebugOut_MpiFileBuffer) -> rosetta.protocols.jd2.DebugOut_MpiFileBuffer Methods inherited from MpiFileBuffer: block_file(...) from builtins.PyCapsule block_file(self : rosetta.protocols.jd2.MpiFileBuffer, filename : str) -> NoneType close_file(...) from builtins.PyCapsule close_file(self : rosetta.protocols.jd2.MpiFileBuffer, fname : str) -> bool garbage_collection(...) from builtins.PyCapsule garbage_collection(rosetta.protocols.jd2.MpiFileBuffer) -> NoneType release_file(...) from builtins.PyCapsule release_file(self : rosetta.protocols.jd2.MpiFileBuffer, filename : str) -> NoneType run(...) from builtins.PyCapsule run(rosetta.protocols.jd2.MpiFileBuffer) -> NoneType set_SlaveCanOpenFile(...) from builtins.PyCapsule set_SlaveCanOpenFile(*args, **kwargs) Overloaded function.   1. set_SlaveCanOpenFile(rosetta.protocols.jd2.MpiFileBuffer) -> NoneType   2. set_SlaveCanOpenFile(self : rosetta.protocols.jd2.MpiFileBuffer, setting : bool) -> NoneType stop(...) from builtins.PyCapsule stop(rosetta.protocols.jd2.MpiFileBuffer) -> NoneType   class EnsembleJobInputter(PDBJobInputter)     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.           Seed Ensemble =============   Randomly choose the starting files using the list of structures given by -s and -l   -jd2:seed_ensemble_weights (RealVector)      - Will give weights to the input PDBs and trigger seed_ensemble mode and the JI.  We then use the weighted sampler to choose the input pdb for    each nstruct.  The weights could be the size of the cluster, the energy, that you like some structure better, etc. Must match number of inputs.   -jd2:seed_ensemble_weight_file (File)      - A file specifying weights to use for each input structure.  Enables seed_ensemble mode and the JI. Two columns.  basename with extension (or    relative path or full path), weight.  Any not given in file will be set to 0 by default.  Can give a line that is [ALL weight] to set all input    pdbs to a given weight. Used for example, to upweight a specific structure:      Example:      #name weight    ALL 1    awesome_model.pdb 3   -jd2:seed_ensemble (Bool)      - Enable seed ensemble mode, but simply randomly choose the input pdb for each nstruct.  For seed ensemble mode, the number of input pdbs can    be larger than nstruct.   Grid Ensemble ============= Use the input files given in -s and -l and nstruct to cover a grid.   -in:jd2:grid_ensemble (Bool)     - Will enable the basic component of the JI.  Here, instead of sampling nstruct for every input pdb, we only sample nstruct no matter the number   of input PDBs (with nstruct split as evenly as possible over the input PDBs).     Method resolution order: EnsembleJobInputter PDBJobInputter JobInputter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.jd2.EnsembleJobInputter) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.EnsembleJobInputter,  : rosetta.protocols.jd2.EnsembleJobInputter) -> rosetta.protocols.jd2.EnsembleJobInputter fill_jobs(...) from builtins.PyCapsule fill_jobs(self : rosetta.protocols.jd2.EnsembleJobInputter, jobs : rosetta.protocols.jd2.JobsContainer) -> NoneType   this function determines what jobs exist from -s/-l Methods inherited from PDBJobInputter: input_source(...) from builtins.PyCapsule input_source(rosetta.protocols.jd2.PDBJobInputter) -> rosetta.protocols.jd2.JobInputterInputSource.Enum   Return the type of input source that the PDBJobInputter is currently   using.      Always PDB_FILE. pose_from_job(...) from builtins.PyCapsule pose_from_job(self : rosetta.protocols.jd2.PDBJobInputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType   this function is responsible for filling the pose reference with the pose indicated by the job.  The Job object (within its InnerJob) contains a PoseCOP.  This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference.  This implementation uses pose_from_pdb Methods inherited from JobInputter: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self const owning pointers.   2. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self owning pointers. get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_const_protocols_jd2_JobInputter_t   Get self const weak pointers.   2. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_protocols_jd2_JobInputter_t   Get self weak pointers. job_inputter_input_source_to_string(...) from builtins.PyCapsule job_inputter_input_source_to_string(source : rosetta.protocols.jd2.JobInputterInputSource.Enum) -> str   call this with input_source() to get the input source of a  particular job inputter update_jobs_list(...) from builtins.PyCapsule update_jobs_list(self : rosetta.protocols.jd2.JobInputter, jobs : protocols::jd2::JobsContainer) -> NoneType   This function is only called by certain JobInputters to update the jobs list after it has already been created.      An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back. updates_jobs_list(...) from builtins.PyCapsule updates_jobs_list(rosetta.protocols.jd2.JobInputter) -> bool   Does this type of JobInputter update the jobs list?      False by default.  Override this function in derived classes to make it true.   class EnsembleJobInputterCreator(JobInputterCreator)       Method resolution order: EnsembleJobInputterCreator JobInputterCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.EnsembleJobInputterCreator,  : rosetta.protocols.jd2.EnsembleJobInputterCreator) -> rosetta.protocols.jd2.EnsembleJobInputterCreator create_JobInputter(...) from builtins.PyCapsule create_JobInputter(rosetta.protocols.jd2.EnsembleJobInputterCreator) -> rosetta.protocols.jd2.JobInputter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.EnsembleJobInputterCreator) -> str   class FileJobOutputter(JobOutputter)     this is a middle-layer implementation of JobOutputter for file-based output.  It handles scorefile output, as scorefiles are common to file-outputting methods.     Method resolution order: FileJobOutputter JobOutputter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.jd2.FileJobOutputter) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. file(...) from builtins.PyCapsule file(self : rosetta.protocols.jd2.FileJobOutputter, job : rosetta.protocols.jd2.Job, data : str) -> NoneType   this function takes a string and writes it to disk (separately from Tracer output). final_pose(...) from builtins.PyCapsule final_pose(self : rosetta.protocols.jd2.FileJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   this function outputs the final result of a job. job_has_completed(...) from builtins.PyCapsule job_has_completed(self : rosetta.protocols.jd2.FileJobOutputter, job : rosetta.protocols.jd2.Job) -> bool   this function is not used for output, but it belongs here since it needs to check the same output locations as the class normally writes to.  This class checks wherever output goes to see if the job's expected output already exists (on disk or whatever).  This is the most basic form of checkpointing.  The base implementation looks for a pdb with the job's name already in existence. other_pose(...) from builtins.PyCapsule other_pose(*args, **kwargs) Overloaded function.   1. other_pose(self : rosetta.protocols.jd2.FileJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol.   2. other_pose(self : rosetta.protocols.jd2.FileJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str, copy_count : int) -> NoneType   this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol.   3. other_pose(self : rosetta.protocols.jd2.FileJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str, copy_count : int, score_only : bool) -> NoneType   this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. output_name(...) from builtins.PyCapsule output_name(self : rosetta.protocols.jd2.FileJobOutputter, job : rosetta.protocols.jd2.Job) -> str   this is the master function for determining the unique output identifier for a job scorefile_name(...) from builtins.PyCapsule scorefile_name(rosetta.protocols.jd2.FileJobOutputter) -> rosetta.utility.file.FileName set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.jd2.FileJobOutputter) -> NoneType write_scorefile(...) from builtins.PyCapsule write_scorefile(rosetta.protocols.jd2.FileJobOutputter) -> bool Methods inherited from JobOutputter: add_evaluation(...) from builtins.PyCapsule add_evaluation(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType   ////////////////////////////// evaluator interface //////////////////////////////////////////// call_output_observers(...) from builtins.PyCapsule call_output_observers(self : rosetta.protocols.jd2.JobOutputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType   call all output_observers clear_evaluators(...) from builtins.PyCapsule clear_evaluators(rosetta.protocols.jd2.JobOutputter) -> NoneType evaluate(...) from builtins.PyCapsule evaluate(self : rosetta.protocols.jd2.JobOutputter, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType evaluators(...) from builtins.PyCapsule evaluators(rosetta.protocols.jd2.JobOutputter) -> rosetta.protocols.evaluation.MetaPoseEvaluator filename(...) from builtins.PyCapsule filename(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.jd2.Job) -> str flush(...) from builtins.PyCapsule flush(rosetta.protocols.jd2.JobOutputter) -> NoneType   this function is meant to be redefined in child classes to allow for flushing of memory buffers.  Here's the long version: The SilentFileJobOutputter wanted to buffer output, but needed to guaruntee that  the output would be flushed at end of runtime.  The original implementation was to A) bend over backward to ensure  that the destructor was run (JobOutputter lives inside static JobDistributor, which was previously not destructed  because it's static) and B) flush the buffers in the destructor.  This caused a problem because the buffer-flushing  tried to use the Tracers, which had already been destructed...boom crash.    New solution: re-forbid use of destructors within the static JobDistributor system, and create a flush  function to force this stuff out.  So here it is: set_evaluators(...) from builtins.PyCapsule set_evaluators(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType starting_pose(...) from builtins.PyCapsule starting_pose(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.core.pose.Pose) -> NoneType   optionally pass a starting (reference) pose to a JobOutputter for later comparison  purposes and/or as interface for initializing evaluators   class FileSystemJobDistributor(JobDistributor)       Method resolution order: FileSystemJobDistributor JobDistributor builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle, rosetta.protocols.jd2.FileSystemJobDistributor) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.FileSystemJobDistributor,  : rosetta.protocols.jd2.FileSystemJobDistributor) -> rosetta.protocols.jd2.FileSystemJobDistributor current_job_finished(...) from builtins.PyCapsule current_job_finished(rosetta.protocols.jd2.FileSystemJobDistributor) -> NoneType get_new_job_id(...) from builtins.PyCapsule get_new_job_id(rosetta.protocols.jd2.FileSystemJobDistributor) -> int go(...) from builtins.PyCapsule go(self : rosetta.protocols.jd2.FileSystemJobDistributor, mover : rosetta.protocols.moves.Mover) -> NoneType mark_current_job_id_for_repetition(...) from builtins.PyCapsule mark_current_job_id_for_repetition(rosetta.protocols.jd2.FileSystemJobDistributor) -> NoneType remove_bad_inputs_from_job_list(...) from builtins.PyCapsule remove_bad_inputs_from_job_list(rosetta.protocols.jd2.FileSystemJobDistributor) -> NoneType restart(...) from builtins.PyCapsule restart(rosetta.protocols.jd2.FileSystemJobDistributor) -> NoneType Methods inherited from JobDistributor: add_batch(...) from builtins.PyCapsule add_batch(*args, **kwargs) Overloaded function.   1. add_batch(self : rosetta.protocols.jd2.JobDistributor,  : str) -> NoneType   add a new batch ( name will be interpreted as flag_file )   2. add_batch(self : rosetta.protocols.jd2.JobDistributor,  : str, id : int) -> NoneType   add a new batch ( name will be interpreted as flag_file ) current_batch_id(...) from builtins.PyCapsule current_batch_id(rosetta.protocols.jd2.JobDistributor) -> int   what is the current batch number ? --- refers to position in batches_ current_job(...) from builtins.PyCapsule current_job(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.Job   Movers may ask their controlling job distributor for information about the current job.  They may also write information to this job for later output, though this use is now discouraged  as the addition of the MultiplePoseMover now means that a single job may include several  separate trajectories. current_job_id(...) from builtins.PyCapsule current_job_id(rosetta.protocols.jd2.JobDistributor) -> int   integer access - which job are we on? current_output_name(...) from builtins.PyCapsule current_output_name(rosetta.protocols.jd2.JobDistributor) -> str   Movers may ask their controlling job distributor for the output name as defined by the Job and JobOutputter. get_current_batch(...) from builtins.PyCapsule get_current_batch(rosetta.protocols.jd2.JobDistributor) -> str   what is the current batch ? --- name refers to the flag-file used for this batch get_instance(...) from builtins.PyCapsule get_instance() -> rosetta.protocols.jd2.JobDistributor job_inputter(...) from builtins.PyCapsule job_inputter(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobInputter   JobInputter access job_inputter_input_source(...) from builtins.PyCapsule job_inputter_input_source(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobInputterInputSource.Enum   The input source for the current JobInputter. job_outputter(...) from builtins.PyCapsule job_outputter(rosetta.protocols.jd2.JobDistributor) -> protocols::jd2::JobOutputter   Movers (or derived classes) may ask for the JobOutputter mpi_finalize(...) from builtins.PyCapsule mpi_finalize(self : rosetta.protocols.jd2.JobDistributor, finalize : bool) -> NoneType   should the go() function call MPI_finalize()? It probably should, this is true by default. set_job_inputter(...) from builtins.PyCapsule set_job_inputter(self : rosetta.protocols.jd2.JobDistributor, new_job_inputter : rosetta.protocols.jd2.JobInputter) -> NoneType   Set the JobInputter and reset the Job list -- this is not something you want to do  after go() has been called, but before it has returned. set_job_outputter(...) from builtins.PyCapsule set_job_outputter(self : rosetta.protocols.jd2.JobDistributor, new_job_outputter : protocols::jd2::JobOutputter) -> NoneType   Movers (or derived classes) may ask for the JobOutputter total_nr_jobs(...) from builtins.PyCapsule total_nr_jobs(rosetta.protocols.jd2.JobDistributor) -> int   class InnerJob(builtins.object)     The InnerJob class is responsible for knowing input requirements for a given job - how many nstruct, and what the input is.  InnerJobs are relatively heavy; there is no need to duplicate a series of InnerJobs for each index into nstruct.  The companion Job class handles the nstruct index and has a pointer to an InnerJob (which is shared across many Jobs). InnerJob also holds a PoseOP to maintain the unmodified input pose for that job.     Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.protocols.jd2.InnerJob, other : rosetta.protocols.jd2.InnerJob) -> bool   Mutual comparison of this inner job to the other inner job  so that if either one thinks it's not the same as the other, then  it returns false.  Invokes the same() function on both this and other      Note: only compare if the pointers to the poses are to the  same location __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, input_tag : str, nstruct_max : int) -> NoneType   2. __init__(self : handle,  : rosetta.core.pose.Pose, input_tag : str, nstruct_max : int) -> NoneType   3. __init__(handle, rosetta.protocols.jd2.InnerJob) -> NoneType __ne__(...) from builtins.PyCapsule __ne__(self : rosetta.protocols.jd2.InnerJob, other : rosetta.protocols.jd2.InnerJob) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.jd2.InnerJob) -> str bad(...) from builtins.PyCapsule bad(rosetta.protocols.jd2.InnerJob) -> bool clone(...) from builtins.PyCapsule clone(rosetta.protocols.jd2.InnerJob) -> rosetta.protocols.jd2.InnerJob   Return an owning pointer to a copy of this object. get_pose(...) from builtins.PyCapsule get_pose(rosetta.protocols.jd2.InnerJob) -> rosetta.core.pose.Pose   return a COP to the input pose  DO NOT USE OUTSIDE OF JD2 NAMESPACE input_tag(...) from builtins.PyCapsule input_tag(rosetta.protocols.jd2.InnerJob) -> str   return the input tag (a string of space separated PDB filenames) nstruct_max(...) from builtins.PyCapsule nstruct_max(rosetta.protocols.jd2.InnerJob) -> int same(...) from builtins.PyCapsule same(self : rosetta.protocols.jd2.InnerJob, other : rosetta.protocols.jd2.InnerJob) -> bool   returns true if this is the same as other;  does not call other.same() set_bad(...) from builtins.PyCapsule set_bad(*args, **kwargs) Overloaded function.   1. set_bad(rosetta.protocols.jd2.InnerJob) -> NoneType   2. set_bad(self : rosetta.protocols.jd2.InnerJob, value : bool) -> NoneType   class InnerMultiThreadingJob(InnerJob)       Method resolution order: InnerMultiThreadingJob InnerJob builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle,  : rosetta.core.pose.Pose, input_tag : str, nstruct_max : int, alns : rosetta.utility.vector1_core_sequence_SequenceAlignment, templates : rosetta.utility.vector1_core_pose_Pose) -> NoneType   2. __init__(handle, rosetta.protocols.jd2.InnerMultiThreadingJob) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. alignments(...) from builtins.PyCapsule alignments(rosetta.protocols.jd2.InnerMultiThreadingJob) -> rosetta.utility.vector1_core_sequence_SequenceAlignment template_poses(...) from builtins.PyCapsule template_poses(rosetta.protocols.jd2.InnerMultiThreadingJob) -> rosetta.utility.vector1_core_pose_Pose Methods inherited from InnerJob: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.protocols.jd2.InnerJob, other : rosetta.protocols.jd2.InnerJob) -> bool   Mutual comparison of this inner job to the other inner job  so that if either one thinks it's not the same as the other, then  it returns false.  Invokes the same() function on both this and other      Note: only compare if the pointers to the poses are to the  same location __ne__(...) from builtins.PyCapsule __ne__(self : rosetta.protocols.jd2.InnerJob, other : rosetta.protocols.jd2.InnerJob) -> bool __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.jd2.InnerJob) -> str bad(...) from builtins.PyCapsule bad(rosetta.protocols.jd2.InnerJob) -> bool clone(...) from builtins.PyCapsule clone(rosetta.protocols.jd2.InnerJob) -> rosetta.protocols.jd2.InnerJob   Return an owning pointer to a copy of this object. get_pose(...) from builtins.PyCapsule get_pose(rosetta.protocols.jd2.InnerJob) -> rosetta.core.pose.Pose   return a COP to the input pose  DO NOT USE OUTSIDE OF JD2 NAMESPACE input_tag(...) from builtins.PyCapsule input_tag(rosetta.protocols.jd2.InnerJob) -> str   return the input tag (a string of space separated PDB filenames) nstruct_max(...) from builtins.PyCapsule nstruct_max(rosetta.protocols.jd2.InnerJob) -> int same(...) from builtins.PyCapsule same(self : rosetta.protocols.jd2.InnerJob, other : rosetta.protocols.jd2.InnerJob) -> bool   returns true if this is the same as other;  does not call other.same() set_bad(...) from builtins.PyCapsule set_bad(*args, **kwargs) Overloaded function.   1. set_bad(rosetta.protocols.jd2.InnerJob) -> NoneType   2. set_bad(self : rosetta.protocols.jd2.InnerJob, value : bool) -> NoneType   class JD2ResourceManager(rosetta.basic.resource_manager.LazyResourceManager)     The %JD2ResourceManager is the ResourceManager that should be used when running protocols under the jd2 JobDistributor.     The purpose of the ResourceManager is to disentangle the process of feeding protocols with Resources they need from the job distribution system in which they run.  When protocols request a resource under the ResourceManager, they do so without knowing what kind of ResourceManager they are communicating with.  Protocols that are designed to run under JD2 could conceivably be run under any other job management scheme (e.g. a complicated MPI protocol).  It's the job of the %JD2ResourceManager to determine the right resource to deliver to a protocol, and the context that the %JD2ResourceManager uses to make that decision is the job.  E.g., when a protocol asks for the "native" (the Pose of the native structure), the %JD2ResourceManager looks up what job is currently running and then delivers the (single) native Pose for that job.   The %JD2ResourceManager is meant to work with the JD2ResourceManagerJobInputter. Jobs are defined in an input XML file and for each of the jobs that are defined, resources can be mapped to them.  Resources are also declared in an XML file and may be declared in the same XML file as the Jobs or in a different XML file. The format of this XML file is specified in full between the documentation in the JD2ResourceManagerJobInputter class and three functions that are documented and implemented in this class.   The %JD2ResourceManager keeps track of which resources are used by which jobs and keeps track of what jobs have completed.  It allocates a Resource the first time that resource is requested by a protoocol, and it deallocates that Resource when all jobs that require that resource have finished.  Thus a protocol that needs an expensive-to-create resource (e.g. a set of 9-mers) can load that resource once and then have that resource shared between all of the jobs that require that resource (e.g. 10K abinitio trajectories) *without having to do any legwork itself.*  If you have 100K abinitio trajectories for 10 different targets, they could all be run in a single job. (Note: as of 9/2013, abinitio does not work with the jd2 or the ResourceManager but it should!)   The main consequence of relying on the ResourceManager to hand resources to jobs is that jobs which require different resources (usually specified on the command line, and therefore requiring that each job run in a separate process) now can be run together in a single process.  For MPI jobs, this is a major improvement, especially in constructing benchmarks, where many separate, (possibly short) jobs need to be run.   (Because Resources are not constructed until they are requested, resources can be declared and never used; you can give a resource file that describes every resource you use in every job, and a job declaration file that only uses one of those resources.)     Method resolution order: JD2ResourceManager rosetta.basic.resource_manager.LazyResourceManager rosetta.basic.resource_manager.ResourceManager builtins.object Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.JD2ResourceManager,  : rosetta.protocols.jd2.JD2ResourceManager) -> rosetta.protocols.jd2.JD2ResourceManager clear(...) from builtins.PyCapsule clear(rosetta.protocols.jd2.JD2ResourceManager) -> NoneType get_jd2_resource_manager_instance(...) from builtins.PyCapsule get_jd2_resource_manager_instance() -> rosetta.protocols.jd2.JD2ResourceManager get_option(...) from builtins.PyCapsule get_option(*args, **kwargs) Overloaded function.   1. get_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.BooleanOptionKey) -> bool   2. get_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.BooleanVectorOptionKey) -> rosetta.utility.vector1_bool   3. get_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.FileOptionKey) -> rosetta.utility.file.FileName   4. get_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.FileVectorOptionKey) -> rosetta.utility.vector1_utility_file_FileName   5. get_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.IntegerOptionKey) -> int   6. get_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.IntegerVectorOptionKey) -> rosetta.utility.vector1_int   7. get_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.PathOptionKey) -> rosetta.utility.file.PathName   8. get_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.PathVectorOptionKey) -> rosetta.utility.vector1_utility_file_PathName   9. get_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.RealOptionKey) -> float   10. get_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.RealVectorOptionKey) -> rosetta.utility.vector1_double   11. get_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.StringOptionKey) -> str   12. get_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.StringVectorOptionKey) -> rosetta.utility.vector1_std_string has_option(...) from builtins.PyCapsule has_option(*args, **kwargs) Overloaded function.   1. has_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.BooleanOptionKey) -> bool   2. has_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.BooleanVectorOptionKey) -> bool   3. has_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.FileOptionKey) -> bool   4. has_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.FileVectorOptionKey) -> bool   5. has_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.IntegerOptionKey) -> bool   6. has_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.IntegerVectorOptionKey) -> bool   7. has_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.PathOptionKey) -> bool   8. has_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.PathVectorOptionKey) -> bool   9. has_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.RealOptionKey) -> bool   10. has_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.RealVectorOptionKey) -> bool   11. has_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.StringOptionKey) -> bool   12. has_option(self : rosetta.protocols.jd2.JD2ResourceManager, key : rosetta.utility.options.StringVectorOptionKey) -> bool has_resource_with_description(...) from builtins.PyCapsule has_resource_with_description(self : rosetta.protocols.jd2.JD2ResourceManager, resource_description : str) -> bool read_resource_locators_tags(...) from builtins.PyCapsule read_resource_locators_tags(self : rosetta.protocols.jd2.JD2ResourceManager, tags : rosetta.utility.tag.Tag) -> NoneType   Read the portion of an XML file that declares ResourceLocator objects read_resource_options_tags(...) from builtins.PyCapsule read_resource_options_tags(self : rosetta.protocols.jd2.JD2ResourceManager, tags : rosetta.utility.tag.Tag) -> NoneType read_resources_tags(...) from builtins.PyCapsule read_resources_tags(self : rosetta.protocols.jd2.JD2ResourceManager, tags : rosetta.utility.tag.Tag) -> NoneType Methods inherited from rosetta.basic.resource_manager.LazyResourceManager: __str__(...) from builtins.PyCapsule __str__(rosetta.basic.resource_manager.LazyResourceManager) -> str add_job_options(...) from builtins.PyCapsule add_job_options(self : rosetta.basic.resource_manager.LazyResourceManager, job_tag : str, job_options : rosetta.basic.resource_manager.JobOptions) -> NoneType add_resource_configuration(...) from builtins.PyCapsule add_resource_configuration(self : rosetta.basic.resource_manager.LazyResourceManager, resource_tag : str, resource_configuration : rosetta.basic.resource_manager.ResourceConfiguration) -> NoneType add_resource_locator(...) from builtins.PyCapsule add_resource_locator(self : rosetta.basic.resource_manager.LazyResourceManager, locator_tag : str, resource_locator : basic::resource_manager::ResourceLocator) -> NoneType add_resource_options(...) from builtins.PyCapsule add_resource_options(self : rosetta.basic.resource_manager.LazyResourceManager, resource_options_tag : str, resource_options : rosetta.basic.resource_manager.ResourceOptions) -> NoneType add_resource_tag_by_job_tag(...) from builtins.PyCapsule add_resource_tag_by_job_tag(self : rosetta.basic.resource_manager.LazyResourceManager, resource_description : str, job_tag : str, resource_tag : str) -> NoneType create_resources(...) from builtins.PyCapsule create_resources(self : rosetta.basic.resource_manager.LazyResourceManager,  : str) -> NoneType   Create all the resources for a particular job; this should be implemented by the derived  class.  The implementation in this class calls utility::exit find_resource_configuration(...) from builtins.PyCapsule find_resource_configuration(self : rosetta.basic.resource_manager.LazyResourceManager, resource_tag : str) -> rosetta.basic.resource_manager.ResourceConfiguration find_resource_locator(...) from builtins.PyCapsule find_resource_locator(self : rosetta.basic.resource_manager.LazyResourceManager, locator_tag : str) -> basic::resource_manager::ResourceLocator find_resource_options(...) from builtins.PyCapsule find_resource_options(self : rosetta.basic.resource_manager.LazyResourceManager, resource_options_tag : str) -> rosetta.basic.resource_manager.ResourceOptions find_resource_tag_by_job_tag(...) from builtins.PyCapsule find_resource_tag_by_job_tag(self : rosetta.basic.resource_manager.LazyResourceManager, resource_description : str, job_tag : str) -> str free_resource_by_job_tag(...) from builtins.PyCapsule free_resource_by_job_tag(self : rosetta.basic.resource_manager.LazyResourceManager, resource_description : str, job_tag : str) -> NoneType free_resource_by_tag(...) from builtins.PyCapsule free_resource_by_tag(self : rosetta.basic.resource_manager.LazyResourceManager, resource_tag : str) -> NoneType get_count_of_jobs_associated_with_resource_tag(...) from builtins.PyCapsule get_count_of_jobs_associated_with_resource_tag(self : rosetta.basic.resource_manager.LazyResourceManager, resource_tag : str) -> int get_job_options(...) from builtins.PyCapsule get_job_options(self : rosetta.basic.resource_manager.LazyResourceManager, job_tag : str) -> rosetta.basic.resource_manager.JobOptions get_resource_tags_for_job_tag(...) from builtins.PyCapsule get_resource_tags_for_job_tag(self : rosetta.basic.resource_manager.LazyResourceManager, job_tag : str) -> rosetta.std.list_std_string_std_allocator_std_string_t has_job_options(...) from builtins.PyCapsule has_job_options(self : rosetta.basic.resource_manager.LazyResourceManager, job_tag : str) -> bool has_resource(...) from builtins.PyCapsule has_resource(self : rosetta.basic.resource_manager.LazyResourceManager, resource_tag : str) -> bool   Does a resource with a given name exist? has_resource_configuration(...) from builtins.PyCapsule has_resource_configuration(self : rosetta.basic.resource_manager.LazyResourceManager, resource_tag : str) -> bool   has a ResourceConfiguration been provided to the LazyResourceManager for a Resource with a particular ResourceTag? has_resource_locator(...) from builtins.PyCapsule has_resource_locator(self : rosetta.basic.resource_manager.LazyResourceManager, locator_tag : str) -> bool   has a ResourceLocator object been provided to the LazyResourceManager which has a particular LocatorTag? has_resource_options(...) from builtins.PyCapsule has_resource_options(self : rosetta.basic.resource_manager.LazyResourceManager, resource_options_tag : str) -> bool   has a ResourceOptions object been provided to the LazyResourceManager which has a particular ResourceOptionsTag? has_resource_tag_by_job_tag(...) from builtins.PyCapsule has_resource_tag_by_job_tag(self : rosetta.basic.resource_manager.LazyResourceManager, resource_description : str, job_tag : str) -> bool mark_job_tag_as_complete(...) from builtins.PyCapsule mark_job_tag_as_complete(self : rosetta.basic.resource_manager.LazyResourceManager, job_tag : str) -> NoneType   remove the Job tag from incomplete_job_sets_ for each resource Methods inherited from rosetta.basic.resource_manager.ResourceManager: get_instance(...) from builtins.PyCapsule get_instance() -> rosetta.basic.resource_manager.ResourceManager   Deprecated access to a global (not-quite singleton) ResourceManager instance that  should be removed   class JD2ResourceManagerCreator(rosetta.basic.resource_manager.ResourceManagerCreator)     The %JD2ResourceManagerCreator is responsible for instantiating the JD2ResourceManager for the ResourceManagerFactory     Method resolution order: JD2ResourceManagerCreator rosetta.basic.resource_manager.ResourceManagerCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.JD2ResourceManagerCreator,  : rosetta.protocols.jd2.JD2ResourceManagerCreator) -> rosetta.protocols.jd2.JD2ResourceManagerCreator create_resource_manager(...) from builtins.PyCapsule create_resource_manager(rosetta.protocols.jd2.JD2ResourceManagerCreator) -> rosetta.basic.resource_manager.ResourceManager manager_type(...) from builtins.PyCapsule manager_type(rosetta.protocols.jd2.JD2ResourceManagerCreator) -> str   class JD2ResourceManagerJobInputter(JobInputter)     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).     Method resolution order: JD2ResourceManagerJobInputter JobInputter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.jd2.JD2ResourceManagerJobInputter) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.JD2ResourceManagerJobInputter,  : rosetta.protocols.jd2.JD2ResourceManagerJobInputter) -> rosetta.protocols.jd2.JD2ResourceManagerJobInputter fill_jobs(...) from builtins.PyCapsule fill_jobs(self : rosetta.protocols.jd2.JD2ResourceManagerJobInputter, jobs : rosetta.protocols.jd2.JobsContainer) -> NoneType   this function determines what jobs exist.  This function neither knows nor cares what jobs are already complete on disk/memory - it just figures out what ones should exist given the input.  NOTE: your JobInputter should order Job objects in the Jobs vector to have as few "transitions" between inputs as possible (group all Jobs of the same input next to each other).  This improves efficiency of the "FAIL_BAD_INPUT" functionality.  Note I said "should", not "must". input_source(...) from builtins.PyCapsule input_source(rosetta.protocols.jd2.JD2ResourceManagerJobInputter) -> rosetta.protocols.jd2.JobInputterInputSource.Enum   return the type of input source that the JobInputter is currently   using pose_from_job(...) from builtins.PyCapsule pose_from_job(self : rosetta.protocols.jd2.JD2ResourceManagerJobInputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType   this function is responsible for filling the pose reference with the pose indicated by the job.  The Job object (within its InnerJob) contains a PoseCOP.  This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference. Methods inherited from JobInputter: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self const owning pointers.   2. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self owning pointers. get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_const_protocols_jd2_JobInputter_t   Get self const weak pointers.   2. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_protocols_jd2_JobInputter_t   Get self weak pointers. job_inputter_input_source_to_string(...) from builtins.PyCapsule job_inputter_input_source_to_string(source : rosetta.protocols.jd2.JobInputterInputSource.Enum) -> str   call this with input_source() to get the input source of a  particular job inputter update_jobs_list(...) from builtins.PyCapsule update_jobs_list(self : rosetta.protocols.jd2.JobInputter, jobs : protocols::jd2::JobsContainer) -> NoneType   This function is only called by certain JobInputters to update the jobs list after it has already been created.      An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back. updates_jobs_list(...) from builtins.PyCapsule updates_jobs_list(rosetta.protocols.jd2.JobInputter) -> bool   Does this type of JobInputter update the jobs list?      False by default.  Override this function in derived classes to make it true.   class JD2ResourceManagerJobInputterCreator(JobInputterCreator)     the %JD2ResourceManagerJobInputterCreator is responsible for instantiating the JD2ResourceManagerJobInputter for the JobDistributorFactory     Method resolution order: JD2ResourceManagerJobInputterCreator JobInputterCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator,  : rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator) -> rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator create_JobInputter(...) from builtins.PyCapsule create_JobInputter(rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator) -> rosetta.protocols.jd2.JobInputter   Create the JD2ResourceManagerJobInputter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator) -> str   Return the name of the JobInputter this class instantiates:  "JD2ResourceManagerJobInputter"   class Job(builtins.object)     The Job class is directly used by the job distributor.  It contains an index into nstruct and a lightweight pointer to an InnerJob (to share those heavier classes).  It also directly contains job-associated output data. The idea here is that your scores, etc are associated with the job, not with a particular pose within that running job.  Thus, the Job object is a better place to store them than the pose.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, inner_job : protocols::jd2::InnerJob, nstruct_index : int) -> NoneType   2. __init__(handle, rosetta.protocols.jd2.Job) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.jd2.Job) -> str add_string(...) from builtins.PyCapsule add_string(self : rosetta.protocols.jd2.Job, string_in : str) -> NoneType   add an output string add_string_real_pair(...) from builtins.PyCapsule add_string_real_pair(self : rosetta.protocols.jd2.Job, string_in : str, real_in : float) -> NoneType   add a string/real pair add_string_string_pair(...) from builtins.PyCapsule add_string_string_pair(self : rosetta.protocols.jd2.Job, string1 : str, string2 : str) -> NoneType   add a string/string pair add_strings(...) from builtins.PyCapsule add_strings(self : rosetta.protocols.jd2.Job,  : rosetta.std.list_std_string_std_allocator_std_string_t) -> NoneType   add output strings bad(...) from builtins.PyCapsule bad(rosetta.protocols.jd2.Job) -> bool call_output_observers(...) from builtins.PyCapsule call_output_observers(self : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose) -> NoneType can_be_deleted(...) from builtins.PyCapsule can_be_deleted(rosetta.protocols.jd2.Job) -> bool   Returns true iff this job can be deleted to free up memory.      Should only be true if the job has completed, is bad, or has failed. clear_output(...) from builtins.PyCapsule clear_output(rosetta.protocols.jd2.Job) -> NoneType   Delete the output strings, string/string pairs, and string/real pairs. clone(...) from builtins.PyCapsule clone(rosetta.protocols.jd2.Job) -> rosetta.protocols.jd2.Job   Return an owning pointer to a copy of this object. completed(...) from builtins.PyCapsule completed(rosetta.protocols.jd2.Job) -> bool copy_without_output(...) from builtins.PyCapsule copy_without_output(rosetta.protocols.jd2.Job) -> rosetta.protocols.jd2.Job   returns a copy of this object whose "output fields" are zeroed  out.  Used by the JobDistributor in cases where the job fails and must be  retried to prevent accumulation of Job state after a failure.  This  implementation was chosen over a clear_all_output function to prevent  mover A from deleting mover B's hard work!  You probably should not be  trying to call this function.  The exception:  If you want an  intermediate-output pose (not the final pose) to not have the aggregated  accessory data in the "real" Job object. elapsed_time(...) from builtins.PyCapsule elapsed_time(rosetta.protocols.jd2.Job) -> int end_time(...) from builtins.PyCapsule end_time(rosetta.protocols.jd2.Job) -> int end_timing(...) from builtins.PyCapsule end_timing(rosetta.protocols.jd2.Job) -> NoneType get_pose(...) from builtins.PyCapsule get_pose(*args, **kwargs) Overloaded function.   1. get_pose(rosetta.protocols.jd2.Job) -> rosetta.core.pose.Pose   return a COP to the input pose   2. get_pose(self : rosetta.protocols.jd2.Job,  : rosetta.core.pose.Pose) -> NoneType   in-place copy of input pose get_string_real_pairs(...) from builtins.PyCapsule get_string_real_pairs(rosetta.protocols.jd2.Job) -> rosetta.std.map_std_string_double get_string_string_pairs(...) from builtins.PyCapsule get_string_string_pairs(rosetta.protocols.jd2.Job) -> rosetta.std.map_std_string_std_string get_strings(...) from builtins.PyCapsule get_strings(rosetta.protocols.jd2.Job) -> rosetta.std.list_std_string_std_allocator_std_string_t   /////////////////////END SECTION////////////////////////////////////////////////////////////////// inner_job(...) from builtins.PyCapsule inner_job(rosetta.protocols.jd2.Job) -> protocols::jd2::InnerJob   access to inner-job ... use is discouraged - use sparingly!  --- DO NOT use my_job->inner_job()->get_pose()  INSTEAD use my_job->get_pose() inner_job_nonconst(...) from builtins.PyCapsule inner_job_nonconst(rosetta.protocols.jd2.Job) -> protocols::jd2::InnerJob   nonconst access is intended only for the JobInputter to load poses into the InnerJob, and the Parser to add constraints, and the JobDistributor to delete completed inputs (recycle memory) input_tag(...) from builtins.PyCapsule input_tag(rosetta.protocols.jd2.Job) -> str   return the input tag (a short string, generally) nstruct_index(...) from builtins.PyCapsule nstruct_index(rosetta.protocols.jd2.Job) -> int nstruct_max(...) from builtins.PyCapsule nstruct_max(rosetta.protocols.jd2.Job) -> int output_string_real_pairs_begin(...) from builtins.PyCapsule output_string_real_pairs_begin(rosetta.protocols.jd2.Job) -> std::_Rb_tree_const_iterator<std::pair<std::string const, double> > output_string_real_pairs_end(...) from builtins.PyCapsule output_string_real_pairs_end(rosetta.protocols.jd2.Job) -> std::_Rb_tree_const_iterator<std::pair<std::string const, double> > output_string_string_pairs_begin(...) from builtins.PyCapsule output_string_string_pairs_begin(rosetta.protocols.jd2.Job) -> std::_Rb_tree_const_iterator<std::pair<std::string const, std::string> > output_string_string_pairs_end(...) from builtins.PyCapsule output_string_string_pairs_end(rosetta.protocols.jd2.Job) -> std::_Rb_tree_const_iterator<std::pair<std::string const, std::string> > output_strings_begin(...) from builtins.PyCapsule output_strings_begin(rosetta.protocols.jd2.Job) -> std::_List_const_iterator<std::string>   /////////////////THIS SECTION OF FUNCTIONS IS FORBIDDEN FOR USE BY MOVERS////////////////////////////////// output_strings_end(...) from builtins.PyCapsule output_strings_end(rosetta.protocols.jd2.Job) -> std::_List_const_iterator<std::string> set_bad(...) from builtins.PyCapsule set_bad(*args, **kwargs) Overloaded function.   1. set_bad(rosetta.protocols.jd2.Job) -> NoneType   2. set_bad(self : rosetta.protocols.jd2.Job, value : bool) -> NoneType set_can_be_deleted(...) from builtins.PyCapsule set_can_be_deleted(*args, **kwargs) Overloaded function.   1. set_can_be_deleted(rosetta.protocols.jd2.Job) -> NoneType   Set whether this job can be deleted to free up memory.   2. set_can_be_deleted(self : rosetta.protocols.jd2.Job, value : bool) -> NoneType   Set whether this job can be deleted to free up memory. set_completed(...) from builtins.PyCapsule set_completed(*args, **kwargs) Overloaded function.   1. set_completed(rosetta.protocols.jd2.Job) -> NoneType   2. set_completed(self : rosetta.protocols.jd2.Job, value : bool) -> NoneType set_status_prefix(...) from builtins.PyCapsule set_status_prefix(self : rosetta.protocols.jd2.Job, prefix : str) -> NoneType start_time(...) from builtins.PyCapsule start_time(rosetta.protocols.jd2.Job) -> int start_timing(...) from builtins.PyCapsule start_timing(rosetta.protocols.jd2.Job) -> NoneType status_prefix(...) from builtins.PyCapsule status_prefix(rosetta.protocols.jd2.Job) -> str timestamp(...) from builtins.PyCapsule timestamp(rosetta.protocols.jd2.Job) -> str to_do(...) from builtins.PyCapsule to_do(rosetta.protocols.jd2.Job) -> bool   class JobDistributor(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.jd2.JobDistributor, rosetta.protocols.jd2.JobDistributor) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_batch(...) from builtins.PyCapsule add_batch(*args, **kwargs) Overloaded function.   1. add_batch(self : rosetta.protocols.jd2.JobDistributor,  : str) -> NoneType   add a new batch ( name will be interpreted as flag_file )   2. add_batch(self : rosetta.protocols.jd2.JobDistributor,  : str, id : int) -> NoneType   add a new batch ( name will be interpreted as flag_file ) assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.JobDistributor,  : rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobDistributor current_batch_id(...) from builtins.PyCapsule current_batch_id(rosetta.protocols.jd2.JobDistributor) -> int   what is the current batch number ? --- refers to position in batches_ current_job(...) from builtins.PyCapsule current_job(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.Job   Movers may ask their controlling job distributor for information about the current job.  They may also write information to this job for later output, though this use is now discouraged  as the addition of the MultiplePoseMover now means that a single job may include several  separate trajectories. current_job_id(...) from builtins.PyCapsule current_job_id(rosetta.protocols.jd2.JobDistributor) -> int   integer access - which job are we on? current_output_name(...) from builtins.PyCapsule current_output_name(rosetta.protocols.jd2.JobDistributor) -> str   Movers may ask their controlling job distributor for the output name as defined by the Job and JobOutputter. get_current_batch(...) from builtins.PyCapsule get_current_batch(rosetta.protocols.jd2.JobDistributor) -> str   what is the current batch ? --- name refers to the flag-file used for this batch get_instance(...) from builtins.PyCapsule get_instance() -> rosetta.protocols.jd2.JobDistributor go(...) from builtins.PyCapsule go(*args, **kwargs) Overloaded function.   1. go(self : rosetta.protocols.jd2.JobDistributor, mover : rosetta.protocols.moves.Mover) -> NoneType   This may be overridden by derived classes.  Default implementation invokes go_main.   2. go(self : rosetta.protocols.jd2.JobDistributor, mover : rosetta.protocols.moves.Mover, jo : protocols::jd2::JobOutputter) -> NoneType   invokes go, after setting JobOutputter   3. go(self : rosetta.protocols.jd2.JobDistributor, mover : rosetta.protocols.moves.Mover, ji : rosetta.protocols.jd2.JobInputter) -> NoneType   invokes go, after setting JobInputter   4. go(self : rosetta.protocols.jd2.JobDistributor, mover : rosetta.protocols.moves.Mover, ji : rosetta.protocols.jd2.JobInputter, jo : protocols::jd2::JobOutputter) -> NoneType   invokes go, after setting JobInputter and JobOutputter job_inputter(...) from builtins.PyCapsule job_inputter(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobInputter   JobInputter access job_inputter_input_source(...) from builtins.PyCapsule job_inputter_input_source(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobInputterInputSource.Enum   The input source for the current JobInputter. job_outputter(...) from builtins.PyCapsule job_outputter(rosetta.protocols.jd2.JobDistributor) -> protocols::jd2::JobOutputter   Movers (or derived classes) may ask for the JobOutputter mpi_finalize(...) from builtins.PyCapsule mpi_finalize(self : rosetta.protocols.jd2.JobDistributor, finalize : bool) -> NoneType   should the go() function call MPI_finalize()? It probably should, this is true by default. restart(...) from builtins.PyCapsule restart(rosetta.protocols.jd2.JobDistributor) -> NoneType set_job_inputter(...) from builtins.PyCapsule set_job_inputter(self : rosetta.protocols.jd2.JobDistributor, new_job_inputter : rosetta.protocols.jd2.JobInputter) -> NoneType   Set the JobInputter and reset the Job list -- this is not something you want to do  after go() has been called, but before it has returned. set_job_outputter(...) from builtins.PyCapsule set_job_outputter(self : rosetta.protocols.jd2.JobDistributor, new_job_outputter : protocols::jd2::JobOutputter) -> NoneType   Movers (or derived classes) may ask for the JobOutputter total_nr_jobs(...) from builtins.PyCapsule total_nr_jobs(rosetta.protocols.jd2.JobDistributor) -> int   class JobDistributorFactory(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.jd2.JobDistributorFactory) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. create_job_distributor(...) from builtins.PyCapsule create_job_distributor() -> rosetta.protocols.jd2.JobDistributor create_job_inputter(...) from builtins.PyCapsule create_job_inputter() -> rosetta.protocols.jd2.JobInputter create_job_outputter(...) from builtins.PyCapsule create_job_outputter(*args, **kwargs) Overloaded function.   1. create_job_outputter() -> rosetta.protocols.jd2.JobOutputter   2. create_job_outputter(default_jobout : rosetta.protocols.jd2.JobOutputter) -> rosetta.protocols.jd2.JobOutputter create_parser(...) from builtins.PyCapsule create_parser() -> protocols::jd2::Parser   class JobInputter(builtins.object)     The %JobInputter class is responsible for - determining what jobs exist, and - taking a job object and returning the starting pose associated with that job.     NOTE: your JobInputter should order Job objects in the Jobs vector to have as few "transitions" between inputs as possible (group all Jobs of the same input next to each other).  This improves efficiency of the "FAIL_BAD_INPUT" functionality.  I said "should", not "must" on purpose.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.jd2.JobInputter) -> NoneType   2. __init__(rosetta.protocols.jd2.JobInputter, rosetta.protocols.jd2.JobInputter) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.JobInputter,  : rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter fill_jobs(...) from builtins.PyCapsule fill_jobs(self : rosetta.protocols.jd2.JobInputter, jobs : protocols::jd2::JobsContainer) -> NoneType   this function determines what jobs exist.  This function neither knows nor  cares what jobs are already complete on disk/memory - it just figures out what  ones should exist given the input.  NOTE: your JobInputter should order Job objects  in the Jobs vector to have as few "transitions" between inputs as possible (group  all Jobs of the same input next to each other).  This improves efficiency of the  "FAIL_BAD_INPUT" functionality.  Note I (Brave Sir Steven) said "should", not "must". get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self const owning pointers.   2. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self owning pointers. get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_const_protocols_jd2_JobInputter_t   Get self const weak pointers.   2. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_protocols_jd2_JobInputter_t   Get self weak pointers. input_source(...) from builtins.PyCapsule input_source(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputterInputSource.Enum   return the type of input source that the JobInputter is currently  using job_inputter_input_source_to_string(...) from builtins.PyCapsule job_inputter_input_source_to_string(source : rosetta.protocols.jd2.JobInputterInputSource.Enum) -> str   call this with input_source() to get the input source of a  particular job inputter pose_from_job(...) from builtins.PyCapsule pose_from_job(self : rosetta.protocols.jd2.JobInputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType   this function is responsible for returning the starting pose to use for  the input job.  The Job object (within its InnerJob) contains a PoseCOP.  This function needs to either create a new Pose from the InnerJob Pose or, on  first demand of a pose from that InnerJob, instantiate the pose, hand off a COP  to the InnerJob, and fill the reference. update_jobs_list(...) from builtins.PyCapsule update_jobs_list(self : rosetta.protocols.jd2.JobInputter, jobs : protocols::jd2::JobsContainer) -> NoneType   This function is only called by certain JobInputters to update the jobs list after it has already been created.      An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back. updates_jobs_list(...) from builtins.PyCapsule updates_jobs_list(rosetta.protocols.jd2.JobInputter) -> bool   Does this type of JobInputter update the jobs list?      False by default.  Override this function in derived classes to make it true.   class JobInputterCreator(builtins.object)     Abstract base class for a JobInputter factory; the Creator class is responsible for creating a particular mover class.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.jd2.JobInputterCreator) -> NoneType   2. __init__(rosetta.protocols.jd2.JobInputterCreator, rosetta.protocols.jd2.JobInputterCreator) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.JobInputterCreator,  : rosetta.protocols.jd2.JobInputterCreator) -> rosetta.protocols.jd2.JobInputterCreator create_JobInputter(...) from builtins.PyCapsule create_JobInputter(rosetta.protocols.jd2.JobInputterCreator) -> rosetta.protocols.jd2.JobInputter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.JobInputterCreator) -> str   class JobInputterFactory(rosetta.utility.SingletonBase_protocols_jd2_JobInputterFactory_t)       Method resolution order: JobInputterFactory rosetta.utility.SingletonBase_protocols_jd2_JobInputterFactory_t builtins.object Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. factory_register(...) from builtins.PyCapsule factory_register(self : rosetta.protocols.jd2.JobInputterFactory, creator : rosetta.protocols.jd2.JobInputterCreator) -> NoneType get_new_JobInputter(...) from builtins.PyCapsule get_new_JobInputter(rosetta.protocols.jd2.JobInputterFactory) -> rosetta.protocols.jd2.JobInputter   return JobInputter defined by input parameters (contained in option system and #defines for MPI, etc) Methods inherited from rosetta.utility.SingletonBase_protocols_jd2_JobInputterFactory_t: get_instance(...) from builtins.PyCapsule get_instance() -> protocols::jd2::JobInputterFactory   class JobOutputter(builtins.object)     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.  Derived classes will be responsible for output such as PDBS, PDBS.tar.gz and silent files.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.jd2.JobOutputter) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_evaluation(...) from builtins.PyCapsule add_evaluation(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType   ////////////////////////////// evaluator interface //////////////////////////////////////////// call_output_observers(...) from builtins.PyCapsule call_output_observers(self : rosetta.protocols.jd2.JobOutputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType   call all output_observers clear_evaluators(...) from builtins.PyCapsule clear_evaluators(rosetta.protocols.jd2.JobOutputter) -> NoneType evaluate(...) from builtins.PyCapsule evaluate(self : rosetta.protocols.jd2.JobOutputter, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType evaluators(...) from builtins.PyCapsule evaluators(rosetta.protocols.jd2.JobOutputter) -> rosetta.protocols.evaluation.MetaPoseEvaluator file(...) from builtins.PyCapsule file(self : rosetta.protocols.jd2.JobOutputter, job : rosetta.protocols.jd2.Job, data : str) -> NoneType   this function takes a string and writes it to disk (separately from Tracer output).  use some sort of extention option system - default .dat?  .data? filename(...) from builtins.PyCapsule filename(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.jd2.Job) -> str final_pose(...) from builtins.PyCapsule final_pose(*args, **kwargs) Overloaded function.   1. final_pose(self : rosetta.protocols.jd2.JobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose) -> NoneType   this function outputs the final result of a job.   2. final_pose(self : rosetta.protocols.jd2.JobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   this function outputs the final result of a job. flush(...) from builtins.PyCapsule flush(rosetta.protocols.jd2.JobOutputter) -> NoneType   this function is meant to be redefined in child classes to allow for flushing of memory buffers.  Here's the long version: The SilentFileJobOutputter wanted to buffer output, but needed to guaruntee that  the output would be flushed at end of runtime.  The original implementation was to A) bend over backward to ensure  that the destructor was run (JobOutputter lives inside static JobDistributor, which was previously not destructed  because it's static) and B) flush the buffers in the destructor.  This caused a problem because the buffer-flushing  tried to use the Tracers, which had already been destructed...boom crash.    New solution: re-forbid use of destructors within the static JobDistributor system, and create a flush  function to force this stuff out.  So here it is: job_has_completed(...) from builtins.PyCapsule job_has_completed(self : rosetta.protocols.jd2.JobOutputter, job : rosetta.protocols.jd2.Job) -> bool   this function is not used for output, but it belongs here since it needs to check  the same output locations as the class normally writes to.  This class checks wherever  output goes to see if the job's expected output already exists (on disk or whatever).  This is the most basic form of checkpointing. other_pose(...) from builtins.PyCapsule other_pose(*args, **kwargs) Overloaded function.   1. other_pose(self : rosetta.protocols.jd2.JobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   this function is intended for saving mid-protocol poses; for example the final  centroid structure before the fullatom stage begins in a combined centroid / fullatom  protocol.   2. other_pose(self : rosetta.protocols.jd2.JobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str, copy_count : int) -> NoneType   this function is intended for saving mid-protocol poses; for example the final  centroid structure before the fullatom stage begins in a combined centroid / fullatom  protocol.   3. other_pose(self : rosetta.protocols.jd2.JobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str, copy_count : int, score_only : bool) -> NoneType   this function is intended for saving mid-protocol poses; for example the final  centroid structure before the fullatom stage begins in a combined centroid / fullatom  protocol. output_name(...) from builtins.PyCapsule output_name(self : rosetta.protocols.jd2.JobOutputter, job : rosetta.protocols.jd2.Job) -> str   this is the master function for determining the unique output identifier for a  job - should this be defined in the base class? set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.jd2.JobOutputter) -> NoneType set_evaluators(...) from builtins.PyCapsule set_evaluators(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType starting_pose(...) from builtins.PyCapsule starting_pose(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.core.pose.Pose) -> NoneType   optionally pass a starting (reference) pose to a JobOutputter for later comparison  purposes and/or as interface for initializing evaluators   class JobOutputterCreator(builtins.object)     Abstract base class for a JobOutputter factory; the Creator class is responsible for creating a particular mover class.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.jd2.JobOutputterCreator) -> NoneType   2. __init__(rosetta.protocols.jd2.JobOutputterCreator, rosetta.protocols.jd2.JobOutputterCreator) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.JobOutputterCreator,  : rosetta.protocols.jd2.JobOutputterCreator) -> rosetta.protocols.jd2.JobOutputterCreator create_JobOutputter(...) from builtins.PyCapsule create_JobOutputter(rosetta.protocols.jd2.JobOutputterCreator) -> rosetta.protocols.jd2.JobOutputter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.JobOutputterCreator) -> str   class JobOutputterFactory(rosetta.utility.SingletonBase_protocols_jd2_JobOutputterFactory_t)       Method resolution order: JobOutputterFactory rosetta.utility.SingletonBase_protocols_jd2_JobOutputterFactory_t builtins.object Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. factory_register(...) from builtins.PyCapsule factory_register(self : rosetta.protocols.jd2.JobOutputterFactory, creator : rosetta.protocols.jd2.JobOutputterCreator) -> NoneType get_new_JobOutputter(...) from builtins.PyCapsule get_new_JobOutputter(*args, **kwargs) Overloaded function.   1. get_new_JobOutputter(rosetta.protocols.jd2.JobOutputterFactory) -> rosetta.protocols.jd2.JobOutputter   return JobOutputter defined by output parameters (contained in option system and #defines for MPI, etc)   2. get_new_JobOutputter(self : rosetta.protocols.jd2.JobOutputterFactory, default_jobout : rosetta.protocols.jd2.JobOutputter) -> rosetta.protocols.jd2.JobOutputter   return JobOutputter defined by output parameters (contained in option system and #defines for MPI, etc).  The difference is that if the option system, etc, says nothing about output (which as of this writing defaults to PDBJobOutputter), this function leaves the input Outputter unchanged.  This allows overriding the default outputter choice in your executable (without abusing the mutability of the options system) Methods inherited from rosetta.utility.SingletonBase_protocols_jd2_JobOutputterFactory_t: get_instance(...) from builtins.PyCapsule get_instance() -> protocols::jd2::JobOutputterFactory   class JobOutputterObserver(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.jd2.JobOutputterObserver) -> NoneType   2. __init__(rosetta.protocols.jd2.JobOutputterObserver, rosetta.protocols.jd2.JobOutputterObserver) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_values_to_job(...) from builtins.PyCapsule add_values_to_job(self : rosetta.protocols.jd2.JobOutputterObserver, pose : rosetta.core.pose.Pose,  : protocols::jd2::Job) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.JobOutputterObserver,  : rosetta.protocols.jd2.JobOutputterObserver) -> rosetta.protocols.jd2.JobOutputterObserver   class JobsContainer(builtins.object)     The JobsContainer class contains a list of JobsOPs. It permits the list to be versatile -- for example, if one wishes to load only a subset of jobs into memory at any given time.     Methods defined here: __getitem__(...) from builtins.PyCapsule __getitem__(*args, **kwargs) Overloaded function.   1. __getitem__(self : rosetta.protocols.jd2.JobsContainer, index : int) -> rosetta.protocols.jd2.Job   Get a specific job, by number.      Should work even if jobs have been deleted, since this uses a  map instead of an array.   2. __getitem__(self : rosetta.protocols.jd2.JobsContainer, index : int) -> rosetta.protocols.jd2.Job   Get a specific job, by number (const-access).      Should work even if jobs have been deleted, since this uses a  map instead of an array. __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.jd2.JobsContainer) -> NoneType   2. __init__(self : rosetta.protocols.jd2.JobsContainer,  : rosetta.protocols.jd2.JobsContainer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.JobsContainer, src : rosetta.protocols.jd2.JobsContainer) -> rosetta.protocols.jd2.JobsContainer   Assignment operator. back(...) from builtins.PyCapsule back(rosetta.protocols.jd2.JobsContainer) -> rosetta.protocols.jd2.Job   Access the last element. can_be_deleted(...) from builtins.PyCapsule can_be_deleted(self : rosetta.protocols.jd2.JobsContainer, index : int) -> bool   Can the job with the given index be deleted? clear(...) from builtins.PyCapsule clear(rosetta.protocols.jd2.JobsContainer) -> NoneType   Clear the jobs list erase(...) from builtins.PyCapsule erase(self : rosetta.protocols.jd2.JobsContainer, index : int) -> NoneType   Erase an element in the jobs list force_job_purging(...) from builtins.PyCapsule force_job_purging(rosetta.protocols.jd2.JobsContainer) -> bool   Get whether or not this JobsContainer forces job purging when higher-numbered jobs are requested.      If true, and if a job inputter is used that limits the number of jobs in memory at any given time,  then when a higher job index is requested than exists in memory, the JobsContainer will force job purging  until that job exists in memory.  If false (the default), then only deletable jobs will be purged, and the  job inputter can attempt to add jobs up to the requested job (which might fail, if the requested job's number  is too high). get_loaded_job_indices(...) from builtins.PyCapsule get_loaded_job_indices(self : rosetta.protocols.jd2.JobsContainer, output : rosetta.utility.vector1_unsigned_long) -> NoneType   Get a list of job indices currently in memory.      The output vector is cleared and populated with the current job indices in memory. get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.jd2.JobsContainer) -> rosetta.protocols.jd2.JobsContainer   Get self const owning pointers.   2. get_self_ptr(rosetta.protocols.jd2.JobsContainer) -> rosetta.protocols.jd2.JobsContainer   Get self owning pointers. has_job(...) from builtins.PyCapsule has_job(self : rosetta.protocols.jd2.JobsContainer, index : int) -> bool   Does the job with the given index exist in the currently-loaded list of jobs? highest_job_index(...) from builtins.PyCapsule highest_job_index(rosetta.protocols.jd2.JobsContainer) -> int   Return the index of the highest job currently loaded in memory. push_back(...) from builtins.PyCapsule push_back(self : rosetta.protocols.jd2.JobsContainer, new_job : rosetta.protocols.jd2.Job) -> NoneType   Add a job to the list of jobs. set_all_current_jobs_as_deletable(...) from builtins.PyCapsule set_all_current_jobs_as_deletable(rosetta.protocols.jd2.JobsContainer) -> NoneType   Mark all jobs currently in memory as deletable.      This will result in all jobs being purged the next time a higher-index job is requeted. set_force_job_purging(...) from builtins.PyCapsule set_force_job_purging(*args, **kwargs) Overloaded function.   1. set_force_job_purging(rosetta.protocols.jd2.JobsContainer) -> NoneType   Set whether or not this JobsContainer forces job purging when higher-numbered jobs are requested.      If true, and if a job inputter is used that limits the number of jobs in memory at any given time,  then when a higher job index is requested than exists in memory, the JobsContainer will force job purging  until that job exists in memory.  If false (the default), then only deletable jobs will be purged, and the  job inputter can attempt to add jobs up to the requested job (which might fail, if the requested job's number  is too high).   2. set_force_job_purging(self : rosetta.protocols.jd2.JobsContainer, val : bool) -> NoneType   Set whether or not this JobsContainer forces job purging when higher-numbered jobs are requested.      If true, and if a job inputter is used that limits the number of jobs in memory at any given time,  then when a higher job index is requested than exists in memory, the JobsContainer will force job purging  until that job exists in memory.  If false (the default), then only deletable jobs will be purged, and the  job inputter can attempt to add jobs up to the requested job (which might fail, if the requested job's number  is too high). set_job_inputter(...) from builtins.PyCapsule set_job_inputter(self : rosetta.protocols.jd2.JobsContainer, jobinputter : rosetta.protocols.jd2.JobInputter) -> NoneType   Set the job inputter.      Needed if the job list is to be updated by the job inputter. set_total_jobs(...) from builtins.PyCapsule set_total_jobs(self : rosetta.protocols.jd2.JobsContainer, total_jobs : int) -> NoneType   Set the total number of jobs.      This overrides whatever the length of the joblist_ is. shuffle(...) from builtins.PyCapsule shuffle(rosetta.protocols.jd2.JobsContainer) -> NoneType   Randomize the order of elements (the map keys) size(...) from builtins.PyCapsule size(rosetta.protocols.jd2.JobsContainer) -> int   Get the total number of jobs.      Might not be the number in the joblist_ map, if we're only holding  a subset in memory at any given time.   class LargeNstructJobInputter(JobInputter)     This is an implementation of JobInputter for cases where it's not possible to list all jobs at once.     Method resolution order: LargeNstructJobInputter JobInputter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.jd2.LargeNstructJobInputter) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.LargeNstructJobInputter,  : rosetta.protocols.jd2.LargeNstructJobInputter) -> rosetta.protocols.jd2.LargeNstructJobInputter fill_jobs(...) from builtins.PyCapsule fill_jobs(self : rosetta.protocols.jd2.LargeNstructJobInputter, jobs : rosetta.protocols.jd2.JobsContainer) -> NoneType   This function determines what jobs exist.       Unlike the GenericJobInputter, this version only ever has a subset of total jobs in  memory at any given time. input_source(...) from builtins.PyCapsule input_source(rosetta.protocols.jd2.LargeNstructJobInputter) -> rosetta.protocols.jd2.JobInputterInputSource.Enum   Return the type of input source that the LargeNstructJobInputter is currently   using.      Always POSE. pose_from_job(...) from builtins.PyCapsule pose_from_job(self : rosetta.protocols.jd2.LargeNstructJobInputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType   this function is responsible for filling the pose reference with  the pose indicated by the job.  The Job object (within its InnerJob)  contains a PoseCOP.  This function needs to either fill the pose  reference from the InnerJob or, on first demand of a pose from that  InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill  the reference. update_jobs_list(...) from builtins.PyCapsule update_jobs_list(self : rosetta.protocols.jd2.LargeNstructJobInputter, jobs : rosetta.protocols.jd2.JobsContainer) -> NoneType   This function is only called by certain JobInputters to update the jobs list after it has already been created.      An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after  the first N have started to come back. updates_jobs_list(...) from builtins.PyCapsule updates_jobs_list(rosetta.protocols.jd2.LargeNstructJobInputter) -> bool   Does this type of JobInputter update the jobs list?      False by default.  Override this function in derived classes to make it true.  The LargeNstructJobInputter overrides this, and returns true. Methods inherited from JobInputter: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self const owning pointers.   2. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self owning pointers. get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_const_protocols_jd2_JobInputter_t   Get self const weak pointers.   2. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_protocols_jd2_JobInputter_t   Get self weak pointers. job_inputter_input_source_to_string(...) from builtins.PyCapsule job_inputter_input_source_to_string(source : rosetta.protocols.jd2.JobInputterInputSource.Enum) -> str   call this with input_source() to get the input source of a  particular job inputter   class LargeNstructJobInputterCreator(JobInputterCreator)       Method resolution order: LargeNstructJobInputterCreator JobInputterCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.LargeNstructJobInputterCreator,  : rosetta.protocols.jd2.LargeNstructJobInputterCreator) -> rosetta.protocols.jd2.LargeNstructJobInputterCreator create_JobInputter(...) from builtins.PyCapsule create_JobInputter(rosetta.protocols.jd2.LargeNstructJobInputterCreator) -> rosetta.protocols.jd2.JobInputter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.LargeNstructJobInputterCreator) -> str   class LazySilentFileJobInputter(JobInputter)       Method resolution order: LazySilentFileJobInputter JobInputter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.jd2.LazySilentFileJobInputter) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.LazySilentFileJobInputter,  : rosetta.protocols.jd2.LazySilentFileJobInputter) -> rosetta.protocols.jd2.LazySilentFileJobInputter fill_jobs(...) from builtins.PyCapsule fill_jobs(self : rosetta.protocols.jd2.LazySilentFileJobInputter, jobs : rosetta.protocols.jd2.JobsContainer) -> NoneType input_source(...) from builtins.PyCapsule input_source(rosetta.protocols.jd2.LazySilentFileJobInputter) -> rosetta.protocols.jd2.JobInputterInputSource.Enum pose_from_job(...) from builtins.PyCapsule pose_from_job(self : rosetta.protocols.jd2.LazySilentFileJobInputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType silent_file_data(...) from builtins.PyCapsule silent_file_data(rosetta.protocols.jd2.LazySilentFileJobInputter) -> rosetta.core.io.silent.SilentFileData struct_from_job(...) from builtins.PyCapsule struct_from_job(self : rosetta.protocols.jd2.LazySilentFileJobInputter, job : rosetta.protocols.jd2.Job) -> rosetta.core.io.silent.SilentStruct Methods inherited from JobInputter: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self const owning pointers.   2. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self owning pointers. get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_const_protocols_jd2_JobInputter_t   Get self const weak pointers.   2. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_protocols_jd2_JobInputter_t   Get self weak pointers. job_inputter_input_source_to_string(...) from builtins.PyCapsule job_inputter_input_source_to_string(source : rosetta.protocols.jd2.JobInputterInputSource.Enum) -> str   call this with input_source() to get the input source of a  particular job inputter update_jobs_list(...) from builtins.PyCapsule update_jobs_list(self : rosetta.protocols.jd2.JobInputter, jobs : protocols::jd2::JobsContainer) -> NoneType   This function is only called by certain JobInputters to update the jobs list after it has already been created.      An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back. updates_jobs_list(...) from builtins.PyCapsule updates_jobs_list(rosetta.protocols.jd2.JobInputter) -> bool   Does this type of JobInputter update the jobs list?      False by default.  Override this function in derived classes to make it true.   class LazySilentFileJobInputterCreator(JobInputterCreator)       Method resolution order: LazySilentFileJobInputterCreator JobInputterCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.LazySilentFileJobInputterCreator,  : rosetta.protocols.jd2.LazySilentFileJobInputterCreator) -> rosetta.protocols.jd2.LazySilentFileJobInputterCreator create_JobInputter(...) from builtins.PyCapsule create_JobInputter(rosetta.protocols.jd2.LazySilentFileJobInputterCreator) -> rosetta.protocols.jd2.JobInputter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.LazySilentFileJobInputterCreator) -> str   class MPIFileBufJobDistributor(JobDistributor)     This JobDistributor is intended for machines where you have a large number of processors. two dedicated processes are used to handle JobDistribution and File-IO. all other processes (higher rank ) are used for computation. the file_buf_rank_ process runs the MpiFileBuffer which is at the receiving end of all ozstream output that is rerouted via MPI from the slave nodes. This means all slaves write to the same file without FileSystem congestion and interlacing in the file -- IO is handled from a single dedicated process The other dedicated process (master_rank) runs the actual JobDistributor and is only used to distribute jobs to slaves and receive their notification of successful or failed execution in case you have only a small number of processors you can put say 10 MPI processes on 8 processors to get optimal CPU usage.     Method resolution order: MPIFileBufJobDistributor JobDistributor builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle, rosetta.protocols.jd2.MPIFileBufJobDistributor) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. get_new_job_id(...) from builtins.PyCapsule get_new_job_id(rosetta.protocols.jd2.MPIFileBufJobDistributor) -> int   dummy for master/slave version go(...) from builtins.PyCapsule go(self : rosetta.protocols.jd2.MPIFileBufJobDistributor, mover : rosetta.protocols.moves.Mover) -> NoneType   dummy for master/slave version increment_client_rank(...) from builtins.PyCapsule increment_client_rank(rosetta.protocols.jd2.MPIFileBufJobDistributor) -> int job_failed(...) from builtins.PyCapsule job_failed(self : rosetta.protocols.jd2.MPIFileBufJobDistributor, pose : rosetta.core.pose.Pose, will_retry : bool) -> NoneType job_succeeded(...) from builtins.PyCapsule job_succeeded(self : rosetta.protocols.jd2.MPIFileBufJobDistributor, pose : rosetta.core.pose.Pose, runtime : float, tag : str) -> NoneType   dummy for master/slave version mark_current_job_id_for_repetition(...) from builtins.PyCapsule mark_current_job_id_for_repetition(rosetta.protocols.jd2.MPIFileBufJobDistributor) -> NoneType   dummy for master/slave version min_client_rank(...) from builtins.PyCapsule min_client_rank(rosetta.protocols.jd2.MPIFileBufJobDistributor) -> int   return rank of first worker process (there might be more dedicated processes, e.g., ArchiveManager...) remove_bad_inputs_from_job_list(...) from builtins.PyCapsule remove_bad_inputs_from_job_list(rosetta.protocols.jd2.MPIFileBufJobDistributor) -> NoneType   dummy for master/slave version Methods inherited from JobDistributor: add_batch(...) from builtins.PyCapsule add_batch(*args, **kwargs) Overloaded function.   1. add_batch(self : rosetta.protocols.jd2.JobDistributor,  : str) -> NoneType   add a new batch ( name will be interpreted as flag_file )   2. add_batch(self : rosetta.protocols.jd2.JobDistributor,  : str, id : int) -> NoneType   add a new batch ( name will be interpreted as flag_file ) assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.JobDistributor,  : rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobDistributor current_batch_id(...) from builtins.PyCapsule current_batch_id(rosetta.protocols.jd2.JobDistributor) -> int   what is the current batch number ? --- refers to position in batches_ current_job(...) from builtins.PyCapsule current_job(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.Job   Movers may ask their controlling job distributor for information about the current job.  They may also write information to this job for later output, though this use is now discouraged  as the addition of the MultiplePoseMover now means that a single job may include several  separate trajectories. current_job_id(...) from builtins.PyCapsule current_job_id(rosetta.protocols.jd2.JobDistributor) -> int   integer access - which job are we on? current_output_name(...) from builtins.PyCapsule current_output_name(rosetta.protocols.jd2.JobDistributor) -> str   Movers may ask their controlling job distributor for the output name as defined by the Job and JobOutputter. get_current_batch(...) from builtins.PyCapsule get_current_batch(rosetta.protocols.jd2.JobDistributor) -> str   what is the current batch ? --- name refers to the flag-file used for this batch get_instance(...) from builtins.PyCapsule get_instance() -> rosetta.protocols.jd2.JobDistributor job_inputter(...) from builtins.PyCapsule job_inputter(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobInputter   JobInputter access job_inputter_input_source(...) from builtins.PyCapsule job_inputter_input_source(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobInputterInputSource.Enum   The input source for the current JobInputter. job_outputter(...) from builtins.PyCapsule job_outputter(rosetta.protocols.jd2.JobDistributor) -> protocols::jd2::JobOutputter   Movers (or derived classes) may ask for the JobOutputter mpi_finalize(...) from builtins.PyCapsule mpi_finalize(self : rosetta.protocols.jd2.JobDistributor, finalize : bool) -> NoneType   should the go() function call MPI_finalize()? It probably should, this is true by default. restart(...) from builtins.PyCapsule restart(rosetta.protocols.jd2.JobDistributor) -> NoneType set_job_inputter(...) from builtins.PyCapsule set_job_inputter(self : rosetta.protocols.jd2.JobDistributor, new_job_inputter : rosetta.protocols.jd2.JobInputter) -> NoneType   Set the JobInputter and reset the Job list -- this is not something you want to do  after go() has been called, but before it has returned. set_job_outputter(...) from builtins.PyCapsule set_job_outputter(self : rosetta.protocols.jd2.JobDistributor, new_job_outputter : protocols::jd2::JobOutputter) -> NoneType   Movers (or derived classes) may ask for the JobOutputter total_nr_jobs(...) from builtins.PyCapsule total_nr_jobs(rosetta.protocols.jd2.JobDistributor) -> int   class MPIMultiCommJobDistributor(MPIFileBufJobDistributor)     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. (2 processes for central JD2 and MPIFileBuf ) derived from MPIFileBufJobDistributor: two dedicated processes are used to handle JobDistribution and File-IO. all other processes (higher rank ) are used for computation.     Method resolution order: MPIMultiCommJobDistributor MPIFileBufJobDistributor JobDistributor builtins.object Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. get_new_job_id(...) from builtins.PyCapsule get_new_job_id(rosetta.protocols.jd2.MPIMultiCommJobDistributor) -> int   dummy for master/slave version job_failed(...) from builtins.PyCapsule job_failed(self : rosetta.protocols.jd2.MPIMultiCommJobDistributor, pose : rosetta.core.pose.Pose,  : bool) -> NoneType   overloaded to suppress message from higher-rank replicas job_succeeded(...) from builtins.PyCapsule job_succeeded(self : rosetta.protocols.jd2.MPIMultiCommJobDistributor, pose : rosetta.core.pose.Pose, run_timei : float, tag : str) -> NoneType   overloaded to suppress message from higher-rank replicas sub_rank(...) from builtins.PyCapsule sub_rank(rosetta.protocols.jd2.MPIMultiCommJobDistributor) -> int Methods inherited from MPIFileBufJobDistributor: go(...) from builtins.PyCapsule go(self : rosetta.protocols.jd2.MPIFileBufJobDistributor, mover : rosetta.protocols.moves.Mover) -> NoneType   dummy for master/slave version increment_client_rank(...) from builtins.PyCapsule increment_client_rank(rosetta.protocols.jd2.MPIFileBufJobDistributor) -> int mark_current_job_id_for_repetition(...) from builtins.PyCapsule mark_current_job_id_for_repetition(rosetta.protocols.jd2.MPIFileBufJobDistributor) -> NoneType   dummy for master/slave version min_client_rank(...) from builtins.PyCapsule min_client_rank(rosetta.protocols.jd2.MPIFileBufJobDistributor) -> int   return rank of first worker process (there might be more dedicated processes, e.g., ArchiveManager...) remove_bad_inputs_from_job_list(...) from builtins.PyCapsule remove_bad_inputs_from_job_list(rosetta.protocols.jd2.MPIFileBufJobDistributor) -> NoneType   dummy for master/slave version Methods inherited from JobDistributor: add_batch(...) from builtins.PyCapsule add_batch(*args, **kwargs) Overloaded function.   1. add_batch(self : rosetta.protocols.jd2.JobDistributor,  : str) -> NoneType   add a new batch ( name will be interpreted as flag_file )   2. add_batch(self : rosetta.protocols.jd2.JobDistributor,  : str, id : int) -> NoneType   add a new batch ( name will be interpreted as flag_file ) assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.JobDistributor,  : rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobDistributor current_batch_id(...) from builtins.PyCapsule current_batch_id(rosetta.protocols.jd2.JobDistributor) -> int   what is the current batch number ? --- refers to position in batches_ current_job(...) from builtins.PyCapsule current_job(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.Job   Movers may ask their controlling job distributor for information about the current job.  They may also write information to this job for later output, though this use is now discouraged  as the addition of the MultiplePoseMover now means that a single job may include several  separate trajectories. current_job_id(...) from builtins.PyCapsule current_job_id(rosetta.protocols.jd2.JobDistributor) -> int   integer access - which job are we on? current_output_name(...) from builtins.PyCapsule current_output_name(rosetta.protocols.jd2.JobDistributor) -> str   Movers may ask their controlling job distributor for the output name as defined by the Job and JobOutputter. get_current_batch(...) from builtins.PyCapsule get_current_batch(rosetta.protocols.jd2.JobDistributor) -> str   what is the current batch ? --- name refers to the flag-file used for this batch get_instance(...) from builtins.PyCapsule get_instance() -> rosetta.protocols.jd2.JobDistributor job_inputter(...) from builtins.PyCapsule job_inputter(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobInputter   JobInputter access job_inputter_input_source(...) from builtins.PyCapsule job_inputter_input_source(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobInputterInputSource.Enum   The input source for the current JobInputter. job_outputter(...) from builtins.PyCapsule job_outputter(rosetta.protocols.jd2.JobDistributor) -> protocols::jd2::JobOutputter   Movers (or derived classes) may ask for the JobOutputter mpi_finalize(...) from builtins.PyCapsule mpi_finalize(self : rosetta.protocols.jd2.JobDistributor, finalize : bool) -> NoneType   should the go() function call MPI_finalize()? It probably should, this is true by default. restart(...) from builtins.PyCapsule restart(rosetta.protocols.jd2.JobDistributor) -> NoneType set_job_inputter(...) from builtins.PyCapsule set_job_inputter(self : rosetta.protocols.jd2.JobDistributor, new_job_inputter : rosetta.protocols.jd2.JobInputter) -> NoneType   Set the JobInputter and reset the Job list -- this is not something you want to do  after go() has been called, but before it has returned. set_job_outputter(...) from builtins.PyCapsule set_job_outputter(self : rosetta.protocols.jd2.JobDistributor, new_job_outputter : protocols::jd2::JobOutputter) -> NoneType   Movers (or derived classes) may ask for the JobOutputter total_nr_jobs(...) from builtins.PyCapsule total_nr_jobs(rosetta.protocols.jd2.JobDistributor) -> int   class MPIWorkPartitionJobDistributor(JobDistributor)     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). It will blindly divide up jobs across processors and then start running them; it will NOT attempt load-balancing by giving more jobs to the processors that finished their original jobs.  This is intended for use on smaller numbers of processors, and/or where the jobs are known to be equal in runtime.  (The WorkPool implementation is meant for when runtimes are uncertain, or you have many many processors). It does not "waste" a processor as a master node, instead all processors run jobs.     Method resolution order: MPIWorkPartitionJobDistributor JobDistributor builtins.object Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.MPIWorkPartitionJobDistributor,  : rosetta.protocols.jd2.MPIWorkPartitionJobDistributor) -> rosetta.protocols.jd2.MPIWorkPartitionJobDistributor get_new_job_id(...) from builtins.PyCapsule get_new_job_id(rosetta.protocols.jd2.MPIWorkPartitionJobDistributor) -> int go(...) from builtins.PyCapsule go(self : rosetta.protocols.jd2.MPIWorkPartitionJobDistributor, mover : rosetta.protocols.moves.Mover) -> NoneType mark_current_job_id_for_repetition(...) from builtins.PyCapsule mark_current_job_id_for_repetition(rosetta.protocols.jd2.MPIWorkPartitionJobDistributor) -> NoneType remove_bad_inputs_from_job_list(...) from builtins.PyCapsule remove_bad_inputs_from_job_list(rosetta.protocols.jd2.MPIWorkPartitionJobDistributor) -> NoneType Methods inherited from JobDistributor: add_batch(...) from builtins.PyCapsule add_batch(*args, **kwargs) Overloaded function.   1. add_batch(self : rosetta.protocols.jd2.JobDistributor,  : str) -> NoneType   add a new batch ( name will be interpreted as flag_file )   2. add_batch(self : rosetta.protocols.jd2.JobDistributor,  : str, id : int) -> NoneType   add a new batch ( name will be interpreted as flag_file ) current_batch_id(...) from builtins.PyCapsule current_batch_id(rosetta.protocols.jd2.JobDistributor) -> int   what is the current batch number ? --- refers to position in batches_ current_job(...) from builtins.PyCapsule current_job(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.Job   Movers may ask their controlling job distributor for information about the current job.  They may also write information to this job for later output, though this use is now discouraged  as the addition of the MultiplePoseMover now means that a single job may include several  separate trajectories. current_job_id(...) from builtins.PyCapsule current_job_id(rosetta.protocols.jd2.JobDistributor) -> int   integer access - which job are we on? current_output_name(...) from builtins.PyCapsule current_output_name(rosetta.protocols.jd2.JobDistributor) -> str   Movers may ask their controlling job distributor for the output name as defined by the Job and JobOutputter. get_current_batch(...) from builtins.PyCapsule get_current_batch(rosetta.protocols.jd2.JobDistributor) -> str   what is the current batch ? --- name refers to the flag-file used for this batch get_instance(...) from builtins.PyCapsule get_instance() -> rosetta.protocols.jd2.JobDistributor job_inputter(...) from builtins.PyCapsule job_inputter(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobInputter   JobInputter access job_inputter_input_source(...) from builtins.PyCapsule job_inputter_input_source(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobInputterInputSource.Enum   The input source for the current JobInputter. job_outputter(...) from builtins.PyCapsule job_outputter(rosetta.protocols.jd2.JobDistributor) -> protocols::jd2::JobOutputter   Movers (or derived classes) may ask for the JobOutputter mpi_finalize(...) from builtins.PyCapsule mpi_finalize(self : rosetta.protocols.jd2.JobDistributor, finalize : bool) -> NoneType   should the go() function call MPI_finalize()? It probably should, this is true by default. restart(...) from builtins.PyCapsule restart(rosetta.protocols.jd2.JobDistributor) -> NoneType set_job_inputter(...) from builtins.PyCapsule set_job_inputter(self : rosetta.protocols.jd2.JobDistributor, new_job_inputter : rosetta.protocols.jd2.JobInputter) -> NoneType   Set the JobInputter and reset the Job list -- this is not something you want to do  after go() has been called, but before it has returned. set_job_outputter(...) from builtins.PyCapsule set_job_outputter(self : rosetta.protocols.jd2.JobDistributor, new_job_outputter : protocols::jd2::JobOutputter) -> NoneType   Movers (or derived classes) may ask for the JobOutputter total_nr_jobs(...) from builtins.PyCapsule total_nr_jobs(rosetta.protocols.jd2.JobDistributor) -> int   class MPIWorkPoolJobDistributor(JobDistributor)     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. It dedicates the head node (whichever processor gets processor rank #0) to handling job requests from the slave nodes (all nonzero ranks). Unlike the MPIWorkPartitionJobDistributor, this JD will not work at all without MPI and the implementations of all but the interface functions have been put inside of ifdef directives. Generally each function has a master and slave version, and the interface functions call one or the other depending on processor rank.     Method resolution order: MPIWorkPoolJobDistributor JobDistributor builtins.object Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.MPIWorkPoolJobDistributor,  : rosetta.protocols.jd2.MPIWorkPoolJobDistributor) -> rosetta.protocols.jd2.MPIWorkPoolJobDistributor get_new_job_id(...) from builtins.PyCapsule get_new_job_id(rosetta.protocols.jd2.MPIWorkPoolJobDistributor) -> int   dummy for master/slave version go(...) from builtins.PyCapsule go(self : rosetta.protocols.jd2.MPIWorkPoolJobDistributor, mover : rosetta.protocols.moves.Mover) -> NoneType   dummy for master/slave version job_failed(...) from builtins.PyCapsule job_failed(self : rosetta.protocols.jd2.MPIWorkPoolJobDistributor, pose : rosetta.core.pose.Pose, will_retry : bool) -> NoneType   Called if job fails. job_succeeded(...) from builtins.PyCapsule job_succeeded(self : rosetta.protocols.jd2.MPIWorkPoolJobDistributor, pose : rosetta.core.pose.Pose, run_time : float, tag : str) -> NoneType   dummy for master/slave version mark_current_job_id_for_repetition(...) from builtins.PyCapsule mark_current_job_id_for_repetition(rosetta.protocols.jd2.MPIWorkPoolJobDistributor) -> NoneType   dummy for master/slave version mpi_finalize(...) from builtins.PyCapsule mpi_finalize(self : rosetta.protocols.jd2.MPIWorkPoolJobDistributor, finalize : bool) -> NoneType   should the go() function call MPI_finalize()? It probably should, this is true by default. remove_bad_inputs_from_job_list(...) from builtins.PyCapsule remove_bad_inputs_from_job_list(rosetta.protocols.jd2.MPIWorkPoolJobDistributor) -> NoneType   dummy for master/slave version Methods inherited from JobDistributor: add_batch(...) from builtins.PyCapsule add_batch(*args, **kwargs) Overloaded function.   1. add_batch(self : rosetta.protocols.jd2.JobDistributor,  : str) -> NoneType   add a new batch ( name will be interpreted as flag_file )   2. add_batch(self : rosetta.protocols.jd2.JobDistributor,  : str, id : int) -> NoneType   add a new batch ( name will be interpreted as flag_file ) current_batch_id(...) from builtins.PyCapsule current_batch_id(rosetta.protocols.jd2.JobDistributor) -> int   what is the current batch number ? --- refers to position in batches_ current_job(...) from builtins.PyCapsule current_job(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.Job   Movers may ask their controlling job distributor for information about the current job.  They may also write information to this job for later output, though this use is now discouraged  as the addition of the MultiplePoseMover now means that a single job may include several  separate trajectories. current_job_id(...) from builtins.PyCapsule current_job_id(rosetta.protocols.jd2.JobDistributor) -> int   integer access - which job are we on? current_output_name(...) from builtins.PyCapsule current_output_name(rosetta.protocols.jd2.JobDistributor) -> str   Movers may ask their controlling job distributor for the output name as defined by the Job and JobOutputter. get_current_batch(...) from builtins.PyCapsule get_current_batch(rosetta.protocols.jd2.JobDistributor) -> str   what is the current batch ? --- name refers to the flag-file used for this batch get_instance(...) from builtins.PyCapsule get_instance() -> rosetta.protocols.jd2.JobDistributor job_inputter(...) from builtins.PyCapsule job_inputter(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobInputter   JobInputter access job_inputter_input_source(...) from builtins.PyCapsule job_inputter_input_source(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobInputterInputSource.Enum   The input source for the current JobInputter. job_outputter(...) from builtins.PyCapsule job_outputter(rosetta.protocols.jd2.JobDistributor) -> protocols::jd2::JobOutputter   Movers (or derived classes) may ask for the JobOutputter restart(...) from builtins.PyCapsule restart(rosetta.protocols.jd2.JobDistributor) -> NoneType set_job_inputter(...) from builtins.PyCapsule set_job_inputter(self : rosetta.protocols.jd2.JobDistributor, new_job_inputter : rosetta.protocols.jd2.JobInputter) -> NoneType   Set the JobInputter and reset the Job list -- this is not something you want to do  after go() has been called, but before it has returned. set_job_outputter(...) from builtins.PyCapsule set_job_outputter(self : rosetta.protocols.jd2.JobDistributor, new_job_outputter : protocols::jd2::JobOutputter) -> NoneType   Movers (or derived classes) may ask for the JobOutputter total_nr_jobs(...) from builtins.PyCapsule total_nr_jobs(rosetta.protocols.jd2.JobDistributor) -> int   class MSDJobDistributor(JobDistributor)       Method resolution order: MSDJobDistributor JobDistributor builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.MSDJobDistributor,  : rosetta.protocols.jd2.MSDJobDistributor) -> rosetta.protocols.jd2.MSDJobDistributor current_job(...) from builtins.PyCapsule current_job(rosetta.protocols.jd2.MSDJobDistributor) -> rosetta.protocols.jd2.Job get_new_job_id(...) from builtins.PyCapsule get_new_job_id(rosetta.protocols.jd2.MSDJobDistributor) -> int go(...) from builtins.PyCapsule go(self : rosetta.protocols.jd2.MSDJobDistributor, mover : rosetta.protocols.moves.Mover) -> NoneType handle_interrupt(...) from builtins.PyCapsule handle_interrupt(rosetta.protocols.jd2.MSDJobDistributor) -> NoneType job_failed(...) from builtins.PyCapsule job_failed(self : rosetta.protocols.jd2.MSDJobDistributor,  : rosetta.core.pose.Pose,  : bool) -> NoneType mark_current_job_id_for_repetition(...) from builtins.PyCapsule mark_current_job_id_for_repetition(rosetta.protocols.jd2.MSDJobDistributor) -> NoneType Methods inherited from JobDistributor: add_batch(...) from builtins.PyCapsule add_batch(*args, **kwargs) Overloaded function.   1. add_batch(self : rosetta.protocols.jd2.JobDistributor,  : str) -> NoneType   add a new batch ( name will be interpreted as flag_file )   2. add_batch(self : rosetta.protocols.jd2.JobDistributor,  : str, id : int) -> NoneType   add a new batch ( name will be interpreted as flag_file ) current_batch_id(...) from builtins.PyCapsule current_batch_id(rosetta.protocols.jd2.JobDistributor) -> int   what is the current batch number ? --- refers to position in batches_ current_job_id(...) from builtins.PyCapsule current_job_id(rosetta.protocols.jd2.JobDistributor) -> int   integer access - which job are we on? current_output_name(...) from builtins.PyCapsule current_output_name(rosetta.protocols.jd2.JobDistributor) -> str   Movers may ask their controlling job distributor for the output name as defined by the Job and JobOutputter. get_current_batch(...) from builtins.PyCapsule get_current_batch(rosetta.protocols.jd2.JobDistributor) -> str   what is the current batch ? --- name refers to the flag-file used for this batch get_instance(...) from builtins.PyCapsule get_instance() -> rosetta.protocols.jd2.JobDistributor job_inputter(...) from builtins.PyCapsule job_inputter(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobInputter   JobInputter access job_inputter_input_source(...) from builtins.PyCapsule job_inputter_input_source(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobInputterInputSource.Enum   The input source for the current JobInputter. job_outputter(...) from builtins.PyCapsule job_outputter(rosetta.protocols.jd2.JobDistributor) -> protocols::jd2::JobOutputter   Movers (or derived classes) may ask for the JobOutputter mpi_finalize(...) from builtins.PyCapsule mpi_finalize(self : rosetta.protocols.jd2.JobDistributor, finalize : bool) -> NoneType   should the go() function call MPI_finalize()? It probably should, this is true by default. restart(...) from builtins.PyCapsule restart(rosetta.protocols.jd2.JobDistributor) -> NoneType set_job_inputter(...) from builtins.PyCapsule set_job_inputter(self : rosetta.protocols.jd2.JobDistributor, new_job_inputter : rosetta.protocols.jd2.JobInputter) -> NoneType   Set the JobInputter and reset the Job list -- this is not something you want to do  after go() has been called, but before it has returned. set_job_outputter(...) from builtins.PyCapsule set_job_outputter(self : rosetta.protocols.jd2.JobDistributor, new_job_outputter : protocols::jd2::JobOutputter) -> NoneType   Movers (or derived classes) may ask for the JobOutputter total_nr_jobs(...) from builtins.PyCapsule total_nr_jobs(rosetta.protocols.jd2.JobDistributor) -> int   class MpiFileBuffer(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.jd2.MpiFileBuffer, file_buf_rank_ : int) -> NoneType   2. __init__(rosetta.protocols.jd2.MpiFileBuffer, rosetta.protocols.jd2.MpiFileBuffer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.MpiFileBuffer,  : rosetta.protocols.jd2.MpiFileBuffer) -> rosetta.protocols.jd2.MpiFileBuffer block_file(...) from builtins.PyCapsule block_file(self : rosetta.protocols.jd2.MpiFileBuffer, filename : str) -> NoneType close_file(...) from builtins.PyCapsule close_file(self : rosetta.protocols.jd2.MpiFileBuffer, fname : str) -> bool garbage_collection(...) from builtins.PyCapsule garbage_collection(rosetta.protocols.jd2.MpiFileBuffer) -> NoneType release_file(...) from builtins.PyCapsule release_file(self : rosetta.protocols.jd2.MpiFileBuffer, filename : str) -> NoneType run(...) from builtins.PyCapsule run(rosetta.protocols.jd2.MpiFileBuffer) -> NoneType set_SlaveCanOpenFile(...) from builtins.PyCapsule set_SlaveCanOpenFile(*args, **kwargs) Overloaded function.   1. set_SlaveCanOpenFile(rosetta.protocols.jd2.MpiFileBuffer) -> NoneType   2. set_SlaveCanOpenFile(self : rosetta.protocols.jd2.MpiFileBuffer, setting : bool) -> NoneType stop(...) from builtins.PyCapsule stop(rosetta.protocols.jd2.MpiFileBuffer) -> NoneType   class MultiThreadingJob(Job)       Method resolution order: MultiThreadingJob Job builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle, rosetta.protocols.jd2.MultiThreadingJob) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. multi_threading_inner_job(...) from builtins.PyCapsule multi_threading_inner_job(rosetta.protocols.jd2.MultiThreadingJob) -> rosetta.protocols.jd2.InnerMultiThreadingJob Methods inherited from Job: __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.jd2.Job) -> str add_string(...) from builtins.PyCapsule add_string(self : rosetta.protocols.jd2.Job, string_in : str) -> NoneType   add an output string add_string_real_pair(...) from builtins.PyCapsule add_string_real_pair(self : rosetta.protocols.jd2.Job, string_in : str, real_in : float) -> NoneType   add a string/real pair add_string_string_pair(...) from builtins.PyCapsule add_string_string_pair(self : rosetta.protocols.jd2.Job, string1 : str, string2 : str) -> NoneType   add a string/string pair add_strings(...) from builtins.PyCapsule add_strings(self : rosetta.protocols.jd2.Job,  : rosetta.std.list_std_string_std_allocator_std_string_t) -> NoneType   add output strings bad(...) from builtins.PyCapsule bad(rosetta.protocols.jd2.Job) -> bool call_output_observers(...) from builtins.PyCapsule call_output_observers(self : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose) -> NoneType can_be_deleted(...) from builtins.PyCapsule can_be_deleted(rosetta.protocols.jd2.Job) -> bool   Returns true iff this job can be deleted to free up memory.      Should only be true if the job has completed, is bad, or has failed. clear_output(...) from builtins.PyCapsule clear_output(rosetta.protocols.jd2.Job) -> NoneType   Delete the output strings, string/string pairs, and string/real pairs. clone(...) from builtins.PyCapsule clone(rosetta.protocols.jd2.Job) -> rosetta.protocols.jd2.Job   Return an owning pointer to a copy of this object. completed(...) from builtins.PyCapsule completed(rosetta.protocols.jd2.Job) -> bool copy_without_output(...) from builtins.PyCapsule copy_without_output(rosetta.protocols.jd2.Job) -> rosetta.protocols.jd2.Job   returns a copy of this object whose "output fields" are zeroed  out.  Used by the JobDistributor in cases where the job fails and must be  retried to prevent accumulation of Job state after a failure.  This  implementation was chosen over a clear_all_output function to prevent  mover A from deleting mover B's hard work!  You probably should not be  trying to call this function.  The exception:  If you want an  intermediate-output pose (not the final pose) to not have the aggregated  accessory data in the "real" Job object. elapsed_time(...) from builtins.PyCapsule elapsed_time(rosetta.protocols.jd2.Job) -> int end_time(...) from builtins.PyCapsule end_time(rosetta.protocols.jd2.Job) -> int end_timing(...) from builtins.PyCapsule end_timing(rosetta.protocols.jd2.Job) -> NoneType get_pose(...) from builtins.PyCapsule get_pose(*args, **kwargs) Overloaded function.   1. get_pose(rosetta.protocols.jd2.Job) -> rosetta.core.pose.Pose   return a COP to the input pose   2. get_pose(self : rosetta.protocols.jd2.Job,  : rosetta.core.pose.Pose) -> NoneType   in-place copy of input pose get_string_real_pairs(...) from builtins.PyCapsule get_string_real_pairs(rosetta.protocols.jd2.Job) -> rosetta.std.map_std_string_double get_string_string_pairs(...) from builtins.PyCapsule get_string_string_pairs(rosetta.protocols.jd2.Job) -> rosetta.std.map_std_string_std_string get_strings(...) from builtins.PyCapsule get_strings(rosetta.protocols.jd2.Job) -> rosetta.std.list_std_string_std_allocator_std_string_t   /////////////////////END SECTION////////////////////////////////////////////////////////////////// inner_job(...) from builtins.PyCapsule inner_job(rosetta.protocols.jd2.Job) -> protocols::jd2::InnerJob   access to inner-job ... use is discouraged - use sparingly!  --- DO NOT use my_job->inner_job()->get_pose()  INSTEAD use my_job->get_pose() inner_job_nonconst(...) from builtins.PyCapsule inner_job_nonconst(rosetta.protocols.jd2.Job) -> protocols::jd2::InnerJob   nonconst access is intended only for the JobInputter to load poses into the InnerJob, and the Parser to add constraints, and the JobDistributor to delete completed inputs (recycle memory) input_tag(...) from builtins.PyCapsule input_tag(rosetta.protocols.jd2.Job) -> str   return the input tag (a short string, generally) nstruct_index(...) from builtins.PyCapsule nstruct_index(rosetta.protocols.jd2.Job) -> int nstruct_max(...) from builtins.PyCapsule nstruct_max(rosetta.protocols.jd2.Job) -> int output_string_real_pairs_begin(...) from builtins.PyCapsule output_string_real_pairs_begin(rosetta.protocols.jd2.Job) -> std::_Rb_tree_const_iterator<std::pair<std::string const, double> > output_string_real_pairs_end(...) from builtins.PyCapsule output_string_real_pairs_end(rosetta.protocols.jd2.Job) -> std::_Rb_tree_const_iterator<std::pair<std::string const, double> > output_string_string_pairs_begin(...) from builtins.PyCapsule output_string_string_pairs_begin(rosetta.protocols.jd2.Job) -> std::_Rb_tree_const_iterator<std::pair<std::string const, std::string> > output_string_string_pairs_end(...) from builtins.PyCapsule output_string_string_pairs_end(rosetta.protocols.jd2.Job) -> std::_Rb_tree_const_iterator<std::pair<std::string const, std::string> > output_strings_begin(...) from builtins.PyCapsule output_strings_begin(rosetta.protocols.jd2.Job) -> std::_List_const_iterator<std::string>   /////////////////THIS SECTION OF FUNCTIONS IS FORBIDDEN FOR USE BY MOVERS////////////////////////////////// output_strings_end(...) from builtins.PyCapsule output_strings_end(rosetta.protocols.jd2.Job) -> std::_List_const_iterator<std::string> set_bad(...) from builtins.PyCapsule set_bad(*args, **kwargs) Overloaded function.   1. set_bad(rosetta.protocols.jd2.Job) -> NoneType   2. set_bad(self : rosetta.protocols.jd2.Job, value : bool) -> NoneType set_can_be_deleted(...) from builtins.PyCapsule set_can_be_deleted(*args, **kwargs) Overloaded function.   1. set_can_be_deleted(rosetta.protocols.jd2.Job) -> NoneType   Set whether this job can be deleted to free up memory.   2. set_can_be_deleted(self : rosetta.protocols.jd2.Job, value : bool) -> NoneType   Set whether this job can be deleted to free up memory. set_completed(...) from builtins.PyCapsule set_completed(*args, **kwargs) Overloaded function.   1. set_completed(rosetta.protocols.jd2.Job) -> NoneType   2. set_completed(self : rosetta.protocols.jd2.Job, value : bool) -> NoneType set_status_prefix(...) from builtins.PyCapsule set_status_prefix(self : rosetta.protocols.jd2.Job, prefix : str) -> NoneType start_time(...) from builtins.PyCapsule start_time(rosetta.protocols.jd2.Job) -> int start_timing(...) from builtins.PyCapsule start_timing(rosetta.protocols.jd2.Job) -> NoneType status_prefix(...) from builtins.PyCapsule status_prefix(rosetta.protocols.jd2.Job) -> str timestamp(...) from builtins.PyCapsule timestamp(rosetta.protocols.jd2.Job) -> str to_do(...) from builtins.PyCapsule to_do(rosetta.protocols.jd2.Job) -> bool   class NoOutputJobOutputter(JobOutputter)     the NoOutputJobOutputter class is responsible for NOT dealing with output     Method resolution order: NoOutputJobOutputter JobOutputter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. file(...) from builtins.PyCapsule file(self : rosetta.protocols.jd2.NoOutputJobOutputter,  : rosetta.protocols.jd2.Job,  : str) -> NoneType   this function takes a string and writes it to disk (separately from Tracer output). use some sort of extention option system - default .dat?  .data? final_pose(...) from builtins.PyCapsule final_pose(self : rosetta.protocols.jd2.NoOutputJobOutputter,  : rosetta.protocols.jd2.Job,  : rosetta.core.pose.Pose,  : str) -> NoneType   this function outputs the final result of a job. job_has_completed(...) from builtins.PyCapsule job_has_completed(self : rosetta.protocols.jd2.NoOutputJobOutputter,  : rosetta.protocols.jd2.Job) -> bool   this function is not used for output, but it belongs here since it needs to check the same output locations as the class normally writes to.  This class checks wherever output goes to see if the job's expected output already exists (on disk or whatever).  This is the most basic form of checkpointing. other_pose(...) from builtins.PyCapsule other_pose(self : rosetta.protocols.jd2.NoOutputJobOutputter,  : rosetta.protocols.jd2.Job,  : rosetta.core.pose.Pose,  : str,  : int,  : bool) -> NoneType   this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. output_name(...) from builtins.PyCapsule output_name(self : rosetta.protocols.jd2.NoOutputJobOutputter, job : rosetta.protocols.jd2.Job) -> str Methods inherited from JobOutputter: add_evaluation(...) from builtins.PyCapsule add_evaluation(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType   ////////////////////////////// evaluator interface //////////////////////////////////////////// call_output_observers(...) from builtins.PyCapsule call_output_observers(self : rosetta.protocols.jd2.JobOutputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType   call all output_observers clear_evaluators(...) from builtins.PyCapsule clear_evaluators(rosetta.protocols.jd2.JobOutputter) -> NoneType evaluate(...) from builtins.PyCapsule evaluate(self : rosetta.protocols.jd2.JobOutputter, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType evaluators(...) from builtins.PyCapsule evaluators(rosetta.protocols.jd2.JobOutputter) -> rosetta.protocols.evaluation.MetaPoseEvaluator filename(...) from builtins.PyCapsule filename(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.jd2.Job) -> str flush(...) from builtins.PyCapsule flush(rosetta.protocols.jd2.JobOutputter) -> NoneType   this function is meant to be redefined in child classes to allow for flushing of memory buffers.  Here's the long version: The SilentFileJobOutputter wanted to buffer output, but needed to guaruntee that  the output would be flushed at end of runtime.  The original implementation was to A) bend over backward to ensure  that the destructor was run (JobOutputter lives inside static JobDistributor, which was previously not destructed  because it's static) and B) flush the buffers in the destructor.  This caused a problem because the buffer-flushing  tried to use the Tracers, which had already been destructed...boom crash.    New solution: re-forbid use of destructors within the static JobDistributor system, and create a flush  function to force this stuff out.  So here it is: set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.jd2.JobOutputter) -> NoneType set_evaluators(...) from builtins.PyCapsule set_evaluators(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType starting_pose(...) from builtins.PyCapsule starting_pose(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.core.pose.Pose) -> NoneType   optionally pass a starting (reference) pose to a JobOutputter for later comparison  purposes and/or as interface for initializing evaluators   class NoOutputJobOutputterCreator(JobOutputterCreator)       Method resolution order: NoOutputJobOutputterCreator JobOutputterCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.NoOutputJobOutputterCreator,  : rosetta.protocols.jd2.NoOutputJobOutputterCreator) -> rosetta.protocols.jd2.NoOutputJobOutputterCreator create_JobOutputter(...) from builtins.PyCapsule create_JobOutputter(rosetta.protocols.jd2.NoOutputJobOutputterCreator) -> rosetta.protocols.jd2.JobOutputter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.NoOutputJobOutputterCreator) -> str   class PDBJobInputter(JobInputter)     This is the simplest implementation of JobInputter, which reads from -s/-l and PDB files.     Method resolution order: PDBJobInputter JobInputter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.jd2.PDBJobInputter) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.PDBJobInputter,  : rosetta.protocols.jd2.PDBJobInputter) -> rosetta.protocols.jd2.PDBJobInputter fill_jobs(...) from builtins.PyCapsule fill_jobs(self : rosetta.protocols.jd2.PDBJobInputter, jobs : rosetta.protocols.jd2.JobsContainer) -> NoneType   this function determines what jobs exist from -s/-l input_source(...) from builtins.PyCapsule input_source(rosetta.protocols.jd2.PDBJobInputter) -> rosetta.protocols.jd2.JobInputterInputSource.Enum   Return the type of input source that the PDBJobInputter is currently   using.      Always PDB_FILE. pose_from_job(...) from builtins.PyCapsule pose_from_job(self : rosetta.protocols.jd2.PDBJobInputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType   this function is responsible for filling the pose reference with the pose indicated by the job.  The Job object (within its InnerJob) contains a PoseCOP.  This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference.  This implementation uses pose_from_pdb Methods inherited from JobInputter: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self const owning pointers.   2. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self owning pointers. get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_const_protocols_jd2_JobInputter_t   Get self const weak pointers.   2. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_protocols_jd2_JobInputter_t   Get self weak pointers. job_inputter_input_source_to_string(...) from builtins.PyCapsule job_inputter_input_source_to_string(source : rosetta.protocols.jd2.JobInputterInputSource.Enum) -> str   call this with input_source() to get the input source of a  particular job inputter update_jobs_list(...) from builtins.PyCapsule update_jobs_list(self : rosetta.protocols.jd2.JobInputter, jobs : protocols::jd2::JobsContainer) -> NoneType   This function is only called by certain JobInputters to update the jobs list after it has already been created.      An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back. updates_jobs_list(...) from builtins.PyCapsule updates_jobs_list(rosetta.protocols.jd2.JobInputter) -> bool   Does this type of JobInputter update the jobs list?      False by default.  Override this function in derived classes to make it true.   class PDBJobInputterCreator(JobInputterCreator)       Method resolution order: PDBJobInputterCreator JobInputterCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.PDBJobInputterCreator,  : rosetta.protocols.jd2.PDBJobInputterCreator) -> rosetta.protocols.jd2.PDBJobInputterCreator create_JobInputter(...) from builtins.PyCapsule create_JobInputter(rosetta.protocols.jd2.PDBJobInputterCreator) -> rosetta.protocols.jd2.JobInputter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.PDBJobInputterCreator) -> str   class PDBJobOutputter(FileJobOutputter)     this simplest implementation of JobOutputter outputs raw PDBs and associated files, uncompressed.     Method resolution order: PDBJobOutputter FileJobOutputter JobOutputter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. final_pose(...) from builtins.PyCapsule final_pose(self : rosetta.protocols.jd2.PDBJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   this function outputs the final result of a job.  This implementation will write a PDB file (plus scores). job_has_completed(...) from builtins.PyCapsule job_has_completed(self : rosetta.protocols.jd2.PDBJobOutputter, job : rosetta.protocols.jd2.Job) -> bool   this function is not used for output, but it belongs here since it needs to check the same output locations as the class normally writes to.  This class checks wherever output goes to see if the job's expected output already exists (on disk or whatever).  This is the most basic form of checkpointing.  The base implementation looks for a pdb with the job's name already in existence. other_pose(...) from builtins.PyCapsule other_pose(*args, **kwargs) Overloaded function.   1. other_pose(self : rosetta.protocols.jd2.PDBJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol.  This implementation will write a PDB file (plus scores).   2. other_pose(self : rosetta.protocols.jd2.PDBJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str, copy_count : int) -> NoneType   this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol.  This implementation will write a PDB file (plus scores).   3. other_pose(self : rosetta.protocols.jd2.PDBJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str, copy_count : int, score_only : bool) -> NoneType   this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol.  This implementation will write a PDB file (plus scores). output_name(...) from builtins.PyCapsule output_name(self : rosetta.protocols.jd2.PDBJobOutputter, job : rosetta.protocols.jd2.Job) -> str   this is the master function for determining the unique output identifier for a job Methods inherited from FileJobOutputter: file(...) from builtins.PyCapsule file(self : rosetta.protocols.jd2.FileJobOutputter, job : rosetta.protocols.jd2.Job, data : str) -> NoneType   this function takes a string and writes it to disk (separately from Tracer output). scorefile_name(...) from builtins.PyCapsule scorefile_name(rosetta.protocols.jd2.FileJobOutputter) -> rosetta.utility.file.FileName set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.jd2.FileJobOutputter) -> NoneType write_scorefile(...) from builtins.PyCapsule write_scorefile(rosetta.protocols.jd2.FileJobOutputter) -> bool Methods inherited from JobOutputter: add_evaluation(...) from builtins.PyCapsule add_evaluation(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType   ////////////////////////////// evaluator interface //////////////////////////////////////////// call_output_observers(...) from builtins.PyCapsule call_output_observers(self : rosetta.protocols.jd2.JobOutputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType   call all output_observers clear_evaluators(...) from builtins.PyCapsule clear_evaluators(rosetta.protocols.jd2.JobOutputter) -> NoneType evaluate(...) from builtins.PyCapsule evaluate(self : rosetta.protocols.jd2.JobOutputter, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType evaluators(...) from builtins.PyCapsule evaluators(rosetta.protocols.jd2.JobOutputter) -> rosetta.protocols.evaluation.MetaPoseEvaluator filename(...) from builtins.PyCapsule filename(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.jd2.Job) -> str flush(...) from builtins.PyCapsule flush(rosetta.protocols.jd2.JobOutputter) -> NoneType   this function is meant to be redefined in child classes to allow for flushing of memory buffers.  Here's the long version: The SilentFileJobOutputter wanted to buffer output, but needed to guaruntee that  the output would be flushed at end of runtime.  The original implementation was to A) bend over backward to ensure  that the destructor was run (JobOutputter lives inside static JobDistributor, which was previously not destructed  because it's static) and B) flush the buffers in the destructor.  This caused a problem because the buffer-flushing  tried to use the Tracers, which had already been destructed...boom crash.    New solution: re-forbid use of destructors within the static JobDistributor system, and create a flush  function to force this stuff out.  So here it is: set_evaluators(...) from builtins.PyCapsule set_evaluators(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType starting_pose(...) from builtins.PyCapsule starting_pose(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.core.pose.Pose) -> NoneType   optionally pass a starting (reference) pose to a JobOutputter for later comparison  purposes and/or as interface for initializing evaluators   class PDBJobOutputterCreator(JobOutputterCreator)       Method resolution order: PDBJobOutputterCreator JobOutputterCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.PDBJobOutputterCreator,  : rosetta.protocols.jd2.PDBJobOutputterCreator) -> rosetta.protocols.jd2.PDBJobOutputterCreator create_JobOutputter(...) from builtins.PyCapsule create_JobOutputter(rosetta.protocols.jd2.PDBJobOutputterCreator) -> rosetta.protocols.jd2.JobOutputter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.PDBJobOutputterCreator) -> str   class Parser(builtins.object)     the Parser class can create a protocol (made of Movers) from an XML file.  This interface class describes its functionality for the August '08 job distributor.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.jd2.Parser) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.Parser,  : rosetta.protocols.jd2.Parser) -> rosetta.protocols.jd2.Parser generate_mover_from_job(...) from builtins.PyCapsule generate_mover_from_job(*args, **kwargs) Overloaded function.   1. generate_mover_from_job(self : rosetta.protocols.jd2.Parser, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, mover : rosetta.protocols.moves.Mover, new_input : bool) -> NoneType   generate_mover_from_job is the function called by the job  distributor to request a mover.  It is defined in the base class (this  class) and handles unpackaging the job and passes the work to  generate_mover_from_pose.  The pose is repackaged into the JobOP so that  jobs starting off that pose are properly modified.      this is the job we're working on (contains the input pose)      The pose that will be used in this job.      this is a mover pointer reference; the function can choose                  to overwrite the input with a new mover      true if this is different input (a different pose)                  from the last job distributor cycle      is true if the Parser is allowed to rewrite                  the Pose inside the input Job after generate_mover_from_pose has                  modified it.      true if the input mover should be replaced                  reguardless of whether or not new_input is true.   2. generate_mover_from_job(self : rosetta.protocols.jd2.Parser, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, mover : rosetta.protocols.moves.Mover, new_input : bool, allow_job_update : bool) -> NoneType   generate_mover_from_job is the function called by the job  distributor to request a mover.  It is defined in the base class (this  class) and handles unpackaging the job and passes the work to  generate_mover_from_pose.  The pose is repackaged into the JobOP so that  jobs starting off that pose are properly modified.      this is the job we're working on (contains the input pose)      The pose that will be used in this job.      this is a mover pointer reference; the function can choose                  to overwrite the input with a new mover      true if this is different input (a different pose)                  from the last job distributor cycle      is true if the Parser is allowed to rewrite                  the Pose inside the input Job after generate_mover_from_pose has                  modified it.      true if the input mover should be replaced                  reguardless of whether or not new_input is true.   3. generate_mover_from_job(self : rosetta.protocols.jd2.Parser, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, mover : rosetta.protocols.moves.Mover, new_input : bool, allow_job_update : bool, guarantee_new_mover : bool) -> NoneType   generate_mover_from_job is the function called by the job  distributor to request a mover.  It is defined in the base class (this  class) and handles unpackaging the job and passes the work to  generate_mover_from_pose.  The pose is repackaged into the JobOP so that  jobs starting off that pose are properly modified.      this is the job we're working on (contains the input pose)      The pose that will be used in this job.      this is a mover pointer reference; the function can choose                  to overwrite the input with a new mover      true if this is different input (a different pose)                  from the last job distributor cycle      is true if the Parser is allowed to rewrite                  the Pose inside the input Job after generate_mover_from_pose has                  modified it.      true if the input mover should be replaced                  reguardless of whether or not new_input is true. generate_mover_from_pose(...) from builtins.PyCapsule generate_mover_from_pose(*args, **kwargs) Overloaded function.   1. generate_mover_from_pose(self : rosetta.protocols.jd2.Parser, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, mover : rosetta.protocols.moves.Mover, new_input : bool, xml_file : str) -> bool   generate_mover_from_pose is overloaded by derived classes to parse  as desired.  The pose is passed by nonconst reference - the function is  thus allowed to modify this pose (preferably not at all, but by adding  constraints if necessary).  This pose will stay modified for jobs starting  off that pose.  The function is expected to use its return bool to signal  whether the pose has changed or not (and thus whether it needs to be  repackaged back into the InnerJob).  This function should return  IMMEDIATELY with false if it chooses not to modify the mover or pose.      job this is the job we're working on (contains the                  input pose's name)      this is the "starting pose" for a series of jobs; the                  function is allowed to modify it by adding constraints if                  necessary      this is a mover; the function can choose to overwrite                  the input with a new mover      new_input true if this is different input (a different                  pose) from the last job distributor cycle      the return value states whether or not the pose has                  been changed - it will be repackaged into the InnerJob only                  as necessary   2. generate_mover_from_pose(self : rosetta.protocols.jd2.Parser, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, mover : rosetta.protocols.moves.Mover, new_input : bool, xml_file : str, guarantee_new_mover : bool) -> bool   generate_mover_from_pose is overloaded by derived classes to parse  as desired.  The pose is passed by nonconst reference - the function is  thus allowed to modify this pose (preferably not at all, but by adding  constraints if necessary).  This pose will stay modified for jobs starting  off that pose.  The function is expected to use its return bool to signal  whether the pose has changed or not (and thus whether it needs to be  repackaged back into the InnerJob).  This function should return  IMMEDIATELY with false if it chooses not to modify the mover or pose.      job this is the job we're working on (contains the                  input pose's name)      this is the "starting pose" for a series of jobs; the                  function is allowed to modify it by adding constraints if                  necessary      this is a mover; the function can choose to overwrite                  the input with a new mover      new_input true if this is different input (a different                  pose) from the last job distributor cycle      the return value states whether or not the pose has                  been changed - it will be repackaged into the InnerJob only                  as necessary   class PoseInputStreamJobInputter(JobInputter)     This is the simplest implementation of JobInputter, which reads from -s/-l and SilentFile files.     Method resolution order: PoseInputStreamJobInputter JobInputter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.jd2.PoseInputStreamJobInputter) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.PoseInputStreamJobInputter,  : rosetta.protocols.jd2.PoseInputStreamJobInputter) -> rosetta.protocols.jd2.PoseInputStreamJobInputter fill_jobs(...) from builtins.PyCapsule fill_jobs(self : rosetta.protocols.jd2.PoseInputStreamJobInputter, jobs : rosetta.protocols.jd2.JobsContainer) -> NoneType input_source(...) from builtins.PyCapsule input_source(rosetta.protocols.jd2.PoseInputStreamJobInputter) -> rosetta.protocols.jd2.JobInputterInputSource.Enum   Return the type of input source that the PoseInputStreamJobInputter is currently   using. pose_from_job(...) from builtins.PyCapsule pose_from_job(self : rosetta.protocols.jd2.PoseInputStreamJobInputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType   This implementation simply calls fill_pose on the PoseInputStream  object. Methods inherited from JobInputter: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self const owning pointers.   2. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self owning pointers. get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_const_protocols_jd2_JobInputter_t   Get self const weak pointers.   2. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_protocols_jd2_JobInputter_t   Get self weak pointers. job_inputter_input_source_to_string(...) from builtins.PyCapsule job_inputter_input_source_to_string(source : rosetta.protocols.jd2.JobInputterInputSource.Enum) -> str   call this with input_source() to get the input source of a  particular job inputter update_jobs_list(...) from builtins.PyCapsule update_jobs_list(self : rosetta.protocols.jd2.JobInputter, jobs : protocols::jd2::JobsContainer) -> NoneType   This function is only called by certain JobInputters to update the jobs list after it has already been created.      An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back. updates_jobs_list(...) from builtins.PyCapsule updates_jobs_list(rosetta.protocols.jd2.JobInputter) -> bool   Does this type of JobInputter update the jobs list?      False by default.  Override this function in derived classes to make it true.   class PoseInputStreamJobInputterCreator(JobInputterCreator)       Method resolution order: PoseInputStreamJobInputterCreator JobInputterCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.PoseInputStreamJobInputterCreator,  : rosetta.protocols.jd2.PoseInputStreamJobInputterCreator) -> rosetta.protocols.jd2.PoseInputStreamJobInputterCreator create_JobInputter(...) from builtins.PyCapsule create_JobInputter(rosetta.protocols.jd2.PoseInputStreamJobInputterCreator) -> rosetta.protocols.jd2.JobInputter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.PoseInputStreamJobInputterCreator) -> str   class ScoreMap(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.jd2.ScoreMap) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.ScoreMap,  : rosetta.protocols.jd2.ScoreMap) -> rosetta.protocols.jd2.ScoreMap nonzero_energies(...) from builtins.PyCapsule nonzero_energies(score_map : rosetta.std.map_std_string_double, score_fxn : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType   full atom energies for output score_map_from_scored_pose(...) from builtins.PyCapsule score_map_from_scored_pose(*args, **kwargs) Overloaded function.   1. score_map_from_scored_pose(score_map : rosetta.std.map_std_string_double, pose : rosetta.core.pose.Pose) -> NoneType   generates a scoremap assuming the pose is already scored (note const w.r.t. pose)   2. score_map_from_scored_pose(pose : rosetta.core.pose.Pose) -> rosetta.std.map_std_string_double   return-by-value version of score_map_from_scored_pose   class ScoreOnlyJobOutputter(FileJobOutputter)     Joboutputter that only outputs score files, useful for screening protocols     Method resolution order: ScoreOnlyJobOutputter FileJobOutputter JobOutputter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. final_pose(...) from builtins.PyCapsule final_pose(self : rosetta.protocols.jd2.ScoreOnlyJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   this function outputs the final result of a job. job_has_completed(...) from builtins.PyCapsule job_has_completed(self : rosetta.protocols.jd2.ScoreOnlyJobOutputter, job : rosetta.protocols.jd2.Job) -> bool   this function is not used for output, but it belongs here since it needs to check the same output locations as the class normally writes to.  This class checks wherever output goes to see if the job's expected output already exists (on disk or whatever).  This is the most basic form of checkpointing. other_pose(...) from builtins.PyCapsule other_pose(*args, **kwargs) Overloaded function.   1. other_pose(self : rosetta.protocols.jd2.ScoreOnlyJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol.   2. other_pose(self : rosetta.protocols.jd2.ScoreOnlyJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str, copy_count : int) -> NoneType   this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol.   3. other_pose(self : rosetta.protocols.jd2.ScoreOnlyJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str, copy_count : int, score_only : bool) -> NoneType   this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. output_name(...) from builtins.PyCapsule output_name(self : rosetta.protocols.jd2.ScoreOnlyJobOutputter, job : rosetta.protocols.jd2.Job) -> str Methods inherited from FileJobOutputter: file(...) from builtins.PyCapsule file(self : rosetta.protocols.jd2.FileJobOutputter, job : rosetta.protocols.jd2.Job, data : str) -> NoneType   this function takes a string and writes it to disk (separately from Tracer output). scorefile_name(...) from builtins.PyCapsule scorefile_name(rosetta.protocols.jd2.FileJobOutputter) -> rosetta.utility.file.FileName set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.jd2.FileJobOutputter) -> NoneType write_scorefile(...) from builtins.PyCapsule write_scorefile(rosetta.protocols.jd2.FileJobOutputter) -> bool Methods inherited from JobOutputter: add_evaluation(...) from builtins.PyCapsule add_evaluation(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType   ////////////////////////////// evaluator interface //////////////////////////////////////////// call_output_observers(...) from builtins.PyCapsule call_output_observers(self : rosetta.protocols.jd2.JobOutputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType   call all output_observers clear_evaluators(...) from builtins.PyCapsule clear_evaluators(rosetta.protocols.jd2.JobOutputter) -> NoneType evaluate(...) from builtins.PyCapsule evaluate(self : rosetta.protocols.jd2.JobOutputter, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType evaluators(...) from builtins.PyCapsule evaluators(rosetta.protocols.jd2.JobOutputter) -> rosetta.protocols.evaluation.MetaPoseEvaluator filename(...) from builtins.PyCapsule filename(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.jd2.Job) -> str flush(...) from builtins.PyCapsule flush(rosetta.protocols.jd2.JobOutputter) -> NoneType   this function is meant to be redefined in child classes to allow for flushing of memory buffers.  Here's the long version: The SilentFileJobOutputter wanted to buffer output, but needed to guaruntee that  the output would be flushed at end of runtime.  The original implementation was to A) bend over backward to ensure  that the destructor was run (JobOutputter lives inside static JobDistributor, which was previously not destructed  because it's static) and B) flush the buffers in the destructor.  This caused a problem because the buffer-flushing  tried to use the Tracers, which had already been destructed...boom crash.    New solution: re-forbid use of destructors within the static JobDistributor system, and create a flush  function to force this stuff out.  So here it is: set_evaluators(...) from builtins.PyCapsule set_evaluators(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType starting_pose(...) from builtins.PyCapsule starting_pose(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.core.pose.Pose) -> NoneType   optionally pass a starting (reference) pose to a JobOutputter for later comparison  purposes and/or as interface for initializing evaluators   class ScoreOnlyJobOutputterCreator(JobOutputterCreator)       Method resolution order: ScoreOnlyJobOutputterCreator JobOutputterCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.ScoreOnlyJobOutputterCreator,  : rosetta.protocols.jd2.ScoreOnlyJobOutputterCreator) -> rosetta.protocols.jd2.ScoreOnlyJobOutputterCreator create_JobOutputter(...) from builtins.PyCapsule create_JobOutputter(rosetta.protocols.jd2.ScoreOnlyJobOutputterCreator) -> rosetta.protocols.jd2.JobOutputter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.ScoreOnlyJobOutputterCreator) -> str   class ScreeningJobInputter(JobInputter)       Method resolution order: ScreeningJobInputter JobInputter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.jd2.ScreeningJobInputter) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.ScreeningJobInputter,  : rosetta.protocols.jd2.ScreeningJobInputter) -> rosetta.protocols.jd2.ScreeningJobInputter fill_jobs(...) from builtins.PyCapsule fill_jobs(self : rosetta.protocols.jd2.ScreeningJobInputter, jobs : rosetta.protocols.jd2.JobsContainer) -> NoneType   fill the jobs based on the specified json file input_source(...) from builtins.PyCapsule input_source(rosetta.protocols.jd2.ScreeningJobInputter) -> rosetta.protocols.jd2.JobInputterInputSource.Enum   return the input source pose_from_job(...) from builtins.PyCapsule pose_from_job(self : rosetta.protocols.jd2.ScreeningJobInputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType   Fill the pose reference with the pose indicated by the job Methods inherited from JobInputter: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self const owning pointers.   2. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self owning pointers. get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_const_protocols_jd2_JobInputter_t   Get self const weak pointers.   2. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_protocols_jd2_JobInputter_t   Get self weak pointers. job_inputter_input_source_to_string(...) from builtins.PyCapsule job_inputter_input_source_to_string(source : rosetta.protocols.jd2.JobInputterInputSource.Enum) -> str   call this with input_source() to get the input source of a  particular job inputter update_jobs_list(...) from builtins.PyCapsule update_jobs_list(self : rosetta.protocols.jd2.JobInputter, jobs : protocols::jd2::JobsContainer) -> NoneType   This function is only called by certain JobInputters to update the jobs list after it has already been created.      An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back. updates_jobs_list(...) from builtins.PyCapsule updates_jobs_list(rosetta.protocols.jd2.JobInputter) -> bool   Does this type of JobInputter update the jobs list?      False by default.  Override this function in derived classes to make it true.   class ScreeningJobInputterCreator(JobInputterCreator)       Method resolution order: ScreeningJobInputterCreator JobInputterCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.ScreeningJobInputterCreator,  : rosetta.protocols.jd2.ScreeningJobInputterCreator) -> rosetta.protocols.jd2.ScreeningJobInputterCreator create_JobInputter(...) from builtins.PyCapsule create_JobInputter(rosetta.protocols.jd2.ScreeningJobInputterCreator) -> rosetta.protocols.jd2.JobInputter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.ScreeningJobInputterCreator) -> str   class ShuffleFileSystemJobDistributor(FileSystemJobDistributor)       Method resolution order: ShuffleFileSystemJobDistributor FileSystemJobDistributor JobDistributor builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle, rosetta.protocols.jd2.ShuffleFileSystemJobDistributor) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.ShuffleFileSystemJobDistributor,  : rosetta.protocols.jd2.ShuffleFileSystemJobDistributor) -> rosetta.protocols.jd2.ShuffleFileSystemJobDistributor get_new_job_id(...) from builtins.PyCapsule get_new_job_id(rosetta.protocols.jd2.ShuffleFileSystemJobDistributor) -> int mark_current_job_id_for_repetition(...) from builtins.PyCapsule mark_current_job_id_for_repetition(rosetta.protocols.jd2.ShuffleFileSystemJobDistributor) -> NoneType next_random_job(...) from builtins.PyCapsule next_random_job(rosetta.protocols.jd2.ShuffleFileSystemJobDistributor) -> int Methods inherited from FileSystemJobDistributor: current_job_finished(...) from builtins.PyCapsule current_job_finished(rosetta.protocols.jd2.FileSystemJobDistributor) -> NoneType go(...) from builtins.PyCapsule go(self : rosetta.protocols.jd2.FileSystemJobDistributor, mover : rosetta.protocols.moves.Mover) -> NoneType remove_bad_inputs_from_job_list(...) from builtins.PyCapsule remove_bad_inputs_from_job_list(rosetta.protocols.jd2.FileSystemJobDistributor) -> NoneType restart(...) from builtins.PyCapsule restart(rosetta.protocols.jd2.FileSystemJobDistributor) -> NoneType Methods inherited from JobDistributor: add_batch(...) from builtins.PyCapsule add_batch(*args, **kwargs) Overloaded function.   1. add_batch(self : rosetta.protocols.jd2.JobDistributor,  : str) -> NoneType   add a new batch ( name will be interpreted as flag_file )   2. add_batch(self : rosetta.protocols.jd2.JobDistributor,  : str, id : int) -> NoneType   add a new batch ( name will be interpreted as flag_file ) current_batch_id(...) from builtins.PyCapsule current_batch_id(rosetta.protocols.jd2.JobDistributor) -> int   what is the current batch number ? --- refers to position in batches_ current_job(...) from builtins.PyCapsule current_job(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.Job   Movers may ask their controlling job distributor for information about the current job.  They may also write information to this job for later output, though this use is now discouraged  as the addition of the MultiplePoseMover now means that a single job may include several  separate trajectories. current_job_id(...) from builtins.PyCapsule current_job_id(rosetta.protocols.jd2.JobDistributor) -> int   integer access - which job are we on? current_output_name(...) from builtins.PyCapsule current_output_name(rosetta.protocols.jd2.JobDistributor) -> str   Movers may ask their controlling job distributor for the output name as defined by the Job and JobOutputter. get_current_batch(...) from builtins.PyCapsule get_current_batch(rosetta.protocols.jd2.JobDistributor) -> str   what is the current batch ? --- name refers to the flag-file used for this batch get_instance(...) from builtins.PyCapsule get_instance() -> rosetta.protocols.jd2.JobDistributor job_inputter(...) from builtins.PyCapsule job_inputter(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobInputter   JobInputter access job_inputter_input_source(...) from builtins.PyCapsule job_inputter_input_source(rosetta.protocols.jd2.JobDistributor) -> rosetta.protocols.jd2.JobInputterInputSource.Enum   The input source for the current JobInputter. job_outputter(...) from builtins.PyCapsule job_outputter(rosetta.protocols.jd2.JobDistributor) -> protocols::jd2::JobOutputter   Movers (or derived classes) may ask for the JobOutputter mpi_finalize(...) from builtins.PyCapsule mpi_finalize(self : rosetta.protocols.jd2.JobDistributor, finalize : bool) -> NoneType   should the go() function call MPI_finalize()? It probably should, this is true by default. set_job_inputter(...) from builtins.PyCapsule set_job_inputter(self : rosetta.protocols.jd2.JobDistributor, new_job_inputter : rosetta.protocols.jd2.JobInputter) -> NoneType   Set the JobInputter and reset the Job list -- this is not something you want to do  after go() has been called, but before it has returned. set_job_outputter(...) from builtins.PyCapsule set_job_outputter(self : rosetta.protocols.jd2.JobDistributor, new_job_outputter : protocols::jd2::JobOutputter) -> NoneType   Movers (or derived classes) may ask for the JobOutputter total_nr_jobs(...) from builtins.PyCapsule total_nr_jobs(rosetta.protocols.jd2.JobDistributor) -> int   class SilentFileJobInputter(JobInputter)     This is the simplest implementation of JobInputter, which reads from -s/-l and SilentFile files.     Method resolution order: SilentFileJobInputter JobInputter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.jd2.SilentFileJobInputter) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.SilentFileJobInputter,  : rosetta.protocols.jd2.SilentFileJobInputter) -> rosetta.protocols.jd2.SilentFileJobInputter fill_jobs(...) from builtins.PyCapsule fill_jobs(self : rosetta.protocols.jd2.SilentFileJobInputter, jobs : rosetta.protocols.jd2.JobsContainer) -> NoneType   this function determines what jobs exist from -in::file::silent and  -in::file::tags. input_source(...) from builtins.PyCapsule input_source(rosetta.protocols.jd2.SilentFileJobInputter) -> rosetta.protocols.jd2.JobInputterInputSource.Enum   Return the type of input source that the SilentFileJobInputter is currently   using.      Always SILENT_FILE. pose_from_job(...) from builtins.PyCapsule pose_from_job(self : rosetta.protocols.jd2.SilentFileJobInputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType   this function is responsible for filling the pose reference with  the pose indicated by the job.  The Job object (within its InnerJob)  contains a PoseCOP.  This function needs to either fill the pose  reference from the InnerJob or, on first demand of a pose from that  InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill  the reference.  This implementation uses pose_from_pdb silent_file_data(...) from builtins.PyCapsule silent_file_data(rosetta.protocols.jd2.SilentFileJobInputter) -> rosetta.core.io.silent.SilentFileData struct_from_job(...) from builtins.PyCapsule struct_from_job(self : rosetta.protocols.jd2.SilentFileJobInputter, job : rosetta.protocols.jd2.Job) -> rosetta.core.io.silent.SilentStruct   this function returns the SilentStruct that belongs to the given job Methods inherited from JobInputter: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self const owning pointers.   2. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self owning pointers. get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_const_protocols_jd2_JobInputter_t   Get self const weak pointers.   2. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_protocols_jd2_JobInputter_t   Get self weak pointers. job_inputter_input_source_to_string(...) from builtins.PyCapsule job_inputter_input_source_to_string(source : rosetta.protocols.jd2.JobInputterInputSource.Enum) -> str   call this with input_source() to get the input source of a  particular job inputter update_jobs_list(...) from builtins.PyCapsule update_jobs_list(self : rosetta.protocols.jd2.JobInputter, jobs : protocols::jd2::JobsContainer) -> NoneType   This function is only called by certain JobInputters to update the jobs list after it has already been created.      An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back. updates_jobs_list(...) from builtins.PyCapsule updates_jobs_list(rosetta.protocols.jd2.JobInputter) -> bool   Does this type of JobInputter update the jobs list?      False by default.  Override this function in derived classes to make it true.   class SilentFileJobInputterCreator(JobInputterCreator)       Method resolution order: SilentFileJobInputterCreator JobInputterCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.SilentFileJobInputterCreator,  : rosetta.protocols.jd2.SilentFileJobInputterCreator) -> rosetta.protocols.jd2.SilentFileJobInputterCreator create_JobInputter(...) from builtins.PyCapsule create_JobInputter(rosetta.protocols.jd2.SilentFileJobInputterCreator) -> rosetta.protocols.jd2.JobInputter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.SilentFileJobInputterCreator) -> str   class SilentFileJobOutputter(FileJobOutputter)     this is a implementation of JobOutputter for silent-file-based output.     Method resolution order: SilentFileJobOutputter FileJobOutputter JobOutputter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. filename(...) from builtins.PyCapsule filename(self : rosetta.protocols.jd2.SilentFileJobOutputter,  : rosetta.protocols.jd2.Job) -> str final_pose(...) from builtins.PyCapsule final_pose(self : rosetta.protocols.jd2.SilentFileJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   ///////////////////////////creating output functions/////////////////////////////////////////      this function outputs the final result of a job. flush(...) from builtins.PyCapsule flush(rosetta.protocols.jd2.SilentFileJobOutputter) -> NoneType   this function flushes any internal buffers - see parent class for explanation job_has_completed(...) from builtins.PyCapsule job_has_completed(self : rosetta.protocols.jd2.SilentFileJobOutputter, job : rosetta.protocols.jd2.Job) -> bool   this function is not used for output, but it  belongs here since it needs to check the same output  locations as the class normally writes to.  This class  checks wherever output goes to see if the job's  expected output already exists (on disk or whatever).  This is the most basic form of checkpointing. other_pose(...) from builtins.PyCapsule other_pose(*args, **kwargs) Overloaded function.   1. other_pose(self : rosetta.protocols.jd2.SilentFileJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   this function is intended for saving  mid-protocol poses; for example the final centroid  structure in a combined centroid/fullatom protocol.  --->these go to file silent_filename+tag   2. other_pose(self : rosetta.protocols.jd2.SilentFileJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str, copy_count : int) -> NoneType   this function is intended for saving  mid-protocol poses; for example the final centroid  structure in a combined centroid/fullatom protocol.  --->these go to file silent_filename+tag   3. other_pose(self : rosetta.protocols.jd2.SilentFileJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str, copy_count : int, score_only : bool) -> NoneType   this function is intended for saving  mid-protocol poses; for example the final centroid  structure in a combined centroid/fullatom protocol.  --->these go to file silent_filename+tag output_name(...) from builtins.PyCapsule output_name(self : rosetta.protocols.jd2.SilentFileJobOutputter, job : rosetta.protocols.jd2.Job) -> str   this is the master function for determining the  unique output identifier for a job set_forced_silent_struct_type(...) from builtins.PyCapsule set_forced_silent_struct_type(self : rosetta.protocols.jd2.SilentFileJobOutputter,  : str) -> NoneType set_silent_file_name(...) from builtins.PyCapsule set_silent_file_name(self : rosetta.protocols.jd2.SilentFileJobOutputter, name : rosetta.utility.file.FileName) -> NoneType set_write_no_structures(...) from builtins.PyCapsule set_write_no_structures(*args, **kwargs) Overloaded function.   1. set_write_no_structures(rosetta.protocols.jd2.SilentFileJobOutputter) -> NoneType   2. set_write_no_structures(self : rosetta.protocols.jd2.SilentFileJobOutputter, value : bool) -> NoneType set_write_separate_scorefile(...) from builtins.PyCapsule set_write_separate_scorefile(self : rosetta.protocols.jd2.SilentFileJobOutputter, write_separate_scorefile : bool) -> NoneType Methods inherited from FileJobOutputter: file(...) from builtins.PyCapsule file(self : rosetta.protocols.jd2.FileJobOutputter, job : rosetta.protocols.jd2.Job, data : str) -> NoneType   this function takes a string and writes it to disk (separately from Tracer output). scorefile_name(...) from builtins.PyCapsule scorefile_name(rosetta.protocols.jd2.FileJobOutputter) -> rosetta.utility.file.FileName set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.jd2.FileJobOutputter) -> NoneType write_scorefile(...) from builtins.PyCapsule write_scorefile(rosetta.protocols.jd2.FileJobOutputter) -> bool Methods inherited from JobOutputter: add_evaluation(...) from builtins.PyCapsule add_evaluation(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType   ////////////////////////////// evaluator interface //////////////////////////////////////////// call_output_observers(...) from builtins.PyCapsule call_output_observers(self : rosetta.protocols.jd2.JobOutputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType   call all output_observers clear_evaluators(...) from builtins.PyCapsule clear_evaluators(rosetta.protocols.jd2.JobOutputter) -> NoneType evaluate(...) from builtins.PyCapsule evaluate(self : rosetta.protocols.jd2.JobOutputter, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType evaluators(...) from builtins.PyCapsule evaluators(rosetta.protocols.jd2.JobOutputter) -> rosetta.protocols.evaluation.MetaPoseEvaluator set_evaluators(...) from builtins.PyCapsule set_evaluators(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType starting_pose(...) from builtins.PyCapsule starting_pose(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.core.pose.Pose) -> NoneType   optionally pass a starting (reference) pose to a JobOutputter for later comparison  purposes and/or as interface for initializing evaluators   class SilentFileJobOutputterCreator(JobOutputterCreator)       Method resolution order: SilentFileJobOutputterCreator JobOutputterCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.SilentFileJobOutputterCreator,  : rosetta.protocols.jd2.SilentFileJobOutputterCreator) -> rosetta.protocols.jd2.SilentFileJobOutputterCreator create_JobOutputter(...) from builtins.PyCapsule create_JobOutputter(rosetta.protocols.jd2.SilentFileJobOutputterCreator) -> rosetta.protocols.jd2.JobOutputter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.jd2.SilentFileJobOutputterCreator) -> str   class SingleFileBuffer(builtins.object)     this is a implementation of Buffer for silent-file-based output.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, filename : str, channel : int, status : int) -> NoneType   2. __init__(handle, rosetta.protocols.jd2.SingleFileBuffer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.SingleFileBuffer,  : rosetta.protocols.jd2.SingleFileBuffer) -> rosetta.protocols.jd2.SingleFileBuffer block(...) from builtins.PyCapsule block(self : rosetta.protocols.jd2.SingleFileBuffer, slave : int) -> NoneType close(...) from builtins.PyCapsule close(self : rosetta.protocols.jd2.SingleFileBuffer, slave : int) -> NoneType filename(...) from builtins.PyCapsule filename(rosetta.protocols.jd2.SingleFileBuffer) -> str flush(...) from builtins.PyCapsule flush(self : rosetta.protocols.jd2.SingleFileBuffer, slave : int) -> NoneType has_open_slaves(...) from builtins.PyCapsule has_open_slaves(rosetta.protocols.jd2.SingleFileBuffer) -> bool length(...) from builtins.PyCapsule length(self : rosetta.protocols.jd2.SingleFileBuffer, slave : int) -> int nr_open_slaves(...) from builtins.PyCapsule nr_open_slaves(rosetta.protocols.jd2.SingleFileBuffer) -> int store_line(...) from builtins.PyCapsule store_line(self : rosetta.protocols.jd2.SingleFileBuffer, slave : int, channel : int, line : str) -> NoneType write_lines(...) from builtins.PyCapsule write_lines(self : rosetta.protocols.jd2.SingleFileBuffer,  : rosetta.utility.vector1_std_string) -> NoneType   class WriteFileSFB(SingleFileBuffer)       Method resolution order: WriteFileSFB SingleFileBuffer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, filename : str, channel : int, append : bool, status : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. block(...) from builtins.PyCapsule block(self : rosetta.protocols.jd2.WriteFileSFB, slave : int) -> NoneType write_lines(...) from builtins.PyCapsule write_lines(self : rosetta.protocols.jd2.WriteFileSFB,  : rosetta.utility.vector1_std_string) -> NoneType Methods inherited from SingleFileBuffer: assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.SingleFileBuffer,  : rosetta.protocols.jd2.SingleFileBuffer) -> rosetta.protocols.jd2.SingleFileBuffer close(...) from builtins.PyCapsule close(self : rosetta.protocols.jd2.SingleFileBuffer, slave : int) -> NoneType filename(...) from builtins.PyCapsule filename(rosetta.protocols.jd2.SingleFileBuffer) -> str flush(...) from builtins.PyCapsule flush(self : rosetta.protocols.jd2.SingleFileBuffer, slave : int) -> NoneType has_open_slaves(...) from builtins.PyCapsule has_open_slaves(rosetta.protocols.jd2.SingleFileBuffer) -> bool length(...) from builtins.PyCapsule length(self : rosetta.protocols.jd2.SingleFileBuffer, slave : int) -> int nr_open_slaves(...) from builtins.PyCapsule nr_open_slaves(rosetta.protocols.jd2.SingleFileBuffer) -> int store_line(...) from builtins.PyCapsule store_line(self : rosetta.protocols.jd2.SingleFileBuffer, slave : int, channel : int, line : str) -> NoneType   class WriteOut_MpiFileBuffer(MpiFileBuffer)       Method resolution order: WriteOut_MpiFileBuffer MpiFileBuffer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, rank : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.WriteOut_MpiFileBuffer,  : rosetta.protocols.jd2.WriteOut_MpiFileBuffer) -> rosetta.protocols.jd2.WriteOut_MpiFileBuffer Methods inherited from MpiFileBuffer: block_file(...) from builtins.PyCapsule block_file(self : rosetta.protocols.jd2.MpiFileBuffer, filename : str) -> NoneType close_file(...) from builtins.PyCapsule close_file(self : rosetta.protocols.jd2.MpiFileBuffer, fname : str) -> bool garbage_collection(...) from builtins.PyCapsule garbage_collection(rosetta.protocols.jd2.MpiFileBuffer) -> NoneType release_file(...) from builtins.PyCapsule release_file(self : rosetta.protocols.jd2.MpiFileBuffer, filename : str) -> NoneType run(...) from builtins.PyCapsule run(rosetta.protocols.jd2.MpiFileBuffer) -> NoneType set_SlaveCanOpenFile(...) from builtins.PyCapsule set_SlaveCanOpenFile(*args, **kwargs) Overloaded function.   1. set_SlaveCanOpenFile(rosetta.protocols.jd2.MpiFileBuffer) -> NoneType   2. set_SlaveCanOpenFile(self : rosetta.protocols.jd2.MpiFileBuffer, setting : bool) -> NoneType stop(...) from builtins.PyCapsule stop(rosetta.protocols.jd2.MpiFileBuffer) -> NoneType