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- rosetta.protocols.jd2.FileSystemJobDistributor(rosetta.protocols.jd2.JobDistributor)
-
- UnfoldedStateEnergyCalculatorJobDistributor
- rosetta.protocols.jd2.MPIWorkPoolJobDistributor(rosetta.protocols.jd2.JobDistributor)
-
- UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
- rosetta.protocols.moves.Mover(builtins.object)
-
- UnfoldedStateEnergyCalculatorMover
class UnfoldedStateEnergyCalculatorJobDistributor(rosetta.protocols.jd2.FileSystemJobDistributor) |
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- Method resolution order:
- UnfoldedStateEnergyCalculatorJobDistributor
- rosetta.protocols.jd2.FileSystemJobDistributor
- rosetta.protocols.jd2.JobDistributor
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_unfolded_energy_data(...) from builtins.PyCapsule
- add_unfolded_energy_data(self : rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor, tlc : str, scores : rosetta.core.scoring.EMapVector) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor, : rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor) -> rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor
- go(...) from builtins.PyCapsule
- go(self : rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor, mover : rosetta.protocols.moves.Mover) -> NoneType
- set_energy_terms(...) from builtins.PyCapsule
- set_energy_terms(self : rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor, weights : rosetta.core.scoring.EMapVector) -> NoneType
Methods inherited from 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
- 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 rosetta.protocols.jd2.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
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class UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor(rosetta.protocols.jd2.MPIWorkPoolJobDistributor) |
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- Method resolution order:
- UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
- rosetta.protocols.jd2.MPIWorkPoolJobDistributor
- rosetta.protocols.jd2.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.
- add_unfolded_energy_data(...) from builtins.PyCapsule
- add_unfolded_energy_data(self : rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor, tlc : str, scores : rosetta.core.scoring.EMapVector) -> NoneType
dummy for master/slave version
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor, : rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor) -> rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
- set_energy_terms(...) from builtins.PyCapsule
- set_energy_terms(self : rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor, weights : rosetta.core.scoring.EMapVector) -> NoneType
dummy for master/slave version
Methods inherited from 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 rosetta.protocols.jd2.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
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class UnfoldedStateEnergyCalculatorMover(rosetta.protocols.moves.Mover) |
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- Method resolution order:
- UnfoldedStateEnergyCalculatorMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, job_dist : rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor, pack_scrfxn : rosetta.core.scoring.ScoreFunction, score_scrfxn : rosetta.core.scoring.ScoreFunction, frag_length : int, mut_aa : str, repack_fragments : bool, native_sequence : bool, seq_match_seq : str, seq_match_pos : int, seq_match_frags : bool) -> NoneType
2. __init__(handle, rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover, pose : rosetta.core.pose.Pose) -> NoneType
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover) -> str
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover) -> bool
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover) -> bool
Methods inherited from rosetta.protocols.moves.Mover:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.moves.Mover, other : rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
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