| | |
- builtins.object
-
- AbstractArchiveBase
-
- ArchiveBase
-
- EvaluatedArchive
-
- NormalizedEvaluatedArchive
- VarianceStatisticsArchive
- BaseArchiveManager
-
- ArchiveManager
- Batch
- rosetta.protocols.jd2.MPIFileBufJobDistributor(rosetta.protocols.jd2.JobDistributor)
-
- MPIArchiveJobDistributor
- rosetta.utility.excn.EXCN_Msg_Exception(rosetta.utility.excn.EXCN_Exception)
-
- EXCN_Archive
class AbstractArchiveBase(builtins.object) |
| |
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.
|
| |
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.archive.AbstractArchiveBase, : rosetta.protocols.jd2.archive.AbstractArchiveBase) -> rosetta.protocols.jd2.archive.AbstractArchiveBase
- finished(...) from builtins.PyCapsule
- finished(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> bool
is archive converged ?
- generate_batch(...) from builtins.PyCapsule
- generate_batch(*args, **kwargs)
Overloaded function.
1. generate_batch(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> NoneType
create a new batch with manager().start_new_batch() and manager().finalize_batch();
2. generate_batch(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, : protocols::jd2::archive::Batch, : int) -> int
create a batch for the current stage, return ct != 0 if more batches should be created at
current stage. (e.g., harvest_batches)
- idle(...) from builtins.PyCapsule
- idle(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> NoneType
do some computations on archive that can be done while we are waiting
- init_from_decoy_set(...) from builtins.PyCapsule
- init_from_decoy_set(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, sfd : rosetta.core.io.silent.SilentFileData) -> NoneType
- initialize(...) from builtins.PyCapsule
- initialize(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> NoneType
- manager(...) from builtins.PyCapsule
- manager(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> protocols::jd2::archive::BaseArchiveManager
access to the ArchiveManager (control of batches)
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> str
- read_structures(...) from builtins.PyCapsule
- read_structures(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, returned_decoys : rosetta.core.io.silent.SilentFileData, alternative_decoys : rosetta.core.io.silent.SilentFileData, batch : protocols::jd2::archive::Batch) -> NoneType
read 'returned_decoys' from 'batch' into archive.
- restore_from_file(...) from builtins.PyCapsule
- restore_from_file(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> bool
restore archive
- save_to_file(...) from builtins.PyCapsule
- save_to_file(*args, **kwargs)
Overloaded function.
1. save_to_file(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> NoneType
save archive to file .. you can put 'suffix' at end of dirname to save other snapshots than the 'current'
2. save_to_file(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, suffix : str) -> NoneType
save archive to file .. you can put 'suffix' at end of dirname to save other snapshots than the 'current'
- set_manager(...) from builtins.PyCapsule
- set_manager(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, manager : protocols::jd2::archive::BaseArchiveManager) -> NoneType
- set_name(...) from builtins.PyCapsule
- set_name(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, set : str) -> NoneType
set name of archive ( used also for save_to_file and restore_from_file )
- still_interested(...) from builtins.PyCapsule
- still_interested(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, : protocols::jd2::archive::Batch) -> bool
old-batches might be outdated and should not be computed anymore
return true for this query if this is the case for old_batch
|
class ArchiveBase(AbstractArchiveBase) |
| | |
- Method resolution order:
- ArchiveBase
- AbstractArchiveBase
- 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.
- accepts_since_last_batch(...) from builtins.PyCapsule
- accepts_since_last_batch(*args, **kwargs)
Overloaded function.
1. accepts_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int
---- methods to keep statistics of acceptance
2. accepts_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int
- add_structure(...) from builtins.PyCapsule
- add_structure(self : rosetta.protocols.jd2.archive.ArchiveBase, new_decoy : rosetta.core.io.silent.SilentStruct, alternative_decoy : rosetta.core.io.silent.SilentStruct, : protocols::jd2::archive::Batch) -> bool
add structure to Archive.. return false if structure is rejected.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.jd2.archive.ArchiveBase, : rosetta.protocols.jd2.archive.ArchiveBase) -> rosetta.protocols.jd2.archive.ArchiveBase
- current_acceptance_ratio(...) from builtins.PyCapsule
- current_acceptance_ratio(rosetta.protocols.jd2.archive.ArchiveBase) -> float
- decoys(...) from builtins.PyCapsule
- decoys(*args, **kwargs)
Overloaded function.
1. decoys(rosetta.protocols.jd2.archive.ArchiveBase) -> rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t
2. decoys(rosetta.protocols.jd2.archive.ArchiveBase) -> rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t
- finished(...) from builtins.PyCapsule
- finished(rosetta.protocols.jd2.archive.ArchiveBase) -> bool
- generate_batch(...) from builtins.PyCapsule
- generate_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType
- idle(...) from builtins.PyCapsule
- idle(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType
called when nothing is happening
- init_from_decoy_set(...) from builtins.PyCapsule
- init_from_decoy_set(self : rosetta.protocols.jd2.archive.ArchiveBase, sfd : rosetta.core.io.silent.SilentFileData) -> NoneType
read externally provided structures from decoy_file into archive
- initialize(...) from builtins.PyCapsule
- initialize(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType
- load_decoys(...) from builtins.PyCapsule
- load_decoys(self : rosetta.protocols.jd2.archive.ArchiveBase, filename : str, decoys : rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType
- nstruct(...) from builtins.PyCapsule
- nstruct(rosetta.protocols.jd2.archive.ArchiveBase) -> int
how many structures should be in archive .. varies from decoys().size() in startup phase.
- proposed_since_last_batch(...) from builtins.PyCapsule
- proposed_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int
- read_structures(...) from builtins.PyCapsule
- read_structures(self : rosetta.protocols.jd2.archive.ArchiveBase, : rosetta.core.io.silent.SilentFileData, alternative_decoys : rosetta.core.io.silent.SilentFileData, batch : protocols::jd2::archive::Batch) -> NoneType
SilentFileData contains the new structures belonging to this batch.
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
2. register_options() -> NoneType
Archive specific options
3. register_options() -> NoneType
Archive specific options
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
- reset_accept_counter(...) from builtins.PyCapsule
- reset_accept_counter(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType
- restore_from_file(...) from builtins.PyCapsule
- restore_from_file(rosetta.protocols.jd2.archive.ArchiveBase) -> bool
- save_decoys(...) from builtins.PyCapsule
- save_decoys(self : rosetta.protocols.jd2.archive.ArchiveBase, dirname : str, name : str, decoys : rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType
helper routine to save decoys properly
- save_to_file(...) from builtins.PyCapsule
- save_to_file(*args, **kwargs)
Overloaded function.
1. save_to_file(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType
save and restore archive to file-system
2. save_to_file(self : rosetta.protocols.jd2.archive.ArchiveBase, suffix : str) -> NoneType
save and restore archive to file-system
- set_nstruct(...) from builtins.PyCapsule
- set_nstruct(self : rosetta.protocols.jd2.archive.ArchiveBase, set : int) -> NoneType
set target size of pool
- statistics_valid(...) from builtins.PyCapsule
- statistics_valid(rosetta.protocols.jd2.archive.ArchiveBase) -> bool
- total_accepts(...) from builtins.PyCapsule
- total_accepts(rosetta.protocols.jd2.archive.ArchiveBase) -> int
- total_proposed(...) from builtins.PyCapsule
- total_proposed(rosetta.protocols.jd2.archive.ArchiveBase) -> int
Methods inherited from AbstractArchiveBase:
- manager(...) from builtins.PyCapsule
- manager(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> protocols::jd2::archive::BaseArchiveManager
access to the ArchiveManager (control of batches)
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> str
- set_manager(...) from builtins.PyCapsule
- set_manager(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, manager : protocols::jd2::archive::BaseArchiveManager) -> NoneType
- set_name(...) from builtins.PyCapsule
- set_name(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, set : str) -> NoneType
set name of archive ( used also for save_to_file and restore_from_file )
- still_interested(...) from builtins.PyCapsule
- still_interested(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, : protocols::jd2::archive::Batch) -> bool
old-batches might be outdated and should not be computed anymore
return true for this query if this is the case for old_batch
|
class ArchiveManager(BaseArchiveManager) |
| |
ArchiveManager is responsible for communication with JobDistributor and organization of Batches and returning decoys
he owns an Archive (AbstractArchiveBase) that will be handed the decoys and is asked to generate_batch() if the QUEUE_EMPTY .
|
| |
- Method resolution order:
- ArchiveManager
- BaseArchiveManager
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : handle, archive_rank : int, jd_master_rank : int, file_buf_rank : int) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- go(...) from builtins.PyCapsule
- go(self : rosetta.protocols.jd2.archive.ArchiveManager, : rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType
- register_options(...) from builtins.PyCapsule
- register_options() -> NoneType
- restore_archive(...) from builtins.PyCapsule
- restore_archive(rosetta.protocols.jd2.archive.ArchiveManager) -> bool
- save_archive(...) from builtins.PyCapsule
- save_archive(rosetta.protocols.jd2.archive.ArchiveManager) -> NoneType
- unfinished_batches(...) from builtins.PyCapsule
- unfinished_batches(rosetta.protocols.jd2.archive.ArchiveManager) -> int
Methods inherited from BaseArchiveManager:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.jd2.archive.BaseArchiveManager, : rosetta.protocols.jd2.archive.BaseArchiveManager) -> rosetta.protocols.jd2.archive.BaseArchiveManager
- batches(...) from builtins.PyCapsule
- batches(rosetta.protocols.jd2.archive.BaseArchiveManager) -> rosetta.utility.vector1_protocols_jd2_archive_Batch
- cancel_batches_previous_to(...) from builtins.PyCapsule
- cancel_batches_previous_to(*args, **kwargs)
Overloaded function.
1. cancel_batches_previous_to(self : rosetta.protocols.jd2.archive.BaseArchiveManager, batch_id : int) -> NoneType
2. cancel_batches_previous_to(self : rosetta.protocols.jd2.archive.BaseArchiveManager, batch_id : int, allow_reading_of_decoys : bool) -> NoneType
- finalize_batch(...) from builtins.PyCapsule
- finalize_batch(*args, **kwargs)
Overloaded function.
1. finalize_batch(self : rosetta.protocols.jd2.archive.BaseArchiveManager, : rosetta.protocols.jd2.archive.Batch) -> NoneType
2. finalize_batch(self : rosetta.protocols.jd2.archive.BaseArchiveManager, : rosetta.protocols.jd2.archive.Batch, reread : bool) -> NoneType
- last_batch_id(...) from builtins.PyCapsule
- last_batch_id(rosetta.protocols.jd2.archive.BaseArchiveManager) -> int
- start_new_batch(...) from builtins.PyCapsule
- start_new_batch(rosetta.protocols.jd2.archive.BaseArchiveManager) -> rosetta.protocols.jd2.archive.Batch
|
class BaseArchiveManager(builtins.object) |
| |
ArchiveManager is responsible for communication with JobDistributor and organization of Batches and returning decoys
he owns an Archive (AbstractArchiveBase) that will be handed the decoys and is asked to generate_batch() if the QUEUE_EMPTY .
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.protocols.jd2.archive.BaseArchiveManager) -> 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.archive.BaseArchiveManager, : rosetta.protocols.jd2.archive.BaseArchiveManager) -> rosetta.protocols.jd2.archive.BaseArchiveManager
- batches(...) from builtins.PyCapsule
- batches(rosetta.protocols.jd2.archive.BaseArchiveManager) -> rosetta.utility.vector1_protocols_jd2_archive_Batch
- cancel_batches_previous_to(...) from builtins.PyCapsule
- cancel_batches_previous_to(*args, **kwargs)
Overloaded function.
1. cancel_batches_previous_to(self : rosetta.protocols.jd2.archive.BaseArchiveManager, batch_id : int) -> NoneType
2. cancel_batches_previous_to(self : rosetta.protocols.jd2.archive.BaseArchiveManager, batch_id : int, allow_reading_of_decoys : bool) -> NoneType
- finalize_batch(...) from builtins.PyCapsule
- finalize_batch(*args, **kwargs)
Overloaded function.
1. finalize_batch(self : rosetta.protocols.jd2.archive.BaseArchiveManager, : rosetta.protocols.jd2.archive.Batch) -> NoneType
2. finalize_batch(self : rosetta.protocols.jd2.archive.BaseArchiveManager, : rosetta.protocols.jd2.archive.Batch, reread : bool) -> NoneType
- last_batch_id(...) from builtins.PyCapsule
- last_batch_id(rosetta.protocols.jd2.archive.BaseArchiveManager) -> int
- restore_archive(...) from builtins.PyCapsule
- restore_archive(rosetta.protocols.jd2.archive.BaseArchiveManager) -> bool
- save_archive(...) from builtins.PyCapsule
- save_archive(rosetta.protocols.jd2.archive.BaseArchiveManager) -> NoneType
- start_new_batch(...) from builtins.PyCapsule
- start_new_batch(rosetta.protocols.jd2.archive.BaseArchiveManager) -> rosetta.protocols.jd2.archive.Batch
|
class Batch(builtins.object) |
| |
a Batch represents a directory "batch_000xxx" that contains flags, broker-setup input-files and output-files
the Batch-class helps to get the correct file- and directory names,
and has some knowledge about its status: finished, unfinished ... decoys already processed by Archive
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.jd2.archive.Batch, options : rosetta.utility.options.OptionCollection, intermediate_structs : bool, has_silent_in : bool, nstruct : int) -> NoneType
2. __init__(self : rosetta.protocols.jd2.archive.Batch, id : int) -> NoneType
3. __init__(self : rosetta.protocols.jd2.archive.Batch, : rosetta.protocols.jd2.archive.Batch) -> 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.archive.Batch) -> str
- all_broker_files(...) from builtins.PyCapsule
- all_broker_files(rosetta.protocols.jd2.archive.Batch) -> str
- allow_reading_cancelled_decoys(...) from builtins.PyCapsule
- allow_reading_cancelled_decoys(rosetta.protocols.jd2.archive.Batch) -> bool
batch has finished
- alternative_decoys_out(...) from builtins.PyCapsule
- alternative_decoys_out(rosetta.protocols.jd2.archive.Batch) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.jd2.archive.Batch, : rosetta.protocols.jd2.archive.Batch) -> rosetta.protocols.jd2.archive.Batch
- batch(...) from builtins.PyCapsule
- batch(rosetta.protocols.jd2.archive.Batch) -> str
some useful file- and directory names
- broker_file(...) from builtins.PyCapsule
- broker_file(rosetta.protocols.jd2.archive.Batch) -> str
- decoys_returned(...) from builtins.PyCapsule
- decoys_returned(rosetta.protocols.jd2.archive.Batch) -> int
how many structures have been processed by archive already
- dir(...) from builtins.PyCapsule
- dir(rosetta.protocols.jd2.archive.Batch) -> str
- extra_broker_files(...) from builtins.PyCapsule
- extra_broker_files(rosetta.protocols.jd2.archive.Batch) -> str
- flag_file(...) from builtins.PyCapsule
- flag_file(rosetta.protocols.jd2.archive.Batch) -> str
- has_finished(...) from builtins.PyCapsule
- has_finished(rosetta.protocols.jd2.archive.Batch) -> bool
batch has finished
- has_silent_in(...) from builtins.PyCapsule
- has_silent_in(rosetta.protocols.jd2.archive.Batch) -> bool
has input decoys
- id(...) from builtins.PyCapsule
- id(rosetta.protocols.jd2.archive.Batch) -> int
batch id
- intermediate_structs(...) from builtins.PyCapsule
- intermediate_structs(rosetta.protocols.jd2.archive.Batch) -> bool
writes out intermediate decoys
- is_cancelled(...) from builtins.PyCapsule
- is_cancelled(rosetta.protocols.jd2.archive.Batch) -> bool
batch has finished
- mark_as_cancelled(...) from builtins.PyCapsule
- mark_as_cancelled(*args, **kwargs)
Overloaded function.
1. mark_as_cancelled(rosetta.protocols.jd2.archive.Batch) -> NoneType
2. mark_as_cancelled(self : rosetta.protocols.jd2.archive.Batch, allow_reading_of_decoys : bool) -> NoneType
- mark_as_finished(...) from builtins.PyCapsule
- mark_as_finished(rosetta.protocols.jd2.archive.Batch) -> NoneType
- mark_as_invalid(...) from builtins.PyCapsule
- mark_as_invalid(rosetta.protocols.jd2.archive.Batch) -> NoneType
- nstruct(...) from builtins.PyCapsule
- nstruct(*args, **kwargs)
Overloaded function.
1. nstruct(rosetta.protocols.jd2.archive.Batch) -> int
nstruct ...
2. nstruct(rosetta.protocols.jd2.archive.Batch) -> int
- read_info_file(...) from builtins.PyCapsule
- read_info_file(rosetta.protocols.jd2.archive.Batch) -> NoneType
- score_file(...) from builtins.PyCapsule
- score_file(rosetta.protocols.jd2.archive.Batch) -> str
- set_decoys_returned(...) from builtins.PyCapsule
- set_decoys_returned(self : rosetta.protocols.jd2.archive.Batch, setting : int) -> NoneType
- set_has_silent_in(...) from builtins.PyCapsule
- set_has_silent_in(*args, **kwargs)
Overloaded function.
1. set_has_silent_in(rosetta.protocols.jd2.archive.Batch) -> NoneType
Setters
2. set_has_silent_in(self : rosetta.protocols.jd2.archive.Batch, setting : bool) -> NoneType
Setters
- set_id(...) from builtins.PyCapsule
- set_id(self : rosetta.protocols.jd2.archive.Batch, id : int) -> NoneType
- set_intermediate_structs(...) from builtins.PyCapsule
- set_intermediate_structs(*args, **kwargs)
Overloaded function.
1. set_intermediate_structs(rosetta.protocols.jd2.archive.Batch) -> NoneType
2. set_intermediate_structs(self : rosetta.protocols.jd2.archive.Batch, setting : bool) -> NoneType
- silent_in(...) from builtins.PyCapsule
- silent_in(rosetta.protocols.jd2.archive.Batch) -> str
- silent_out(...) from builtins.PyCapsule
- silent_out(rosetta.protocols.jd2.archive.Batch) -> str
- user_options(...) from builtins.PyCapsule
- user_options(*args, **kwargs)
Overloaded function.
1. user_options(rosetta.protocols.jd2.archive.Batch) -> rosetta.utility.options.OptionCollection
2. user_options(rosetta.protocols.jd2.archive.Batch) -> rosetta.utility.options.OptionCollection
- valid(...) from builtins.PyCapsule
- valid(rosetta.protocols.jd2.archive.Batch) -> bool
- write_info_file(...) from builtins.PyCapsule
- write_info_file(rosetta.protocols.jd2.archive.Batch) -> NoneType
read and write BATCH_INFO ( decoys_returned/ finished etc.. )
|
class EvaluatedArchive(ArchiveBase) |
| |
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:
- EvaluatedArchive
- ArchiveBase
- AbstractArchiveBase
- 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.
- add_evaluated_structure(...) from builtins.PyCapsule
- add_evaluated_structure(self : rosetta.protocols.jd2.archive.EvaluatedArchive, evaluated_decoy : rosetta.core.io.silent.SilentStruct, alternative_decoy : rosetta.core.io.silent.SilentStruct, : protocols::jd2::archive::Batch) -> bool
add an evaluated decoy to Archive (i.e, evaluated_decoy = evaluate( some_decoy ) );
- add_evaluation(...) from builtins.PyCapsule
- add_evaluation(*args, **kwargs)
Overloaded function.
1. add_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive, : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType
add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()
2. add_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive, : rosetta.protocols.evaluation.PoseEvaluator, weight : float) -> NoneType
add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()
- add_structure(...) from builtins.PyCapsule
- add_structure(self : rosetta.protocols.jd2.archive.EvaluatedArchive, new_decoy : rosetta.core.io.silent.SilentStruct, alternative_decoy : rosetta.core.io.silent.SilentStruct, batch : protocols::jd2::archive::Batch) -> bool
add decoy to Archive
evaluate decoy and call add_evaluated_structure
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.jd2.archive.EvaluatedArchive, : rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.protocols.jd2.archive.EvaluatedArchive
- evaluate_local(...) from builtins.PyCapsule
- evaluate_local(rosetta.protocols.jd2.archive.EvaluatedArchive) -> bool
specify if decoys are evaluated on the master or (non-local i.e., on the individual slave nodes)
- evaluate_silent_struct(...) from builtins.PyCapsule
- evaluate_silent_struct(self : rosetta.protocols.jd2.archive.EvaluatedArchive, from_batch : rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct
yields an "evaluated" silent-struct which can be queried with select_score
will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct
- evaluators(...) from builtins.PyCapsule
- evaluators(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t
- get_weight(...) from builtins.PyCapsule
- get_weight(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> float
- has_evaluator(...) from builtins.PyCapsule
- has_evaluator(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> bool
is a certain elvaluator present ?
- init_from_decoy_set(...) from builtins.PyCapsule
- init_from_decoy_set(self : rosetta.protocols.jd2.archive.EvaluatedArchive, sfd : rosetta.core.io.silent.SilentFileData) -> NoneType
overloaded to make input decoys appear the same as decoys coming from batches
- read_structures(...) from builtins.PyCapsule
- read_structures(self : rosetta.protocols.jd2.archive.EvaluatedArchive, sfd : rosetta.core.io.silent.SilentFileData, alternative_decoys : rosetta.core.io.silent.SilentFileData, batch : protocols::jd2::archive::Batch) -> NoneType
only overloaded this to add some verbosity each time we read structures
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
2. register_options() -> NoneType
Archive specific options
3. register_options() -> NoneType
Archive specific options
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
- remove_evaluation(...) from builtins.PyCapsule
- remove_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> NoneType
remove Evaluator
- rescore(...) from builtins.PyCapsule
- rescore(rosetta.protocols.jd2.archive.EvaluatedArchive) -> NoneType
recompute all score-values of all decoys and re-order the archive by (new) select_score
- restore_from_file(...) from builtins.PyCapsule
- restore_from_file(rosetta.protocols.jd2.archive.EvaluatedArchive) -> bool
overloaded that we can sort the pool after reading
- save_to_file(...) from builtins.PyCapsule
- save_to_file(*args, **kwargs)
Overloaded function.
1. save_to_file(rosetta.protocols.jd2.archive.EvaluatedArchive) -> NoneType
overloaded to save / restore the variance_archive_
2. save_to_file(self : rosetta.protocols.jd2.archive.EvaluatedArchive, suffix : str) -> NoneType
overloaded to save / restore the variance_archive_
- score_variation(...) from builtins.PyCapsule
- score_variation(self : rosetta.protocols.jd2.archive.EvaluatedArchive, col : str) -> float
- score_variations(...) from builtins.PyCapsule
- score_variations(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.std.map_std_string_double
- scorefxn(...) from builtins.PyCapsule
- scorefxn(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.core.scoring.ScoreFunction
- select_score(...) from builtins.PyCapsule
- select_score(self : rosetta.protocols.jd2.archive.EvaluatedArchive, evaluated_decoy : rosetta.core.io.silent.SilentStruct) -> float
compute score according to select_weights --- this can contain any evaluator columns
- set_evaluate_local(...) from builtins.PyCapsule
- set_evaluate_local(self : rosetta.protocols.jd2.archive.EvaluatedArchive, setting : bool) -> NoneType
- set_evaluators(...) from builtins.PyCapsule
- set_evaluators(self : rosetta.protocols.jd2.archive.EvaluatedArchive, : rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t, : rosetta.std.map_std_string_double) -> NoneType
- set_scorefxn(...) from builtins.PyCapsule
- set_scorefxn(self : rosetta.protocols.jd2.archive.EvaluatedArchive, scorefxn_ : rosetta.core.scoring.ScoreFunction) -> NoneType
set scorefxn used for evaluation
- set_weight(...) from builtins.PyCapsule
- set_weight(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str, weight : float) -> NoneType
set weight of an evaluator or a column otherwise present in silent-structs
(i.e, score, chainbreak, external evaluation like score_final )
- set_weights(...) from builtins.PyCapsule
- set_weights(self : rosetta.protocols.jd2.archive.EvaluatedArchive, setting : rosetta.std.map_std_string_double) -> NoneType
- setup_default_evaluators(...) from builtins.PyCapsule
- setup_default_evaluators(rosetta.protocols.jd2.archive.EvaluatedArchive) -> NoneType
set common evaluators: eg. ConstraintEvaluator if -cst_file is present
- start_evaluation_timer(...) from builtins.PyCapsule
- start_evaluation_timer(rosetta.protocols.jd2.archive.EvaluatedArchive) -> NoneType
- weights(...) from builtins.PyCapsule
- weights(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.std.map_std_string_double
Methods inherited from ArchiveBase:
- accepts_since_last_batch(...) from builtins.PyCapsule
- accepts_since_last_batch(*args, **kwargs)
Overloaded function.
1. accepts_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int
---- methods to keep statistics of acceptance
2. accepts_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int
- current_acceptance_ratio(...) from builtins.PyCapsule
- current_acceptance_ratio(rosetta.protocols.jd2.archive.ArchiveBase) -> float
- decoys(...) from builtins.PyCapsule
- decoys(*args, **kwargs)
Overloaded function.
1. decoys(rosetta.protocols.jd2.archive.ArchiveBase) -> rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t
2. decoys(rosetta.protocols.jd2.archive.ArchiveBase) -> rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t
- finished(...) from builtins.PyCapsule
- finished(rosetta.protocols.jd2.archive.ArchiveBase) -> bool
- generate_batch(...) from builtins.PyCapsule
- generate_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType
- idle(...) from builtins.PyCapsule
- idle(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType
called when nothing is happening
- initialize(...) from builtins.PyCapsule
- initialize(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType
- load_decoys(...) from builtins.PyCapsule
- load_decoys(self : rosetta.protocols.jd2.archive.ArchiveBase, filename : str, decoys : rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType
- nstruct(...) from builtins.PyCapsule
- nstruct(rosetta.protocols.jd2.archive.ArchiveBase) -> int
how many structures should be in archive .. varies from decoys().size() in startup phase.
- proposed_since_last_batch(...) from builtins.PyCapsule
- proposed_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int
- reset_accept_counter(...) from builtins.PyCapsule
- reset_accept_counter(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType
- save_decoys(...) from builtins.PyCapsule
- save_decoys(self : rosetta.protocols.jd2.archive.ArchiveBase, dirname : str, name : str, decoys : rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType
helper routine to save decoys properly
- set_nstruct(...) from builtins.PyCapsule
- set_nstruct(self : rosetta.protocols.jd2.archive.ArchiveBase, set : int) -> NoneType
set target size of pool
- statistics_valid(...) from builtins.PyCapsule
- statistics_valid(rosetta.protocols.jd2.archive.ArchiveBase) -> bool
- total_accepts(...) from builtins.PyCapsule
- total_accepts(rosetta.protocols.jd2.archive.ArchiveBase) -> int
- total_proposed(...) from builtins.PyCapsule
- total_proposed(rosetta.protocols.jd2.archive.ArchiveBase) -> int
Methods inherited from AbstractArchiveBase:
- manager(...) from builtins.PyCapsule
- manager(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> protocols::jd2::archive::BaseArchiveManager
access to the ArchiveManager (control of batches)
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> str
- set_manager(...) from builtins.PyCapsule
- set_manager(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, manager : protocols::jd2::archive::BaseArchiveManager) -> NoneType
- set_name(...) from builtins.PyCapsule
- set_name(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, set : str) -> NoneType
set name of archive ( used also for save_to_file and restore_from_file )
- still_interested(...) from builtins.PyCapsule
- still_interested(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, : protocols::jd2::archive::Batch) -> bool
old-batches might be outdated and should not be computed anymore
return true for this query if this is the case for old_batch
|
class MPIArchiveJobDistributor(rosetta.protocols.jd2.MPIFileBufJobDistributor) |
| |
JobDistributor for the iterative ArchiveManager/Archive Framework
This job distributor is meant for running iterative jobs with the ArchiveManager/Archive Framework.
could vary greatly. In this configuration the three first nodes are dedicated processes (JobDistributor, FileBuffer, and ArchiveManger )
and the remaining CPUs form slave or worker nodes. 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:
- MPIArchiveJobDistributor
- rosetta.protocols.jd2.MPIFileBufJobDistributor
- rosetta.protocols.jd2.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.
- go(...) from builtins.PyCapsule
- go(self : rosetta.protocols.jd2.archive.MPIArchiveJobDistributor, mover : rosetta.protocols.moves.Mover) -> NoneType
overloaded to also start the ArchiveManager process
- is_archive_rank(...) from builtins.PyCapsule
- is_archive_rank(rosetta.protocols.jd2.archive.MPIArchiveJobDistributor) -> bool
- set_archive(...) from builtins.PyCapsule
- set_archive(self : rosetta.protocols.jd2.archive.MPIArchiveJobDistributor, : rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType
Methods inherited from rosetta.protocols.jd2.MPIFileBufJobDistributor:
- get_new_job_id(...) from builtins.PyCapsule
- get_new_job_id(rosetta.protocols.jd2.MPIFileBufJobDistributor) -> int
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 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 )
- 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 NormalizedEvaluatedArchive(EvaluatedArchive) |
| |
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:
- NormalizedEvaluatedArchive
- EvaluatedArchive
- ArchiveBase
- AbstractArchiveBase
- 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.
- add_evaluated_structure(...) from builtins.PyCapsule
- add_evaluated_structure(self : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, from_batch : rosetta.core.io.silent.SilentStruct, alternative_decoy : rosetta.core.io.silent.SilentStruct, : protocols::jd2::archive::Batch) -> bool
add decoy to Archive
evaluate decoy and call add_evaluated_structure
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive
- determine_score_variations(...) from builtins.PyCapsule
- determine_score_variations(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> bool
determine variation of scores (those that are non-zeros in select_weights_ )
- init_from_options(...) from builtins.PyCapsule
- init_from_options(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> NoneType
- initialize(...) from builtins.PyCapsule
- initialize(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> NoneType
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
2. register_options() -> NoneType
Archive specific options
3. register_options() -> NoneType
Archive specific options
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
- rescore(...) from builtins.PyCapsule
- rescore(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> NoneType
recompute all score-values of all decoys and re-order the archive by (new) select_score
- restore_from_file(...) from builtins.PyCapsule
- restore_from_file(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> bool
overloaded that we can sort the pool after reading
- save_to_file(...) from builtins.PyCapsule
- save_to_file(*args, **kwargs)
Overloaded function.
1. save_to_file(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> NoneType
overloaded to save / restore the variance_archive_
2. save_to_file(self : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, suffix : str) -> NoneType
overloaded to save / restore the variance_archive_
- score_variation(...) from builtins.PyCapsule
- score_variation(self : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, col : str) -> float
- score_variations(...) from builtins.PyCapsule
- score_variations(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> rosetta.std.map_std_string_double
Methods inherited from EvaluatedArchive:
- add_evaluation(...) from builtins.PyCapsule
- add_evaluation(*args, **kwargs)
Overloaded function.
1. add_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive, : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType
add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()
2. add_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive, : rosetta.protocols.evaluation.PoseEvaluator, weight : float) -> NoneType
add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()
- add_structure(...) from builtins.PyCapsule
- add_structure(self : rosetta.protocols.jd2.archive.EvaluatedArchive, new_decoy : rosetta.core.io.silent.SilentStruct, alternative_decoy : rosetta.core.io.silent.SilentStruct, batch : protocols::jd2::archive::Batch) -> bool
add decoy to Archive
evaluate decoy and call add_evaluated_structure
- evaluate_local(...) from builtins.PyCapsule
- evaluate_local(rosetta.protocols.jd2.archive.EvaluatedArchive) -> bool
specify if decoys are evaluated on the master or (non-local i.e., on the individual slave nodes)
- evaluate_silent_struct(...) from builtins.PyCapsule
- evaluate_silent_struct(self : rosetta.protocols.jd2.archive.EvaluatedArchive, from_batch : rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct
yields an "evaluated" silent-struct which can be queried with select_score
will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct
- evaluators(...) from builtins.PyCapsule
- evaluators(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t
- get_weight(...) from builtins.PyCapsule
- get_weight(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> float
- has_evaluator(...) from builtins.PyCapsule
- has_evaluator(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> bool
is a certain elvaluator present ?
- init_from_decoy_set(...) from builtins.PyCapsule
- init_from_decoy_set(self : rosetta.protocols.jd2.archive.EvaluatedArchive, sfd : rosetta.core.io.silent.SilentFileData) -> NoneType
overloaded to make input decoys appear the same as decoys coming from batches
- read_structures(...) from builtins.PyCapsule
- read_structures(self : rosetta.protocols.jd2.archive.EvaluatedArchive, sfd : rosetta.core.io.silent.SilentFileData, alternative_decoys : rosetta.core.io.silent.SilentFileData, batch : protocols::jd2::archive::Batch) -> NoneType
only overloaded this to add some verbosity each time we read structures
- remove_evaluation(...) from builtins.PyCapsule
- remove_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> NoneType
remove Evaluator
- scorefxn(...) from builtins.PyCapsule
- scorefxn(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.core.scoring.ScoreFunction
- select_score(...) from builtins.PyCapsule
- select_score(self : rosetta.protocols.jd2.archive.EvaluatedArchive, evaluated_decoy : rosetta.core.io.silent.SilentStruct) -> float
compute score according to select_weights --- this can contain any evaluator columns
- set_evaluate_local(...) from builtins.PyCapsule
- set_evaluate_local(self : rosetta.protocols.jd2.archive.EvaluatedArchive, setting : bool) -> NoneType
- set_evaluators(...) from builtins.PyCapsule
- set_evaluators(self : rosetta.protocols.jd2.archive.EvaluatedArchive, : rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t, : rosetta.std.map_std_string_double) -> NoneType
- set_scorefxn(...) from builtins.PyCapsule
- set_scorefxn(self : rosetta.protocols.jd2.archive.EvaluatedArchive, scorefxn_ : rosetta.core.scoring.ScoreFunction) -> NoneType
set scorefxn used for evaluation
- set_weight(...) from builtins.PyCapsule
- set_weight(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str, weight : float) -> NoneType
set weight of an evaluator or a column otherwise present in silent-structs
(i.e, score, chainbreak, external evaluation like score_final )
- set_weights(...) from builtins.PyCapsule
- set_weights(self : rosetta.protocols.jd2.archive.EvaluatedArchive, setting : rosetta.std.map_std_string_double) -> NoneType
- setup_default_evaluators(...) from builtins.PyCapsule
- setup_default_evaluators(rosetta.protocols.jd2.archive.EvaluatedArchive) -> NoneType
set common evaluators: eg. ConstraintEvaluator if -cst_file is present
- start_evaluation_timer(...) from builtins.PyCapsule
- start_evaluation_timer(rosetta.protocols.jd2.archive.EvaluatedArchive) -> NoneType
- weights(...) from builtins.PyCapsule
- weights(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.std.map_std_string_double
Methods inherited from ArchiveBase:
- accepts_since_last_batch(...) from builtins.PyCapsule
- accepts_since_last_batch(*args, **kwargs)
Overloaded function.
1. accepts_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int
---- methods to keep statistics of acceptance
2. accepts_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int
- current_acceptance_ratio(...) from builtins.PyCapsule
- current_acceptance_ratio(rosetta.protocols.jd2.archive.ArchiveBase) -> float
- decoys(...) from builtins.PyCapsule
- decoys(*args, **kwargs)
Overloaded function.
1. decoys(rosetta.protocols.jd2.archive.ArchiveBase) -> rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t
2. decoys(rosetta.protocols.jd2.archive.ArchiveBase) -> rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t
- finished(...) from builtins.PyCapsule
- finished(rosetta.protocols.jd2.archive.ArchiveBase) -> bool
- generate_batch(...) from builtins.PyCapsule
- generate_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType
- idle(...) from builtins.PyCapsule
- idle(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType
called when nothing is happening
- load_decoys(...) from builtins.PyCapsule
- load_decoys(self : rosetta.protocols.jd2.archive.ArchiveBase, filename : str, decoys : rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType
- nstruct(...) from builtins.PyCapsule
- nstruct(rosetta.protocols.jd2.archive.ArchiveBase) -> int
how many structures should be in archive .. varies from decoys().size() in startup phase.
- proposed_since_last_batch(...) from builtins.PyCapsule
- proposed_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int
- reset_accept_counter(...) from builtins.PyCapsule
- reset_accept_counter(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType
- save_decoys(...) from builtins.PyCapsule
- save_decoys(self : rosetta.protocols.jd2.archive.ArchiveBase, dirname : str, name : str, decoys : rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType
helper routine to save decoys properly
- set_nstruct(...) from builtins.PyCapsule
- set_nstruct(self : rosetta.protocols.jd2.archive.ArchiveBase, set : int) -> NoneType
set target size of pool
- statistics_valid(...) from builtins.PyCapsule
- statistics_valid(rosetta.protocols.jd2.archive.ArchiveBase) -> bool
- total_accepts(...) from builtins.PyCapsule
- total_accepts(rosetta.protocols.jd2.archive.ArchiveBase) -> int
- total_proposed(...) from builtins.PyCapsule
- total_proposed(rosetta.protocols.jd2.archive.ArchiveBase) -> int
Methods inherited from AbstractArchiveBase:
- manager(...) from builtins.PyCapsule
- manager(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> protocols::jd2::archive::BaseArchiveManager
access to the ArchiveManager (control of batches)
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> str
- set_manager(...) from builtins.PyCapsule
- set_manager(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, manager : protocols::jd2::archive::BaseArchiveManager) -> NoneType
- set_name(...) from builtins.PyCapsule
- set_name(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, set : str) -> NoneType
set name of archive ( used also for save_to_file and restore_from_file )
- still_interested(...) from builtins.PyCapsule
- still_interested(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, : protocols::jd2::archive::Batch) -> bool
old-batches might be outdated and should not be computed anymore
return true for this query if this is the case for old_batch
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class VarianceStatisticsArchive(EvaluatedArchive) |
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- Method resolution order:
- VarianceStatisticsArchive
- EvaluatedArchive
- ArchiveBase
- AbstractArchiveBase
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, name : str) -> NoneType
2. __init__(handle, rosetta.protocols.jd2.archive.VarianceStatisticsArchive) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_evaluated_structure(...) from builtins.PyCapsule
- add_evaluated_structure(self : rosetta.protocols.jd2.archive.VarianceStatisticsArchive, : rosetta.core.io.silent.SilentStruct, alternative_decoy : rosetta.core.io.silent.SilentStruct, : rosetta.protocols.jd2.archive.Batch) -> bool
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.jd2.archive.VarianceStatisticsArchive, : rosetta.protocols.jd2.archive.VarianceStatisticsArchive) -> rosetta.protocols.jd2.archive.VarianceStatisticsArchive
- generate_batch(...) from builtins.PyCapsule
- generate_batch(rosetta.protocols.jd2.archive.VarianceStatisticsArchive) -> NoneType
- init_from_decoy_set(...) from builtins.PyCapsule
- init_from_decoy_set(self : rosetta.protocols.jd2.archive.VarianceStatisticsArchive, : rosetta.core.io.silent.SilentFileData) -> NoneType
overloaded to make input decoys appear the same as decoys coming from batches
- set_insertion_prob(...) from builtins.PyCapsule
- set_insertion_prob(self : rosetta.protocols.jd2.archive.VarianceStatisticsArchive, setting : float) -> NoneType
Methods inherited from EvaluatedArchive:
- add_evaluation(...) from builtins.PyCapsule
- add_evaluation(*args, **kwargs)
Overloaded function.
1. add_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive, : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType
add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()
2. add_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive, : rosetta.protocols.evaluation.PoseEvaluator, weight : float) -> NoneType
add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()
- add_structure(...) from builtins.PyCapsule
- add_structure(self : rosetta.protocols.jd2.archive.EvaluatedArchive, new_decoy : rosetta.core.io.silent.SilentStruct, alternative_decoy : rosetta.core.io.silent.SilentStruct, batch : protocols::jd2::archive::Batch) -> bool
add decoy to Archive
evaluate decoy and call add_evaluated_structure
- evaluate_local(...) from builtins.PyCapsule
- evaluate_local(rosetta.protocols.jd2.archive.EvaluatedArchive) -> bool
specify if decoys are evaluated on the master or (non-local i.e., on the individual slave nodes)
- evaluate_silent_struct(...) from builtins.PyCapsule
- evaluate_silent_struct(self : rosetta.protocols.jd2.archive.EvaluatedArchive, from_batch : rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct
yields an "evaluated" silent-struct which can be queried with select_score
will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct
- evaluators(...) from builtins.PyCapsule
- evaluators(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t
- get_weight(...) from builtins.PyCapsule
- get_weight(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> float
- has_evaluator(...) from builtins.PyCapsule
- has_evaluator(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> bool
is a certain elvaluator present ?
- read_structures(...) from builtins.PyCapsule
- read_structures(self : rosetta.protocols.jd2.archive.EvaluatedArchive, sfd : rosetta.core.io.silent.SilentFileData, alternative_decoys : rosetta.core.io.silent.SilentFileData, batch : protocols::jd2::archive::Batch) -> NoneType
only overloaded this to add some verbosity each time we read structures
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
2. register_options() -> NoneType
Archive specific options
3. register_options() -> NoneType
Archive specific options
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
- remove_evaluation(...) from builtins.PyCapsule
- remove_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> NoneType
remove Evaluator
- rescore(...) from builtins.PyCapsule
- rescore(rosetta.protocols.jd2.archive.EvaluatedArchive) -> NoneType
recompute all score-values of all decoys and re-order the archive by (new) select_score
- restore_from_file(...) from builtins.PyCapsule
- restore_from_file(rosetta.protocols.jd2.archive.EvaluatedArchive) -> bool
overloaded that we can sort the pool after reading
- save_to_file(...) from builtins.PyCapsule
- save_to_file(*args, **kwargs)
Overloaded function.
1. save_to_file(rosetta.protocols.jd2.archive.EvaluatedArchive) -> NoneType
overloaded to save / restore the variance_archive_
2. save_to_file(self : rosetta.protocols.jd2.archive.EvaluatedArchive, suffix : str) -> NoneType
overloaded to save / restore the variance_archive_
- score_variation(...) from builtins.PyCapsule
- score_variation(self : rosetta.protocols.jd2.archive.EvaluatedArchive, col : str) -> float
- score_variations(...) from builtins.PyCapsule
- score_variations(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.std.map_std_string_double
- scorefxn(...) from builtins.PyCapsule
- scorefxn(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.core.scoring.ScoreFunction
- select_score(...) from builtins.PyCapsule
- select_score(self : rosetta.protocols.jd2.archive.EvaluatedArchive, evaluated_decoy : rosetta.core.io.silent.SilentStruct) -> float
compute score according to select_weights --- this can contain any evaluator columns
- set_evaluate_local(...) from builtins.PyCapsule
- set_evaluate_local(self : rosetta.protocols.jd2.archive.EvaluatedArchive, setting : bool) -> NoneType
- set_evaluators(...) from builtins.PyCapsule
- set_evaluators(self : rosetta.protocols.jd2.archive.EvaluatedArchive, : rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t, : rosetta.std.map_std_string_double) -> NoneType
- set_scorefxn(...) from builtins.PyCapsule
- set_scorefxn(self : rosetta.protocols.jd2.archive.EvaluatedArchive, scorefxn_ : rosetta.core.scoring.ScoreFunction) -> NoneType
set scorefxn used for evaluation
- set_weight(...) from builtins.PyCapsule
- set_weight(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str, weight : float) -> NoneType
set weight of an evaluator or a column otherwise present in silent-structs
(i.e, score, chainbreak, external evaluation like score_final )
- set_weights(...) from builtins.PyCapsule
- set_weights(self : rosetta.protocols.jd2.archive.EvaluatedArchive, setting : rosetta.std.map_std_string_double) -> NoneType
- setup_default_evaluators(...) from builtins.PyCapsule
- setup_default_evaluators(rosetta.protocols.jd2.archive.EvaluatedArchive) -> NoneType
set common evaluators: eg. ConstraintEvaluator if -cst_file is present
- start_evaluation_timer(...) from builtins.PyCapsule
- start_evaluation_timer(rosetta.protocols.jd2.archive.EvaluatedArchive) -> NoneType
- weights(...) from builtins.PyCapsule
- weights(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.std.map_std_string_double
Methods inherited from ArchiveBase:
- accepts_since_last_batch(...) from builtins.PyCapsule
- accepts_since_last_batch(*args, **kwargs)
Overloaded function.
1. accepts_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int
---- methods to keep statistics of acceptance
2. accepts_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int
- current_acceptance_ratio(...) from builtins.PyCapsule
- current_acceptance_ratio(rosetta.protocols.jd2.archive.ArchiveBase) -> float
- decoys(...) from builtins.PyCapsule
- decoys(*args, **kwargs)
Overloaded function.
1. decoys(rosetta.protocols.jd2.archive.ArchiveBase) -> rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t
2. decoys(rosetta.protocols.jd2.archive.ArchiveBase) -> rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t
- finished(...) from builtins.PyCapsule
- finished(rosetta.protocols.jd2.archive.ArchiveBase) -> bool
- idle(...) from builtins.PyCapsule
- idle(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType
called when nothing is happening
- initialize(...) from builtins.PyCapsule
- initialize(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType
- load_decoys(...) from builtins.PyCapsule
- load_decoys(self : rosetta.protocols.jd2.archive.ArchiveBase, filename : str, decoys : rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType
- nstruct(...) from builtins.PyCapsule
- nstruct(rosetta.protocols.jd2.archive.ArchiveBase) -> int
how many structures should be in archive .. varies from decoys().size() in startup phase.
- proposed_since_last_batch(...) from builtins.PyCapsule
- proposed_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int
- reset_accept_counter(...) from builtins.PyCapsule
- reset_accept_counter(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType
- save_decoys(...) from builtins.PyCapsule
- save_decoys(self : rosetta.protocols.jd2.archive.ArchiveBase, dirname : str, name : str, decoys : rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType
helper routine to save decoys properly
- set_nstruct(...) from builtins.PyCapsule
- set_nstruct(self : rosetta.protocols.jd2.archive.ArchiveBase, set : int) -> NoneType
set target size of pool
- statistics_valid(...) from builtins.PyCapsule
- statistics_valid(rosetta.protocols.jd2.archive.ArchiveBase) -> bool
- total_accepts(...) from builtins.PyCapsule
- total_accepts(rosetta.protocols.jd2.archive.ArchiveBase) -> int
- total_proposed(...) from builtins.PyCapsule
- total_proposed(rosetta.protocols.jd2.archive.ArchiveBase) -> int
Methods inherited from AbstractArchiveBase:
- manager(...) from builtins.PyCapsule
- manager(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> protocols::jd2::archive::BaseArchiveManager
access to the ArchiveManager (control of batches)
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> str
- set_manager(...) from builtins.PyCapsule
- set_manager(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, manager : protocols::jd2::archive::BaseArchiveManager) -> NoneType
- set_name(...) from builtins.PyCapsule
- set_name(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, set : str) -> NoneType
set name of archive ( used also for save_to_file and restore_from_file )
- still_interested(...) from builtins.PyCapsule
- still_interested(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, : protocols::jd2::archive::Batch) -> bool
old-batches might be outdated and should not be computed anymore
return true for this query if this is the case for old_batch
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