| | |
- builtins.object
-
- AlignmentCluster
- AlignmentClustering
- AlignmentSet
- rosetta.core.scoring.constraints.ConstraintSet(builtins.object)
-
- IgnoreSubsetConstraintSet
- rosetta.protocols.evaluation.AlignEvaluator(rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t)
-
- Align_RmsdEvaluator
- Align_RotamerEvaluator
- rosetta.protocols.evaluation.EvaluatorCreator(builtins.object)
-
- AlignRmsdTargetEvaluatorCreator
- rosetta.protocols.jd2.InnerJob(builtins.object)
-
- ThreadingJob
- rosetta.protocols.jd2.JobInputter(builtins.object)
-
- GenericJobInputter
- ThreadingJobInputter
- rosetta.protocols.jd2.JobInputterCreator(builtins.object)
-
- GenericJobInputterCreator
- ThreadingJobInputterCreator
- rosetta.protocols.moves.Mover(builtins.object)
-
- ExtraThreadingMover
- LoopRelaxMover
- LoopRelaxThreadingMover
- MultiThreadingMover
- RecoverSideChainsMover
- StealLigandMover
- StealSideChainsMover
- ThreadingMover
-
- PartialThreadingMover
- rosetta.protocols.moves.MoverCreator(builtins.object)
-
- LoopRelaxMoverCreator
class Align_RmsdEvaluator(rosetta.protocols.evaluation.AlignEvaluator) |
| | |
- Method resolution order:
- Align_RmsdEvaluator
- rosetta.protocols.evaluation.AlignEvaluator
- rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t
- rosetta.protocols.evaluation.PoseEvaluator
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle, rosetta.core.pose.Pose) -> NoneType
doc
2. __init__(handle, rosetta.core.pose.Pose, str) -> NoneType
doc
3. __init__(handle, rosetta.core.pose.Pose, str, bool) -> NoneType
doc
4. __init__(handle, rosetta.core.pose.Pose, str, bool, rosetta.core.sequence.SequenceAlignment) -> NoneType
doc
5. __init__(self : handle, native_pose : rosetta.core.pose.Pose, tag : str, calc_gdt : bool, aln : rosetta.core.sequence.SequenceAlignment, gdt_by_TM : bool) -> NoneType
6. __init__(handle, rosetta.protocols.comparative_modeling.Align_RmsdEvaluator) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(*args, **kwargs)
Overloaded function.
1. apply(self : rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, pose : rosetta.core.pose.Pose, tag : str, ss : rosetta.core.io.silent.SilentStruct) -> NoneType
2. apply(self : rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, : rosetta.core.pose.Pose) -> float
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, : rosetta.protocols.comparative_modeling.Align_RmsdEvaluator) -> rosetta.protocols.comparative_modeling.Align_RmsdEvaluator
- calc_gdt(...) from builtins.PyCapsule
- calc_gdt(*args, **kwargs)
Overloaded function.
1. calc_gdt(self : rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, setting : bool) -> NoneType
2. calc_gdt(rosetta.protocols.comparative_modeling.Align_RmsdEvaluator) -> bool
- gdt_by_TM(...) from builtins.PyCapsule
- gdt_by_TM(*args, **kwargs)
Overloaded function.
1. gdt_by_TM(self : rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, setting : bool) -> NoneType
2. gdt_by_TM(rosetta.protocols.comparative_modeling.Align_RmsdEvaluator) -> bool
- report_gdt_components(...) from builtins.PyCapsule
- report_gdt_components(*args, **kwargs)
Overloaded function.
1. report_gdt_components(self : rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, setting : bool) -> NoneType
2. report_gdt_components(rosetta.protocols.comparative_modeling.Align_RmsdEvaluator) -> bool
Methods inherited from rosetta.protocols.evaluation.AlignEvaluator:
- get_alignment(...) from builtins.PyCapsule
- get_alignment(self : rosetta.protocols.evaluation.AlignEvaluator, pose : rosetta.core.pose.Pose) -> rosetta.core.sequence.SequenceAlignment
- native_pose(...) from builtins.PyCapsule
- native_pose(rosetta.protocols.evaluation.AlignEvaluator) -> rosetta.core.pose.Pose
- report_aln_components(...) from builtins.PyCapsule
- report_aln_components(*args, **kwargs)
Overloaded function.
1. report_aln_components(self : rosetta.protocols.evaluation.AlignEvaluator, setting : bool) -> NoneType
2. report_aln_components(rosetta.protocols.evaluation.AlignEvaluator) -> bool
- tag(...) from builtins.PyCapsule
- tag(rosetta.protocols.evaluation.AlignEvaluator) -> str
Methods inherited from rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t:
- applicable(...) from builtins.PyCapsule
- applicable(*args, **kwargs)
Overloaded function.
1. applicable(self : rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t, : rosetta.core.pose.Pose) -> bool
2. applicable(self : rosetta.protocols.evaluation.PoseEvaluator, : rosetta.core.pose.Pose) -> bool
- name(...) from builtins.PyCapsule
- name(*args, **kwargs)
Overloaded function.
1. name(self : rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t, : int) -> str
2. name(self : rosetta.protocols.evaluation.PoseEvaluator, : int) -> str
- size(...) from builtins.PyCapsule
- size(*args, **kwargs)
Overloaded function.
1. size(rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t) -> int
2. size(rosetta.protocols.evaluation.PoseEvaluator) -> int
|
class Align_RotamerEvaluator(rosetta.protocols.evaluation.AlignEvaluator) |
| | |
- Method resolution order:
- Align_RotamerEvaluator
- rosetta.protocols.evaluation.AlignEvaluator
- rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t
- rosetta.protocols.evaluation.PoseEvaluator
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle, rosetta.core.pose.Pose) -> NoneType
doc
2. __init__(handle, rosetta.core.pose.Pose, str) -> NoneType
doc
3. __init__(handle, rosetta.core.pose.Pose, str, float) -> NoneType
doc
4. __init__(self : handle, native_pose : rosetta.core.pose.Pose, tag : str, chi_dev : float, aln : rosetta.core.sequence.SequenceAlignment) -> NoneType
5. __init__(handle, rosetta.protocols.comparative_modeling.Align_RotamerEvaluator) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(*args, **kwargs)
Overloaded function.
1. apply(self : rosetta.protocols.comparative_modeling.Align_RotamerEvaluator, pose : rosetta.core.pose.Pose, tag : str, ss : rosetta.core.io.silent.SilentStruct) -> NoneType
2. apply(self : rosetta.protocols.comparative_modeling.Align_RotamerEvaluator, : rosetta.core.pose.Pose) -> float
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.comparative_modeling.Align_RotamerEvaluator, : rosetta.protocols.comparative_modeling.Align_RotamerEvaluator) -> rosetta.protocols.comparative_modeling.Align_RotamerEvaluator
- chi_dev(...) from builtins.PyCapsule
- chi_dev(rosetta.protocols.comparative_modeling.Align_RotamerEvaluator) -> float
Methods inherited from rosetta.protocols.evaluation.AlignEvaluator:
- get_alignment(...) from builtins.PyCapsule
- get_alignment(self : rosetta.protocols.evaluation.AlignEvaluator, pose : rosetta.core.pose.Pose) -> rosetta.core.sequence.SequenceAlignment
- native_pose(...) from builtins.PyCapsule
- native_pose(rosetta.protocols.evaluation.AlignEvaluator) -> rosetta.core.pose.Pose
- report_aln_components(...) from builtins.PyCapsule
- report_aln_components(*args, **kwargs)
Overloaded function.
1. report_aln_components(self : rosetta.protocols.evaluation.AlignEvaluator, setting : bool) -> NoneType
2. report_aln_components(rosetta.protocols.evaluation.AlignEvaluator) -> bool
- tag(...) from builtins.PyCapsule
- tag(rosetta.protocols.evaluation.AlignEvaluator) -> str
Methods inherited from rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t:
- applicable(...) from builtins.PyCapsule
- applicable(*args, **kwargs)
Overloaded function.
1. applicable(self : rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t, : rosetta.core.pose.Pose) -> bool
2. applicable(self : rosetta.protocols.evaluation.PoseEvaluator, : rosetta.core.pose.Pose) -> bool
- name(...) from builtins.PyCapsule
- name(*args, **kwargs)
Overloaded function.
1. name(self : rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t, : int) -> str
2. name(self : rosetta.protocols.evaluation.PoseEvaluator, : int) -> str
- size(...) from builtins.PyCapsule
- size(*args, **kwargs)
Overloaded function.
1. size(rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t) -> int
2. size(rosetta.protocols.evaluation.PoseEvaluator) -> int
|
class AlignmentSet(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.protocols.comparative_modeling.AlignmentSet) -> 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.comparative_modeling.AlignmentSet) -> rosetta.utility.vector1_core_sequence_SequenceAlignment
Gets the next alignment from the stream. Might be the same
alignment every time, or might be a different alignment after each
call to this function.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.comparative_modeling.AlignmentSet, : rosetta.protocols.comparative_modeling.AlignmentSet) -> rosetta.protocols.comparative_modeling.AlignmentSet
- insert(...) from builtins.PyCapsule
- insert(self : rosetta.protocols.comparative_modeling.AlignmentSet, aln : rosetta.core.sequence.SequenceAlignment) -> NoneType
- size(...) from builtins.PyCapsule
- size(rosetta.protocols.comparative_modeling.AlignmentSet) -> int
|
class ExtraThreadingMover(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- ExtraThreadingMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, align : rosetta.core.sequence.SequenceAlignment, template_pose : rosetta.core.pose.Pose, residue_selection : rosetta.utility.vector1_unsigned_long) -> NoneType
2. __init__(handle, rosetta.protocols.comparative_modeling.ExtraThreadingMover) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- alignment(...) from builtins.PyCapsule
- alignment(rosetta.protocols.comparative_modeling.ExtraThreadingMover) -> rosetta.core.sequence.SequenceAlignment
Returns the SequenceAlignment object used in threading.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.comparative_modeling.ExtraThreadingMover, query_pose : rosetta.core.pose.Pose) -> NoneType
Threads the given Pose onto the template_pose with the
SequenceAlignment provided.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.comparative_modeling.ExtraThreadingMover, : rosetta.protocols.comparative_modeling.ExtraThreadingMover) -> rosetta.protocols.comparative_modeling.ExtraThreadingMover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.comparative_modeling.ExtraThreadingMover) -> str
- get_qt_mapping(...) from builtins.PyCapsule
- get_qt_mapping(self : rosetta.protocols.comparative_modeling.ExtraThreadingMover, query_pose : rosetta.core.pose.Pose) -> rosetta.core.id.SequenceMapping
Returns the SequenceMapping between query and template.
- query_index(...) from builtins.PyCapsule
- query_index(rosetta.protocols.comparative_modeling.ExtraThreadingMover) -> int
Returns the index of the query sequence in SequenceAlignment
object.
- template_index(...) from builtins.PyCapsule
- template_index(rosetta.protocols.comparative_modeling.ExtraThreadingMover) -> int
Returns the index of the template sequence in SequenceAlignment
object.
Methods inherited from 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
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- 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
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- 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
|
class GenericJobInputter(rosetta.protocols.jd2.JobInputter) |
| |
This is the simplest implementation of JobInputter
|
| |
- Method resolution order:
- GenericJobInputter
- rosetta.protocols.jd2.JobInputter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.comparative_modeling.GenericJobInputter) -> 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.comparative_modeling.GenericJobInputter, : rosetta.protocols.comparative_modeling.GenericJobInputter) -> rosetta.protocols.comparative_modeling.GenericJobInputter
- fill_jobs(...) from builtins.PyCapsule
- fill_jobs(self : rosetta.protocols.comparative_modeling.GenericJobInputter, jobs : rosetta.protocols.jd2.JobsContainer) -> NoneType
this function determines what jobs exist
- input_source(...) from builtins.PyCapsule
- input_source(rosetta.protocols.comparative_modeling.GenericJobInputter) -> rosetta.protocols.jd2.JobInputterInputSource.Enum
Return the type of input source that the GenericJobInputter is currently
using.
Always POSE.
- pose_from_job(...) from builtins.PyCapsule
- pose_from_job(self : rosetta.protocols.comparative_modeling.GenericJobInputter, 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 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 IgnoreSubsetConstraintSet(rosetta.core.scoring.constraints.ConstraintSet) |
| | |
- Method resolution order:
- IgnoreSubsetConstraintSet
- rosetta.core.scoring.constraints.ConstraintSet
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle, rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet) -> NoneType
2. __init__(self : handle, residues_to_ignore : rosetta.std.set_int_std_less_int_std_allocator_int_t, other : rosetta.core.scoring.constraints.ConstraintSet) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(*args, **kwargs)
Overloaded function.
1. assign(self : rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, rhs : rosetta.core.scoring.constraints.ConstraintSet) -> rosetta.core.scoring.constraints.ConstraintSet
2. assign(self : rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, : rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet) -> rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet) -> rosetta.core.scoring.constraints.ConstraintSet
- detached_clone(...) from builtins.PyCapsule
- detached_clone(rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet) -> rosetta.core.scoring.constraints.ConstraintSet
- detached_copy(...) from builtins.PyCapsule
- detached_copy(self : rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, src : rosetta.core.scoring.constraints.ConstraintSet) -> NoneType
- ignore(...) from builtins.PyCapsule
- ignore(self : rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, pos : int) -> bool
Returns true if we're supposed to ignore this sequence position,
false otherwise.
- ignore_list(...) from builtins.PyCapsule
- ignore_list(rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet) -> rosetta.std.set_int_std_less_int_std_allocator_int_t
- ignore_residue(...) from builtins.PyCapsule
- ignore_residue(self : rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, pos : int) -> NoneType
- residue_pair_constraint_exists(...) from builtins.PyCapsule
- residue_pair_constraint_exists(self : rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, pos1 : int, pos2 : int) -> bool
- residue_pair_energy(...) from builtins.PyCapsule
- residue_pair_energy(self : rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, emap : rosetta.core.scoring.EMapVector) -> NoneType
- same_type_as_me(...) from builtins.PyCapsule
- same_type_as_me(*args, **kwargs)
Overloaded function.
1. same_type_as_me(self : rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, other : rosetta.core.scoring.constraints.ConstraintSet) -> bool
2. same_type_as_me(self : rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, other : rosetta.core.scoring.constraints.ConstraintSet, recurse : bool) -> bool
- setup_for_minimizing_for_residue(...) from builtins.PyCapsule
- setup_for_minimizing_for_residue(self : rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, minmap : rosetta.core.kinematics.MinimizerMapBase, res_data_cache : rosetta.core.scoring.ResSingleMinimizationData) -> NoneType
Allow the parent class implementation to add the residue constraints
for this residue to the res_data_cache if this residue is not being ignored.
- setup_for_minimizing_for_residue_pair(...) from builtins.PyCapsule
- setup_for_minimizing_for_residue_pair(self : rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, minmap : rosetta.core.kinematics.MinimizerMapBase, res1_data_cache : rosetta.core.scoring.ResSingleMinimizationData, res2_data_cache : rosetta.core.scoring.ResSingleMinimizationData, respair_data_cache : rosetta.core.scoring.ResPairMinimizationData) -> NoneType
Allow the parent class implenetation to add the residue-pair constraints
for this residue pair to the respair_data_cache if neither residues are being ignored.
Methods inherited from rosetta.core.scoring.constraints.ConstraintSet:
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.scoring.constraints.ConstraintSet) -> str
- add_constraint(...) from builtins.PyCapsule
- add_constraint(self : rosetta.core.scoring.constraints.ConstraintSet, cst : rosetta.core.scoring.constraints.Constraint) -> NoneType
- add_constraints(...) from builtins.PyCapsule
- add_constraints(*args, **kwargs)
Overloaded function.
1. add_constraints(self : rosetta.core.scoring.constraints.ConstraintSet, cst_list : rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t) -> NoneType
2. add_constraints(self : rosetta.core.scoring.constraints.ConstraintSet, cst_set : rosetta.core.scoring.constraints.ConstraintSet) -> NoneType
add another constraint set to this constraint set
- add_dof_constraint(...) from builtins.PyCapsule
- add_dof_constraint(*args, **kwargs)
Overloaded function.
1. add_dof_constraint(self : rosetta.core.scoring.constraints.ConstraintSet, id : rosetta.core.id.DOF_ID, func : rosetta.core.scoring.func.Func) -> NoneType
Note -- still hacky. Will not be included in packing, just scoring
and minimization
2. add_dof_constraint(self : rosetta.core.scoring.constraints.ConstraintSet, id : rosetta.core.id.DOF_ID, func : rosetta.core.scoring.func.Func, t : rosetta.core.scoring.ScoreType) -> NoneType
Note -- still hacky. Will not be included in packing, just scoring
and minimization
- attach_to_conformation(...) from builtins.PyCapsule
- attach_to_conformation(self : rosetta.core.scoring.constraints.ConstraintSet, conformation : rosetta.std.weak_ptr_const_core_conformation_Conformation_t) -> NoneType
- clear(...) from builtins.PyCapsule
- clear(rosetta.core.scoring.constraints.ConstraintSet) -> NoneType
- clear_sequence_constraints(...) from builtins.PyCapsule
- clear_sequence_constraints(rosetta.core.scoring.constraints.ConstraintSet) -> NoneType
Discard any and all sequence constraints in the sequence_constraints_ list.
- deprecated_eval_atom_derivative(...) from builtins.PyCapsule
- deprecated_eval_atom_derivative(self : rosetta.core.scoring.constraints.ConstraintSet, atom_id : rosetta.core.id.AtomID, pose : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, weights : rosetta.core.scoring.EMapVector, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t) -> NoneType
Switching over to a pairwise decomposable eval-atom-deriv system for
RTMin means deprecating the old "evaluate an atom's derivative wrt the entire structure"
This function is preserved (for now) for use by the RNA_TorsionEnergy
- detach_from_conformation(...) from builtins.PyCapsule
- detach_from_conformation(rosetta.core.scoring.constraints.ConstraintSet) -> NoneType
- eval_intrares_energy(...) from builtins.PyCapsule
- eval_intrares_energy(*args, **kwargs)
Overloaded function.
1. eval_intrares_energy(self : rosetta.core.scoring.constraints.ConstraintSet, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, emap : rosetta.core.scoring.EMapVector) -> NoneType
2. eval_intrares_energy(self : rosetta.core.scoring.constraints.ConstraintSet, rsd : rosetta.core.conformation.Residue, emap : rosetta.core.scoring.EMapVector) -> NoneType
- eval_multibody_atom_derivative(...) from builtins.PyCapsule
- eval_multibody_atom_derivative(self : rosetta.core.scoring.constraints.ConstraintSet, atom_id : rosetta.core.id.AtomID, pose : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, weights : rosetta.core.scoring.EMapVector, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t) -> NoneType
evaluate the derivatives for an atom that contains 3- or higher-body
constraints. Such derivatives cannot be evalauated in an extra-posal context
(e.g. such as in RTMin).
- eval_non_residue_pair_energy(...) from builtins.PyCapsule
- eval_non_residue_pair_energy(self : rosetta.core.scoring.constraints.ConstraintSet, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, emap : rosetta.core.scoring.EMapVector) -> NoneType
Does *NOT* zero the emap values, just adds the additional contribution to the
existing emap energies (so can be called inside finalize_total_energies)
- get_all_constraints(...) from builtins.PyCapsule
- get_all_constraints(rosetta.core.scoring.constraints.ConstraintSet) -> rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t
Returns all constraints in the set as a flat list, regardless of
type.
- has_constraints(...) from builtins.PyCapsule
- has_constraints(rosetta.core.scoring.constraints.ConstraintSet) -> bool
- has_dof_constraints(...) from builtins.PyCapsule
- has_dof_constraints(rosetta.core.scoring.constraints.ConstraintSet) -> bool
- has_intra_residue_constraints(...) from builtins.PyCapsule
- has_intra_residue_constraints(rosetta.core.scoring.constraints.ConstraintSet) -> bool
- has_non_residue_pair_constraints(...) from builtins.PyCapsule
- has_non_residue_pair_constraints(rosetta.core.scoring.constraints.ConstraintSet) -> bool
- has_residue_pair_constraints(...) from builtins.PyCapsule
- has_residue_pair_constraints(rosetta.core.scoring.constraints.ConstraintSet) -> bool
- is_empty(...) from builtins.PyCapsule
- is_empty(rosetta.core.scoring.constraints.ConstraintSet) -> bool
- n_sequence_constraints(...) from builtins.PyCapsule
- n_sequence_constraints(rosetta.core.scoring.constraints.ConstraintSet) -> int
Get the number of sequence constraints.
- on_connection_change(...) from builtins.PyCapsule
- on_connection_change(self : rosetta.core.scoring.constraints.ConstraintSet, event : rosetta.core.conformation.signals.ConnectionEvent) -> NoneType
- on_length_change(...) from builtins.PyCapsule
- on_length_change(self : rosetta.core.scoring.constraints.ConstraintSet, event : rosetta.core.conformation.signals.LengthEvent) -> NoneType
- remap_residue_positions(...) from builtins.PyCapsule
- remap_residue_positions(self : rosetta.core.scoring.constraints.ConstraintSet, smap : rosetta.core.id.SequenceMapping) -> NoneType
remaps the constraints in this particular constraint set according
to brief the passed in sequence mapping --- redundant with
remapped_clone!!!
- remapped_clone(...) from builtins.PyCapsule
- remapped_clone(*args, **kwargs)
Overloaded function.
1. remapped_clone(self : rosetta.core.scoring.constraints.ConstraintSet, src : rosetta.core.pose.Pose, dest : rosetta.core.pose.Pose) -> rosetta.core.scoring.constraints.ConstraintSet
Copies the data from this ConstraintSet into a new object and
returns its OP; atoms are mapped to atoms with the same name in dest pose
( e.g. for switch from centroid to fullatom ) if a sequence_mapping is
present it is used to map residue numbers .. NULL = identity mapping to
the new object. This will really clone all constraints since they have to
change their atom-numbers and residue-numbers
2. remapped_clone(self : rosetta.core.scoring.constraints.ConstraintSet, src : rosetta.core.pose.Pose, dest : rosetta.core.pose.Pose, smap : rosetta.core.id.SequenceMapping) -> rosetta.core.scoring.constraints.ConstraintSet
Copies the data from this ConstraintSet into a new object and
returns its OP; atoms are mapped to atoms with the same name in dest pose
( e.g. for switch from centroid to fullatom ) if a sequence_mapping is
present it is used to map residue numbers .. NULL = identity mapping to
the new object. This will really clone all constraints since they have to
change their atom-numbers and residue-numbers
- remove_constraint(...) from builtins.PyCapsule
- remove_constraint(self : rosetta.core.scoring.constraints.ConstraintSet, cst : rosetta.core.scoring.constraints.Constraint, object_comparison : bool) -> bool
Returns true if the constraint was successfully found and removed.
if object comparison is set to true, the constraint to be removed is found
through the Constraint::== operator and not through pointer comparison
- remove_constraints(...) from builtins.PyCapsule
- remove_constraints(self : rosetta.core.scoring.constraints.ConstraintSet, cst_list : rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t, object_comparison : bool) -> bool
- residue_pair_constraints_begin(...) from builtins.PyCapsule
- residue_pair_constraints_begin(self : rosetta.core.scoring.constraints.ConstraintSet, resid : int) -> std::_Rb_tree_const_iterator<std::pair<unsigned long const, std::shared_ptr<core::scoring::constraints::Constraints> > >
- residue_pair_constraints_end(...) from builtins.PyCapsule
- residue_pair_constraints_end(self : rosetta.core.scoring.constraints.ConstraintSet, resid : int) -> std::_Rb_tree_const_iterator<std::pair<unsigned long const, std::shared_ptr<core::scoring::constraints::Constraints> > >
- residue_pair_constraints_exists(...) from builtins.PyCapsule
- residue_pair_constraints_exists(self : rosetta.core.scoring.constraints.ConstraintSet, pos : int) -> bool
- revision_id(...) from builtins.PyCapsule
- revision_id(rosetta.core.scoring.constraints.ConstraintSet) -> int
- sequence_constraint(...) from builtins.PyCapsule
- sequence_constraint(self : rosetta.core.scoring.constraints.ConstraintSet, index : int) -> rosetta.core.scoring.aa_composition_energy.SequenceConstraint
Get the owning pointer to the Nth sequence constraint.
- setup_for_derivatives(...) from builtins.PyCapsule
- setup_for_derivatives(self : rosetta.core.scoring.constraints.ConstraintSet, pose : rosetta.core.pose.Pose, scfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- setup_for_scoring(...) from builtins.PyCapsule
- setup_for_scoring(self : rosetta.core.scoring.constraints.ConstraintSet, pose : rosetta.core.pose.Pose, scfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- steal_def_clone(...) from builtins.PyCapsule
- steal_def_clone(*args, **kwargs)
Overloaded function.
1. steal_def_clone(self : rosetta.core.scoring.constraints.ConstraintSet, src : rosetta.core.pose.Pose, dest : rosetta.core.pose.Pose) -> rosetta.core.scoring.constraints.ConstraintSet
like remapped_clone, but constraints also steal_def from src-pose
use, e.g., to get a new set of CoordinateConstraints for given xyz
coordinates in src-pose
2. steal_def_clone(self : rosetta.core.scoring.constraints.ConstraintSet, src : rosetta.core.pose.Pose, dest : rosetta.core.pose.Pose, smap : rosetta.core.id.SequenceMapping) -> rosetta.core.scoring.constraints.ConstraintSet
like remapped_clone, but constraints also steal_def from src-pose
use, e.g., to get a new set of CoordinateConstraints for given xyz
coordinates in src-pose
|
class LoopRelaxMover(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- LoopRelaxMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, remodel : str, intermedrelax : str, refine : str, relax : str, loops : rosetta.protocols.loops.Loops) -> NoneType
3. __init__(self : handle, remodel : str, intermedrelax : str, refine : str, relax : str, loops_from_file : protocols::loops::LoopsFileData) -> NoneType
4. __init__(self : handle, remodel : str, intermedrelax : str, refine : str, relax : str, guarded_loops : protocols::loops::GuardedLoopsFromFile) -> NoneType
5. __init__(handle, rosetta.protocols.comparative_modeling.LoopRelaxMover) -> 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.comparative_modeling.LoopRelaxMover, pose : rosetta.core.pose.Pose) -> NoneType
Apply the loop-relax protocol to a Pose. At the call to this function, the
loop indices originating from the loop file (which may list indices with PDB identifiers
i.e. res+insertioncode+chain ) will be resolved. Until this point, the Loops object
in the LoopRelaxMover cannot be used.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.comparative_modeling.LoopRelaxMover, rhs : rosetta.protocols.comparative_modeling.LoopRelaxMover) -> rosetta.protocols.comparative_modeling.LoopRelaxMover
assignment operator; Shallow copy of all data.
- cen_scorefxn(...) from builtins.PyCapsule
- cen_scorefxn(self : rosetta.protocols.comparative_modeling.LoopRelaxMover, cen_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.comparative_modeling.LoopRelaxMover) -> rosetta.protocols.moves.Mover
- cmd_line_csts(...) from builtins.PyCapsule
- cmd_line_csts(*args, **kwargs)
Overloaded function.
1. cmd_line_csts(self : rosetta.protocols.comparative_modeling.LoopRelaxMover, setting : bool) -> NoneType
2. cmd_line_csts(rosetta.protocols.comparative_modeling.LoopRelaxMover) -> bool
- compute_rmsd(...) from builtins.PyCapsule
- compute_rmsd(*args, **kwargs)
Overloaded function.
1. compute_rmsd(self : rosetta.protocols.comparative_modeling.LoopRelaxMover, c : bool) -> NoneType
2. compute_rmsd(rosetta.protocols.comparative_modeling.LoopRelaxMover) -> bool
- copy_sidechains(...) from builtins.PyCapsule
- copy_sidechains(*args, **kwargs)
Overloaded function.
1. copy_sidechains(self : rosetta.protocols.comparative_modeling.LoopRelaxMover, setting : bool) -> NoneType
2. copy_sidechains(rosetta.protocols.comparative_modeling.LoopRelaxMover) -> bool
- fa_scorefxn(...) from builtins.PyCapsule
- fa_scorefxn(self : rosetta.protocols.comparative_modeling.LoopRelaxMover, fa_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- frag_libs(...) from builtins.PyCapsule
- frag_libs(*args, **kwargs)
Overloaded function.
1. frag_libs(self : rosetta.protocols.comparative_modeling.LoopRelaxMover, new_libs : rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t) -> NoneType
2. frag_libs(rosetta.protocols.comparative_modeling.LoopRelaxMover) -> rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.comparative_modeling.LoopRelaxMover) -> rosetta.protocols.moves.Mover
- get_loops(...) from builtins.PyCapsule
- get_loops(*args, **kwargs)
Overloaded function.
1. get_loops(rosetta.protocols.comparative_modeling.LoopRelaxMover) -> rosetta.protocols.loops.Loops
Loops accessor. May only be retrieved after the loop indices have been resolved
in a call to apply.
2. get_loops(rosetta.protocols.comparative_modeling.LoopRelaxMover) -> rosetta.protocols.loops.Loops
Loops accessor. May only be retrieved after the loop indices have been resolved
in a call to apply.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.comparative_modeling.LoopRelaxMover) -> str
- intermedrelax(...) from builtins.PyCapsule
- intermedrelax(*args, **kwargs)
Overloaded function.
1. intermedrelax(self : rosetta.protocols.comparative_modeling.LoopRelaxMover, val : str) -> NoneType
2. intermedrelax(rosetta.protocols.comparative_modeling.LoopRelaxMover) -> str
- loops(...) from builtins.PyCapsule
- loops(self : rosetta.protocols.comparative_modeling.LoopRelaxMover, val : rosetta.protocols.loops.Loops) -> NoneType
set the Loops object (with resolved indices) directly. This would override
the unresolved-indices held in the LoopsFileData if that data were set in the constructor
- loops_file_data(...) from builtins.PyCapsule
- loops_file_data(self : rosetta.protocols.comparative_modeling.LoopRelaxMover, loopfiledata : protocols::loops::LoopsFileData) -> NoneType
Set the loop file data. This will require that a Pose be presented to
the LoopRelax object before get_loops() can be called.
- n_rebuild_tries(...) from builtins.PyCapsule
- n_rebuild_tries(*args, **kwargs)
Overloaded function.
1. n_rebuild_tries(self : rosetta.protocols.comparative_modeling.LoopRelaxMover, setting : int) -> NoneType
2. n_rebuild_tries(rosetta.protocols.comparative_modeling.LoopRelaxMover) -> int
- rebuild_filter(...) from builtins.PyCapsule
- rebuild_filter(*args, **kwargs)
Overloaded function.
1. rebuild_filter(self : rosetta.protocols.comparative_modeling.LoopRelaxMover, setting : float) -> NoneType
2. rebuild_filter(rosetta.protocols.comparative_modeling.LoopRelaxMover) -> float
- refine(...) from builtins.PyCapsule
- refine(*args, **kwargs)
Overloaded function.
1. refine(self : rosetta.protocols.comparative_modeling.LoopRelaxMover, val : str) -> NoneType
2. refine(rosetta.protocols.comparative_modeling.LoopRelaxMover) -> str
- relax(...) from builtins.PyCapsule
- relax(*args, **kwargs)
Overloaded function.
1. relax(self : rosetta.protocols.comparative_modeling.LoopRelaxMover, val : str) -> NoneType
2. relax(rosetta.protocols.comparative_modeling.LoopRelaxMover) -> str
- remodel(...) from builtins.PyCapsule
- remodel(*args, **kwargs)
Overloaded function.
1. remodel(self : rosetta.protocols.comparative_modeling.LoopRelaxMover, val : str) -> NoneType
2. remodel(rosetta.protocols.comparative_modeling.LoopRelaxMover) -> str
- resolve_loopfile_indices(...) from builtins.PyCapsule
- resolve_loopfile_indices(self : rosetta.protocols.comparative_modeling.LoopRelaxMover, pose : rosetta.core.pose.Pose) -> NoneType
Must be called before the Loops data can be read from.
- scorefxns(...) from builtins.PyCapsule
- scorefxns(self : rosetta.protocols.comparative_modeling.LoopRelaxMover, cen_scorefxn : rosetta.core.scoring.ScoreFunction, fa_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
Methods inherited from 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
- 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
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- 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
|
class LoopRelaxThreadingMover(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- LoopRelaxThreadingMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover) -> 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.comparative_modeling.LoopRelaxThreadingMover, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover, : rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover) -> rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover) -> str
- setup(...) from builtins.PyCapsule
- setup(rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover) -> NoneType
Methods inherited from 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
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- 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
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- 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
|
class MultiThreadingMover(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- MultiThreadingMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, aligns : rosetta.utility.vector1_core_sequence_SequenceAlignment, template_poses : rosetta.utility.vector1_core_pose_Pose) -> NoneType
2. __init__(handle, rosetta.protocols.comparative_modeling.MultiThreadingMover) -> 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.comparative_modeling.MultiThreadingMover, query_pose : rosetta.core.pose.Pose) -> NoneType
Threads the given Pose onto the template_pose with the
SequenceAlignment provided.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.comparative_modeling.MultiThreadingMover, : rosetta.protocols.comparative_modeling.MultiThreadingMover) -> rosetta.protocols.comparative_modeling.MultiThreadingMover
- build_loops(...) from builtins.PyCapsule
- build_loops(*args, **kwargs)
Overloaded function.
1. build_loops(self : rosetta.protocols.comparative_modeling.MultiThreadingMover, setting : bool) -> NoneType
2. build_loops(rosetta.protocols.comparative_modeling.MultiThreadingMover) -> bool
- frag_libs(...) from builtins.PyCapsule
- frag_libs(*args, **kwargs)
Overloaded function.
1. frag_libs(rosetta.protocols.comparative_modeling.MultiThreadingMover) -> rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t
2. frag_libs(self : rosetta.protocols.comparative_modeling.MultiThreadingMover, new_libs : rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t) -> NoneType
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.comparative_modeling.MultiThreadingMover) -> str
- min_loop_size(...) from builtins.PyCapsule
- min_loop_size(*args, **kwargs)
Overloaded function.
1. min_loop_size(self : rosetta.protocols.comparative_modeling.MultiThreadingMover, new_size : int) -> NoneType
2. min_loop_size(rosetta.protocols.comparative_modeling.MultiThreadingMover) -> int
- randomize_loop_coords(...) from builtins.PyCapsule
- randomize_loop_coords(*args, **kwargs)
Overloaded function.
1. randomize_loop_coords(self : rosetta.protocols.comparative_modeling.MultiThreadingMover, setting : bool) -> NoneType
2. randomize_loop_coords(rosetta.protocols.comparative_modeling.MultiThreadingMover) -> bool
- repack_query(...) from builtins.PyCapsule
- repack_query(*args, **kwargs)
Overloaded function.
1. repack_query(self : rosetta.protocols.comparative_modeling.MultiThreadingMover, setting : bool) -> NoneType
2. repack_query(rosetta.protocols.comparative_modeling.MultiThreadingMover) -> bool
Methods inherited from 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
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- 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
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- 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
|
class PartialThreadingMover(ThreadingMover) |
| | |
- Method resolution order:
- PartialThreadingMover
- ThreadingMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, align : rosetta.core.sequence.SequenceAlignment, template_pose : rosetta.core.pose.Pose) -> NoneType
2. __init__(handle, rosetta.protocols.comparative_modeling.PartialThreadingMover) -> 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.comparative_modeling.PartialThreadingMover, query_pose : rosetta.core.pose.Pose) -> NoneType
Threads the given Pose onto the template_pose with the
SequenceAlignment provided.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.comparative_modeling.PartialThreadingMover, : rosetta.protocols.comparative_modeling.PartialThreadingMover) -> rosetta.protocols.comparative_modeling.PartialThreadingMover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.comparative_modeling.PartialThreadingMover) -> str
Methods inherited from ThreadingMover:
- alignment(...) from builtins.PyCapsule
- alignment(*args, **kwargs)
Overloaded function.
1. alignment(rosetta.protocols.comparative_modeling.ThreadingMover) -> rosetta.core.sequence.SequenceAlignment
Returns the SequenceAlignment object used in threading.
2. alignment(self : rosetta.protocols.comparative_modeling.ThreadingMover, new_align : rosetta.core.sequence.SequenceAlignment) -> NoneType
Sets the SequenceAlignment associated with this object.
- build_loops(...) from builtins.PyCapsule
- build_loops(*args, **kwargs)
Overloaded function.
1. build_loops(self : rosetta.protocols.comparative_modeling.ThreadingMover, setting : bool) -> NoneType
2. build_loops(rosetta.protocols.comparative_modeling.ThreadingMover) -> bool
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.comparative_modeling.ThreadingMover) -> rosetta.protocols.moves.Mover
- frag_libs(...) from builtins.PyCapsule
- frag_libs(*args, **kwargs)
Overloaded function.
1. frag_libs(rosetta.protocols.comparative_modeling.ThreadingMover) -> rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t
2. frag_libs(self : rosetta.protocols.comparative_modeling.ThreadingMover, new_libs : rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t) -> NoneType
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.comparative_modeling.ThreadingMover) -> rosetta.protocols.moves.Mover
- get_qt_mapping(...) from builtins.PyCapsule
- get_qt_mapping(self : rosetta.protocols.comparative_modeling.ThreadingMover, query_pose : rosetta.core.pose.Pose) -> rosetta.core.id.SequenceMapping
Returns the SequenceMapping between query and template.
- min_loop_size(...) from builtins.PyCapsule
- min_loop_size(*args, **kwargs)
Overloaded function.
1. min_loop_size(self : rosetta.protocols.comparative_modeling.ThreadingMover, new_size : int) -> NoneType
2. min_loop_size(rosetta.protocols.comparative_modeling.ThreadingMover) -> int
- query_index(...) from builtins.PyCapsule
- query_index(*args, **kwargs)
Overloaded function.
1. query_index(rosetta.protocols.comparative_modeling.ThreadingMover) -> int
Returns the index of the query sequence in SequenceAlignment
object.
2. query_index(self : rosetta.protocols.comparative_modeling.ThreadingMover, new_index : int) -> NoneType
Sets the index of the query sequence in SequenceAlignment object.
- randomize_loop_coords(...) from builtins.PyCapsule
- randomize_loop_coords(*args, **kwargs)
Overloaded function.
1. randomize_loop_coords(self : rosetta.protocols.comparative_modeling.ThreadingMover, setting : bool) -> NoneType
2. randomize_loop_coords(rosetta.protocols.comparative_modeling.ThreadingMover) -> bool
- repack_query(...) from builtins.PyCapsule
- repack_query(*args, **kwargs)
Overloaded function.
1. repack_query(self : rosetta.protocols.comparative_modeling.ThreadingMover, setting : bool) -> NoneType
2. repack_query(rosetta.protocols.comparative_modeling.ThreadingMover) -> bool
- template_index(...) from builtins.PyCapsule
- template_index(*args, **kwargs)
Overloaded function.
1. template_index(rosetta.protocols.comparative_modeling.ThreadingMover) -> int
Returns the index of the template sequence in SequenceAlignment
object.
2. template_index(self : rosetta.protocols.comparative_modeling.ThreadingMover, new_index : int) -> NoneType
Sets the index of the template sequence in SequenceAlignment
object.
- template_pose(...) from builtins.PyCapsule
- template_pose(self : rosetta.protocols.comparative_modeling.ThreadingMover, template_pose : rosetta.core.pose.Pose) -> NoneType
Methods inherited from 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
- 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
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- 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
|
class RecoverSideChainsMover(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- RecoverSideChainsMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, mover : rosetta.protocols.moves.Mover) -> NoneType
2. __init__(handle, rosetta.protocols.comparative_modeling.RecoverSideChainsMover) -> 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.comparative_modeling.RecoverSideChainsMover, pose : rosetta.core.pose.Pose) -> NoneType
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.comparative_modeling.RecoverSideChainsMover) -> str
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
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- 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
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- 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
|
class StealLigandMover(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- StealLigandMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, source : rosetta.core.pose.Pose, anchor_atom_dest : rosetta.core.id.NamedAtomID, anchor_atom_source : rosetta.core.id.NamedAtomID, ligand_indices : rosetta.utility.vector1_core_id_NamedAtomID) -> NoneType
2. __init__(handle, rosetta.protocols.comparative_modeling.StealLigandMover) -> 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.comparative_modeling.StealLigandMover, pose : rosetta.core.pose.Pose) -> NoneType
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.comparative_modeling.StealLigandMover) -> str
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
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- 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
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- 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
|
class StealSideChainsMover(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- StealSideChainsMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, source : rosetta.core.pose.Pose, map : rosetta.core.id.SequenceMapping) -> NoneType
2. __init__(handle, rosetta.protocols.comparative_modeling.StealSideChainsMover) -> 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.comparative_modeling.StealSideChainsMover, pose : rosetta.core.pose.Pose) -> NoneType
maps from pose to source_
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.comparative_modeling.StealSideChainsMover) -> str
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
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- 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
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- 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
|
class ThreadingJob(rosetta.protocols.jd2.InnerJob) |
| |
The InnerThreadingJob class is responsible for knowing input requirements for a given job - how many nstruct, and what the input is. InnerThreadingJobs are relatively heavy; there is no need to duplicate a series of InnerThreadingJobs for each index into nstruct. The companion ThreadingJob class handles the nstruct index and has a pointer to an InnerThreadingJob (which is shared across many ThreadingJobs). InnerThreadingJob also holds a PoseOP to maintain the unmodified input pose for that job.
|
| |
- Method resolution order:
- ThreadingJob
- rosetta.protocols.jd2.InnerJob
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, template_pdb : rosetta.core.pose.Pose, alignment : rosetta.core.sequence.SequenceAlignment, input_tag : str, nstruct_max : int) -> NoneType
2. __init__(handle, rosetta.protocols.comparative_modeling.ThreadingJob) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- alignment(...) from builtins.PyCapsule
- alignment(rosetta.protocols.comparative_modeling.ThreadingJob) -> rosetta.core.sequence.SequenceAlignment
the alignment for this Job
- alignment_id(...) from builtins.PyCapsule
- alignment_id(rosetta.protocols.comparative_modeling.ThreadingJob) -> str
convenience : alignment id
- extra_residues_to_steal(...) from builtins.PyCapsule
- extra_residues_to_steal(*args, **kwargs)
Overloaded function.
1. extra_residues_to_steal(rosetta.protocols.comparative_modeling.ThreadingJob) -> rosetta.utility.vector1_unsigned_long
returns list of extra residues to steal
2. extra_residues_to_steal(self : rosetta.protocols.comparative_modeling.ThreadingJob, res : rosetta.utility.vector1_unsigned_long) -> NoneType
- loops(...) from builtins.PyCapsule
- loops(self : rosetta.protocols.comparative_modeling.ThreadingJob, nres : int) -> rosetta.protocols.loops.Loops
returns the "standard" loop definition (as conservative as possible)
Methods inherited from rosetta.protocols.jd2.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
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class ThreadingJobInputter(rosetta.protocols.jd2.JobInputter) |
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This is the simplest implementation of JobInputter
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- Method resolution order:
- ThreadingJobInputter
- rosetta.protocols.jd2.JobInputter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.comparative_modeling.ThreadingJobInputter) -> 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.comparative_modeling.ThreadingJobInputter, : rosetta.protocols.comparative_modeling.ThreadingJobInputter) -> rosetta.protocols.comparative_modeling.ThreadingJobInputter
- fill_jobs(...) from builtins.PyCapsule
- fill_jobs(self : rosetta.protocols.comparative_modeling.ThreadingJobInputter, jobs : rosetta.protocols.jd2.JobsContainer) -> NoneType
this function determines what jobs exist
- input_source(...) from builtins.PyCapsule
- input_source(rosetta.protocols.comparative_modeling.ThreadingJobInputter) -> rosetta.protocols.jd2.JobInputterInputSource.Enum
Return the type of input source that the ThreadingJobInputter is
currently using for template structures.
- pose_from_job(...) from builtins.PyCapsule
- pose_from_job(self : rosetta.protocols.comparative_modeling.ThreadingJobInputter, 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 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.
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class ThreadingMover(rosetta.protocols.moves.Mover) |
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- Method resolution order:
- ThreadingMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.comparative_modeling.ThreadingMover) -> NoneType
3. __init__(self : handle, align : rosetta.core.sequence.SequenceAlignment, template_pose : rosetta.core.pose.Pose) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- alignment(...) from builtins.PyCapsule
- alignment(*args, **kwargs)
Overloaded function.
1. alignment(rosetta.protocols.comparative_modeling.ThreadingMover) -> rosetta.core.sequence.SequenceAlignment
Returns the SequenceAlignment object used in threading.
2. alignment(self : rosetta.protocols.comparative_modeling.ThreadingMover, new_align : rosetta.core.sequence.SequenceAlignment) -> NoneType
Sets the SequenceAlignment associated with this object.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.comparative_modeling.ThreadingMover, query_pose : rosetta.core.pose.Pose) -> NoneType
Threads the given Pose onto the template_pose with the
SequenceAlignment provided.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.comparative_modeling.ThreadingMover, : rosetta.protocols.comparative_modeling.ThreadingMover) -> rosetta.protocols.comparative_modeling.ThreadingMover
- build_loops(...) from builtins.PyCapsule
- build_loops(*args, **kwargs)
Overloaded function.
1. build_loops(self : rosetta.protocols.comparative_modeling.ThreadingMover, setting : bool) -> NoneType
2. build_loops(rosetta.protocols.comparative_modeling.ThreadingMover) -> bool
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.comparative_modeling.ThreadingMover) -> rosetta.protocols.moves.Mover
- frag_libs(...) from builtins.PyCapsule
- frag_libs(*args, **kwargs)
Overloaded function.
1. frag_libs(rosetta.protocols.comparative_modeling.ThreadingMover) -> rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t
2. frag_libs(self : rosetta.protocols.comparative_modeling.ThreadingMover, new_libs : rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t) -> NoneType
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.comparative_modeling.ThreadingMover) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.comparative_modeling.ThreadingMover) -> str
- get_qt_mapping(...) from builtins.PyCapsule
- get_qt_mapping(self : rosetta.protocols.comparative_modeling.ThreadingMover, query_pose : rosetta.core.pose.Pose) -> rosetta.core.id.SequenceMapping
Returns the SequenceMapping between query and template.
- min_loop_size(...) from builtins.PyCapsule
- min_loop_size(*args, **kwargs)
Overloaded function.
1. min_loop_size(self : rosetta.protocols.comparative_modeling.ThreadingMover, new_size : int) -> NoneType
2. min_loop_size(rosetta.protocols.comparative_modeling.ThreadingMover) -> int
- query_index(...) from builtins.PyCapsule
- query_index(*args, **kwargs)
Overloaded function.
1. query_index(rosetta.protocols.comparative_modeling.ThreadingMover) -> int
Returns the index of the query sequence in SequenceAlignment
object.
2. query_index(self : rosetta.protocols.comparative_modeling.ThreadingMover, new_index : int) -> NoneType
Sets the index of the query sequence in SequenceAlignment object.
- randomize_loop_coords(...) from builtins.PyCapsule
- randomize_loop_coords(*args, **kwargs)
Overloaded function.
1. randomize_loop_coords(self : rosetta.protocols.comparative_modeling.ThreadingMover, setting : bool) -> NoneType
2. randomize_loop_coords(rosetta.protocols.comparative_modeling.ThreadingMover) -> bool
- repack_query(...) from builtins.PyCapsule
- repack_query(*args, **kwargs)
Overloaded function.
1. repack_query(self : rosetta.protocols.comparative_modeling.ThreadingMover, setting : bool) -> NoneType
2. repack_query(rosetta.protocols.comparative_modeling.ThreadingMover) -> bool
- template_index(...) from builtins.PyCapsule
- template_index(*args, **kwargs)
Overloaded function.
1. template_index(rosetta.protocols.comparative_modeling.ThreadingMover) -> int
Returns the index of the template sequence in SequenceAlignment
object.
2. template_index(self : rosetta.protocols.comparative_modeling.ThreadingMover, new_index : int) -> NoneType
Sets the index of the template sequence in SequenceAlignment
object.
- template_pose(...) from builtins.PyCapsule
- template_pose(self : rosetta.protocols.comparative_modeling.ThreadingMover, template_pose : rosetta.core.pose.Pose) -> NoneType
Methods inherited from 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
- 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
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- 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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