| | |
- rosetta.protocols.loop_modeling.LoopMover(rosetta.protocols.moves.Mover)
-
- AcceptanceCheck
- LoopFilter
- LoopMoverGroup
- PrepareForCentroid
- PrepareForFullatom
- rosetta.protocols.moves.MoverCreator(builtins.object)
-
- PrepareForCentroidCreator
- PrepareForFullatomCreator
class AcceptanceCheck(rosetta.protocols.loop_modeling.LoopMover) |
| |
Apply an additional Monte Carlo acceptance check.
This class is meant to be used when you have a complex loop
sampling protocol (e.g. when you are stringing together a large number of
loop movers) and you want to add intermediate acceptance checks. Note that
you don't usually have to use this class, because LoopProtocol always makes
an acceptance check after all the loop movers have been applied.
|
| |
- Method resolution order:
- AcceptanceCheck
- rosetta.protocols.loop_modeling.LoopMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle, rosetta.protocols.moves.MonteCarlo) -> NoneType
doc
2. __init__(self : handle, monte_carlo : rosetta.protocols.moves.MonteCarlo, name : str) -> NoneType
3. __init__(handle, rosetta.protocols.loop_modeling.utilities.AcceptanceCheck) -> 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.loop_modeling.utilities.AcceptanceCheck, : rosetta.protocols.loop_modeling.utilities.AcceptanceCheck) -> rosetta.protocols.loop_modeling.utilities.AcceptanceCheck
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.loop_modeling.utilities.AcceptanceCheck) -> str
LoopMover::get_name
Methods inherited from rosetta.protocols.loop_modeling.LoopMover:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.loop_modeling.LoopMover, pose : rosetta.core.pose.Pose) -> NoneType
Sample the pose in the regions specified by get_loops().
The parent class apply() method automatically sets up a fold
tree (if necessary) and keeps track of whether or not the move succeeded.
Child classes should reimplement do_apply() instead of this method.
- get_children_names(...) from builtins.PyCapsule
- get_children_names(*args, **kwargs)
Overloaded function.
1. get_children_names(self : rosetta.protocols.loop_modeling.LoopMover, names : rosetta.utility.vector1_std_string) -> NoneType
Add the names of all the algorithms invoked by this loop mover to
the given list. Indentation is used to represent hierarchy.
2. get_children_names(self : rosetta.protocols.loop_modeling.LoopMover, names : rosetta.utility.vector1_std_string, indent : str) -> NoneType
Add the names of all the algorithms invoked by this loop mover to
the given list. Indentation is used to represent hierarchy.
- get_loop(...) from builtins.PyCapsule
- get_loop(self : rosetta.protocols.loop_modeling.LoopMover, index : int) -> rosetta.protocols.loops.Loop
Return the specified loop.
- get_loops(...) from builtins.PyCapsule
- get_loops(*args, **kwargs)
Overloaded function.
1. get_loops(rosetta.protocols.loop_modeling.LoopMover) -> rosetta.protocols.loops.Loops
Return the loops to be sampled on the next call to apply().
2. get_loops(rosetta.protocols.loop_modeling.LoopMover) -> rosetta.protocols.loops.Loops
Return the loops to be sampled on the next call to apply().
- request_fold_tree(...) from builtins.PyCapsule
- request_fold_tree(rosetta.protocols.loop_modeling.LoopMover) -> rosetta.protocols.loop_modeling.FoldTreeRequest
Return an enum representing the kind of fold tree that is
compatible with this mover.
The FoldTreeRequest enum values can be combined using the
bitwise logical operators. For example, you can request either the
standard fold tree or a simple fold tree with `FTR_LOOPS_WITH_CUTS |
FTR_SIMPLE_TREE.`
- set_loop(...) from builtins.PyCapsule
- set_loop(self : rosetta.protocols.loop_modeling.LoopMover, loop : rosetta.protocols.loops.Loop) -> NoneType
Set the loop to be sampled on the next call to apply().
- set_loops(...) from builtins.PyCapsule
- set_loops(*args, **kwargs)
Overloaded function.
1. set_loops(self : rosetta.protocols.loop_modeling.LoopMover, loops : rosetta.protocols.loops.Loops) -> NoneType
Set the loops to be sampled on the next call to apply().
2. set_loops(self : rosetta.protocols.loop_modeling.LoopMover, loops : rosetta.protocols.loops.Loops) -> NoneType
Set the loops to be sampled on the next call to apply().
- setup_fold_tree(...) from builtins.PyCapsule
- setup_fold_tree(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, request : rosetta.protocols.loop_modeling.FoldTreeRequest) -> NoneType
Setup the given pose with a fold tree that is compatible with the
given loops and requests.
- trust_fold_tree(...) from builtins.PyCapsule
- trust_fold_tree(rosetta.protocols.loop_modeling.LoopMover) -> NoneType
Promise that the calling code will setup a fold tree compatible
with request_fold_tree(). If this method is not called, this mover will
setup a fold tree on its own every time apply() is called.
- was_successful(...) from builtins.PyCapsule
- was_successful(rosetta.protocols.loop_modeling.LoopMover) -> bool
Return true if the previous move was successful.
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 LoopFilter(rosetta.protocols.loop_modeling.LoopMover) |
| |
Apply any filter in the context of a loop modeling simulation.
|
| |
- Method resolution order:
- LoopFilter
- rosetta.protocols.loop_modeling.LoopMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, filter : rosetta.protocols.filters.Filter) -> NoneType
2. __init__(handle, rosetta.protocols.loop_modeling.utilities.LoopFilter) -> 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.loop_modeling.utilities.LoopFilter, : rosetta.protocols.loop_modeling.utilities.LoopFilter) -> rosetta.protocols.loop_modeling.utilities.LoopFilter
- do_apply(...) from builtins.PyCapsule
- do_apply(self : rosetta.protocols.loop_modeling.utilities.LoopFilter, pose : rosetta.core.pose.Pose) -> bool
Apply the given filter and return the result.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.loop_modeling.utilities.LoopFilter) -> str
LoopMover::get_name
Methods inherited from rosetta.protocols.loop_modeling.LoopMover:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.loop_modeling.LoopMover, pose : rosetta.core.pose.Pose) -> NoneType
Sample the pose in the regions specified by get_loops().
The parent class apply() method automatically sets up a fold
tree (if necessary) and keeps track of whether or not the move succeeded.
Child classes should reimplement do_apply() instead of this method.
- get_children_names(...) from builtins.PyCapsule
- get_children_names(*args, **kwargs)
Overloaded function.
1. get_children_names(self : rosetta.protocols.loop_modeling.LoopMover, names : rosetta.utility.vector1_std_string) -> NoneType
Add the names of all the algorithms invoked by this loop mover to
the given list. Indentation is used to represent hierarchy.
2. get_children_names(self : rosetta.protocols.loop_modeling.LoopMover, names : rosetta.utility.vector1_std_string, indent : str) -> NoneType
Add the names of all the algorithms invoked by this loop mover to
the given list. Indentation is used to represent hierarchy.
- get_loop(...) from builtins.PyCapsule
- get_loop(self : rosetta.protocols.loop_modeling.LoopMover, index : int) -> rosetta.protocols.loops.Loop
Return the specified loop.
- get_loops(...) from builtins.PyCapsule
- get_loops(*args, **kwargs)
Overloaded function.
1. get_loops(rosetta.protocols.loop_modeling.LoopMover) -> rosetta.protocols.loops.Loops
Return the loops to be sampled on the next call to apply().
2. get_loops(rosetta.protocols.loop_modeling.LoopMover) -> rosetta.protocols.loops.Loops
Return the loops to be sampled on the next call to apply().
- request_fold_tree(...) from builtins.PyCapsule
- request_fold_tree(rosetta.protocols.loop_modeling.LoopMover) -> rosetta.protocols.loop_modeling.FoldTreeRequest
Return an enum representing the kind of fold tree that is
compatible with this mover.
The FoldTreeRequest enum values can be combined using the
bitwise logical operators. For example, you can request either the
standard fold tree or a simple fold tree with `FTR_LOOPS_WITH_CUTS |
FTR_SIMPLE_TREE.`
- set_loop(...) from builtins.PyCapsule
- set_loop(self : rosetta.protocols.loop_modeling.LoopMover, loop : rosetta.protocols.loops.Loop) -> NoneType
Set the loop to be sampled on the next call to apply().
- set_loops(...) from builtins.PyCapsule
- set_loops(*args, **kwargs)
Overloaded function.
1. set_loops(self : rosetta.protocols.loop_modeling.LoopMover, loops : rosetta.protocols.loops.Loops) -> NoneType
Set the loops to be sampled on the next call to apply().
2. set_loops(self : rosetta.protocols.loop_modeling.LoopMover, loops : rosetta.protocols.loops.Loops) -> NoneType
Set the loops to be sampled on the next call to apply().
- setup_fold_tree(...) from builtins.PyCapsule
- setup_fold_tree(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, request : rosetta.protocols.loop_modeling.FoldTreeRequest) -> NoneType
Setup the given pose with a fold tree that is compatible with the
given loops and requests.
- trust_fold_tree(...) from builtins.PyCapsule
- trust_fold_tree(rosetta.protocols.loop_modeling.LoopMover) -> NoneType
Promise that the calling code will setup a fold tree compatible
with request_fold_tree(). If this method is not called, this mover will
setup a fold tree on its own every time apply() is called.
- was_successful(...) from builtins.PyCapsule
- was_successful(rosetta.protocols.loop_modeling.LoopMover) -> bool
Return true if the previous move was successful.
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 LoopMoverGroup(rosetta.protocols.loop_modeling.LoopMover) |
| |
Manage a collection of loop-sampling algorithms.
This class is meant to make a group of LoopMover objects behave
like a single LoopMover. Methods like add_mover() and add_filter() are
also provided to add movers to the group.
|
| |
- Method resolution order:
- LoopMoverGroup
- rosetta.protocols.loop_modeling.LoopMover
- 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.loop_modeling.utilities.LoopMoverGroup) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_filter(...) from builtins.PyCapsule
- add_filter(self : rosetta.protocols.loop_modeling.utilities.LoopMoverGroup, filter : rosetta.protocols.filters.Filter) -> rosetta.protocols.loop_modeling.LoopMover
Add a filter to this group.
- add_mover(...) from builtins.PyCapsule
- add_mover(self : rosetta.protocols.loop_modeling.utilities.LoopMoverGroup, task : rosetta.protocols.loop_modeling.LoopMover) -> rosetta.protocols.loop_modeling.LoopMover
Add a mover to this group.
- add_mover_group(...) from builtins.PyCapsule
- add_mover_group(rosetta.protocols.loop_modeling.utilities.LoopMoverGroup) -> rosetta.protocols.loop_modeling.utilities.LoopMoverGroup
Add a nested group to this group.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.loop_modeling.utilities.LoopMoverGroup, : rosetta.protocols.loop_modeling.utilities.LoopMoverGroup) -> rosetta.protocols.loop_modeling.utilities.LoopMoverGroup
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.loop_modeling.utilities.LoopMoverGroup) -> NoneType
Remove all movers and filters from this group.
- empty(...) from builtins.PyCapsule
- empty(rosetta.protocols.loop_modeling.utilities.LoopMoverGroup) -> bool
Return true if no movers are contained in this group.
- get_children_names(...) from builtins.PyCapsule
- get_children_names(*args, **kwargs)
Overloaded function.
1. get_children_names(self : rosetta.protocols.loop_modeling.utilities.LoopMoverGroup, names : rosetta.utility.vector1_std_string) -> NoneType
Add the names of all the algorithms invoked by this loop mover to
the given list. Indentation is used to represent hierarchy.
2. get_children_names(self : rosetta.protocols.loop_modeling.utilities.LoopMoverGroup, names : rosetta.utility.vector1_std_string, indent : str) -> NoneType
Add the names of all the algorithms invoked by this loop mover to
the given list. Indentation is used to represent hierarchy.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.loop_modeling.utilities.LoopMoverGroup) -> str
Return the name of this mover.
- mark_as_default(...) from builtins.PyCapsule
- mark_as_default(rosetta.protocols.loop_modeling.utilities.LoopMoverGroup) -> NoneType
Indicate that the current set of movers in this group is meant as
some sort of default, and should be cleared when a new mover is added.
Methods inherited from rosetta.protocols.loop_modeling.LoopMover:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.loop_modeling.LoopMover, pose : rosetta.core.pose.Pose) -> NoneType
Sample the pose in the regions specified by get_loops().
The parent class apply() method automatically sets up a fold
tree (if necessary) and keeps track of whether or not the move succeeded.
Child classes should reimplement do_apply() instead of this method.
- get_loop(...) from builtins.PyCapsule
- get_loop(self : rosetta.protocols.loop_modeling.LoopMover, index : int) -> rosetta.protocols.loops.Loop
Return the specified loop.
- get_loops(...) from builtins.PyCapsule
- get_loops(*args, **kwargs)
Overloaded function.
1. get_loops(rosetta.protocols.loop_modeling.LoopMover) -> rosetta.protocols.loops.Loops
Return the loops to be sampled on the next call to apply().
2. get_loops(rosetta.protocols.loop_modeling.LoopMover) -> rosetta.protocols.loops.Loops
Return the loops to be sampled on the next call to apply().
- request_fold_tree(...) from builtins.PyCapsule
- request_fold_tree(rosetta.protocols.loop_modeling.LoopMover) -> rosetta.protocols.loop_modeling.FoldTreeRequest
Return an enum representing the kind of fold tree that is
compatible with this mover.
The FoldTreeRequest enum values can be combined using the
bitwise logical operators. For example, you can request either the
standard fold tree or a simple fold tree with `FTR_LOOPS_WITH_CUTS |
FTR_SIMPLE_TREE.`
- set_loop(...) from builtins.PyCapsule
- set_loop(self : rosetta.protocols.loop_modeling.LoopMover, loop : rosetta.protocols.loops.Loop) -> NoneType
Set the loop to be sampled on the next call to apply().
- set_loops(...) from builtins.PyCapsule
- set_loops(*args, **kwargs)
Overloaded function.
1. set_loops(self : rosetta.protocols.loop_modeling.LoopMover, loops : rosetta.protocols.loops.Loops) -> NoneType
Set the loops to be sampled on the next call to apply().
2. set_loops(self : rosetta.protocols.loop_modeling.LoopMover, loops : rosetta.protocols.loops.Loops) -> NoneType
Set the loops to be sampled on the next call to apply().
- setup_fold_tree(...) from builtins.PyCapsule
- setup_fold_tree(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, request : rosetta.protocols.loop_modeling.FoldTreeRequest) -> NoneType
Setup the given pose with a fold tree that is compatible with the
given loops and requests.
- trust_fold_tree(...) from builtins.PyCapsule
- trust_fold_tree(rosetta.protocols.loop_modeling.LoopMover) -> NoneType
Promise that the calling code will setup a fold tree compatible
with request_fold_tree(). If this method is not called, this mover will
setup a fold tree on its own every time apply() is called.
- was_successful(...) from builtins.PyCapsule
- was_successful(rosetta.protocols.loop_modeling.LoopMover) -> bool
Return true if the previous move was successful.
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 PrepareForCentroid(rosetta.protocols.loop_modeling.LoopMover) |
| |
Convert a pose to centroid mode for low-resolution loop modeling.
|
| |
- Method resolution order:
- PrepareForCentroid
- rosetta.protocols.loop_modeling.LoopMover
- 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.loop_modeling.utilities.PrepareForCentroid) -> 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.loop_modeling.utilities.PrepareForCentroid, : rosetta.protocols.loop_modeling.utilities.PrepareForCentroid) -> rosetta.protocols.loop_modeling.utilities.PrepareForCentroid
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.loop_modeling.utilities.PrepareForCentroid) -> str
LoopMover::get_name
Methods inherited from rosetta.protocols.loop_modeling.LoopMover:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.loop_modeling.LoopMover, pose : rosetta.core.pose.Pose) -> NoneType
Sample the pose in the regions specified by get_loops().
The parent class apply() method automatically sets up a fold
tree (if necessary) and keeps track of whether or not the move succeeded.
Child classes should reimplement do_apply() instead of this method.
- get_children_names(...) from builtins.PyCapsule
- get_children_names(*args, **kwargs)
Overloaded function.
1. get_children_names(self : rosetta.protocols.loop_modeling.LoopMover, names : rosetta.utility.vector1_std_string) -> NoneType
Add the names of all the algorithms invoked by this loop mover to
the given list. Indentation is used to represent hierarchy.
2. get_children_names(self : rosetta.protocols.loop_modeling.LoopMover, names : rosetta.utility.vector1_std_string, indent : str) -> NoneType
Add the names of all the algorithms invoked by this loop mover to
the given list. Indentation is used to represent hierarchy.
- get_loop(...) from builtins.PyCapsule
- get_loop(self : rosetta.protocols.loop_modeling.LoopMover, index : int) -> rosetta.protocols.loops.Loop
Return the specified loop.
- get_loops(...) from builtins.PyCapsule
- get_loops(*args, **kwargs)
Overloaded function.
1. get_loops(rosetta.protocols.loop_modeling.LoopMover) -> rosetta.protocols.loops.Loops
Return the loops to be sampled on the next call to apply().
2. get_loops(rosetta.protocols.loop_modeling.LoopMover) -> rosetta.protocols.loops.Loops
Return the loops to be sampled on the next call to apply().
- request_fold_tree(...) from builtins.PyCapsule
- request_fold_tree(rosetta.protocols.loop_modeling.LoopMover) -> rosetta.protocols.loop_modeling.FoldTreeRequest
Return an enum representing the kind of fold tree that is
compatible with this mover.
The FoldTreeRequest enum values can be combined using the
bitwise logical operators. For example, you can request either the
standard fold tree or a simple fold tree with `FTR_LOOPS_WITH_CUTS |
FTR_SIMPLE_TREE.`
- set_loop(...) from builtins.PyCapsule
- set_loop(self : rosetta.protocols.loop_modeling.LoopMover, loop : rosetta.protocols.loops.Loop) -> NoneType
Set the loop to be sampled on the next call to apply().
- set_loops(...) from builtins.PyCapsule
- set_loops(*args, **kwargs)
Overloaded function.
1. set_loops(self : rosetta.protocols.loop_modeling.LoopMover, loops : rosetta.protocols.loops.Loops) -> NoneType
Set the loops to be sampled on the next call to apply().
2. set_loops(self : rosetta.protocols.loop_modeling.LoopMover, loops : rosetta.protocols.loops.Loops) -> NoneType
Set the loops to be sampled on the next call to apply().
- setup_fold_tree(...) from builtins.PyCapsule
- setup_fold_tree(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, request : rosetta.protocols.loop_modeling.FoldTreeRequest) -> NoneType
Setup the given pose with a fold tree that is compatible with the
given loops and requests.
- trust_fold_tree(...) from builtins.PyCapsule
- trust_fold_tree(rosetta.protocols.loop_modeling.LoopMover) -> NoneType
Promise that the calling code will setup a fold tree compatible
with request_fold_tree(). If this method is not called, this mover will
setup a fold tree on its own every time apply() is called.
- was_successful(...) from builtins.PyCapsule
- was_successful(rosetta.protocols.loop_modeling.LoopMover) -> bool
Return true if the previous move was successful.
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
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class PrepareForFullatom(rosetta.protocols.loop_modeling.LoopMover) |
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Convert a pose to fullatom mode for high-resolution loop modeling.
Before we start high-resolution loop modeling, we need to make
sure that all the residues in the pose have sidechains. There are three
ways this could happen. This first is that the pose is already in fullatom
mode and we don't have to do anything. This is important to check, because
we don't want to mess anything up if low-resolution loop modeling was
skipped. The second is by copying sidechains from the original structure,
except for those in regions where the backbone was moved, which have to be
repacked. This is the default action. The third option, which has to be
explicitly requested, is to simply repack everything.
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- Method resolution order:
- PrepareForFullatom
- rosetta.protocols.loop_modeling.LoopMover
- 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.loop_modeling.utilities.PrepareForFullatom) -> 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.loop_modeling.utilities.PrepareForFullatom, : rosetta.protocols.loop_modeling.utilities.PrepareForFullatom) -> rosetta.protocols.loop_modeling.utilities.PrepareForFullatom
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.loop_modeling.utilities.PrepareForFullatom) -> str
LoopMover::get_name
- get_score_function(...) from builtins.PyCapsule
- get_score_function(rosetta.protocols.loop_modeling.utilities.PrepareForFullatom) -> rosetta.core.scoring.ScoreFunction
Get the score function to be used on the next call to apply().
- set_force_repack(...) from builtins.PyCapsule
- set_force_repack(self : rosetta.protocols.loop_modeling.utilities.PrepareForFullatom, value : bool) -> NoneType
Guarantee the pose is repacked before the fullatom stage.
- set_original_pose(...) from builtins.PyCapsule
- set_original_pose(self : rosetta.protocols.loop_modeling.utilities.PrepareForFullatom, pose : rosetta.core.pose.Pose) -> NoneType
Set the original pose. This must be called before apply().
- set_score_function(...) from builtins.PyCapsule
- set_score_function(self : rosetta.protocols.loop_modeling.utilities.PrepareForFullatom, score_function : rosetta.core.scoring.ScoreFunction) -> NoneType
Set the score function to be used on the next call to apply().
Methods inherited from rosetta.protocols.loop_modeling.LoopMover:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.loop_modeling.LoopMover, pose : rosetta.core.pose.Pose) -> NoneType
Sample the pose in the regions specified by get_loops().
The parent class apply() method automatically sets up a fold
tree (if necessary) and keeps track of whether or not the move succeeded.
Child classes should reimplement do_apply() instead of this method.
- get_children_names(...) from builtins.PyCapsule
- get_children_names(*args, **kwargs)
Overloaded function.
1. get_children_names(self : rosetta.protocols.loop_modeling.LoopMover, names : rosetta.utility.vector1_std_string) -> NoneType
Add the names of all the algorithms invoked by this loop mover to
the given list. Indentation is used to represent hierarchy.
2. get_children_names(self : rosetta.protocols.loop_modeling.LoopMover, names : rosetta.utility.vector1_std_string, indent : str) -> NoneType
Add the names of all the algorithms invoked by this loop mover to
the given list. Indentation is used to represent hierarchy.
- get_loop(...) from builtins.PyCapsule
- get_loop(self : rosetta.protocols.loop_modeling.LoopMover, index : int) -> rosetta.protocols.loops.Loop
Return the specified loop.
- get_loops(...) from builtins.PyCapsule
- get_loops(*args, **kwargs)
Overloaded function.
1. get_loops(rosetta.protocols.loop_modeling.LoopMover) -> rosetta.protocols.loops.Loops
Return the loops to be sampled on the next call to apply().
2. get_loops(rosetta.protocols.loop_modeling.LoopMover) -> rosetta.protocols.loops.Loops
Return the loops to be sampled on the next call to apply().
- request_fold_tree(...) from builtins.PyCapsule
- request_fold_tree(rosetta.protocols.loop_modeling.LoopMover) -> rosetta.protocols.loop_modeling.FoldTreeRequest
Return an enum representing the kind of fold tree that is
compatible with this mover.
The FoldTreeRequest enum values can be combined using the
bitwise logical operators. For example, you can request either the
standard fold tree or a simple fold tree with `FTR_LOOPS_WITH_CUTS |
FTR_SIMPLE_TREE.`
- set_loop(...) from builtins.PyCapsule
- set_loop(self : rosetta.protocols.loop_modeling.LoopMover, loop : rosetta.protocols.loops.Loop) -> NoneType
Set the loop to be sampled on the next call to apply().
- set_loops(...) from builtins.PyCapsule
- set_loops(*args, **kwargs)
Overloaded function.
1. set_loops(self : rosetta.protocols.loop_modeling.LoopMover, loops : rosetta.protocols.loops.Loops) -> NoneType
Set the loops to be sampled on the next call to apply().
2. set_loops(self : rosetta.protocols.loop_modeling.LoopMover, loops : rosetta.protocols.loops.Loops) -> NoneType
Set the loops to be sampled on the next call to apply().
- setup_fold_tree(...) from builtins.PyCapsule
- setup_fold_tree(pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, request : rosetta.protocols.loop_modeling.FoldTreeRequest) -> NoneType
Setup the given pose with a fold tree that is compatible with the
given loops and requests.
- trust_fold_tree(...) from builtins.PyCapsule
- trust_fold_tree(rosetta.protocols.loop_modeling.LoopMover) -> NoneType
Promise that the calling code will setup a fold tree compatible
with request_fold_tree(). If this method is not called, this mover will
setup a fold tree on its own every time apply() is called.
- was_successful(...) from builtins.PyCapsule
- was_successful(rosetta.protocols.loop_modeling.LoopMover) -> bool
Return true if the previous move was successful.
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
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