| | |
- rosetta.protocols.loops.loop_mover.IndependentLoopMover(rosetta.protocols.loops.loop_mover.LoopMover)
-
- LoopMover_Perturb_CCD
- LoopMover_Perturb_KIC
- LoopMover_Perturb_QuickCCD
-
- LoopMover_Perturb_QuickCCD_Moves
- rosetta.protocols.moves.MoverCreator(builtins.object)
-
- LoopMover_Perturb_CCDCreator
- LoopMover_Perturb_KICCreator
- LoopMover_Perturb_QuickCCDCreator
- LoopMover_Perturb_QuickCCD_MovesCreator
class LoopMover_Perturb_CCD(rosetta.protocols.loops.loop_mover.IndependentLoopMover) |
| |
/////////////////////////////////////////////////////////////////////////////////////
the main function to model one single loop in centroid mode. The
modeling algorithm is fragment_ccd_min_trial, which consists of perturbing
the loop conformation by fragment insertion , then close the loop by CCD loop
closure, then minimize the loop conformation and finally subject it to Monte
Carlo acceptance or rejection. The loop conformation will be initialized as
extended conformation if it is specified in the loop definition, resembling
ab initio loop modeling in real practice. The loop has to be long enough for
inserting certain length of fragments.
//////////////////////////////////////////////////////////////////////////////////////
|
| |
- Method resolution order:
- LoopMover_Perturb_CCD
- rosetta.protocols.loops.loop_mover.IndependentLoopMover
- rosetta.protocols.loops.loop_mover.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__(self : handle, loops_in : rosetta.protocols.loops.Loops) -> NoneType
3. __init__(self : handle, loops_in : rosetta.protocols.loops.Loops, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
4. __init__(self : handle, loops_in : rosetta.protocols.loops.Loops, scorefxn : rosetta.core.scoring.ScoreFunction, fragset : rosetta.core.fragment.FragSet) -> NoneType
5. __init__(handle, rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD, : rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD) -> rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD) -> rosetta.protocols.moves.Mover
Clone this object
- get_loops(...) from builtins.PyCapsule
- get_loops(rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD) -> rosetta.protocols.loops.Loops
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD) -> str
- get_scorefxn(...) from builtins.PyCapsule
- get_scorefxn(rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD) -> rosetta.core.scoring.ScoreFunction
- set_default_settings(...) from builtins.PyCapsule
- set_default_settings(rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD) -> NoneType
Methods inherited from rosetta.protocols.loops.loop_mover.IndependentLoopMover:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, pose : rosetta.core.pose.Pose) -> NoneType
Apply the loop-build protocol to the input pose
- get_accept_aborted_loops(...) from builtins.PyCapsule
- get_accept_aborted_loops(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- get_all_loops_closed(...) from builtins.PyCapsule
- get_all_loops_closed(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- get_build_all_loops(...) from builtins.PyCapsule
- get_build_all_loops(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- get_build_attempts(...) from builtins.PyCapsule
- get_build_attempts(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> int
- get_grow_attempts(...) from builtins.PyCapsule
- get_grow_attempts(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> int
- get_loop_combine_rate(...) from builtins.PyCapsule
- get_loop_combine_rate(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- get_random_order(...) from builtins.PyCapsule
- get_random_order(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- get_strict_loops(...) from builtins.PyCapsule
- get_strict_loops(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- set_accept_aborted_loops_(...) from builtins.PyCapsule
- set_accept_aborted_loops_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : bool) -> NoneType
- set_build_all_loops_(...) from builtins.PyCapsule
- set_build_all_loops_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : bool) -> NoneType
- set_build_attempts_(...) from builtins.PyCapsule
- set_build_attempts_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : int) -> NoneType
Accessors:
- set_defaults(...) from builtins.PyCapsule
- set_defaults(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> NoneType
- set_grow_attempts_(...) from builtins.PyCapsule
- set_grow_attempts_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : int) -> NoneType
- set_loop_combine_rate_(...) from builtins.PyCapsule
- set_loop_combine_rate_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : float) -> NoneType
- set_random_order_(...) from builtins.PyCapsule
- set_random_order_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : bool) -> NoneType
- set_strict_loops(...) from builtins.PyCapsule
- set_strict_loops(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : bool) -> NoneType
Methods inherited from rosetta.protocols.loops.loop_mover.LoopMover:
- add_fragments(...) from builtins.PyCapsule
- add_fragments(self : rosetta.protocols.loops.loop_mover.LoopMover, fragset : rosetta.core.fragment.FragSet) -> NoneType
add a fragment set
- clear_fragments(...) from builtins.PyCapsule
- clear_fragments(rosetta.protocols.loops.loop_mover.LoopMover) -> NoneType
clear the list of fragment sets
- false_movemap(...) from builtins.PyCapsule
- false_movemap(*args, **kwargs)
Overloaded function.
1. false_movemap(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.core.kinematics.MoveMap
explicit False settings in this MoveMap will override any
automatically generated MoveMap settings during the loop modeling
protocol
2. false_movemap(self : rosetta.protocols.loops.loop_mover.LoopMover, mm : rosetta.core.kinematics.MoveMap) -> NoneType
explicit False settings in this MoveMap will override any
automatically generated MoveMap settings during the loop modeling
protocol
- frag_libs(...) from builtins.PyCapsule
- frag_libs(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t
- get_checkpoints(...) from builtins.PyCapsule
- get_checkpoints(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.checkpoint.CheckPointer
- loops(...) from builtins.PyCapsule
- loops(*args, **kwargs)
Overloaded function.
1. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, lptr : rosetta.protocols.loops.Loops) -> NoneType
Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets
the GuardedLoopsFromFile object into a "not in charge" state (since something else
must be controlling the the Loops object). The GuardedLoopFromFile object copies the pointer,
not the data.
2. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, loop_file_data : protocols::loops::LoopsFileData) -> NoneType
Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ).
3. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, guarded_loops : protocols::loops::GuardedLoopsFromFile) -> NoneType
Set the guarded_loops pointer
4. loops(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.loops.Loops
Accessor for the loops data. Requires that the loop indices have been resolved; do not call this before
apply() has been called.
5. loops(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.loops.Loops
non-const accessor for the loops data. Requires that the loop indices have been resolved; do not call this
before apply() has been called.
- scorefxn(...) from builtins.PyCapsule
- scorefxn(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.core.scoring.ScoreFunction
- set_extended_torsions(...) from builtins.PyCapsule
- set_extended_torsions(self : rosetta.protocols.loops.loop_mover.LoopMover, pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop) -> NoneType
Extend a loop
- set_guarded_loops_not_in_charge(...) from builtins.PyCapsule
- set_guarded_loops_not_in_charge(rosetta.protocols.loops.loop_mover.LoopMover) -> NoneType
Inform the GuardedLoopsFromFile object that it is not in charge of
updating its Loops object at the beginning of apply()
- set_scorefxn(...) from builtins.PyCapsule
- set_scorefxn(self : rosetta.protocols.loops.loop_mover.LoopMover, score_in : rosetta.core.scoring.ScoreFunction) -> NoneType
- torsion_features_string(...) from builtins.PyCapsule
- torsion_features_string(self : rosetta.protocols.loops.loop_mover.LoopMover, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector0_core_conformation_ppo_torsion_bin
create a string representing the torsion bins (ABEGX) for the loops defined in the
guarded_loops_ object. A sentinal value of ppo_torbin_U is used to mark the boundaries
between the separate loops (unused as long as there's only one Loop object in the
guarded_loops_ 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
- 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 LoopMover_Perturb_KIC(rosetta.protocols.loops.loop_mover.IndependentLoopMover) |
| | |
- Method resolution order:
- LoopMover_Perturb_KIC
- rosetta.protocols.loops.loop_mover.IndependentLoopMover
- rosetta.protocols.loops.loop_mover.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__(self : handle, loops_in : rosetta.protocols.loops.Loops) -> NoneType
3. __init__(self : handle, loops_in : rosetta.protocols.loops.Loops, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
4. __init__(handle, rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC, : rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC) -> rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC) -> rosetta.protocols.moves.Mover
Clone this object
- get_max_kic_build_attempts(...) from builtins.PyCapsule
- get_max_kic_build_attempts(rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC) -> int
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC) -> str
- set_default_settings(...) from builtins.PyCapsule
- set_default_settings(rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC) -> NoneType
- set_extended_torsions(...) from builtins.PyCapsule
- set_extended_torsions(self : rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC, pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop) -> NoneType
- set_max_kic_build_attempts(...) from builtins.PyCapsule
- set_max_kic_build_attempts(self : rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC, max_kic_build_attempts : int) -> NoneType
Methods inherited from rosetta.protocols.loops.loop_mover.IndependentLoopMover:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, pose : rosetta.core.pose.Pose) -> NoneType
Apply the loop-build protocol to the input pose
- get_accept_aborted_loops(...) from builtins.PyCapsule
- get_accept_aborted_loops(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- get_all_loops_closed(...) from builtins.PyCapsule
- get_all_loops_closed(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- get_build_all_loops(...) from builtins.PyCapsule
- get_build_all_loops(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- get_build_attempts(...) from builtins.PyCapsule
- get_build_attempts(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> int
- get_grow_attempts(...) from builtins.PyCapsule
- get_grow_attempts(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> int
- get_loop_combine_rate(...) from builtins.PyCapsule
- get_loop_combine_rate(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- get_random_order(...) from builtins.PyCapsule
- get_random_order(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- get_strict_loops(...) from builtins.PyCapsule
- get_strict_loops(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- set_accept_aborted_loops_(...) from builtins.PyCapsule
- set_accept_aborted_loops_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : bool) -> NoneType
- set_build_all_loops_(...) from builtins.PyCapsule
- set_build_all_loops_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : bool) -> NoneType
- set_build_attempts_(...) from builtins.PyCapsule
- set_build_attempts_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : int) -> NoneType
Accessors:
- set_defaults(...) from builtins.PyCapsule
- set_defaults(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> NoneType
- set_grow_attempts_(...) from builtins.PyCapsule
- set_grow_attempts_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : int) -> NoneType
- set_loop_combine_rate_(...) from builtins.PyCapsule
- set_loop_combine_rate_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : float) -> NoneType
- set_random_order_(...) from builtins.PyCapsule
- set_random_order_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : bool) -> NoneType
- set_strict_loops(...) from builtins.PyCapsule
- set_strict_loops(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : bool) -> NoneType
Methods inherited from rosetta.protocols.loops.loop_mover.LoopMover:
- add_fragments(...) from builtins.PyCapsule
- add_fragments(self : rosetta.protocols.loops.loop_mover.LoopMover, fragset : rosetta.core.fragment.FragSet) -> NoneType
add a fragment set
- clear_fragments(...) from builtins.PyCapsule
- clear_fragments(rosetta.protocols.loops.loop_mover.LoopMover) -> NoneType
clear the list of fragment sets
- false_movemap(...) from builtins.PyCapsule
- false_movemap(*args, **kwargs)
Overloaded function.
1. false_movemap(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.core.kinematics.MoveMap
explicit False settings in this MoveMap will override any
automatically generated MoveMap settings during the loop modeling
protocol
2. false_movemap(self : rosetta.protocols.loops.loop_mover.LoopMover, mm : rosetta.core.kinematics.MoveMap) -> NoneType
explicit False settings in this MoveMap will override any
automatically generated MoveMap settings during the loop modeling
protocol
- frag_libs(...) from builtins.PyCapsule
- frag_libs(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t
- get_checkpoints(...) from builtins.PyCapsule
- get_checkpoints(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.checkpoint.CheckPointer
- loops(...) from builtins.PyCapsule
- loops(*args, **kwargs)
Overloaded function.
1. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, lptr : rosetta.protocols.loops.Loops) -> NoneType
Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets
the GuardedLoopsFromFile object into a "not in charge" state (since something else
must be controlling the the Loops object). The GuardedLoopFromFile object copies the pointer,
not the data.
2. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, loop_file_data : protocols::loops::LoopsFileData) -> NoneType
Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ).
3. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, guarded_loops : protocols::loops::GuardedLoopsFromFile) -> NoneType
Set the guarded_loops pointer
4. loops(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.loops.Loops
Accessor for the loops data. Requires that the loop indices have been resolved; do not call this before
apply() has been called.
5. loops(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.loops.Loops
non-const accessor for the loops data. Requires that the loop indices have been resolved; do not call this
before apply() has been called.
- scorefxn(...) from builtins.PyCapsule
- scorefxn(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.core.scoring.ScoreFunction
- set_guarded_loops_not_in_charge(...) from builtins.PyCapsule
- set_guarded_loops_not_in_charge(rosetta.protocols.loops.loop_mover.LoopMover) -> NoneType
Inform the GuardedLoopsFromFile object that it is not in charge of
updating its Loops object at the beginning of apply()
- set_scorefxn(...) from builtins.PyCapsule
- set_scorefxn(self : rosetta.protocols.loops.loop_mover.LoopMover, score_in : rosetta.core.scoring.ScoreFunction) -> NoneType
- torsion_features_string(...) from builtins.PyCapsule
- torsion_features_string(self : rosetta.protocols.loops.loop_mover.LoopMover, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector0_core_conformation_ppo_torsion_bin
create a string representing the torsion bins (ABEGX) for the loops defined in the
guarded_loops_ object. A sentinal value of ppo_torbin_U is used to mark the boundaries
between the separate loops (unused as long as there's only one Loop object in the
guarded_loops_ 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
- 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 LoopMover_Perturb_QuickCCD(rosetta.protocols.loops.loop_mover.IndependentLoopMover) |
| |
LoopMover utilizing fragment insertion, ccd loop closure, and
minimization
|
| |
- Method resolution order:
- LoopMover_Perturb_QuickCCD
- rosetta.protocols.loops.loop_mover.IndependentLoopMover
- rosetta.protocols.loops.loop_mover.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__(self : handle, loops_in : rosetta.protocols.loops.Loops) -> NoneType
3. __init__(self : handle, loops_in : rosetta.protocols.loops.Loops, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
4. __init__(self : handle, loops_in : rosetta.protocols.loops.Loops, scorefxn : rosetta.core.scoring.ScoreFunction, fragset : rosetta.core.fragment.FragSet) -> NoneType
5. __init__(handle, rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD) -> 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.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD, : rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD) -> rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD) -> rosetta.protocols.moves.Mover
clone this object
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD) -> str
- randomize_loop(...) from builtins.PyCapsule
- randomize_loop(*args, **kwargs)
Overloaded function.
1. randomize_loop(rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD) -> bool
randomize loops prior to loop modeling?
2. randomize_loop(self : rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD, flag : bool) -> NoneType
indicate whether loops should be randomized prior to modeling
- set_default_settings(...) from builtins.PyCapsule
- set_default_settings(rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD) -> NoneType
set default settings
default settings are as follows:
randomize_loop() = true
Methods inherited from rosetta.protocols.loops.loop_mover.IndependentLoopMover:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, pose : rosetta.core.pose.Pose) -> NoneType
Apply the loop-build protocol to the input pose
- get_accept_aborted_loops(...) from builtins.PyCapsule
- get_accept_aborted_loops(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- get_all_loops_closed(...) from builtins.PyCapsule
- get_all_loops_closed(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- get_build_all_loops(...) from builtins.PyCapsule
- get_build_all_loops(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- get_build_attempts(...) from builtins.PyCapsule
- get_build_attempts(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> int
- get_grow_attempts(...) from builtins.PyCapsule
- get_grow_attempts(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> int
- get_loop_combine_rate(...) from builtins.PyCapsule
- get_loop_combine_rate(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- get_random_order(...) from builtins.PyCapsule
- get_random_order(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- get_strict_loops(...) from builtins.PyCapsule
- get_strict_loops(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- set_accept_aborted_loops_(...) from builtins.PyCapsule
- set_accept_aborted_loops_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : bool) -> NoneType
- set_build_all_loops_(...) from builtins.PyCapsule
- set_build_all_loops_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : bool) -> NoneType
- set_build_attempts_(...) from builtins.PyCapsule
- set_build_attempts_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : int) -> NoneType
Accessors:
- set_defaults(...) from builtins.PyCapsule
- set_defaults(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> NoneType
- set_grow_attempts_(...) from builtins.PyCapsule
- set_grow_attempts_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : int) -> NoneType
- set_loop_combine_rate_(...) from builtins.PyCapsule
- set_loop_combine_rate_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : float) -> NoneType
- set_random_order_(...) from builtins.PyCapsule
- set_random_order_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : bool) -> NoneType
- set_strict_loops(...) from builtins.PyCapsule
- set_strict_loops(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : bool) -> NoneType
Methods inherited from rosetta.protocols.loops.loop_mover.LoopMover:
- add_fragments(...) from builtins.PyCapsule
- add_fragments(self : rosetta.protocols.loops.loop_mover.LoopMover, fragset : rosetta.core.fragment.FragSet) -> NoneType
add a fragment set
- clear_fragments(...) from builtins.PyCapsule
- clear_fragments(rosetta.protocols.loops.loop_mover.LoopMover) -> NoneType
clear the list of fragment sets
- false_movemap(...) from builtins.PyCapsule
- false_movemap(*args, **kwargs)
Overloaded function.
1. false_movemap(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.core.kinematics.MoveMap
explicit False settings in this MoveMap will override any
automatically generated MoveMap settings during the loop modeling
protocol
2. false_movemap(self : rosetta.protocols.loops.loop_mover.LoopMover, mm : rosetta.core.kinematics.MoveMap) -> NoneType
explicit False settings in this MoveMap will override any
automatically generated MoveMap settings during the loop modeling
protocol
- frag_libs(...) from builtins.PyCapsule
- frag_libs(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t
- get_checkpoints(...) from builtins.PyCapsule
- get_checkpoints(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.checkpoint.CheckPointer
- loops(...) from builtins.PyCapsule
- loops(*args, **kwargs)
Overloaded function.
1. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, lptr : rosetta.protocols.loops.Loops) -> NoneType
Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets
the GuardedLoopsFromFile object into a "not in charge" state (since something else
must be controlling the the Loops object). The GuardedLoopFromFile object copies the pointer,
not the data.
2. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, loop_file_data : protocols::loops::LoopsFileData) -> NoneType
Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ).
3. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, guarded_loops : protocols::loops::GuardedLoopsFromFile) -> NoneType
Set the guarded_loops pointer
4. loops(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.loops.Loops
Accessor for the loops data. Requires that the loop indices have been resolved; do not call this before
apply() has been called.
5. loops(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.loops.Loops
non-const accessor for the loops data. Requires that the loop indices have been resolved; do not call this
before apply() has been called.
- scorefxn(...) from builtins.PyCapsule
- scorefxn(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.core.scoring.ScoreFunction
- set_extended_torsions(...) from builtins.PyCapsule
- set_extended_torsions(self : rosetta.protocols.loops.loop_mover.LoopMover, pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop) -> NoneType
Extend a loop
- set_guarded_loops_not_in_charge(...) from builtins.PyCapsule
- set_guarded_loops_not_in_charge(rosetta.protocols.loops.loop_mover.LoopMover) -> NoneType
Inform the GuardedLoopsFromFile object that it is not in charge of
updating its Loops object at the beginning of apply()
- set_scorefxn(...) from builtins.PyCapsule
- set_scorefxn(self : rosetta.protocols.loops.loop_mover.LoopMover, score_in : rosetta.core.scoring.ScoreFunction) -> NoneType
- torsion_features_string(...) from builtins.PyCapsule
- torsion_features_string(self : rosetta.protocols.loops.loop_mover.LoopMover, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector0_core_conformation_ppo_torsion_bin
create a string representing the torsion bins (ABEGX) for the loops defined in the
guarded_loops_ object. A sentinal value of ppo_torbin_U is used to mark the boundaries
between the separate loops (unused as long as there's only one Loop object in the
guarded_loops_ 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
- 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 LoopMover_Perturb_QuickCCD_Moves(LoopMover_Perturb_QuickCCD) |
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/////////////////////////////////////////////////////////////////////////////////////
The Old stuff from Looprelax
//////////////////////////////////////////////////////////////////////////////////////
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- Method resolution order:
- LoopMover_Perturb_QuickCCD_Moves
- LoopMover_Perturb_QuickCCD
- rosetta.protocols.loops.loop_mover.IndependentLoopMover
- rosetta.protocols.loops.loop_mover.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__(self : handle, loops_in : rosetta.protocols.loops.Loops) -> NoneType
3. __init__(self : handle, loops_in : rosetta.protocols.loops.Loops, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
4. __init__(handle, rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves) -> 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.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves, : rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves) -> rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves) -> rosetta.protocols.moves.Mover
Clone this object
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves) -> str
Methods inherited from LoopMover_Perturb_QuickCCD:
- randomize_loop(...) from builtins.PyCapsule
- randomize_loop(*args, **kwargs)
Overloaded function.
1. randomize_loop(rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD) -> bool
randomize loops prior to loop modeling?
2. randomize_loop(self : rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD, flag : bool) -> NoneType
indicate whether loops should be randomized prior to modeling
- set_default_settings(...) from builtins.PyCapsule
- set_default_settings(rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD) -> NoneType
set default settings
default settings are as follows:
randomize_loop() = true
Methods inherited from rosetta.protocols.loops.loop_mover.IndependentLoopMover:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, pose : rosetta.core.pose.Pose) -> NoneType
Apply the loop-build protocol to the input pose
- get_accept_aborted_loops(...) from builtins.PyCapsule
- get_accept_aborted_loops(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- get_all_loops_closed(...) from builtins.PyCapsule
- get_all_loops_closed(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- get_build_all_loops(...) from builtins.PyCapsule
- get_build_all_loops(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- get_build_attempts(...) from builtins.PyCapsule
- get_build_attempts(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> int
- get_grow_attempts(...) from builtins.PyCapsule
- get_grow_attempts(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> int
- get_loop_combine_rate(...) from builtins.PyCapsule
- get_loop_combine_rate(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- get_random_order(...) from builtins.PyCapsule
- get_random_order(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- get_strict_loops(...) from builtins.PyCapsule
- get_strict_loops(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> bool
- set_accept_aborted_loops_(...) from builtins.PyCapsule
- set_accept_aborted_loops_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : bool) -> NoneType
- set_build_all_loops_(...) from builtins.PyCapsule
- set_build_all_loops_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : bool) -> NoneType
- set_build_attempts_(...) from builtins.PyCapsule
- set_build_attempts_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : int) -> NoneType
Accessors:
- set_defaults(...) from builtins.PyCapsule
- set_defaults(rosetta.protocols.loops.loop_mover.IndependentLoopMover) -> NoneType
- set_grow_attempts_(...) from builtins.PyCapsule
- set_grow_attempts_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : int) -> NoneType
- set_loop_combine_rate_(...) from builtins.PyCapsule
- set_loop_combine_rate_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : float) -> NoneType
- set_random_order_(...) from builtins.PyCapsule
- set_random_order_(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : bool) -> NoneType
- set_strict_loops(...) from builtins.PyCapsule
- set_strict_loops(self : rosetta.protocols.loops.loop_mover.IndependentLoopMover, value : bool) -> NoneType
Methods inherited from rosetta.protocols.loops.loop_mover.LoopMover:
- add_fragments(...) from builtins.PyCapsule
- add_fragments(self : rosetta.protocols.loops.loop_mover.LoopMover, fragset : rosetta.core.fragment.FragSet) -> NoneType
add a fragment set
- clear_fragments(...) from builtins.PyCapsule
- clear_fragments(rosetta.protocols.loops.loop_mover.LoopMover) -> NoneType
clear the list of fragment sets
- false_movemap(...) from builtins.PyCapsule
- false_movemap(*args, **kwargs)
Overloaded function.
1. false_movemap(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.core.kinematics.MoveMap
explicit False settings in this MoveMap will override any
automatically generated MoveMap settings during the loop modeling
protocol
2. false_movemap(self : rosetta.protocols.loops.loop_mover.LoopMover, mm : rosetta.core.kinematics.MoveMap) -> NoneType
explicit False settings in this MoveMap will override any
automatically generated MoveMap settings during the loop modeling
protocol
- frag_libs(...) from builtins.PyCapsule
- frag_libs(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t
- get_checkpoints(...) from builtins.PyCapsule
- get_checkpoints(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.checkpoint.CheckPointer
- loops(...) from builtins.PyCapsule
- loops(*args, **kwargs)
Overloaded function.
1. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, lptr : rosetta.protocols.loops.Loops) -> NoneType
Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets
the GuardedLoopsFromFile object into a "not in charge" state (since something else
must be controlling the the Loops object). The GuardedLoopFromFile object copies the pointer,
not the data.
2. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, loop_file_data : protocols::loops::LoopsFileData) -> NoneType
Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ).
3. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, guarded_loops : protocols::loops::GuardedLoopsFromFile) -> NoneType
Set the guarded_loops pointer
4. loops(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.loops.Loops
Accessor for the loops data. Requires that the loop indices have been resolved; do not call this before
apply() has been called.
5. loops(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.loops.Loops
non-const accessor for the loops data. Requires that the loop indices have been resolved; do not call this
before apply() has been called.
- scorefxn(...) from builtins.PyCapsule
- scorefxn(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.core.scoring.ScoreFunction
- set_extended_torsions(...) from builtins.PyCapsule
- set_extended_torsions(self : rosetta.protocols.loops.loop_mover.LoopMover, pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop) -> NoneType
Extend a loop
- set_guarded_loops_not_in_charge(...) from builtins.PyCapsule
- set_guarded_loops_not_in_charge(rosetta.protocols.loops.loop_mover.LoopMover) -> NoneType
Inform the GuardedLoopsFromFile object that it is not in charge of
updating its Loops object at the beginning of apply()
- set_scorefxn(...) from builtins.PyCapsule
- set_scorefxn(self : rosetta.protocols.loops.loop_mover.LoopMover, score_in : rosetta.core.scoring.ScoreFunction) -> NoneType
- torsion_features_string(...) from builtins.PyCapsule
- torsion_features_string(self : rosetta.protocols.loops.loop_mover.LoopMover, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector0_core_conformation_ppo_torsion_bin
create a string representing the torsion bins (ABEGX) for the loops defined in the
guarded_loops_ object. A sentinal value of ppo_torbin_U is used to mark the boundaries
between the separate loops (unused as long as there's only one Loop object in the
guarded_loops_ 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
- 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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