rosetta.protocols.stepwise.modeler.rna.phosphate
index
(built-in)

Bindings for protocols::stepwise::modeler::rna::phosphate namespace

 
Classes
       
builtins.object
PhosphateMove
PhosphateTerminus
rosetta.protocols.moves.Mover(builtins.object)
MultiPhosphateSampler
PhosphateMover

 
class MultiPhosphateSampler(rosetta.protocols.moves.Mover)
    
Method resolution order:
MultiPhosphateSampler
rosetta.protocols.moves.Mover
builtins.object

Methods defined here:
__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs)
Overloaded function.
 
1. __init__(self : handle, reference_pose : rosetta.core.pose.Pose) -> NoneType
 
2. __init__(self : handle, pose_to_prepack : rosetta.core.pose.Pose, moving_res : int) -> NoneType
 
3. __init__(handle, rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler) -> NoneType
__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.
apply(...) from builtins.PyCapsule
apply(self : rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler, pose : rosetta.core.pose.Pose) -> NoneType
assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler,  : rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler) -> rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler
clone(...) from builtins.PyCapsule
clone(rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler) -> rosetta.protocols.moves.Mover
clone_sampler(...) from builtins.PyCapsule
clone_sampler(rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler) -> rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler
copy_phosphates(...) from builtins.PyCapsule
copy_phosphates(self : rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler, mod_pose : rosetta.core.pose.Pose) -> NoneType
do_prepack(...) from builtins.PyCapsule
do_prepack(self : rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler, pose : rosetta.core.pose.Pose, moving_res_list : rosetta.utility.vector1_unsigned_long) -> NoneType
force_phosphate_instantiation(...) from builtins.PyCapsule
force_phosphate_instantiation(rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler) -> bool
get_name(...) from builtins.PyCapsule
get_name(rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler) -> str
get_scorefxn(...) from builtins.PyCapsule
get_scorefxn(rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler) -> rosetta.core.scoring.ScoreFunction
initialize_by_prepack(...) from builtins.PyCapsule
initialize_by_prepack(*args, **kwargs)
Overloaded function.
 
1. initialize_by_prepack(self : rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler, pose : rosetta.core.pose.Pose, moving_res : int) -> NoneType
 
2. initialize_by_prepack(self : rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler, pose : rosetta.core.pose.Pose, moving_res_list : rosetta.utility.vector1_unsigned_long) -> NoneType
instantiated_some_phosphate(...) from builtins.PyCapsule
instantiated_some_phosphate(rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler) -> bool
moving_partition_res(...) from builtins.PyCapsule
moving_partition_res(rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler) -> rosetta.utility.vector1_unsigned_long
phosphate_move_list(...) from builtins.PyCapsule
phosphate_move_list(rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler) -> rosetta.utility.vector1_protocols_stepwise_modeler_rna_phosphate_PhosphateMove
pose(...) from builtins.PyCapsule
pose(rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler) -> rosetta.core.pose.Pose
reset(...) from builtins.PyCapsule
reset(self : rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler, pose : rosetta.core.pose.Pose) -> NoneType
reset_to_original_pose(...) from builtins.PyCapsule
reset_to_original_pose(rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler) -> NoneType
sample_phosphates(...) from builtins.PyCapsule
sample_phosphates(*args, **kwargs)
Overloaded function.
 
1. sample_phosphates(rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler) -> NoneType
 
2. sample_phosphates(self : rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler, viewer_pose_op : rosetta.core.pose.Pose) -> NoneType
screen_all(...) from builtins.PyCapsule
screen_all(rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler) -> bool
set_five_prime_phosphate_res(...) from builtins.PyCapsule
set_five_prime_phosphate_res(self : rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler, setting : rosetta.utility.vector1_unsigned_long) -> NoneType
set_force_phosphate_instantiation(...) from builtins.PyCapsule
set_force_phosphate_instantiation(self : rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler, setting : bool) -> NoneType
set_moving_partition_res(...) from builtins.PyCapsule
set_moving_partition_res(self : rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler, setting : rosetta.utility.vector1_unsigned_long) -> NoneType
set_phosphate_move_list(...) from builtins.PyCapsule
set_phosphate_move_list(self : rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler, setting : rosetta.utility.vector1_protocols_stepwise_modeler_rna_phosphate_PhosphateMove) -> NoneType
set_scorefxn(...) from builtins.PyCapsule
set_scorefxn(self : rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
set_screen_all(...) from builtins.PyCapsule
set_screen_all(self : rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler, setting : bool) -> NoneType
set_three_prime_phosphate_res(...) from builtins.PyCapsule
set_three_prime_phosphate_res(self : rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler, setting : rosetta.utility.vector1_unsigned_long) -> NoneType

Methods inherited from rosetta.protocols.moves.Mover:
clear_info(...) from builtins.PyCapsule
clear_info(rosetta.protocols.moves.Mover) -> NoneType
 
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
 
 
 clear_info is called by jd2 before calling apply
create(...) from builtins.PyCapsule
create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
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 Moverget_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 PhosphateMove(builtins.object)
     Methods defined here:
__eq__(...) from builtins.PyCapsule
__eq__(self : rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMove, other : rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMove) -> bool
__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs)
Overloaded function.
 
1. __init__(self : rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMove, rsd : int, terminus : rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateTerminus) -> NoneType
 
2. __init__(self : rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMove,  : rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMove) -> 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.stepwise.modeler.rna.phosphate.PhosphateMove) -> str
assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMove,  : rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMove) -> rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMove
rsd(...) from builtins.PyCapsule
rsd(rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMove) -> int
terminus(...) from builtins.PyCapsule
terminus(rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMove) -> rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateTerminus

 
class PhosphateMover(rosetta.protocols.moves.Mover)
    ////////////////////////////////////////////////////////////
 
 
Method resolution order:
PhosphateMover
rosetta.protocols.moves.Mover
builtins.object

Methods defined here:
__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs)
Overloaded function.
 
1. __init__(self : handle, sample_res : int, which_terminus_ : rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateTerminus, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
 
2. __init__(self : handle, phosphate_move : rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMove, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
 
3. __init__(handle, rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover) -> NoneType
__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.
apply(...) from builtins.PyCapsule
apply(self : rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover, pose_to_visualize : rosetta.core.pose.Pose) -> NoneType
force_phosphate_instantiation(...) from builtins.PyCapsule
force_phosphate_instantiation(rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover) -> bool
get_name(...) from builtins.PyCapsule
get_name(rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover) -> str
instantiated_phosphate(...) from builtins.PyCapsule
instantiated_phosphate(rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover) -> bool
screen_phosphate(...) from builtins.PyCapsule
screen_phosphate(self : rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover, pose : rosetta.core.pose.Pose) -> NoneType
set_force_phosphate_instantiation(...) from builtins.PyCapsule
set_force_phosphate_instantiation(self : rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover, setting : bool) -> NoneType

Methods inherited from rosetta.protocols.moves.Mover:
assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.moves.Mover, other : rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
clear_info(...) from builtins.PyCapsule
clear_info(rosetta.protocols.moves.Mover) -> NoneType
 
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
 
 
 clear_info is called by jd2 before calling apply
clone(...) from builtins.PyCapsule
clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
 
Return a clone of the Mover object.
create(...) from builtins.PyCapsule
create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
fresh_instance(...) from builtins.PyCapsule
fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
 
Generates a new Mover object freshly created with the default ctor.
get_additional_output(...) from builtins.PyCapsule
get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
 
fpd
 
 
 Mechanism by which a mover may return multiple output poses from a single input pose.
get_current_job(...) from builtins.PyCapsule
get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
get_current_tag(...) from builtins.PyCapsule
get_current_tag(rosetta.protocols.moves.Mover) -> str
 
A tag is a unique identifier used to identify structures produced
 by this Moverget_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 PhosphateTerminus(builtins.object)
     Methods defined here:
__eq__(...) from builtins.PyCapsule
__eq__(rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateTerminus, rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateTerminus) -> bool
__hash__(...) from builtins.PyCapsule
__hash__(rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateTerminus) -> int
__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs)
Overloaded function.
 
1. __init__(rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateTerminus, int) -> NoneType
 
2. __init__(rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateTerminus, int) -> NoneType
__int__(...) from builtins.PyCapsule
__int__(rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateTerminus) -> int
__ne__(...) from builtins.PyCapsule
__ne__(rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateTerminus, rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateTerminus) -> bool
__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.
__repr__(...) from builtins.PyCapsule
__repr__(rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateTerminus) -> str

Data and other attributes defined here:
FIVE_PRIME_PHOSPHATE = PhosphateTerminus.FIVE_PRIME_PHOSPHATE
NONE = PhosphateTerminus.NONE
THREE_PRIME_PHOSPHATE = PhosphateTerminus.THREE_PRIME_PHOSPHATE

 
Functions
       
check_phosphate_contacts_donor(...) method of builtins.PyCapsule instance
check_phosphate_contacts_donor(*args, **kwargs)
Overloaded function.
 
1. check_phosphate_contacts_donor(op_xyz_list : rosetta.utility.vector1_numeric_xyzVector_double_t, donor_atom_xyz_list : rosetta.utility.vector1_numeric_xyzVector_double_t, donor_base_atom_xyz_list : rosetta.utility.vector1_numeric_xyzVector_double_t) -> bool
 
2. check_phosphate_contacts_donor(pose : rosetta.core.pose.Pose, n : int) -> bool
copy_over_phosphate_variants(...) method of builtins.PyCapsule instance
copy_over_phosphate_variants(*args, **kwargs)
Overloaded function.
 
1. copy_over_phosphate_variants(pose : rosetta.core.pose.Pose, reference_pose : rosetta.core.pose.Pose, phosphate_move_list : rosetta.utility.vector1_protocols_stepwise_modeler_rna_phosphate_PhosphateMove) -> NoneType
 
2. copy_over_phosphate_variants(pose : rosetta.core.pose.Pose, reference_pose : rosetta.core.pose.Pose, res_list : rosetta.utility.vector1_unsigned_long) -> NoneType
correctly_position_five_prime_phosphate(...) method of builtins.PyCapsule instance
correctly_position_five_prime_phosphate(pose : rosetta.core.pose.Pose, res : int) -> NoneType
detect_phosphate_contacts(...) method of builtins.PyCapsule instance
detect_phosphate_contacts(pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool
get_phosphate_atom_and_neighbor_list(...) method of builtins.PyCapsule instance
get_phosphate_atom_and_neighbor_list(pose : rosetta.core.pose.Pose, phosphate_move_ : rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMove, donor_atom_xyz_list : rosetta.utility.vector1_numeric_xyzVector_double_t, donor_base_atom_xyz_list : rosetta.utility.vector1_numeric_xyzVector_double_t, neighbor_copy_dofs : rosetta.utility.vector1_unsigned_long) -> NoneType
get_phosphate_scorefxn(...) method of builtins.PyCapsule instance
get_phosphate_scorefxn(*args, **kwargs)
Overloaded function.
 
1. get_phosphate_scorefxn() -> rosetta.core.scoring.ScoreFunction
 
2. get_phosphate_scorefxn(options : rosetta.core.scoring.methods.EnergyMethodOptions) -> rosetta.core.scoring.ScoreFunction
remove_terminal_phosphates(...) method of builtins.PyCapsule instance
remove_terminal_phosphates(*args, **kwargs)
Overloaded function.
 
1. remove_terminal_phosphates(pose : rosetta.core.pose.Pose) -> NoneType
 
2. remove_terminal_phosphates(pose : rosetta.core.pose.Pose, res_list : rosetta.utility.vector1_unsigned_long) -> NoneType
setup_three_prime_phosphate_based_on_next_residue(...) method of builtins.PyCapsule instance
setup_three_prime_phosphate_based_on_next_residue(pose : rosetta.core.pose.Pose, n : int) -> NoneType
to_string(...) method of builtins.PyCapsule instance
to_string(phosphate_terminus : rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateTerminus) -> str

 
Data
        FIVE_PRIME_PHOSPHATE = PhosphateTerminus.FIVE_PRIME_PHOSPHATE
NONE = PhosphateTerminus.NONE
THREE_PRIME_PHOSPHATE = PhosphateTerminus.THREE_PRIME_PHOSPHATE