Bindings for protocols::farna namespace

Modules
		rosetta.protocols.farna.base_pairs rosetta.protocols.farna.fragments rosetta.protocols.farna.libraries rosetta.protocols.farna.movers rosetta.protocols.farna.options rosetta.protocols.farna.secstruct rosetta.protocols.farna.setup

Classes
		rosetta.protocols.moves.Mover(builtins.object) FARNA_Optimizer MultipleDomainMover RNA_DeNovoProtocol RNA_FragmentMonteCarlo   class FARNA_Optimizer(rosetta.protocols.moves.Mover)       Method resolution order: FARNA_Optimizer rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle, rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, rosetta.core.scoring.ScoreFunction) -> NoneType   doc   2. __init__(self : handle, pose_list : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, scorefxn : rosetta.core.scoring.ScoreFunction, cycles : int) -> NoneType   3. __init__(handle, rosetta.protocols.farna.FARNA_Optimizer) -> 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.farna.FARNA_Optimizer, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.farna.FARNA_Optimizer,  : rosetta.protocols.farna.FARNA_Optimizer) -> rosetta.protocols.farna.FARNA_Optimizer cycles(...) from builtins.PyCapsule cycles(rosetta.protocols.farna.FARNA_Optimizer) -> int get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.farna.FARNA_Optimizer) -> str rna_fragment_monte_carlo(...) from builtins.PyCapsule rna_fragment_monte_carlo(rosetta.protocols.farna.FARNA_Optimizer) -> protocols::farna::RNA_FragmentMonteCarlo set_cycles(...) from builtins.PyCapsule set_cycles(self : rosetta.protocols.farna.FARNA_Optimizer, setting : int) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply clone(...) from builtins.PyCapsule clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Return a clone of the Mover object. create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class MultipleDomainMover(rosetta.protocols.moves.Mover)     The RNA de novo structure modeling protocol     Method resolution order: MultipleDomainMover rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, pose : rosetta.core.pose.Pose, rna_loop_closer : rosetta.protocols.coarse_rna.CoarseRNA_LoopCloser) -> NoneType   2. __init__(handle, rosetta.protocols.farna.MultipleDomainMover) -> 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.farna.MultipleDomainMover, pose : rosetta.core.pose.Pose) -> NoneType   Apply the loop-rebuild protocol to the input pose apply_and_return_jump(...) from builtins.PyCapsule apply_and_return_jump(self : rosetta.protocols.farna.MultipleDomainMover, pose : rosetta.core.pose.Pose) -> int apply_at_domain(...) from builtins.PyCapsule apply_at_domain(self : rosetta.protocols.farna.MultipleDomainMover, pose : rosetta.core.pose.Pose, n : int) -> int assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.farna.MultipleDomainMover,  : rosetta.protocols.farna.MultipleDomainMover) -> rosetta.protocols.farna.MultipleDomainMover clone(...) from builtins.PyCapsule clone(rosetta.protocols.farna.MultipleDomainMover) -> rosetta.protocols.moves.Mover   Clone this object get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.farna.MultipleDomainMover) -> str num_domains(...) from builtins.PyCapsule num_domains(rosetta.protocols.farna.MultipleDomainMover) -> int randomize_pose_rigid_bodies(...) from builtins.PyCapsule randomize_pose_rigid_bodies(self : rosetta.protocols.farna.MultipleDomainMover, pose : rosetta.core.pose.Pose) -> NoneType slide_back_to_origin(...) from builtins.PyCapsule slide_back_to_origin(self : rosetta.protocols.farna.MultipleDomainMover, pose : rosetta.core.pose.Pose) -> NoneType update_rot_trans_mag(...) from builtins.PyCapsule update_rot_trans_mag(self : rosetta.protocols.farna.MultipleDomainMover, rot_mag : float, trans_mag : float) -> 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 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 RNA_DeNovoProtocol(rosetta.protocols.moves.Mover)     The RNA de novo structure modeling protocol     Method resolution order: RNA_DeNovoProtocol rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   doc   2. __init__(handle, protocols::farna::options::RNA_DeNovoProtocolOptions) -> NoneType   doc   3. __init__(self : handle, options : protocols::farna::options::RNA_DeNovoProtocolOptions, params : rosetta.protocols.farna.setup.RNA_DeNovoParameters) -> NoneType   4. __init__(handle, rosetta.protocols.farna.RNA_DeNovoProtocol) -> 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.farna.RNA_DeNovoProtocol) -> str align_and_output_to_silent_file(...) from builtins.PyCapsule align_and_output_to_silent_file(self : rosetta.protocols.farna.RNA_DeNovoProtocol, pose : rosetta.core.pose.Pose, silent_file : str, out_file_tag : str) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.farna.RNA_DeNovoProtocol, pose : rosetta.core.pose.Pose) -> NoneType   Apply the RNA denovo modeling protocol to the input pose assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.farna.RNA_DeNovoProtocol,  : rosetta.protocols.farna.RNA_DeNovoProtocol) -> rosetta.protocols.farna.RNA_DeNovoProtocol clone(...) from builtins.PyCapsule clone(rosetta.protocols.farna.RNA_DeNovoProtocol) -> rosetta.protocols.moves.Mover   Clone this object get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.farna.RNA_DeNovoProtocol) -> str options(...) from builtins.PyCapsule options(rosetta.protocols.farna.RNA_DeNovoProtocol) -> protocols::farna::options::RNA_DeNovoProtocolOptions output_to_silent_file(...) from builtins.PyCapsule output_to_silent_file(*args, **kwargs) Overloaded function.   1. output_to_silent_file(self : rosetta.protocols.farna.RNA_DeNovoProtocol, pose : rosetta.core.pose.Pose, silent_file : str, out_file_tag : str) -> NoneType   2. output_to_silent_file(self : rosetta.protocols.farna.RNA_DeNovoProtocol, pose : rosetta.core.pose.Pose, silent_file : str, out_file_tag : str, score_only : bool) -> NoneType rna_fragment_monte_carlo(...) from builtins.PyCapsule rna_fragment_monte_carlo(rosetta.protocols.farna.RNA_DeNovoProtocol) -> protocols::farna::RNA_FragmentMonteCarlo set_refine_pose_list(...) from builtins.PyCapsule set_refine_pose_list(self : rosetta.protocols.farna.RNA_DeNovoProtocol, setting : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) -> 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 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 RNA_FragmentMonteCarlo(rosetta.protocols.moves.Mover)       Method resolution order: RNA_FragmentMonteCarlo rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   doc   2. __init__(self : handle,  : protocols::farna::options::RNA_FragmentMonteCarloOptions) -> NoneType   3. __init__(handle, rosetta.protocols.farna.RNA_FragmentMonteCarlo) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. align_pose(...) from builtins.PyCapsule align_pose(*args, **kwargs) Overloaded function.   1. align_pose(self : rosetta.protocols.farna.RNA_FragmentMonteCarlo, pose : rosetta.core.pose.Pose) -> NoneType   2. align_pose(self : rosetta.protocols.farna.RNA_FragmentMonteCarlo, pose : rosetta.core.pose.Pose, verbose : bool) -> NoneType all_lores_score_final(...) from builtins.PyCapsule all_lores_score_final(rosetta.protocols.farna.RNA_FragmentMonteCarlo) -> rosetta.std.list_double_std_allocator_double_t apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.farna.RNA_FragmentMonteCarlo, pose : rosetta.core.pose.Pose) -> NoneType   Apply the loop-rebuild protocol to the input pose atom_level_domain_map(...) from builtins.PyCapsule atom_level_domain_map(rosetta.protocols.farna.RNA_FragmentMonteCarlo) -> rosetta.protocols.toolbox.AtomLevelDomainMap get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.farna.RNA_FragmentMonteCarlo) -> str get_rmsd_no_superimpose(...) from builtins.PyCapsule get_rmsd_no_superimpose(self : rosetta.protocols.farna.RNA_FragmentMonteCarlo, pose : rosetta.core.pose.Pose) -> float get_rmsd_stems_no_superimpose(...) from builtins.PyCapsule get_rmsd_stems_no_superimpose(self : rosetta.protocols.farna.RNA_FragmentMonteCarlo, pose : rosetta.core.pose.Pose) -> float loop_modeling(...) from builtins.PyCapsule loop_modeling(rosetta.protocols.farna.RNA_FragmentMonteCarlo) -> bool lores_pose(...) from builtins.PyCapsule lores_pose(rosetta.protocols.farna.RNA_FragmentMonteCarlo) -> rosetta.core.pose.Pose lores_score_early(...) from builtins.PyCapsule lores_score_early(rosetta.protocols.farna.RNA_FragmentMonteCarlo) -> float lores_score_final(...) from builtins.PyCapsule lores_score_final(rosetta.protocols.farna.RNA_FragmentMonteCarlo) -> float rna_base_pair_handler(...) from builtins.PyCapsule rna_base_pair_handler(rosetta.protocols.farna.RNA_FragmentMonteCarlo) -> protocols::farna::base_pairs::RNA_BasePairHandler rna_chunk_library(...) from builtins.PyCapsule rna_chunk_library(rosetta.protocols.farna.RNA_FragmentMonteCarlo) -> protocols::farna::libraries::RNA_ChunkLibrary rna_loop_closer(...) from builtins.PyCapsule rna_loop_closer(rosetta.protocols.farna.RNA_FragmentMonteCarlo) -> protocols::farna::movers::RNA_LoopCloser set_all_lores_score_final(...) from builtins.PyCapsule set_all_lores_score_final(self : rosetta.protocols.farna.RNA_FragmentMonteCarlo, setting : rosetta.std.list_double_std_allocator_double_t) -> NoneType set_chunk_coverage(...) from builtins.PyCapsule set_chunk_coverage(self : rosetta.protocols.farna.RNA_FragmentMonteCarlo, setting : float) -> NoneType set_denovo_scorefxn(...) from builtins.PyCapsule set_denovo_scorefxn(self : rosetta.protocols.farna.RNA_FragmentMonteCarlo, setting : rosetta.core.scoring.ScoreFunction) -> NoneType set_hires_scorefxn(...) from builtins.PyCapsule set_hires_scorefxn(self : rosetta.protocols.farna.RNA_FragmentMonteCarlo, setting : rosetta.core.scoring.ScoreFunction) -> NoneType set_out_file_tag(...) from builtins.PyCapsule set_out_file_tag(self : rosetta.protocols.farna.RNA_FragmentMonteCarlo, setting : str) -> NoneType set_refine_pose(...) from builtins.PyCapsule set_refine_pose(self : rosetta.protocols.farna.RNA_FragmentMonteCarlo, setting : bool) -> NoneType set_rna_base_pair_handler(...) from builtins.PyCapsule set_rna_base_pair_handler(self : rosetta.protocols.farna.RNA_FragmentMonteCarlo, setting : protocols::farna::base_pairs::RNA_BasePairHandler) -> NoneType set_rna_de_novo_pose_setup(...) from builtins.PyCapsule set_rna_de_novo_pose_setup(self : rosetta.protocols.farna.RNA_FragmentMonteCarlo, setting : rosetta.protocols.farna.setup.RNA_DeNovoPoseInitializer) -> NoneType set_user_input_chunk_library(...) from builtins.PyCapsule set_user_input_chunk_library(self : rosetta.protocols.farna.RNA_FragmentMonteCarlo, setting : protocols::farna::libraries::RNA_ChunkLibrary) -> NoneType set_vdw_grid(...) from builtins.PyCapsule set_vdw_grid(self : rosetta.protocols.farna.RNA_FragmentMonteCarlo, setting : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker) -> 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 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

Functions
		assert_phosphate_nomenclature_matches_mini(...) method of builtins.PyCapsule instance assert_phosphate_nomenclature_matches_mini(pose : rosetta.core.pose.Pose) -> NoneType check_base_pair(...) method of builtins.PyCapsule instance check_base_pair(pose : rosetta.core.pose.Pose, struct_type : ObjexxFCL::FArray1D<int>) -> NoneType classify_base_pairs_lores(...) method of builtins.PyCapsule instance classify_base_pairs_lores(pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_core_pose_rna_BasePair compare_RNA_char(...) method of builtins.PyCapsule instance compare_RNA_char(char1 : str, char2 : str) -> bool compare_RNA_secstruct(...) method of builtins.PyCapsule instance compare_RNA_secstruct(char1 : str, char2 : str) -> bool convert_based_on_match_type(...) method of builtins.PyCapsule instance convert_based_on_match_type(RNA_string : str, type : int) -> str create_rna_vall_torsions(...) method of builtins.PyCapsule instance create_rna_vall_torsions(*args, **kwargs) Overloaded function.   1. create_rna_vall_torsions(pose : rosetta.core.pose.Pose, torsions_out : rosetta.utility.io.ozstream, exclude_res_list : rosetta.utility.vector1_unsigned_long) -> NoneType   2. create_rna_vall_torsions(pose : rosetta.core.pose.Pose, outfile : str, exclude_res_list : rosetta.utility.vector1_unsigned_long) -> NoneType ensure_phosphate_nomenclature_matches_mini(...) method of builtins.PyCapsule instance ensure_phosphate_nomenclature_matches_mini(pose : rosetta.core.pose.Pose) -> NoneType export_packer_results(...) method of builtins.PyCapsule instance export_packer_results(*args, **kwargs) Overloaded function.   1. export_packer_results(results : rosetta.utility.vector1_std_pair_double_std_string_t, pose_list : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, scorefxn : rosetta.core.scoring.ScoreFunction, outfile : str) -> NoneType   2. export_packer_results(results : rosetta.utility.vector1_std_pair_double_std_string_t, pose_list : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, scorefxn : rosetta.core.scoring.ScoreFunction, outfile : str, dumo : bool) -> NoneType figure_out_base_pair_partner(...) method of builtins.PyCapsule instance figure_out_base_pair_partner(*args, **kwargs) Overloaded function.   1. figure_out_base_pair_partner(pose : rosetta.core.pose.Pose, partner : rosetta.std.map_unsigned_long_unsigned_long) -> NoneType   2. figure_out_base_pair_partner(pose : rosetta.core.pose.Pose, partner : rosetta.std.map_unsigned_long_unsigned_long, strict : bool) -> NoneType figure_out_secstruct(...) method of builtins.PyCapsule instance figure_out_secstruct(pose : rosetta.core.pose.Pose) -> NoneType fill_in_default_jump_atoms(...) method of builtins.PyCapsule instance fill_in_default_jump_atoms(f : rosetta.core.kinematics.FoldTree, pose : rosetta.core.pose.Pose) -> NoneType get_base_pairing_info(...) method of builtins.PyCapsule instance get_base_pairing_info(pose : rosetta.core.pose.Pose, seqpos : int, secstruct : str, edge_is_base_pairing : ObjexxFCL::FArray1D<bool>) -> NoneType get_base_pairing_list(...) method of builtins.PyCapsule instance get_base_pairing_list(pose : rosetta.core.pose.Pose, base_pairing_list : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> NoneType get_moving_res(...) method of builtins.PyCapsule instance get_moving_res(pose : rosetta.core.pose.Pose, atom_level_domain_map : rosetta.protocols.toolbox.AtomLevelDomainMap) -> rosetta.utility.vector1_unsigned_long get_rigid_body_jumps(...) method of builtins.PyCapsule instance get_rigid_body_jumps(pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long get_rna_hires_scorefxn(...) method of builtins.PyCapsule instance get_rna_hires_scorefxn() -> rosetta.core.scoring.ScoreFunction get_sugar_centroid(...) method of builtins.PyCapsule instance get_sugar_centroid(rsd : rosetta.core.conformation.Residue) -> rosetta.numeric.xyzVector_double_t involved_in_phosphate_torsion(...) method of builtins.PyCapsule instance involved_in_phosphate_torsion(atomname : str) -> bool is_num_in_list(...) method of builtins.PyCapsule instance is_num_in_list(i : int, list : rosetta.utility.vector1_unsigned_long) -> bool let_rigid_body_jumps_move(...) method of builtins.PyCapsule instance let_rigid_body_jumps_move(*args, **kwargs) Overloaded function.   1. let_rigid_body_jumps_move(movemap : rosetta.core.kinematics.MoveMap, pose : rosetta.core.pose.Pose) -> bool   2. let_rigid_body_jumps_move(movemap : rosetta.core.kinematics.MoveMap, pose : rosetta.core.pose.Pose, move_first_rigid_body : bool) -> bool make_coarse_pose(...) method of builtins.PyCapsule instance make_coarse_pose(pose : rosetta.core.pose.Pose, coarse_pose : rosetta.core.pose.Pose) -> NoneType make_extended_coarse_pose(...) method of builtins.PyCapsule instance make_extended_coarse_pose(coarse_pose : rosetta.core.pose.Pose, full_sequence : str) -> NoneType moveable_jump(...) method of builtins.PyCapsule instance moveable_jump(*args, **kwargs) Overloaded function.   1. moveable_jump(jump_atom_id1 : rosetta.core.id.AtomID, jump_atom_id2 : rosetta.core.id.AtomID, atom_level_domain_map : rosetta.protocols.toolbox.AtomLevelDomainMap) -> bool   2. moveable_jump(jump_pos1 : int, jump_pos2 : int, atom_level_domain_map : rosetta.protocols.toolbox.AtomLevelDomainMap) -> bool possible_root(...) method of builtins.PyCapsule instance possible_root(f : rosetta.core.kinematics.FoldTree, n : int) -> bool print_hbonds(...) method of builtins.PyCapsule instance print_hbonds(pose : rosetta.core.pose.Pose) -> NoneType print_internal_coords(...) method of builtins.PyCapsule instance print_internal_coords(pose : rosetta.core.pose.Pose) -> NoneType process_input_file(...) method of builtins.PyCapsule instance process_input_file(*args, **kwargs) Overloaded function.   1. process_input_file(silent_file : str, pose_list : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) -> NoneType   2. process_input_file(silent_file : str, pose_list : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, is_pdb : bool) -> NoneType   3. process_input_file(silent_file : str, pose_list : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, is_pdb : bool, coarse_rna : bool) -> NoneType remove_cutpoint_closed(...) method of builtins.PyCapsule instance remove_cutpoint_closed(pose : rosetta.core.pose.Pose, i : int) -> NoneType remove_cutpoints_closed(...) method of builtins.PyCapsule instance remove_cutpoints_closed(pose : rosetta.core.pose.Pose) -> NoneType set_output_res_and_chain(...) method of builtins.PyCapsule instance set_output_res_and_chain(extended_pose : rosetta.core.pose.Pose, output_resnum_and_chain : (rosetta.utility.vector1_int, rosetta.utility.vector1_char)) -> NoneType setup_base_pair_constraints(...) method of builtins.PyCapsule instance setup_base_pair_constraints(*args, **kwargs) Overloaded function.   1. setup_base_pair_constraints(pose : rosetta.core.pose.Pose, pairings : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> NoneType   2. setup_base_pair_constraints(pose : rosetta.core.pose.Pose, pairings : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, suppress_factor : float) -> NoneType setup_coarse_chainbreak_constraints(...) method of builtins.PyCapsule instance setup_coarse_chainbreak_constraints(pose : rosetta.core.pose.Pose, n : int) -> NoneType translate_virtual_anchor_to_first_rigid_body(...) method of builtins.PyCapsule instance translate_virtual_anchor_to_first_rigid_body(pose : rosetta.core.pose.Pose) -> NoneType virtualize_bulges(...) method of builtins.PyCapsule instance virtualize_bulges(input_pose : rosetta.core.pose.Pose, in_allow_bulge_res_list : rosetta.utility.vector1_unsigned_long, scorefxn : rosetta.core.scoring.ScoreFunction, tag : str, allow_pre_virtualize : bool, allow_consecutive_bulges : bool, verbose : bool) -> int