Bindings for protocols::hybridization namespace

Classes
		builtins.object AlignOption DDomainParse FragmentBiasAssigner HybridizeFoldtreeDynamic TMalign rosetta.basic.datacache.CacheableData(builtins.object) TemplateHistory rosetta.protocols.moves.Mover(builtins.object) BackboneTorsionPerturbation BackboneTorsionSampler CartesianHybridize CartesianSampler ChunkTrialMover DomainAssembly FoldTreeHybridize HybridizeProtocol InsertChunkMover MRMover WeightedFragmentSmoothTrialMover WeightedFragmentTrialMover rosetta.protocols.moves.MoverCreator(builtins.object) BackboneTorsionPerturbationCreator BackboneTorsionSamplerCreator CartesianSamplerCreator HybridizeProtocolCreator rosetta.protocols.moves.PoseCondition(builtins.object) AllResiduesChanged   class AlignOption(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.protocols.hybridization.AlignOption, rosetta.protocols.hybridization.AlignOption) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.protocols.hybridization.AlignOption) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.hybridization.AlignOption, int) -> NoneType   2. __init__(rosetta.protocols.hybridization.AlignOption, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.protocols.hybridization.AlignOption) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.protocols.hybridization.AlignOption, rosetta.protocols.hybridization.AlignOption) -> 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.hybridization.AlignOption) -> str Data and other attributes defined here: all_chunks = AlignOption.all_chunks random_chunk = AlignOption.random_chunk   class AllResiduesChanged(rosetta.protocols.moves.PoseCondition)     (helper) functor class which keeps track of initial phi/psi values.        calls of operator ( pose ) compare the initial phi/psi values /to the current values of the given pose. Returns false once all phi/psi values  have been modified.     Method resolution order: AllResiduesChanged rosetta.protocols.moves.PoseCondition builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.protocols.hybridization.AllResiduesChanged, pose : rosetta.core.pose.Pose) -> bool __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle, rosetta.core.pose.Pose, rosetta.utility.vector1_double) -> NoneType   doc   2. __init__(self : handle, pose : rosetta.core.pose.Pose, residue_weights : rosetta.utility.vector1_double, anchor_residues : rosetta.utility.vector1_unsigned_long) -> NoneType   3. __init__(self : handle, pose : rosetta.core.pose.Pose) -> NoneType   4. __init__(handle, rosetta.protocols.hybridization.AllResiduesChanged) -> 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.hybridization.AllResiduesChanged,  : rosetta.protocols.hybridization.AllResiduesChanged) -> rosetta.protocols.hybridization.AllResiduesChanged   class BackboneTorsionPerturbation(rosetta.protocols.moves.Mover)       Method resolution order: BackboneTorsionPerturbation rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.hybridization.BackboneTorsionPerturbation) -> 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.hybridization.BackboneTorsionPerturbation, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.hybridization.BackboneTorsionPerturbation,  : rosetta.protocols.hybridization.BackboneTorsionPerturbation) -> rosetta.protocols.hybridization.BackboneTorsionPerturbation clone(...) from builtins.PyCapsule clone(rosetta.protocols.hybridization.BackboneTorsionPerturbation) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.hybridization.BackboneTorsionPerturbation) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.hybridization.BackboneTorsionPerturbation) -> str init(...) from builtins.PyCapsule init(rosetta.protocols.hybridization.BackboneTorsionPerturbation) -> NoneType perturb(...) from builtins.PyCapsule perturb(*args, **kwargs) Overloaded function.   1. perturb(self : rosetta.protocols.hybridization.BackboneTorsionPerturbation, pose : rosetta.core.pose.Pose, max_delta_torsion : float) -> NoneType   2. perturb(self : rosetta.protocols.hybridization.BackboneTorsionPerturbation, pose : rosetta.core.pose.Pose, level : int, max_delta_torsion : float, local : int, rama_biased : bool, repack : bool, minimize : bool) -> NoneType set_scorefunction(...) from builtins.PyCapsule set_scorefunction(self : rosetta.protocols.hybridization.BackboneTorsionPerturbation, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType task_factory(...) from builtins.PyCapsule task_factory(self : rosetta.protocols.hybridization.BackboneTorsionPerturbation, tf : rosetta.core.pack.task.TaskFactory) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class BackboneTorsionPerturbationCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: BackboneTorsionPerturbationCreator rosetta.protocols.moves.MoverCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> 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.hybridization.BackboneTorsionPerturbationCreator,  : rosetta.protocols.hybridization.BackboneTorsionPerturbationCreator) -> rosetta.protocols.hybridization.BackboneTorsionPerturbationCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.hybridization.BackboneTorsionPerturbationCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.hybridization.BackboneTorsionPerturbationCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class BackboneTorsionSampler(rosetta.protocols.moves.Mover)       Method resolution order: BackboneTorsionSampler rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.hybridization.BackboneTorsionSampler) -> 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.hybridization.BackboneTorsionSampler, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.hybridization.BackboneTorsionSampler,  : rosetta.protocols.hybridization.BackboneTorsionSampler) -> rosetta.protocols.hybridization.BackboneTorsionSampler clone(...) from builtins.PyCapsule clone(rosetta.protocols.hybridization.BackboneTorsionSampler) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.hybridization.BackboneTorsionSampler) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.hybridization.BackboneTorsionSampler) -> str init(...) from builtins.PyCapsule init(rosetta.protocols.hybridization.BackboneTorsionSampler) -> NoneType local_perturb(...) from builtins.PyCapsule local_perturb(self : rosetta.protocols.hybridization.BackboneTorsionSampler, pose : rosetta.core.pose.Pose, max_delta_torsion : float) -> NoneType perturb(...) from builtins.PyCapsule perturb(self : rosetta.protocols.hybridization.BackboneTorsionSampler, pose : rosetta.core.pose.Pose, level : int, max_delta_torsion : float, local : int, rama_biased : bool, repack : bool, minimize : bool) -> NoneType set_scorefunction(...) from builtins.PyCapsule set_scorefunction(self : rosetta.protocols.hybridization.BackboneTorsionSampler, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType task_factory(...) from builtins.PyCapsule task_factory(self : rosetta.protocols.hybridization.BackboneTorsionSampler, tf : rosetta.core.pack.task.TaskFactory) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class BackboneTorsionSamplerCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: BackboneTorsionSamplerCreator rosetta.protocols.moves.MoverCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> 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.hybridization.BackboneTorsionSamplerCreator,  : rosetta.protocols.hybridization.BackboneTorsionSamplerCreator) -> rosetta.protocols.hybridization.BackboneTorsionSamplerCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.hybridization.BackboneTorsionSamplerCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.hybridization.BackboneTorsionSamplerCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class CartesianHybridize(rosetta.protocols.moves.Mover)       Method resolution order: CartesianHybridize 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, templates_in : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, template_wts_in : rosetta.utility.vector1_double, template_chunks_in : rosetta.utility.vector1_protocols_loops_Loops, template_contigs_in : rosetta.utility.vector1_protocols_loops_Loops, fragments9_in : rosetta.core.fragment.FragSet) -> NoneType   3. __init__(handle, rosetta.protocols.hybridization.CartesianHybridize) -> 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.hybridization.CartesianHybridize, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.hybridization.CartesianHybridize,  : rosetta.protocols.hybridization.CartesianHybridize) -> rosetta.protocols.hybridization.CartesianHybridize clone(...) from builtins.PyCapsule clone(rosetta.protocols.hybridization.CartesianHybridize) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.hybridization.CartesianHybridize) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.hybridization.CartesianHybridize) -> str init(...) from builtins.PyCapsule init(rosetta.protocols.hybridization.CartesianHybridize) -> NoneType set_cartfrag_overlap(...) from builtins.PyCapsule set_cartfrag_overlap(self : rosetta.protocols.hybridization.CartesianHybridize, cartfrag_overlap_in : int) -> NoneType set_cenrot(...) from builtins.PyCapsule set_cenrot(self : rosetta.protocols.hybridization.CartesianHybridize, cenrot_in : bool) -> NoneType set_fragment_probs(...) from builtins.PyCapsule set_fragment_probs(self : rosetta.protocols.hybridization.CartesianHybridize, prob : float, randprob : float) -> NoneType set_increase_cycles(...) from builtins.PyCapsule set_increase_cycles(self : rosetta.protocols.hybridization.CartesianHybridize, increase_cycles_in : float) -> NoneType set_linmin_only(...) from builtins.PyCapsule set_linmin_only(self : rosetta.protocols.hybridization.CartesianHybridize, linmin_only_in : bool) -> NoneType set_max_insertion(...) from builtins.PyCapsule set_max_insertion(self : rosetta.protocols.hybridization.CartesianHybridize, max_in : int) -> NoneType set_min_scorefunction(...) from builtins.PyCapsule set_min_scorefunction(self : rosetta.protocols.hybridization.CartesianHybridize, scorefxn_in : rosetta.core.scoring.ScoreFunction) -> NoneType set_no_global_frame(...) from builtins.PyCapsule set_no_global_frame(self : rosetta.protocols.hybridization.CartesianHybridize, no_global_frame_in : bool) -> NoneType set_pack_scorefunction(...) from builtins.PyCapsule set_pack_scorefunction(self : rosetta.protocols.hybridization.CartesianHybridize, scorefxn_in : rosetta.core.scoring.ScoreFunction) -> NoneType set_per_residue_controls(...) from builtins.PyCapsule set_per_residue_controls(self : rosetta.protocols.hybridization.CartesianHybridize, residue_sample_template_in : rosetta.utility.vector1_bool, residue_sample_abinitio_in : rosetta.utility.vector1_bool) -> NoneType set_scorefunction(...) from builtins.PyCapsule set_scorefunction(self : rosetta.protocols.hybridization.CartesianHybridize, scorefxn_in : rosetta.core.scoring.ScoreFunction) -> NoneType set_seqfrags_only(...) from builtins.PyCapsule set_seqfrags_only(self : rosetta.protocols.hybridization.CartesianHybridize, seqfrags_only_in : bool) -> NoneType set_skip_long_min(...) from builtins.PyCapsule set_skip_long_min(self : rosetta.protocols.hybridization.CartesianHybridize, skip_long_min_in : bool) -> NoneType set_temperature(...) from builtins.PyCapsule set_temperature(self : rosetta.protocols.hybridization.CartesianHybridize, temp_in : 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 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 CartesianSampler(rosetta.protocols.moves.Mover)       Method resolution order: CartesianSampler 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, fragments_in : rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t) -> NoneType   3. __init__(handle, rosetta.protocols.hybridization.CartesianSampler) -> 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.hybridization.CartesianSampler, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.hybridization.CartesianSampler,  : rosetta.protocols.hybridization.CartesianSampler) -> rosetta.protocols.hybridization.CartesianSampler clone(...) from builtins.PyCapsule clone(rosetta.protocols.hybridization.CartesianSampler) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.hybridization.CartesianSampler) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.hybridization.CartesianSampler) -> str init(...) from builtins.PyCapsule init(rosetta.protocols.hybridization.CartesianSampler) -> NoneType set_bbmove(...) from builtins.PyCapsule set_bbmove(self : rosetta.protocols.hybridization.CartesianSampler, bbmove_in : bool) -> NoneType set_fa_scorefunction(...) from builtins.PyCapsule set_fa_scorefunction(self : rosetta.protocols.hybridization.CartesianSampler, scorefxn_in : rosetta.core.scoring.ScoreFunction) -> NoneType set_frag_sizes(...) from builtins.PyCapsule set_frag_sizes(self : rosetta.protocols.hybridization.CartesianSampler, frag_sizes_in : rosetta.utility.vector1_unsigned_long) -> NoneType set_fullatom(...) from builtins.PyCapsule set_fullatom(self : rosetta.protocols.hybridization.CartesianSampler, fullatom_in : bool) -> NoneType set_mc_scorefunction(...) from builtins.PyCapsule set_mc_scorefunction(self : rosetta.protocols.hybridization.CartesianSampler, scorefxn_in : rosetta.core.scoring.ScoreFunction) -> NoneType set_ncycles(...) from builtins.PyCapsule set_ncycles(self : rosetta.protocols.hybridization.CartesianSampler, ncycles_in : int) -> NoneType set_nfrags(...) from builtins.PyCapsule set_nfrags(self : rosetta.protocols.hybridization.CartesianSampler, nfrags_in : int) -> NoneType set_nminsteps(...) from builtins.PyCapsule set_nminsteps(self : rosetta.protocols.hybridization.CartesianSampler, nminsteps_in : int) -> NoneType set_overlap(...) from builtins.PyCapsule set_overlap(self : rosetta.protocols.hybridization.CartesianSampler, overlap_in : int) -> NoneType set_restore_csts(...) from builtins.PyCapsule set_restore_csts(self : rosetta.protocols.hybridization.CartesianSampler, restore_csts_in : bool) -> NoneType set_rms_cutoff(...) from builtins.PyCapsule set_rms_cutoff(self : rosetta.protocols.hybridization.CartesianSampler, rms_cutoff_in : float) -> NoneType set_scorefunction(...) from builtins.PyCapsule set_scorefunction(self : rosetta.protocols.hybridization.CartesianSampler, scorefxn_in : rosetta.core.scoring.ScoreFunction) -> NoneType set_strategy(...) from builtins.PyCapsule set_strategy(self : rosetta.protocols.hybridization.CartesianSampler, strategy_in : str) -> NoneType set_temp(...) from builtins.PyCapsule set_temp(self : rosetta.protocols.hybridization.CartesianSampler, temp_in : float) -> NoneType set_userpos(...) from builtins.PyCapsule set_userpos(self : rosetta.protocols.hybridization.CartesianSampler, user_pos_in : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_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 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 CartesianSamplerCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: CartesianSamplerCreator rosetta.protocols.moves.MoverCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> 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.hybridization.CartesianSamplerCreator,  : rosetta.protocols.hybridization.CartesianSamplerCreator) -> rosetta.protocols.hybridization.CartesianSamplerCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.hybridization.CartesianSamplerCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.hybridization.CartesianSamplerCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class ChunkTrialMover(rosetta.protocols.moves.Mover)       Method resolution order: ChunkTrialMover 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_const_core_pose_Pose_t, rosetta.utility.vector1_protocols_loops_Loops) -> NoneType   doc   2. __init__(handle, rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, rosetta.utility.vector1_protocols_loops_Loops, bool) -> NoneType   doc   3. __init__(handle, rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, rosetta.utility.vector1_protocols_loops_Loops, bool, rosetta.protocols.hybridization.AlignOption) -> NoneType   doc   4. __init__(self : handle, template_poses : rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, template_chunks : rosetta.utility.vector1_protocols_loops_Loops, random_template : bool, align_option : rosetta.protocols.hybridization.AlignOption, residue_sample_template : rosetta.utility.vector1_bool) -> NoneType   5. __init__(handle, rosetta.protocols.hybridization.ChunkTrialMover) -> 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.hybridization.ChunkTrialMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.hybridization.ChunkTrialMover,  : rosetta.protocols.hybridization.ChunkTrialMover) -> rosetta.protocols.hybridization.ChunkTrialMover get_alignment_from_template(...) from builtins.PyCapsule get_alignment_from_template(self : rosetta.protocols.hybridization.ChunkTrialMover, template_pose : rosetta.core.pose.Pose, seqpos_alignment : rosetta.std.map_unsigned_long_unsigned_long) -> NoneType get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.hybridization.ChunkTrialMover) -> str has_valid_moves(...) from builtins.PyCapsule has_valid_moves(rosetta.protocols.hybridization.ChunkTrialMover) -> bool pick_random_chunk(...) from builtins.PyCapsule pick_random_chunk(self : rosetta.protocols.hybridization.ChunkTrialMover, pose : rosetta.core.pose.Pose) -> NoneType pick_random_template(...) from builtins.PyCapsule pick_random_template(rosetta.protocols.hybridization.ChunkTrialMover) -> NoneType set_max_registry_shift(...) from builtins.PyCapsule set_max_registry_shift(self : rosetta.protocols.hybridization.ChunkTrialMover, max_registry_shift_in : int) -> NoneType set_template(...) from builtins.PyCapsule set_template(self : rosetta.protocols.hybridization.ChunkTrialMover, template_number : int) -> NoneType set_templates_to_ignore(...) from builtins.PyCapsule set_templates_to_ignore(self : rosetta.protocols.hybridization.ChunkTrialMover, template_indices_in : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType template_number(...) from builtins.PyCapsule template_number(rosetta.protocols.hybridization.ChunkTrialMover) -> int trial_counter(...) from builtins.PyCapsule trial_counter(self : rosetta.protocols.hybridization.ChunkTrialMover, ires : int) -> int 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 DDomainParse(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.hybridization.DDomainParse) -> NoneType   2. __init__(self : rosetta.protocols.hybridization.DDomainParse, pcut_in : float, hcut_in : float, length_in : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. split(...) from builtins.PyCapsule split(self : rosetta.protocols.hybridization.DDomainParse, templ : rosetta.core.pose.Pose) -> rosetta.utility.vector1_protocols_loops_Loops   class DomainAssembly(rosetta.protocols.moves.Mover)       Method resolution order: DomainAssembly rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, poses : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, domain_assembly_weights : rosetta.utility.vector1_double) -> NoneType   2. __init__(self : handle, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   3. __init__(handle, rosetta.protocols.hybridization.DomainAssembly) -> 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.hybridization.DomainAssembly, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.hybridization.DomainAssembly,  : rosetta.protocols.hybridization.DomainAssembly) -> rosetta.protocols.hybridization.DomainAssembly get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.hybridization.DomainAssembly) -> str run(...) from builtins.PyCapsule run(rosetta.protocols.hybridization.DomainAssembly) -> 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 FoldTreeHybridize(rosetta.protocols.moves.Mover)       Method resolution order: FoldTreeHybridize 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, initial_template_index : int, template_poses : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, template_weights : rosetta.utility.vector1_double, template_chunks : rosetta.utility.vector1_protocols_loops_Loops, fragments_small_in : rosetta.core.fragment.FragSet, fragments_big_in : rosetta.core.fragment.FragSet) -> NoneType   3. __init__(handle, rosetta.protocols.hybridization.FoldTreeHybridize) -> 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.hybridization.FoldTreeHybridize, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.hybridization.FoldTreeHybridize,  : rosetta.protocols.hybridization.FoldTreeHybridize) -> rosetta.protocols.hybridization.FoldTreeHybridize center_of_mass(...) from builtins.PyCapsule center_of_mass(self : rosetta.protocols.hybridization.FoldTreeHybridize, pose : rosetta.core.pose.Pose) -> rosetta.numeric.xyzVector_double_t get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.hybridization.FoldTreeHybridize) -> str get_pairings_residues(...) from builtins.PyCapsule get_pairings_residues(rosetta.protocols.hybridization.FoldTreeHybridize) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t get_residue_weights(...) from builtins.PyCapsule get_residue_weights(self : rosetta.protocols.hybridization.FoldTreeHybridize, pose : rosetta.core.pose.Pose, wt1 : rosetta.utility.vector1_double, wt3 : rosetta.utility.vector1_double, wt9 : rosetta.utility.vector1_double) -> NoneType get_strand_pairs(...) from builtins.PyCapsule get_strand_pairs(rosetta.protocols.hybridization.FoldTreeHybridize) -> rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t init(...) from builtins.PyCapsule init(rosetta.protocols.hybridization.FoldTreeHybridize) -> NoneType restore_original_foldtree(...) from builtins.PyCapsule restore_original_foldtree(self : rosetta.protocols.hybridization.FoldTreeHybridize, pose : rosetta.core.pose.Pose) -> NoneType set_add_hetatm(...) from builtins.PyCapsule set_add_hetatm(self : rosetta.protocols.hybridization.FoldTreeHybridize, add_hetatm_in : bool, hetatm_self_cst_weight_in : float, hetatm_prot_cst_weight_in : float) -> NoneType set_add_non_init_chunks(...) from builtins.PyCapsule set_add_non_init_chunks(self : rosetta.protocols.hybridization.FoldTreeHybridize, add_non_init_chunks_in : float) -> NoneType set_auto_frag_insertion_weight(...) from builtins.PyCapsule set_auto_frag_insertion_weight(self : rosetta.protocols.hybridization.FoldTreeHybridize, auto_frag_insertion_weight_in : bool) -> NoneType set_big_frag_insertion_weight(...) from builtins.PyCapsule set_big_frag_insertion_weight(self : rosetta.protocols.hybridization.FoldTreeHybridize, big_frag_insertion_weight_in : float) -> NoneType set_chunk_insertion_weight(...) from builtins.PyCapsule set_chunk_insertion_weight(self : rosetta.protocols.hybridization.FoldTreeHybridize, chunk_insertion_weight_in : float) -> NoneType set_constraint_file(...) from builtins.PyCapsule set_constraint_file(self : rosetta.protocols.hybridization.FoldTreeHybridize, cst_file_in : str) -> NoneType set_filter_templates(...) from builtins.PyCapsule set_filter_templates(self : rosetta.protocols.hybridization.FoldTreeHybridize, filter_templates_in : bool) -> NoneType set_frag_1mer_insertion_weight(...) from builtins.PyCapsule set_frag_1mer_insertion_weight(self : rosetta.protocols.hybridization.FoldTreeHybridize, frag_1mer_insertion_weight_in : float) -> NoneType set_frag_weight_aligned(...) from builtins.PyCapsule set_frag_weight_aligned(self : rosetta.protocols.hybridization.FoldTreeHybridize, frag_weight_aligned_in : float) -> NoneType set_increase_cycles(...) from builtins.PyCapsule set_increase_cycles(self : rosetta.protocols.hybridization.FoldTreeHybridize, increase_cycles_in : float) -> NoneType set_max_insertion(...) from builtins.PyCapsule set_max_insertion(self : rosetta.protocols.hybridization.FoldTreeHybridize, max_in : int) -> NoneType set_max_registry_shift(...) from builtins.PyCapsule set_max_registry_shift(self : rosetta.protocols.hybridization.FoldTreeHybridize, max_registry_shift_in : int) -> NoneType set_minimize_at_end(...) from builtins.PyCapsule set_minimize_at_end(self : rosetta.protocols.hybridization.FoldTreeHybridize, min_at_end_in : bool) -> NoneType set_minimize_sf(...) from builtins.PyCapsule set_minimize_sf(self : rosetta.protocols.hybridization.FoldTreeHybridize, minscorefxn_in : rosetta.core.scoring.ScoreFunction) -> NoneType set_pairings_file(...) from builtins.PyCapsule set_pairings_file(self : rosetta.protocols.hybridization.FoldTreeHybridize, pairings_file_in : str) -> NoneType set_per_residue_controls(...) from builtins.PyCapsule set_per_residue_controls(self : rosetta.protocols.hybridization.FoldTreeHybridize, residue_sample_template_in : rosetta.utility.vector1_bool, residue_sample_abinitio_in : rosetta.utility.vector1_bool) -> NoneType set_random_sheets(...) from builtins.PyCapsule set_random_sheets(self : rosetta.protocols.hybridization.FoldTreeHybridize, random_sheets_in : rosetta.utility.vector1_unsigned_long) -> NoneType set_scorefunction(...) from builtins.PyCapsule set_scorefunction(self : rosetta.protocols.hybridization.FoldTreeHybridize, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_sheets(...) from builtins.PyCapsule set_sheets(self : rosetta.protocols.hybridization.FoldTreeHybridize, sheets_in : rosetta.utility.vector1_unsigned_long) -> NoneType set_small_frag_insertion_weight(...) from builtins.PyCapsule set_small_frag_insertion_weight(self : rosetta.protocols.hybridization.FoldTreeHybridize, small_frag_insertion_weight_in : float) -> NoneType set_stage1_1_cycles(...) from builtins.PyCapsule set_stage1_1_cycles(self : rosetta.protocols.hybridization.FoldTreeHybridize, stage1_1_cycles_in : int) -> NoneType set_stage1_2_cycles(...) from builtins.PyCapsule set_stage1_2_cycles(self : rosetta.protocols.hybridization.FoldTreeHybridize, stage1_2_cycles_in : int) -> NoneType set_stage1_3_cycles(...) from builtins.PyCapsule set_stage1_3_cycles(self : rosetta.protocols.hybridization.FoldTreeHybridize, stage1_3_cycles_in : int) -> NoneType set_stage1_4_cycles(...) from builtins.PyCapsule set_stage1_4_cycles(self : rosetta.protocols.hybridization.FoldTreeHybridize, stage1_4_cycles_in : int) -> NoneType set_top_n_big_frag(...) from builtins.PyCapsule set_top_n_big_frag(self : rosetta.protocols.hybridization.FoldTreeHybridize, top_n_big_frag_in : int) -> NoneType set_top_n_small_frag(...) from builtins.PyCapsule set_top_n_small_frag(self : rosetta.protocols.hybridization.FoldTreeHybridize, top_n_small_frag_in : int) -> NoneType set_user_csts(...) from builtins.PyCapsule set_user_csts(self : rosetta.protocols.hybridization.FoldTreeHybridize, user_csts_in : rosetta.utility.vector1_unsigned_long) -> NoneType setup_foldtree(...) from builtins.PyCapsule setup_foldtree(self : rosetta.protocols.hybridization.FoldTreeHybridize, pose : rosetta.core.pose.Pose) -> NoneType setup_scorefunctions(...) from builtins.PyCapsule setup_scorefunctions(self : rosetta.protocols.hybridization.FoldTreeHybridize, score0 : rosetta.core.scoring.ScoreFunction, score1 : rosetta.core.scoring.ScoreFunction, score2 : rosetta.core.scoring.ScoreFunction, score5 : rosetta.core.scoring.ScoreFunction, score3 : rosetta.core.scoring.ScoreFunction) -> NoneType translate_virt_to_CoM(...) from builtins.PyCapsule translate_virt_to_CoM(self : rosetta.protocols.hybridization.FoldTreeHybridize, pose : rosetta.core.pose.Pose) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply 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 FragmentBiasAssigner(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.protocols.hybridization.FragmentBiasAssigner, pose : rosetta.core.pose.Pose) -> 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.hybridization.FragmentBiasAssigner,  : rosetta.protocols.hybridization.FragmentBiasAssigner) -> rosetta.protocols.hybridization.FragmentBiasAssigner automode(...) from builtins.PyCapsule automode(self : rosetta.protocols.hybridization.FragmentBiasAssigner, pose : rosetta.core.pose.Pose, score_cut : float) -> NoneType   ///////////////////////////////// automode_scores(...) from builtins.PyCapsule automode_scores(self : rosetta.protocols.hybridization.FragmentBiasAssigner, pose : rosetta.core.pose.Pose, scores : rosetta.utility.vector1_double) -> NoneType bfactors(...) from builtins.PyCapsule bfactors(self : rosetta.protocols.hybridization.FragmentBiasAssigner, pose : rosetta.core.pose.Pose) -> NoneType chainbreak(...) from builtins.PyCapsule chainbreak(self : rosetta.protocols.hybridization.FragmentBiasAssigner, pose : rosetta.core.pose.Pose) -> NoneType compute_frag_bias(...) from builtins.PyCapsule compute_frag_bias(self : rosetta.protocols.hybridization.FragmentBiasAssigner, frag_bias : rosetta.utility.vector1_numeric_random_WeightedSampler, pose : rosetta.core.pose.Pose, fragments : rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t) -> NoneType cumulate_probability(...) from builtins.PyCapsule cumulate_probability(rosetta.protocols.hybridization.FragmentBiasAssigner) -> NoneType density(...) from builtins.PyCapsule density(self : rosetta.protocols.hybridization.FragmentBiasAssigner, pose : rosetta.core.pose.Pose) -> NoneType density_nbr(...) from builtins.PyCapsule density_nbr(self : rosetta.protocols.hybridization.FragmentBiasAssigner, pose : rosetta.core.pose.Pose) -> NoneType   ///////////////////////////////// exclude_residues(...) from builtins.PyCapsule exclude_residues(self : rosetta.protocols.hybridization.FragmentBiasAssigner, residues_to_exclude : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType fragbias_reporter(...) from builtins.PyCapsule fragbias_reporter(self : rosetta.protocols.hybridization.FragmentBiasAssigner, pose : rosetta.core.pose.Pose) -> NoneType geometry(...) from builtins.PyCapsule geometry(*args, **kwargs) Overloaded function.   1. geometry(self : rosetta.protocols.hybridization.FragmentBiasAssigner, pose : rosetta.core.pose.Pose) -> NoneType   2. geometry(self : rosetta.protocols.hybridization.FragmentBiasAssigner, pose : rosetta.core.pose.Pose, weight : float) -> NoneType include_residues(...) from builtins.PyCapsule include_residues(self : rosetta.protocols.hybridization.FragmentBiasAssigner, residues_to_include : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType init(...) from builtins.PyCapsule init(self : rosetta.protocols.hybridization.FragmentBiasAssigner, pose : rosetta.core.pose.Pose) -> NoneType old_rama(...) from builtins.PyCapsule old_rama(self : rosetta.protocols.hybridization.FragmentBiasAssigner, pose : rosetta.core.pose.Pose) -> NoneType   ///////////////////////////// rama(...) from builtins.PyCapsule rama(*args, **kwargs) Overloaded function.   1. rama(self : rosetta.protocols.hybridization.FragmentBiasAssigner, pose : rosetta.core.pose.Pose) -> NoneType   2. rama(self : rosetta.protocols.hybridization.FragmentBiasAssigner, pose : rosetta.core.pose.Pose, weight : float) -> NoneType set_rsd_wdw_to_assign_prob(...) from builtins.PyCapsule set_rsd_wdw_to_assign_prob(*args, **kwargs) Overloaded function.   1. set_rsd_wdw_to_assign_prob(rosetta.protocols.hybridization.FragmentBiasAssigner) -> NoneType   2. set_rsd_wdw_to_assign_prob(self : rosetta.protocols.hybridization.FragmentBiasAssigner, wdw : int) -> NoneType set_score_threshold(...) from builtins.PyCapsule set_score_threshold(*args, **kwargs) Overloaded function.   1. set_score_threshold(rosetta.protocols.hybridization.FragmentBiasAssigner) -> NoneType   2. set_score_threshold(self : rosetta.protocols.hybridization.FragmentBiasAssigner, threshold : float) -> NoneType set_wdw_to_freeze(...) from builtins.PyCapsule set_wdw_to_freeze(*args, **kwargs) Overloaded function.   1. set_wdw_to_freeze(rosetta.protocols.hybridization.FragmentBiasAssigner) -> NoneType   2. set_wdw_to_freeze(self : rosetta.protocols.hybridization.FragmentBiasAssigner, wdw : int) -> NoneType uniform(...) from builtins.PyCapsule uniform(rosetta.protocols.hybridization.FragmentBiasAssigner) -> NoneType   ////////////////////////////////////////////////////////// user(...) from builtins.PyCapsule user(self : rosetta.protocols.hybridization.FragmentBiasAssigner, user_pos : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, loops : rosetta.protocols.loops.Loops) -> NoneType   //////////////////////////////////////////////////////////   class HybridizeFoldtreeDynamic(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.hybridization.HybridizeFoldtreeDynamic) -> NoneType   2. __init__(self : rosetta.protocols.hybridization.HybridizeFoldtreeDynamic,  : rosetta.protocols.hybridization.HybridizeFoldtreeDynamic) -> 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.hybridization.HybridizeFoldtreeDynamic,  : rosetta.protocols.hybridization.HybridizeFoldtreeDynamic) -> rosetta.protocols.hybridization.HybridizeFoldtreeDynamic get_anchors(...) from builtins.PyCapsule get_anchors(rosetta.protocols.hybridization.HybridizeFoldtreeDynamic) -> rosetta.utility.vector1_unsigned_long initialize(...) from builtins.PyCapsule initialize(self : rosetta.protocols.hybridization.HybridizeFoldtreeDynamic, pose : rosetta.core.pose.Pose, core_chunks : rosetta.protocols.loops.Loops, strand_pairs : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, strand_pair_library_positions : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType reset(...) from builtins.PyCapsule reset(self : rosetta.protocols.hybridization.HybridizeFoldtreeDynamic, pose : rosetta.core.pose.Pose) -> NoneType   class HybridizeProtocol(rosetta.protocols.moves.Mover)       Method resolution order: HybridizeProtocol rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.hybridization.HybridizeProtocol) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_big_fragments(...) from builtins.PyCapsule add_big_fragments(self : rosetta.protocols.hybridization.HybridizeProtocol, newval : rosetta.core.fragment.FragSet) -> NoneType add_fragment_csts(...) from builtins.PyCapsule add_fragment_csts(self : rosetta.protocols.hybridization.HybridizeProtocol, pose : rosetta.core.pose.Pose) -> NoneType add_null_template(...) from builtins.PyCapsule add_null_template(*args, **kwargs) Overloaded function.   1. add_null_template(self : rosetta.protocols.hybridization.HybridizeProtocol, template_pose : rosetta.core.pose.Pose, cst_fn : str) -> NoneType   2. add_null_template(self : rosetta.protocols.hybridization.HybridizeProtocol, template_pose : rosetta.core.pose.Pose, cst_fn : str, symmdef_file : str) -> NoneType   3. add_null_template(self : rosetta.protocols.hybridization.HybridizeProtocol, template_pose : rosetta.core.pose.Pose, cst_fn : str, symmdef_file : str, weight : float) -> NoneType add_small_fragments(...) from builtins.PyCapsule add_small_fragments(self : rosetta.protocols.hybridization.HybridizeProtocol, newval : rosetta.core.fragment.FragSet) -> NoneType add_template(...) from builtins.PyCapsule add_template(*args, **kwargs) Overloaded function.   1. add_template(self : rosetta.protocols.hybridization.HybridizeProtocol, template_fn : str, cst_fn : str) -> NoneType   2. add_template(self : rosetta.protocols.hybridization.HybridizeProtocol, template_fn : str, cst_fn : str, symmdef_file : str) -> NoneType   3. add_template(self : rosetta.protocols.hybridization.HybridizeProtocol, template_fn : str, cst_fn : str, symmdef_file : str, weight : float) -> NoneType   4. add_template(self : rosetta.protocols.hybridization.HybridizeProtocol, template_fn : str, cst_fn : str, symmdef_file : str, weight : float, rand_chains : rosetta.utility.vector1_char) -> NoneType   5. add_template(self : rosetta.protocols.hybridization.HybridizeProtocol, template_pose : rosetta.core.pose.Pose, cst_fn : str) -> NoneType   6. add_template(self : rosetta.protocols.hybridization.HybridizeProtocol, template_pose : rosetta.core.pose.Pose, cst_fn : str, symmdef_file : str) -> NoneType   7. add_template(self : rosetta.protocols.hybridization.HybridizeProtocol, template_pose : rosetta.core.pose.Pose, cst_fn : str, symmdef_file : str, weight : float) -> NoneType   8. add_template(self : rosetta.protocols.hybridization.HybridizeProtocol, template_pose : rosetta.core.pose.Pose, cst_fn : str, symmdef_file : str, weight : float, rand_chains : rosetta.utility.vector1_char) -> NoneType   9. add_template(self : rosetta.protocols.hybridization.HybridizeProtocol, template_pose : rosetta.core.pose.Pose, cst_fn : str, symmdef_file : str, weight : float, rand_chains : rosetta.utility.vector1_char, filename : str) -> NoneType align_by_domain(...) from builtins.PyCapsule align_by_domain(self : rosetta.protocols.hybridization.HybridizeProtocol, pose : rosetta.core.pose.Pose, ref_pose : rosetta.core.pose.Pose, domains : rosetta.utility.vector1_protocols_loops_Loops) -> NoneType align_templates_by_domain(...) from builtins.PyCapsule align_templates_by_domain(*args, **kwargs) Overloaded function.   1. align_templates_by_domain(self : rosetta.protocols.hybridization.HybridizeProtocol, ref_pose : rosetta.core.pose.Pose) -> NoneType   2. align_templates_by_domain(self : rosetta.protocols.hybridization.HybridizeProtocol, ref_pose : rosetta.core.pose.Pose, domains : rosetta.utility.vector1_protocols_loops_Loops) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.hybridization.HybridizeProtocol,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.hybridization.HybridizeProtocol,  : rosetta.protocols.hybridization.HybridizeProtocol) -> rosetta.protocols.hybridization.HybridizeProtocol check_and_create_fragments(...) from builtins.PyCapsule check_and_create_fragments(self : rosetta.protocols.hybridization.HybridizeProtocol,  : rosetta.core.pose.Pose) -> NoneType clone(...) from builtins.PyCapsule clone(rosetta.protocols.hybridization.HybridizeProtocol) -> rosetta.protocols.moves.Mover do_intrastage_docking(...) from builtins.PyCapsule do_intrastage_docking(self : rosetta.protocols.hybridization.HybridizeProtocol, pose : rosetta.core.pose.Pose) -> NoneType domain_parse_templates(...) from builtins.PyCapsule domain_parse_templates(self : rosetta.protocols.hybridization.HybridizeProtocol, nres : int) -> NoneType fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.hybridization.HybridizeProtocol) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.hybridization.HybridizeProtocol) -> str init(...) from builtins.PyCapsule init(rosetta.protocols.hybridization.HybridizeProtocol) -> NoneType initialize_and_sample_loops(...) from builtins.PyCapsule initialize_and_sample_loops(self : rosetta.protocols.hybridization.HybridizeProtocol, pose : rosetta.core.pose.Pose, chosen_templ : rosetta.core.pose.Pose, template_contigs_icluster : rosetta.protocols.loops.Loops, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType pick_starting_template(...) from builtins.PyCapsule pick_starting_template(rosetta.protocols.hybridization.HybridizeProtocol) -> int set_batch_relax(...) from builtins.PyCapsule set_batch_relax(self : rosetta.protocols.hybridization.HybridizeProtocol, newval : int) -> NoneType set_fullatom_scorefxn(...) from builtins.PyCapsule set_fullatom_scorefxn(self : rosetta.protocols.hybridization.HybridizeProtocol, newval : rosetta.core.scoring.ScoreFunction) -> NoneType set_stage1_increase_cycles(...) from builtins.PyCapsule set_stage1_increase_cycles(self : rosetta.protocols.hybridization.HybridizeProtocol, newval : float) -> NoneType set_stage1_scorefxn(...) from builtins.PyCapsule set_stage1_scorefxn(self : rosetta.protocols.hybridization.HybridizeProtocol, newval : rosetta.core.scoring.ScoreFunction) -> NoneType set_stage2_increase_cycles(...) from builtins.PyCapsule set_stage2_increase_cycles(self : rosetta.protocols.hybridization.HybridizeProtocol, newval : float) -> NoneType set_stage2_scorefxn(...) from builtins.PyCapsule set_stage2_scorefxn(self : rosetta.protocols.hybridization.HybridizeProtocol, newval : rosetta.core.scoring.ScoreFunction) -> NoneType set_stage2min_scorefxn(...) from builtins.PyCapsule set_stage2min_scorefxn(self : rosetta.protocols.hybridization.HybridizeProtocol, newval : rosetta.core.scoring.ScoreFunction) -> NoneType set_stage2pack_scorefxn(...) from builtins.PyCapsule set_stage2pack_scorefxn(self : rosetta.protocols.hybridization.HybridizeProtocol, newval : rosetta.core.scoring.ScoreFunction) -> NoneType update_last_template(...) from builtins.PyCapsule update_last_template(rosetta.protocols.hybridization.HybridizeProtocol) -> NoneType validate_template(...) from builtins.PyCapsule validate_template(self : rosetta.protocols.hybridization.HybridizeProtocol, filename : str, fasta : str, template_pose : rosetta.core.pose.Pose, align_pdb_info : bool) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class HybridizeProtocolCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: HybridizeProtocolCreator rosetta.protocols.moves.MoverCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> 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.hybridization.HybridizeProtocolCreator,  : rosetta.protocols.hybridization.HybridizeProtocolCreator) -> rosetta.protocols.hybridization.HybridizeProtocolCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.hybridization.HybridizeProtocolCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.hybridization.HybridizeProtocolCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class InsertChunkMover(rosetta.protocols.moves.Mover)       Method resolution order: InsertChunkMover rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.hybridization.InsertChunkMover) -> 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.hybridization.InsertChunkMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.hybridization.InsertChunkMover,  : rosetta.protocols.hybridization.InsertChunkMover) -> rosetta.protocols.hybridization.InsertChunkMover check_overlap(...) from builtins.PyCapsule check_overlap(self : rosetta.protocols.hybridization.InsertChunkMover, pose : rosetta.core.pose.Pose) -> NoneType get_local_sequence_mapping(...) from builtins.PyCapsule get_local_sequence_mapping(*args, **kwargs) Overloaded function.   1. get_local_sequence_mapping(self : rosetta.protocols.hybridization.InsertChunkMover, pose : rosetta.core.pose.Pose) -> bool   2. get_local_sequence_mapping(self : rosetta.protocols.hybridization.InsertChunkMover, pose : rosetta.core.pose.Pose, registry_shift : int) -> bool   3. get_local_sequence_mapping(self : rosetta.protocols.hybridization.InsertChunkMover, pose : rosetta.core.pose.Pose, registry_shift : int, MAX_TRIAL : int) -> bool get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.hybridization.InsertChunkMover) -> str init(...) from builtins.PyCapsule init(rosetta.protocols.hybridization.InsertChunkMover) -> NoneType set_aligned_chunk(...) from builtins.PyCapsule set_aligned_chunk(self : rosetta.protocols.hybridization.InsertChunkMover, pose : rosetta.core.pose.Pose, jump_number : int, anchor_insert_only_in : bool) -> NoneType set_bb_xyz_aligned(...) from builtins.PyCapsule set_bb_xyz_aligned(self : rosetta.protocols.hybridization.InsertChunkMover, pose : rosetta.core.pose.Pose) -> NoneType set_registry_shift(...) from builtins.PyCapsule set_registry_shift(self : rosetta.protocols.hybridization.InsertChunkMover, registry_shift : int) -> NoneType set_template(...) from builtins.PyCapsule set_template(self : rosetta.protocols.hybridization.InsertChunkMover, template_pose : rosetta.core.pose.Pose, template_id : int, sequence_alignment : rosetta.std.map_unsigned_long_unsigned_long) -> NoneType success(...) from builtins.PyCapsule success(rosetta.protocols.hybridization.InsertChunkMover) -> bool trial_counter(...) from builtins.PyCapsule trial_counter(self : rosetta.protocols.hybridization.InsertChunkMover, ires : int) -> int 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 MRMover(rosetta.protocols.moves.Mover)       Method resolution order: MRMover rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.hybridization.MRMover) -> 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.hybridization.MRMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.hybridization.MRMover,  : rosetta.protocols.hybridization.MRMover) -> rosetta.protocols.hybridization.MRMover clone(...) from builtins.PyCapsule clone(rosetta.protocols.hybridization.MRMover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.hybridization.MRMover) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.hybridization.MRMover) -> str init(...) from builtins.PyCapsule init(rosetta.protocols.hybridization.MRMover) -> NoneType set_big_fragments(...) from builtins.PyCapsule set_big_fragments(self : rosetta.protocols.hybridization.MRMover, newval : rosetta.core.fragment.FragSet) -> NoneType set_cen_cst_weight(...) from builtins.PyCapsule set_cen_cst_weight(self : rosetta.protocols.hybridization.MRMover, newval : float) -> NoneType set_censcale(...) from builtins.PyCapsule set_censcale(self : rosetta.protocols.hybridization.MRMover, newval : float) -> NoneType set_centroid_density_weight(...) from builtins.PyCapsule set_centroid_density_weight(self : rosetta.protocols.hybridization.MRMover, newval : float) -> NoneType set_disulf(...) from builtins.PyCapsule set_disulf(self : rosetta.protocols.hybridization.MRMover, newval : rosetta.utility.vector1_std_string) -> NoneType set_fa_cst_weight(...) from builtins.PyCapsule set_fa_cst_weight(self : rosetta.protocols.hybridization.MRMover, newval : float) -> NoneType set_fullatom_density_weight(...) from builtins.PyCapsule set_fullatom_density_weight(self : rosetta.protocols.hybridization.MRMover, newval : float, fast : bool) -> NoneType set_max_gaplength_to_model(...) from builtins.PyCapsule set_max_gaplength_to_model(self : rosetta.protocols.hybridization.MRMover, newval : int) -> NoneType set_small_fragments(...) from builtins.PyCapsule set_small_fragments(self : rosetta.protocols.hybridization.MRMover, newval : rosetta.core.fragment.FragSet) -> NoneType set_symmdef_file(...) from builtins.PyCapsule set_symmdef_file(self : rosetta.protocols.hybridization.MRMover, newval : str) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class TMalign(builtins.object)       Methods defined here: DP_iter(...) from builtins.PyCapsule DP_iter(self : rosetta.protocols.hybridization.TMalign, x : rosetta.std.vector_numeric_xyzVector_double_t, y : rosetta.std.vector_numeric_xyzVector_double_t, x_len : int, y_len : int, t : rosetta.numeric.xyzVector_double_t, u : rosetta.numeric.xyzMatrix_double_t, invmap0 : rosetta.std.vector_int, g1 : int, g2 : int, iteration_max : int) -> float Kabsch(...) from builtins.PyCapsule Kabsch(*args, **kwargs) Overloaded function.   1. Kabsch(self : rosetta.protocols.hybridization.TMalign, x : rosetta.std.vector_numeric_xyzVector_double_t, y : rosetta.std.vector_numeric_xyzVector_double_t, n : int, mode : int, rms : float, t : rosetta.numeric.xyzVector_double_t, u : rosetta.numeric.xyzMatrix_double_t) -> bool   2. Kabsch(self : rosetta.protocols.hybridization.TMalign, x : rosetta.std.vector_std_vector_double_std_allocator_double_t, y : rosetta.std.vector_std_vector_double_std_allocator_double_t, n : int, mode : int, rms : float, t : rosetta.std.vector_double, u : rosetta.std.vector_std_vector_double_std_allocator_double_t) -> bool NWDP_TM(...) from builtins.PyCapsule NWDP_TM(*args, **kwargs) Overloaded function.   1. NWDP_TM(self : rosetta.protocols.hybridization.TMalign, len1 : int, len2 : int, gap_open : float, j2i : rosetta.std.vector_int) -> NoneType   2. NWDP_TM(self : rosetta.protocols.hybridization.TMalign, x : rosetta.std.vector_numeric_xyzVector_double_t, y : rosetta.std.vector_numeric_xyzVector_double_t, len1 : int, len2 : int, t : rosetta.numeric.xyzVector_double_t, u : rosetta.numeric.xyzMatrix_double_t, d02 : float, gap_open : float, j2i : rosetta.std.vector_int) -> NoneType   3. NWDP_TM(self : rosetta.protocols.hybridization.TMalign, secx : rosetta.std.vector_int, secy : rosetta.std.vector_int, len1 : int, len2 : int, gap_open : float, j2i : rosetta.std.vector_int) -> NoneType PrintErrorAndQuit(...) from builtins.PyCapsule PrintErrorAndQuit(self : rosetta.protocols.hybridization.TMalign, sErrorString : str) -> NoneType TMscore(...) from builtins.PyCapsule TMscore(self : rosetta.protocols.hybridization.TMalign, length : int) -> float TMscore8_search(...) from builtins.PyCapsule TMscore8_search(self : rosetta.protocols.hybridization.TMalign, xtm : rosetta.std.vector_numeric_xyzVector_double_t, ytm : rosetta.std.vector_numeric_xyzVector_double_t, Lali : int, t0 : rosetta.numeric.xyzVector_double_t, u0 : rosetta.numeric.xyzMatrix_double_t, simplify_step : int, score_sum_method : int, Rcomm : float) -> float __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.hybridization.TMalign) -> NoneType   2. __init__(self : rosetta.protocols.hybridization.TMalign,  : rosetta.protocols.hybridization.TMalign) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. alignment2AtomMap(...) from builtins.PyCapsule alignment2AtomMap(*args, **kwargs) Overloaded function.   1. alignment2AtomMap(self : rosetta.protocols.hybridization.TMalign, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, atom_map : rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> NoneType   2. alignment2AtomMap(self : rosetta.protocols.hybridization.TMalign, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, n_mapped_residues : int, atom_map : rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> NoneType   3. alignment2AtomMap(self : rosetta.protocols.hybridization.TMalign, pose : rosetta.core.pose.Pose, ref_pose : rosetta.core.pose.Pose, residue_list : rosetta.std.list_unsigned_long_std_allocator_unsigned_long_t, ref_residue_list : rosetta.std.list_unsigned_long_std_allocator_unsigned_long_t, n_mapped_residues : int, atom_map : rosetta.core.id.AtomID_Map_core_id_AtomID_t) -> NoneType alignment2strings(...) from builtins.PyCapsule alignment2strings(self : rosetta.protocols.hybridization.TMalign, seqxA : str, seqyA : str, seqM : str) -> NoneType apply(...) from builtins.PyCapsule apply(*args, **kwargs) Overloaded function.   1. apply(self : rosetta.protocols.hybridization.TMalign, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose) -> int   2. apply(self : rosetta.protocols.hybridization.TMalign, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, residue_list1 : rosetta.std.list_unsigned_long_std_allocator_unsigned_long_t, residue_list2 : rosetta.std.list_unsigned_long_std_allocator_unsigned_long_t) -> int assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.hybridization.TMalign,  : rosetta.protocols.hybridization.TMalign) -> rosetta.protocols.hybridization.TMalign convert_matrix_to_xyz(...) from builtins.PyCapsule convert_matrix_to_xyz(self : rosetta.protocols.hybridization.TMalign, x : rosetta.std.vector_std_vector_double_std_allocator_double_t, xx : rosetta.numeric.xyzMatrix_double_t) -> NoneType convert_vector_to_xyz(...) from builtins.PyCapsule convert_vector_to_xyz(self : rosetta.protocols.hybridization.TMalign, x : rosetta.std.vector_double, xx : rosetta.numeric.xyzVector_double_t) -> NoneType convert_xyz_to_matrix(...) from builtins.PyCapsule convert_xyz_to_matrix(self : rosetta.protocols.hybridization.TMalign, x : rosetta.numeric.xyzMatrix_double_t, xx : rosetta.std.vector_std_vector_double_std_allocator_double_t) -> NoneType convert_xyz_to_vector(...) from builtins.PyCapsule convert_xyz_to_vector(self : rosetta.protocols.hybridization.TMalign, x : rosetta.numeric.xyzVector_double_t, xx : rosetta.std.vector_double) -> NoneType convert_xyz_v_to_vectors(...) from builtins.PyCapsule convert_xyz_v_to_vectors(self : rosetta.protocols.hybridization.TMalign, x : rosetta.std.vector_numeric_xyzVector_double_t, xx : rosetta.std.vector_std_vector_double_std_allocator_double_t) -> NoneType detailed_search(...) from builtins.PyCapsule detailed_search(self : rosetta.protocols.hybridization.TMalign, x : rosetta.std.vector_numeric_xyzVector_double_t, y : rosetta.std.vector_numeric_xyzVector_double_t,  : int, y_len : int, invmap0 : rosetta.std.vector_int, t : rosetta.numeric.xyzVector_double_t, u : rosetta.numeric.xyzMatrix_double_t, simplify_step : int, score_sum_method : int) -> float dist(...) from builtins.PyCapsule dist(self : rosetta.protocols.hybridization.TMalign, x : rosetta.numeric.xyzVector_double_t, y : rosetta.numeric.xyzVector_double_t) -> float do_rotation(...) from builtins.PyCapsule do_rotation(self : rosetta.protocols.hybridization.TMalign, x : rosetta.std.vector_numeric_xyzVector_double_t, x1 : rosetta.std.vector_numeric_xyzVector_double_t, len : int, t : rosetta.numeric.xyzVector_double_t, u : rosetta.numeric.xyzMatrix_double_t) -> NoneType find_max_frag(...) from builtins.PyCapsule find_max_frag(self : rosetta.protocols.hybridization.TMalign, x : rosetta.std.vector_numeric_xyzVector_double_t, resno : rosetta.std.vector_int, len : int, start_max : int, end_max : int) -> NoneType get_initial(...) from builtins.PyCapsule get_initial(self : rosetta.protocols.hybridization.TMalign, x : rosetta.std.vector_numeric_xyzVector_double_t, y : rosetta.std.vector_numeric_xyzVector_double_t, x_len : int, y_len : int, y2x : rosetta.std.vector_int) -> float get_initial_fgt(...) from builtins.PyCapsule get_initial_fgt(self : rosetta.protocols.hybridization.TMalign, x : rosetta.std.vector_numeric_xyzVector_double_t, y : rosetta.std.vector_numeric_xyzVector_double_t, x_len : int, y_len : int, xresno : rosetta.std.vector_int, yresno : rosetta.std.vector_int, y2x : rosetta.std.vector_int) -> float get_initial_local(...) from builtins.PyCapsule get_initial_local(self : rosetta.protocols.hybridization.TMalign, x : rosetta.std.vector_numeric_xyzVector_double_t, y : rosetta.std.vector_numeric_xyzVector_double_t, x_len : int, y_len : int, y2x : rosetta.std.vector_int) -> bool get_initial_ss(...) from builtins.PyCapsule get_initial_ss(self : rosetta.protocols.hybridization.TMalign, x : rosetta.std.vector_numeric_xyzVector_double_t, y : rosetta.std.vector_numeric_xyzVector_double_t, x_len : int, y_len : int, y2x : rosetta.std.vector_int) -> NoneType get_initial_ssplus(...) from builtins.PyCapsule get_initial_ssplus(self : rosetta.protocols.hybridization.TMalign, x : rosetta.std.vector_numeric_xyzVector_double_t, y : rosetta.std.vector_numeric_xyzVector_double_t, x_len : int, y_len : int, y2x0 : rosetta.std.vector_int, y2x : rosetta.std.vector_int) -> NoneType get_score_fast(...) from builtins.PyCapsule get_score_fast(self : rosetta.protocols.hybridization.TMalign, x : rosetta.std.vector_numeric_xyzVector_double_t, y : rosetta.std.vector_numeric_xyzVector_double_t,  : int, y_len : int, invmap : rosetta.std.vector_int) -> float load_pose_allocate_memory(...) from builtins.PyCapsule load_pose_allocate_memory(self : rosetta.protocols.hybridization.TMalign, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, residue_list1 : rosetta.std.list_unsigned_long_std_allocator_unsigned_long_t, residue_list2 : rosetta.std.list_unsigned_long_std_allocator_unsigned_long_t) -> NoneType make_sec(...) from builtins.PyCapsule make_sec(self : rosetta.protocols.hybridization.TMalign, x : rosetta.std.vector_numeric_xyzVector_double_t, len : int, sec : rosetta.std.vector_int) -> NoneType parameter_set4final(...) from builtins.PyCapsule parameter_set4final(self : rosetta.protocols.hybridization.TMalign, len : float) -> NoneType parameter_set4scale(...) from builtins.PyCapsule parameter_set4scale(self : rosetta.protocols.hybridization.TMalign, len : int, d_s : float) -> NoneType parameter_set4search(...) from builtins.PyCapsule parameter_set4search(self : rosetta.protocols.hybridization.TMalign, xlen : int, ylen : int) -> NoneType read_pose(...) from builtins.PyCapsule read_pose(self : rosetta.protocols.hybridization.TMalign, pose : rosetta.core.pose.Pose, residue_list : rosetta.std.list_unsigned_long_std_allocator_unsigned_long_t, a : rosetta.std.vector_numeric_xyzVector_double_t, seq : str, resno : rosetta.std.vector_int) -> int score_fun8(...) from builtins.PyCapsule score_fun8(self : rosetta.protocols.hybridization.TMalign, xa : rosetta.std.vector_numeric_xyzVector_double_t, ya : rosetta.std.vector_numeric_xyzVector_double_t, n_ali : int, d : float, i_ali : rosetta.std.vector_int, score1 : float, score_sum_method : int) -> int score_matrix_rmsd(...) from builtins.PyCapsule score_matrix_rmsd(self : rosetta.protocols.hybridization.TMalign, x : rosetta.std.vector_numeric_xyzVector_double_t, y : rosetta.std.vector_numeric_xyzVector_double_t, x_len : int, y_len : int, y2x : rosetta.std.vector_int) -> NoneType score_matrix_rmsd_sec(...) from builtins.PyCapsule score_matrix_rmsd_sec(self : rosetta.protocols.hybridization.TMalign, x : rosetta.std.vector_numeric_xyzVector_double_t, y : rosetta.std.vector_numeric_xyzVector_double_t, x_len : int, y_len : int, y2x : rosetta.std.vector_int) -> NoneType sec_str(...) from builtins.PyCapsule sec_str(self : rosetta.protocols.hybridization.TMalign, dis13 : float, dis14 : float, dis15 : float, dis24 : float, dis25 : float, dis35 : float) -> int smooth(...) from builtins.PyCapsule smooth(self : rosetta.protocols.hybridization.TMalign, sec : rosetta.std.vector_int, len : int) -> NoneType transform(...) from builtins.PyCapsule transform(self : rosetta.protocols.hybridization.TMalign, t : rosetta.numeric.xyzVector_double_t, u : rosetta.numeric.xyzMatrix_double_t, x : rosetta.numeric.xyzVector_double_t, x1 : rosetta.numeric.xyzVector_double_t) -> NoneType   class TemplateHistory(rosetta.basic.datacache.CacheableData)     ////////////////////////////////////////////////////////////////////////////     Method resolution order: TemplateHistory rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, pose : rosetta.core.pose.Pose) -> NoneType   2. __init__(handle, rosetta.protocols.hybridization.TemplateHistory) -> 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.hybridization.TemplateHistory,  : rosetta.protocols.hybridization.TemplateHistory) -> rosetta.protocols.hybridization.TemplateHistory clone(...) from builtins.PyCapsule clone(rosetta.protocols.hybridization.TemplateHistory) -> rosetta.basic.datacache.CacheableData get(...) from builtins.PyCapsule get(self : rosetta.protocols.hybridization.TemplateHistory, resid : int) -> int set(...) from builtins.PyCapsule set(self : rosetta.protocols.hybridization.TemplateHistory, res_start : int, res_stop : int, template_id : int) -> NoneType setall(...) from builtins.PyCapsule setall(self : rosetta.protocols.hybridization.TemplateHistory, template_id : int) -> NoneType size(...) from builtins.PyCapsule size(rosetta.protocols.hybridization.TemplateHistory) -> int Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class WeightedFragmentSmoothTrialMover(rosetta.protocols.moves.Mover)       Method resolution order: WeightedFragmentSmoothTrialMover rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, frag_libs : rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t, residue_weights : rosetta.utility.vector1_double, anchor_residues : rosetta.utility.vector1_unsigned_long, nr_frags : int, cost : rosetta.protocols.simple_moves.FragmentCost) -> NoneType   2. __init__(handle, rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover) -> 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.hybridization.WeightedFragmentSmoothTrialMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover,  : rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover) -> rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover) -> str get_nr_frags(...) from builtins.PyCapsule get_nr_frags(rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover) -> int get_total_frames(...) from builtins.PyCapsule get_total_frames(rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover) -> int update_sampler_weights(...) from builtins.PyCapsule update_sampler_weights(self : rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover, residue_weights : rosetta.utility.vector1_double) -> 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 WeightedFragmentTrialMover(rosetta.protocols.moves.Mover)       Method resolution order: WeightedFragmentTrialMover 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_fragment_FragSet_t, rosetta.utility.vector1_double) -> NoneType   doc   2. __init__(handle, rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t, rosetta.utility.vector1_double, rosetta.utility.vector1_unsigned_long) -> NoneType   doc   3. __init__(self : handle, frag_libs : rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t, residue_weights : rosetta.utility.vector1_double, anchor_residues : rosetta.utility.vector1_unsigned_long, nr_frags : int) -> NoneType   4. __init__(handle, rosetta.protocols.hybridization.WeightedFragmentTrialMover) -> 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.hybridization.WeightedFragmentTrialMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.hybridization.WeightedFragmentTrialMover,  : rosetta.protocols.hybridization.WeightedFragmentTrialMover) -> rosetta.protocols.hybridization.WeightedFragmentTrialMover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.hybridization.WeightedFragmentTrialMover) -> str get_nr_frags(...) from builtins.PyCapsule get_nr_frags(rosetta.protocols.hybridization.WeightedFragmentTrialMover) -> int get_total_frames(...) from builtins.PyCapsule get_total_frames(rosetta.protocols.hybridization.WeightedFragmentTrialMover) -> int update_sampler_weights(...) from builtins.PyCapsule update_sampler_weights(self : rosetta.protocols.hybridization.WeightedFragmentTrialMover, residue_weights : rosetta.utility.vector1_double) -> 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