Bindings for protocols::loops::loop_mover::refine namespace

Classes
		builtins.object LoopRefineInnerCycleName rosetta.protocols.loops.loop_mover.LoopMover(rosetta.protocols.moves.Mover) LoopMover_Refine_Backrub LoopMover_Refine_CCD LoopMover_Refine_KIC rosetta.protocols.moves.Mover(builtins.object) LoopRefineInnerCycle LoopRefineInnerCycleContainer RepackTrial ShearMinCCDTrial SmallMinCCDTrial rosetta.protocols.moves.MoverCreator(builtins.object) LoopMover_Refine_BackrubCreator LoopMover_Refine_CCDCreator LoopMover_Refine_KICCreator LoopRefineInnerCycleContainerCreator RepackTrialCreator ShearMinCCDTrialCreator SmallMinCCDTrialCreator rosetta.utility.SingletonBase_protocols_loops_loop_mover_refine_LoopRefineInnerCycleFactory_t(builtins.object) LoopRefineInnerCycleFactory   class LoopMover_Refine_Backrub(rosetta.protocols.loops.loop_mover.LoopMover)       Method resolution order: LoopMover_Refine_Backrub rosetta.protocols.loops.loop_mover.LoopMover rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, loops_in : rosetta.protocols.loops.Loops) -> NoneType   3. __init__(self : handle, loops_in : rosetta.protocols.loops.Loops, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   4. __init__(handle, rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub) -> 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.loops.loop_mover.refine.LoopMover_Refine_Backrub, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub,  : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub) -> rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub clone(...) from builtins.PyCapsule clone(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub) -> rosetta.protocols.moves.Mover   Clone this object get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub) -> str get_redesign_loop(...) from builtins.PyCapsule get_redesign_loop(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub) -> bool get_task_factory(...) from builtins.PyCapsule get_task_factory(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub) -> bool set_default_settings(...) from builtins.PyCapsule set_default_settings(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub) -> NoneType set_redesign_loop(...) from builtins.PyCapsule set_redesign_loop(*args, **kwargs) Overloaded function.   1. set_redesign_loop(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub) -> NoneType   2. set_redesign_loop(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub, value : bool) -> NoneType set_task_factory(...) from builtins.PyCapsule set_task_factory(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub, value : rosetta.core.pack.task.TaskFactory) -> NoneType Methods inherited from rosetta.protocols.loops.loop_mover.LoopMover: add_fragments(...) from builtins.PyCapsule add_fragments(self : rosetta.protocols.loops.loop_mover.LoopMover, fragset : rosetta.core.fragment.FragSet) -> NoneType   add a fragment set clear_fragments(...) from builtins.PyCapsule clear_fragments(rosetta.protocols.loops.loop_mover.LoopMover) -> NoneType   clear the list of fragment sets false_movemap(...) from builtins.PyCapsule false_movemap(*args, **kwargs) Overloaded function.   1. false_movemap(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.core.kinematics.MoveMap   explicit False settings in this MoveMap will override any   automatically generated MoveMap settings during the loop modeling   protocol   2. false_movemap(self : rosetta.protocols.loops.loop_mover.LoopMover, mm : rosetta.core.kinematics.MoveMap) -> NoneType   explicit False settings in this MoveMap will override any   automatically generated MoveMap settings during the loop modeling   protocol frag_libs(...) from builtins.PyCapsule frag_libs(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t get_checkpoints(...) from builtins.PyCapsule get_checkpoints(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.checkpoint.CheckPointer loops(...) from builtins.PyCapsule loops(*args, **kwargs) Overloaded function.   1. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, lptr : rosetta.protocols.loops.Loops) -> NoneType   Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets  the GuardedLoopsFromFile object into a "not in charge" state (since something else  must be controlling the the Loops object).  The GuardedLoopFromFile object copies the pointer,  not the data.   2. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, loop_file_data : protocols::loops::LoopsFileData) -> NoneType   Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ).   3. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, guarded_loops : protocols::loops::GuardedLoopsFromFile) -> NoneType   Set the guarded_loops pointer   4. loops(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.loops.Loops   Accessor for the loops data.  Requires that the loop indices have been resolved; do not call this before  apply() has been called.   5. loops(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.loops.Loops   non-const accessor for the loops data.  Requires that the loop indices have been resolved; do not call this  before apply() has been called. scorefxn(...) from builtins.PyCapsule scorefxn(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.core.scoring.ScoreFunction set_extended_torsions(...) from builtins.PyCapsule set_extended_torsions(self : rosetta.protocols.loops.loop_mover.LoopMover, pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop) -> NoneType   Extend a loop set_guarded_loops_not_in_charge(...) from builtins.PyCapsule set_guarded_loops_not_in_charge(rosetta.protocols.loops.loop_mover.LoopMover) -> NoneType   Inform the GuardedLoopsFromFile object that it is not in charge of  updating its Loops object at the beginning of apply() set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.loops.loop_mover.LoopMover, score_in : rosetta.core.scoring.ScoreFunction) -> NoneType torsion_features_string(...) from builtins.PyCapsule torsion_features_string(self : rosetta.protocols.loops.loop_mover.LoopMover, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector0_core_conformation_ppo_torsion_bin   create a string representing the torsion bins (ABEGX) for the loops defined in the  guarded_loops_ object.  A sentinal value of ppo_torbin_U is used to mark the boundaries  between the separate loops (unused as long as there's only one Loop object in the  guarded_loops_ object). Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class LoopMover_Refine_BackrubCreator(rosetta.protocols.moves.MoverCreator)     creator for the LoopMover_Refine_BackrubCreator class     Method resolution order: LoopMover_Refine_BackrubCreator 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.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator,  : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator) -> rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator) -> str   class LoopMover_Refine_CCD(rosetta.protocols.loops.loop_mover.LoopMover)       Method resolution order: LoopMover_Refine_CCD rosetta.protocols.loops.loop_mover.LoopMover rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, loops_in : rosetta.protocols.loops.Loops) -> NoneType   3. __init__(self : handle, loops_in : rosetta.protocols.loops.Loops, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   4. __init__(handle, rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> str apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD,  : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD clone(...) from builtins.PyCapsule clone(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> rosetta.protocols.moves.Mover   Clone this object current_cycle_number(...) from builtins.PyCapsule current_cycle_number(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> int flank_residue_min(...) from builtins.PyCapsule flank_residue_min(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> bool get_loops(...) from builtins.PyCapsule get_loops(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> rosetta.protocols.loops.Loops get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> str get_redesign_loop(...) from builtins.PyCapsule get_redesign_loop(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> bool get_task_factory(...) from builtins.PyCapsule get_task_factory(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> rosetta.core.pack.task.TaskFactory inner_cycles(...) from builtins.PyCapsule inner_cycles(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> int max_inner_cycles(...) from builtins.PyCapsule max_inner_cycles(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, value : int) -> NoneType move_map(...) from builtins.PyCapsule move_map(*args, **kwargs) Overloaded function.   1. move_map(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> rosetta.core.kinematics.MoveMap   2. move_map(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, mm : rosetta.core.kinematics.MoveMap) -> NoneType outer_cycles(...) from builtins.PyCapsule outer_cycles(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, value : int) -> NoneType repack_neighbors(...) from builtins.PyCapsule repack_neighbors(*args, **kwargs) Overloaded function.   1. repack_neighbors(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, s : bool) -> NoneType   2. repack_neighbors(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> bool repack_period(...) from builtins.PyCapsule repack_period(*args, **kwargs) Overloaded function.   1. repack_period(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, value : int) -> NoneType   2. repack_period(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> int set_default_settings(...) from builtins.PyCapsule set_default_settings(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> NoneType set_flank_residue_min(...) from builtins.PyCapsule set_flank_residue_min(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, value : bool) -> NoneType set_fold_tree_from_loops(...) from builtins.PyCapsule set_fold_tree_from_loops(*args, **kwargs) Overloaded function.   1. set_fold_tree_from_loops(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, s : bool) -> NoneType   2. set_fold_tree_from_loops(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> bool set_redesign_loop(...) from builtins.PyCapsule set_redesign_loop(*args, **kwargs) Overloaded function.   1. set_redesign_loop(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD) -> NoneType   2. set_redesign_loop(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, value : bool) -> NoneType set_task_factory(...) from builtins.PyCapsule set_task_factory(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, task_factory_in : rosetta.core.pack.task.TaskFactory) -> NoneType setup_movemap(...) from builtins.PyCapsule setup_movemap(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, pose : rosetta.core.pose.Pose, loops : rosetta.protocols.loops.Loops, allow_repack : rosetta.utility.vector1_bool, movemap : rosetta.core.kinematics.MoveMap) -> NoneType   setup an appropriate movemap for the given loops      The loops to model.      Indicates whether or not to allow a position to   repack.      Output movemap, all settings added here.      will enforce the false movemap temp_final(...) from builtins.PyCapsule temp_final(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, value : float) -> NoneType temp_initial(...) from builtins.PyCapsule temp_initial(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD, value : float) -> NoneType Methods inherited from rosetta.protocols.loops.loop_mover.LoopMover: add_fragments(...) from builtins.PyCapsule add_fragments(self : rosetta.protocols.loops.loop_mover.LoopMover, fragset : rosetta.core.fragment.FragSet) -> NoneType   add a fragment set clear_fragments(...) from builtins.PyCapsule clear_fragments(rosetta.protocols.loops.loop_mover.LoopMover) -> NoneType   clear the list of fragment sets false_movemap(...) from builtins.PyCapsule false_movemap(*args, **kwargs) Overloaded function.   1. false_movemap(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.core.kinematics.MoveMap   explicit False settings in this MoveMap will override any   automatically generated MoveMap settings during the loop modeling   protocol   2. false_movemap(self : rosetta.protocols.loops.loop_mover.LoopMover, mm : rosetta.core.kinematics.MoveMap) -> NoneType   explicit False settings in this MoveMap will override any   automatically generated MoveMap settings during the loop modeling   protocol frag_libs(...) from builtins.PyCapsule frag_libs(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t get_checkpoints(...) from builtins.PyCapsule get_checkpoints(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.checkpoint.CheckPointer loops(...) from builtins.PyCapsule loops(*args, **kwargs) Overloaded function.   1. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, lptr : rosetta.protocols.loops.Loops) -> NoneType   Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets  the GuardedLoopsFromFile object into a "not in charge" state (since something else  must be controlling the the Loops object).  The GuardedLoopFromFile object copies the pointer,  not the data.   2. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, loop_file_data : protocols::loops::LoopsFileData) -> NoneType   Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ).   3. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, guarded_loops : protocols::loops::GuardedLoopsFromFile) -> NoneType   Set the guarded_loops pointer   4. loops(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.loops.Loops   Accessor for the loops data.  Requires that the loop indices have been resolved; do not call this before  apply() has been called.   5. loops(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.loops.Loops   non-const accessor for the loops data.  Requires that the loop indices have been resolved; do not call this  before apply() has been called. scorefxn(...) from builtins.PyCapsule scorefxn(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.core.scoring.ScoreFunction set_extended_torsions(...) from builtins.PyCapsule set_extended_torsions(self : rosetta.protocols.loops.loop_mover.LoopMover, pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop) -> NoneType   Extend a loop set_guarded_loops_not_in_charge(...) from builtins.PyCapsule set_guarded_loops_not_in_charge(rosetta.protocols.loops.loop_mover.LoopMover) -> NoneType   Inform the GuardedLoopsFromFile object that it is not in charge of  updating its Loops object at the beginning of apply() set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.loops.loop_mover.LoopMover, score_in : rosetta.core.scoring.ScoreFunction) -> NoneType torsion_features_string(...) from builtins.PyCapsule torsion_features_string(self : rosetta.protocols.loops.loop_mover.LoopMover, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector0_core_conformation_ppo_torsion_bin   create a string representing the torsion bins (ABEGX) for the loops defined in the  guarded_loops_ object.  A sentinal value of ppo_torbin_U is used to mark the boundaries  between the separate loops (unused as long as there's only one Loop object in the  guarded_loops_ object). Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class LoopMover_Refine_CCDCreator(rosetta.protocols.moves.MoverCreator)     creator for the LoopMover_Refine_CCDCreator class     Method resolution order: LoopMover_Refine_CCDCreator 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.loops.loop_mover.refine.LoopMover_Refine_CCDCreator,  : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator) -> rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator) -> str   class LoopMover_Refine_KIC(rosetta.protocols.loops.loop_mover.LoopMover)       Method resolution order: LoopMover_Refine_KIC rosetta.protocols.loops.loop_mover.LoopMover rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, loops_in : rosetta.protocols.loops.Loops) -> NoneType   3. __init__(self : handle, loops_in : rosetta.protocols.loops.Loops, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   4. __init__(handle, rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC) -> str apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC,  : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC) -> rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC clone(...) from builtins.PyCapsule clone(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC) -> rosetta.protocols.moves.Mover   Clone this object get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC) -> str get_redesign_loop(...) from builtins.PyCapsule get_redesign_loop(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC) -> bool get_task_factory(...) from builtins.PyCapsule get_task_factory(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC) -> bool init(...) from builtins.PyCapsule init(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_default_settings(...) from builtins.PyCapsule set_default_settings(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC) -> NoneType set_flank_residue_min(...) from builtins.PyCapsule set_flank_residue_min(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC, value : bool) -> NoneType set_movemap_from_kic_segment(...) from builtins.PyCapsule set_movemap_from_kic_segment(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC, pose : rosetta.core.pose.Pose, cur_mm : rosetta.core.kinematics.MoveMap, kic_start : int, kic_end : int) -> NoneType set_redesign_loop(...) from builtins.PyCapsule set_redesign_loop(*args, **kwargs) Overloaded function.   1. set_redesign_loop(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC) -> NoneType   2. set_redesign_loop(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC, value : bool) -> NoneType set_rottrials_from_kic_segment(...) from builtins.PyCapsule set_rottrials_from_kic_segment(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC, pose : rosetta.core.pose.Pose, rottrials_packer_task : rosetta.core.pack.task.PackerTask, kic_start : int, kic_end : int) -> NoneType set_task_factory(...) from builtins.PyCapsule set_task_factory(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC, value : rosetta.core.pack.task.TaskFactory) -> NoneType update_allow_sc_vectors(...) from builtins.PyCapsule update_allow_sc_vectors(self : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC, pose : rosetta.core.pose.Pose, allow_sc_vectors : rosetta.utility.vector1_utility_vector1_bool_std_allocator_bool_t) -> NoneType   update the vector of vectors of moveable side-chain positions, one for each loop in loops_ Methods inherited from rosetta.protocols.loops.loop_mover.LoopMover: add_fragments(...) from builtins.PyCapsule add_fragments(self : rosetta.protocols.loops.loop_mover.LoopMover, fragset : rosetta.core.fragment.FragSet) -> NoneType   add a fragment set clear_fragments(...) from builtins.PyCapsule clear_fragments(rosetta.protocols.loops.loop_mover.LoopMover) -> NoneType   clear the list of fragment sets false_movemap(...) from builtins.PyCapsule false_movemap(*args, **kwargs) Overloaded function.   1. false_movemap(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.core.kinematics.MoveMap   explicit False settings in this MoveMap will override any   automatically generated MoveMap settings during the loop modeling   protocol   2. false_movemap(self : rosetta.protocols.loops.loop_mover.LoopMover, mm : rosetta.core.kinematics.MoveMap) -> NoneType   explicit False settings in this MoveMap will override any   automatically generated MoveMap settings during the loop modeling   protocol frag_libs(...) from builtins.PyCapsule frag_libs(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t get_checkpoints(...) from builtins.PyCapsule get_checkpoints(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.checkpoint.CheckPointer loops(...) from builtins.PyCapsule loops(*args, **kwargs) Overloaded function.   1. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, lptr : rosetta.protocols.loops.Loops) -> NoneType   Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets  the GuardedLoopsFromFile object into a "not in charge" state (since something else  must be controlling the the Loops object).  The GuardedLoopFromFile object copies the pointer,  not the data.   2. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, loop_file_data : protocols::loops::LoopsFileData) -> NoneType   Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ).   3. loops(self : rosetta.protocols.loops.loop_mover.LoopMover, guarded_loops : protocols::loops::GuardedLoopsFromFile) -> NoneType   Set the guarded_loops pointer   4. loops(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.loops.Loops   Accessor for the loops data.  Requires that the loop indices have been resolved; do not call this before  apply() has been called.   5. loops(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.protocols.loops.Loops   non-const accessor for the loops data.  Requires that the loop indices have been resolved; do not call this  before apply() has been called. scorefxn(...) from builtins.PyCapsule scorefxn(rosetta.protocols.loops.loop_mover.LoopMover) -> rosetta.core.scoring.ScoreFunction set_extended_torsions(...) from builtins.PyCapsule set_extended_torsions(self : rosetta.protocols.loops.loop_mover.LoopMover, pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop) -> NoneType   Extend a loop set_guarded_loops_not_in_charge(...) from builtins.PyCapsule set_guarded_loops_not_in_charge(rosetta.protocols.loops.loop_mover.LoopMover) -> NoneType   Inform the GuardedLoopsFromFile object that it is not in charge of  updating its Loops object at the beginning of apply() set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.loops.loop_mover.LoopMover, score_in : rosetta.core.scoring.ScoreFunction) -> NoneType torsion_features_string(...) from builtins.PyCapsule torsion_features_string(self : rosetta.protocols.loops.loop_mover.LoopMover, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector0_core_conformation_ppo_torsion_bin   create a string representing the torsion bins (ABEGX) for the loops defined in the  guarded_loops_ object.  A sentinal value of ppo_torbin_U is used to mark the boundaries  between the separate loops (unused as long as there's only one Loop object in the  guarded_loops_ object). Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class LoopMover_Refine_KICCreator(rosetta.protocols.moves.MoverCreator)     creator for the LoopMover_Perturb_KICCreator class     Method resolution order: LoopMover_Refine_KICCreator 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.loops.loop_mover.refine.LoopMover_Refine_KICCreator,  : rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator) -> rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator) -> str   class LoopRefineInnerCycle(rosetta.protocols.moves.Mover)       Method resolution order: LoopRefineInnerCycle rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> NoneType   2. __init__(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> NoneType   3. __init__(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, loop_mover : rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t, mc : rosetta.protocols.moves.MonteCarlo, scorefxn : rosetta.core.scoring.ScoreFunction, tf : rosetta.core.pack.task.TaskFactory) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> str apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, rhs : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle debug(...) from builtins.PyCapsule debug(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> bool get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> str loop_mover(...) from builtins.PyCapsule loop_mover(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t mc(...) from builtins.PyCapsule mc(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.protocols.moves.MonteCarlo 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_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> bool   This mover retains state such that a fresh version is needed if the input Pose is about to change scorefxn(...) from builtins.PyCapsule scorefxn(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.core.scoring.ScoreFunction set_debug(...) from builtins.PyCapsule set_debug(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, debug : bool) -> NoneType set_loop_mover(...) from builtins.PyCapsule set_loop_mover(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, new_owner_in_town : rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t) -> NoneType set_mc(...) from builtins.PyCapsule set_mc(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, mc : rosetta.protocols.moves.MonteCarlo) -> NoneType set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_task_factory(...) from builtins.PyCapsule set_task_factory(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, tf : rosetta.core.pack.task.TaskFactory) -> NoneType task_factory(...) from builtins.PyCapsule task_factory(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.core.pack.task.TaskFactory 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 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. 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 LoopRefineInnerCycleContainer(LoopRefineInnerCycle)       Method resolution order: LoopRefineInnerCycleContainer LoopRefineInnerCycle 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.loops.loop_mover.refine.LoopRefineInnerCycleContainer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer) -> str add_inner_cycle_step(...) from builtins.PyCapsule add_inner_cycle_step(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer, inner_cycle_step : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer, rhs : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer) -> rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer clone(...) from builtins.PyCapsule clone(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer) -> 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_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer) -> bool   This mover retains state such that a fresh version is needed if the input Pose is about to change set_loop_mover(...) from builtins.PyCapsule set_loop_mover(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer, new_owner_in_town : rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t) -> NoneType set_mc(...) from builtins.PyCapsule set_mc(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer, mc : rosetta.protocols.moves.MonteCarlo) -> NoneType set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer, pose : rosetta.core.pose.Pose) -> NoneType set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_task_factory(...) from builtins.PyCapsule set_task_factory(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer, tf : rosetta.core.pack.task.TaskFactory) -> NoneType Methods inherited from LoopRefineInnerCycle: debug(...) from builtins.PyCapsule debug(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> bool loop_mover(...) from builtins.PyCapsule loop_mover(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t mc(...) from builtins.PyCapsule mc(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.protocols.moves.MonteCarlo scorefxn(...) from builtins.PyCapsule scorefxn(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.core.scoring.ScoreFunction set_debug(...) from builtins.PyCapsule set_debug(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, debug : bool) -> NoneType task_factory(...) from builtins.PyCapsule task_factory(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.core.pack.task.TaskFactory 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 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. 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_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 LoopRefineInnerCycleContainerCreator(rosetta.protocols.moves.MoverCreator)     creator for the LoopRefineInnerCycleContainer class     Method resolution order: LoopRefineInnerCycleContainerCreator 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.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator,  : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator) -> rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator) -> str   class LoopRefineInnerCycleFactory(rosetta.utility.SingletonBase_protocols_loops_loop_mover_refine_LoopRefineInnerCycleFactory_t)     Create LoopMover Reporters     Method resolution order: LoopRefineInnerCycleFactory rosetta.utility.SingletonBase_protocols_loops_loop_mover_refine_LoopRefineInnerCycleFactory_t builtins.object Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. create_inner_cycle(...) from builtins.PyCapsule create_inner_cycle(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory, type_name : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleName, loop_mover : rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t, mc : rosetta.protocols.moves.MonteCarlo, scorefxn : rosetta.core.scoring.ScoreFunction, tf : rosetta.core.pack.task.TaskFactory) -> rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle   Create a LoopRefineInnerCycle giving it a pointer to the data it needs to function Methods inherited from rosetta.utility.SingletonBase_protocols_loops_loop_mover_refine_LoopRefineInnerCycleFactory_t: get_instance(...) from builtins.PyCapsule get_instance() -> protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory   class LoopRefineInnerCycleName(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleName, rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleName) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleName) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleName, int) -> NoneType   2. __init__(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleName, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleName) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleName, rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleName) -> 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.loops.loop_mover.refine.LoopRefineInnerCycleName) -> str Data and other attributes defined here: IC_RefineCCDStandard = LoopRefineInnerCycleName.number_of_loop_refine_inner_cycle_names IC_RepackTrial = LoopRefineInnerCycleName.IC_RepackTrial IC_ShearMinCCDTrial = LoopRefineInnerCycleName.IC_ShearMinCCDTrial IC_SmallMinCCDTrial = LoopRefineInnerCycleName.IC_SmallMinCCDTrial number_of_loop_refine_inner_cycle_names = LoopRefineInnerCycleName.number_of_loop_refine_inner_cycle_names   class RepackTrial(LoopRefineInnerCycle)       Method resolution order: RepackTrial LoopRefineInnerCycle 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.loops.loop_mover.refine.RepackTrial) -> NoneType   3. __init__(self : handle, loop_mover : rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t, mc : rosetta.protocols.moves.MonteCarlo, scorefxn : rosetta.core.scoring.ScoreFunction, tf : rosetta.core.pack.task.TaskFactory) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.loops.loop_mover.refine.RepackTrial) -> str apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.loops.loop_mover.refine.RepackTrial,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loops.loop_mover.refine.RepackTrial, rhs : rosetta.protocols.loops.loop_mover.refine.RepackTrial) -> rosetta.protocols.loops.loop_mover.refine.RepackTrial clone(...) from builtins.PyCapsule clone(rosetta.protocols.loops.loop_mover.refine.RepackTrial) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.loops.loop_mover.refine.RepackTrial) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.loops.loop_mover.refine.RepackTrial) -> 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_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.loops.loop_mover.refine.RepackTrial) -> bool   This mover retains state such that a fresh version is needed if the input Pose is about to change Methods inherited from LoopRefineInnerCycle: debug(...) from builtins.PyCapsule debug(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> bool loop_mover(...) from builtins.PyCapsule loop_mover(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t mc(...) from builtins.PyCapsule mc(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.protocols.moves.MonteCarlo scorefxn(...) from builtins.PyCapsule scorefxn(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.core.scoring.ScoreFunction set_debug(...) from builtins.PyCapsule set_debug(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, debug : bool) -> NoneType set_loop_mover(...) from builtins.PyCapsule set_loop_mover(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, new_owner_in_town : rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t) -> NoneType set_mc(...) from builtins.PyCapsule set_mc(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, mc : rosetta.protocols.moves.MonteCarlo) -> NoneType set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_task_factory(...) from builtins.PyCapsule set_task_factory(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, tf : rosetta.core.pack.task.TaskFactory) -> NoneType task_factory(...) from builtins.PyCapsule task_factory(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.core.pack.task.TaskFactory 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 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. 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 RepackTrialCreator(rosetta.protocols.moves.MoverCreator)     creator for the RepackTrial class     Method resolution order: RepackTrialCreator 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.loops.loop_mover.refine.RepackTrialCreator,  : rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator) -> rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator) -> str   class ShearMinCCDTrial(LoopRefineInnerCycle)       Method resolution order: ShearMinCCDTrial LoopRefineInnerCycle 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, loop_mover : rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t, mc : rosetta.protocols.moves.MonteCarlo, scorefxn : rosetta.core.scoring.ScoreFunction, tf : rosetta.core.pack.task.TaskFactory) -> NoneType   3. __init__(handle, rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial) -> str apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial, rhs : rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial) -> rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial clone(...) from builtins.PyCapsule clone(rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial) -> str reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial) -> bool   This mover retains state such that a fresh version is needed if the input Pose is about to change Methods inherited from LoopRefineInnerCycle: debug(...) from builtins.PyCapsule debug(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> bool loop_mover(...) from builtins.PyCapsule loop_mover(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t mc(...) from builtins.PyCapsule mc(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.protocols.moves.MonteCarlo 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 scorefxn(...) from builtins.PyCapsule scorefxn(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.core.scoring.ScoreFunction set_debug(...) from builtins.PyCapsule set_debug(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, debug : bool) -> NoneType set_loop_mover(...) from builtins.PyCapsule set_loop_mover(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, new_owner_in_town : rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t) -> NoneType set_mc(...) from builtins.PyCapsule set_mc(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, mc : rosetta.protocols.moves.MonteCarlo) -> NoneType set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_task_factory(...) from builtins.PyCapsule set_task_factory(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, tf : rosetta.core.pack.task.TaskFactory) -> NoneType task_factory(...) from builtins.PyCapsule task_factory(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.core.pack.task.TaskFactory 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 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. 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 ShearMinCCDTrialCreator(rosetta.protocols.moves.MoverCreator)     creator for the ShearMinCCDTrial class     Method resolution order: ShearMinCCDTrialCreator 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.loops.loop_mover.refine.ShearMinCCDTrialCreator,  : rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator) -> rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator) -> str   class SmallMinCCDTrial(LoopRefineInnerCycle)       Method resolution order: SmallMinCCDTrial LoopRefineInnerCycle 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.loops.loop_mover.refine.SmallMinCCDTrial) -> NoneType   3. __init__(self : handle, loop_mover : rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t, mc : rosetta.protocols.moves.MonteCarlo, scorefxn : rosetta.core.scoring.ScoreFunction, tf : rosetta.core.pack.task.TaskFactory) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial) -> str apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial, rhs : rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial) -> rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial clone(...) from builtins.PyCapsule clone(rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial) -> str minimizer_options(...) from builtins.PyCapsule minimizer_options(rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial) -> rosetta.core.optimization.MinimizerOptions number_of_moves(...) from builtins.PyCapsule number_of_moves(rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial) -> int 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_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial) -> bool   This mover retains state such that a fresh version is needed if the input Pose is about to change set_minimizer_options(...) from builtins.PyCapsule set_minimizer_options(self : rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial, minimizer_options : rosetta.core.optimization.MinimizerOptions) -> NoneType set_number_of_moves(...) from builtins.PyCapsule set_number_of_moves(self : rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial, nmoves : int) -> NoneType Methods inherited from LoopRefineInnerCycle: debug(...) from builtins.PyCapsule debug(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> bool loop_mover(...) from builtins.PyCapsule loop_mover(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t mc(...) from builtins.PyCapsule mc(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.protocols.moves.MonteCarlo scorefxn(...) from builtins.PyCapsule scorefxn(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.core.scoring.ScoreFunction set_debug(...) from builtins.PyCapsule set_debug(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, debug : bool) -> NoneType set_loop_mover(...) from builtins.PyCapsule set_loop_mover(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, new_owner_in_town : rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t) -> NoneType set_mc(...) from builtins.PyCapsule set_mc(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, mc : rosetta.protocols.moves.MonteCarlo) -> NoneType set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_task_factory(...) from builtins.PyCapsule set_task_factory(self : rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle, tf : rosetta.core.pack.task.TaskFactory) -> NoneType task_factory(...) from builtins.PyCapsule task_factory(rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle) -> rosetta.core.pack.task.TaskFactory 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 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. 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 SmallMinCCDTrialCreator(rosetta.protocols.moves.MoverCreator)     creator for the SmallMinCCDTrial class     Method resolution order: SmallMinCCDTrialCreator 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.loops.loop_mover.refine.SmallMinCCDTrialCreator,  : rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator) -> rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator) -> str

Data
		IC_RefineCCDStandard = LoopRefineInnerCycleName.number_of_loop_refine_inner_cycle_names IC_RepackTrial = LoopRefineInnerCycleName.IC_RepackTrial IC_ShearMinCCDTrial = LoopRefineInnerCycleName.IC_ShearMinCCDTrial IC_SmallMinCCDTrial = LoopRefineInnerCycleName.IC_SmallMinCCDTrial number_of_loop_refine_inner_cycle_names = LoopRefineInnerCycleName.number_of_loop_refine_inner_cycle_names