Bindings for protocols::loops::loop_closure::kinematic_closure namespace

Classes
		builtins.object KinematicPerturber BaseTabooPerturber NeighborDependentTabooSamplingKinematicPerturber TabooSamplingKinematicPerturber NeighborDependentTorsionSamplingKinematicPerturber TorsionRestrictedKinematicPerturber TorsionSamplingKinematicPerturber TorsionSweepingKinematicPerturber VicinitySamplingKinematicPerturber rosetta.protocols.moves.Mover(builtins.object) KinematicMover KinematicWrapper   class BaseTabooPerturber(KinematicPerturber)     Taboo-sampling perturber base class, the two variants of which, share much code in common, but interface with separate Ramachandran potentials.     Method resolution order: BaseTabooPerturber KinematicPerturber 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. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber,  : rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber) -> rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber clear_torsion_string_stack(...) from builtins.PyCapsule clear_torsion_string_stack(rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber) -> NoneType next_torsion_string(...) from builtins.PyCapsule next_torsion_string(rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber) -> rosetta.utility.vector0_core_conformation_ppo_torsion_bin num_strings(...) from builtins.PyCapsule num_strings(rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber) -> int perturb_chain(...) from builtins.PyCapsule perturb_chain(self : rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber, pose : rosetta.core.pose.Pose, torsions : rosetta.utility.vector1_double, bond_ang : rosetta.utility.vector1_double,  : rosetta.utility.vector1_double) -> NoneType set_pose_after_closure(...) from builtins.PyCapsule set_pose_after_closure(self : rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber, pose : rosetta.core.pose.Pose, torsions : rosetta.utility.vector1_double, bond_ang : rosetta.utility.vector1_double, bond_len : rosetta.utility.vector1_double, closure_successful : bool) -> NoneType set_vary_ca_bond_angles(...) from builtins.PyCapsule set_vary_ca_bond_angles(self : rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber, vary_ca_bond_angles : bool) -> NoneType Methods inherited from KinematicPerturber: get_movemap(...) from builtins.PyCapsule get_movemap(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.core.kinematics.MoveMap kinmover(...) from builtins.PyCapsule kinmover(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t max_sample_iterations(...) from builtins.PyCapsule max_sample_iterations(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> int perturber_exhausted(...) from builtins.PyCapsule perturber_exhausted(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> bool perturber_type(...) from builtins.PyCapsule perturber_type(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> str set_kinmover(...) from builtins.PyCapsule set_kinmover(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, kinmover : rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t) -> NoneType set_max_sample_iterations(...) from builtins.PyCapsule set_max_sample_iterations(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, sample_its : int) -> NoneType set_movemap(...) from builtins.PyCapsule set_movemap(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, mm : rosetta.core.kinematics.MoveMap) -> NoneType   class KinematicMover(rosetta.protocols.moves.Mover)     A mover class for performing kinematic loop closure on a peptide segment       ////////////////////////////////////////////////////////////////////////////     Method resolution order: KinematicMover rosetta.protocols.moves.Mover builtins.object Methods defined here: BANGLE_MIN(...) from builtins.PyCapsule BANGLE_MIN(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> float BANGLE_SD(...) from builtins.PyCapsule BANGLE_SD(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> float __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_filter(...) from builtins.PyCapsule add_filter(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, filter : rosetta.protocols.filters.Filter) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover,  : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover check_rama(...) from builtins.PyCapsule check_rama(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, old_rama_score : float, new_rama_score : float) -> bool clear_filters(...) from builtins.PyCapsule clear_filters(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> NoneType count_bb_atoms(...) from builtins.PyCapsule count_bb_atoms(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, pose : rosetta.core.pose.Pose, start_res : int, end_res : int) -> int count_bb_atoms_in_residue(...) from builtins.PyCapsule count_bb_atoms_in_residue(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, pose : rosetta.core.pose.Pose, position : int) -> int end_res(...) from builtins.PyCapsule end_res(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> int frequency_in_taboo_map(...) from builtins.PyCapsule frequency_in_taboo_map(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, pos : int,  : rosetta.core.conformation.ppo_torsion_bin) -> float get_bb_atoms_for_residue(...) from builtins.PyCapsule get_bb_atoms_for_residue(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, res : rosetta.core.conformation.Residue, bb_atom_index : int) -> str get_bump_overlap_factor(...) from builtins.PyCapsule get_bump_overlap_factor(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> float get_bumpcheck_atom_count_for_residue(...) from builtins.PyCapsule get_bumpcheck_atom_count_for_residue(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, rsd : rosetta.core.conformation.Residue) -> int get_bumpcheck_atoms_for_residue(...) from builtins.PyCapsule get_bumpcheck_atoms_for_residue(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, rsd : rosetta.core.conformation.Residue, bumpcheck_atom_index : int) -> str get_hardsphere_bump_check(...) from builtins.PyCapsule get_hardsphere_bump_check(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> bool get_idealize_loop_first(...) from builtins.PyCapsule get_idealize_loop_first(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> bool get_loop_sequence(...) from builtins.PyCapsule get_loop_sequence(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> rosetta.utility.vector1_core_chemical_AA get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> str get_rama_check(...) from builtins.PyCapsule get_rama_check(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> bool get_sample_nonpivot_torsions(...) from builtins.PyCapsule get_sample_nonpivot_torsions(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> bool get_vary_bondangles(...) from builtins.PyCapsule get_vary_bondangles(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> bool insert_sampled_torsion_string_into_taboo_map(...) from builtins.PyCapsule insert_sampled_torsion_string_into_taboo_map(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, ts : rosetta.utility.vector0_core_conformation_ppo_torsion_bin) -> NoneType is_beta_aminoacid(...) from builtins.PyCapsule is_beta_aminoacid(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, res : rosetta.core.conformation.Residue) -> bool is_in_taboo_map(...) from builtins.PyCapsule is_in_taboo_map(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, ts : rosetta.utility.vector0_core_conformation_ppo_torsion_bin) -> bool last_move_succeeded(...) from builtins.PyCapsule last_move_succeeded(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> bool loop_begin(...) from builtins.PyCapsule loop_begin(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> int loop_end(...) from builtins.PyCapsule loop_end(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> int middle_res(...) from builtins.PyCapsule middle_res(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> int perturber(...) from builtins.PyCapsule perturber(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber segment_length(...) from builtins.PyCapsule segment_length(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> int set_bump_overlap_factor(...) from builtins.PyCapsule set_bump_overlap_factor(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, bump_overlap_factor : float) -> NoneType set_do_sfxn_eval_every_iteration(...) from builtins.PyCapsule set_do_sfxn_eval_every_iteration(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, do_sfxn_eval : bool) -> NoneType set_filters(...) from builtins.PyCapsule set_filters(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, filters_in : rosetta.utility.vector1_std_shared_ptr_const_protocols_filters_Filter_t) -> NoneType set_hardsphere_bump_check(...) from builtins.PyCapsule set_hardsphere_bump_check(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, do_bump_check : bool) -> NoneType set_idealize_loop_first(...) from builtins.PyCapsule set_idealize_loop_first(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, idealize : bool) -> NoneType set_loop_begin_and_end(...) from builtins.PyCapsule set_loop_begin_and_end(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, loop_begin : int, loop_end : int) -> NoneType set_nonpivot_bb_torsion_id(...) from builtins.PyCapsule set_nonpivot_bb_torsion_id(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, bbtorids : rosetta.utility.vector1_unsigned_long) -> NoneType set_nonpivot_res_to_sweep(...) from builtins.PyCapsule set_nonpivot_res_to_sweep(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, resids : rosetta.utility.vector1_unsigned_long) -> NoneType set_perturber(...) from builtins.PyCapsule set_perturber(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, perturber_in : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> NoneType set_pivots(...) from builtins.PyCapsule set_pivots(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, start_res : int, middle_res : int, end_res : int) -> NoneType set_rama_check(...) from builtins.PyCapsule set_rama_check(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, do_rama_check : bool) -> NoneType set_sample_nonpivot_torsions(...) from builtins.PyCapsule set_sample_nonpivot_torsions(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, sample : bool) -> NoneType set_sfxn(...) from builtins.PyCapsule set_sfxn(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, sfxn_in : rosetta.core.scoring.ScoreFunction) -> NoneType set_sweep_nonpivot_torsions(...) from builtins.PyCapsule set_sweep_nonpivot_torsions(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, sweep : bool) -> NoneType set_sweep_nsteps(...) from builtins.PyCapsule set_sweep_nsteps(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, nsteps : rosetta.utility.vector1_unsigned_long) -> NoneType set_sweep_start_angle(...) from builtins.PyCapsule set_sweep_start_angle(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, angles_in_degrees : rosetta.utility.vector1_double) -> NoneType set_sweep_step_size(...) from builtins.PyCapsule set_sweep_step_size(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, angle_steps_in_degrees : rosetta.utility.vector1_double) -> NoneType set_temperature(...) from builtins.PyCapsule set_temperature(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, temp_in : float) -> NoneType set_vary_bondangles(...) from builtins.PyCapsule set_vary_bondangles(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, vary : bool) -> NoneType start_res(...) from builtins.PyCapsule start_res(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> int sweep_incomplete(...) from builtins.PyCapsule sweep_incomplete(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover) -> bool   returns true as long as the Lexicographical iterator has not covered all  angles -- useful in a while-loop. torsion_features_string(...) from builtins.PyCapsule torsion_features_string(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector0_core_conformation_ppo_torsion_bin update_sequence(...) from builtins.PyCapsule update_sequence(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, sequence : rosetta.utility.vector1_core_chemical_AA) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply clone(...) from builtins.PyCapsule clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Return a clone of the Mover object. create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class KinematicPerturber(builtins.object)     pure virtual base class for KinematicPerturber.  KinematicPerturbers determine HOW loops should be perturbed.  The base class contains a provision for determining WHERE they should be perturbed: MoveMap sensitivity.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> NoneType   2. __init__(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> 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_closure.kinematic_closure.KinematicPerturber,  : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber clear_torsion_string_stack(...) from builtins.PyCapsule clear_torsion_string_stack(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> NoneType get_movemap(...) from builtins.PyCapsule get_movemap(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.core.kinematics.MoveMap kinmover(...) from builtins.PyCapsule kinmover(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t max_sample_iterations(...) from builtins.PyCapsule max_sample_iterations(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> int perturb_chain(...) from builtins.PyCapsule perturb_chain(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, pose : rosetta.core.pose.Pose, torsions : rosetta.utility.vector1_double, bond_ang : rosetta.utility.vector1_double, bond_len : rosetta.utility.vector1_double) -> NoneType   function that perturbs the chain, i.e. sets new values  for the torsions, bond angles and bond lengths  note: the torsions/angles/lengths that are input to this  function will be identical to the ones in the pose,  i.e. only the dof values that are explicitly set by  this function plus the pivots will have changed after loop closure perturber_exhausted(...) from builtins.PyCapsule perturber_exhausted(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> bool perturber_type(...) from builtins.PyCapsule perturber_type(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> str set_kinmover(...) from builtins.PyCapsule set_kinmover(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, kinmover : rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t) -> NoneType set_max_sample_iterations(...) from builtins.PyCapsule set_max_sample_iterations(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, sample_its : int) -> NoneType set_movemap(...) from builtins.PyCapsule set_movemap(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, mm : rosetta.core.kinematics.MoveMap) -> NoneType set_pose_after_closure(...) from builtins.PyCapsule set_pose_after_closure(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, pose : rosetta.core.pose.Pose, torsions : rosetta.utility.vector1_double,  : rosetta.utility.vector1_double,  : rosetta.utility.vector1_double,  : bool) -> NoneType   after the kinmover has closed the loop, the perturber needs  to put the solutions into the pose  note: the base class version of this function sets the torsions,  so any KinematicPerturber that only changes the torsions will not have  to implement this function   class KinematicWrapper(rosetta.protocols.moves.Mover)     This class extends KinematicMover by composition (has-a KinematicMover).  The idea is to make KinematicMover useful when ONLY the apply() function is available (as in MoverContainers, etc.).  It will reapply KinematicMover until the KinematicMover reports a success.  This class uses searches through loop begin/middle/end points while searching for solutions.  You can pass a MoveMap; it will refuse to put pivots where the MoveMap is not mobile.     Method resolution order: KinematicWrapper rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle, rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, rosetta.protocols.loops.Loop) -> NoneType   doc   2. __init__(self : handle, kinmover_in : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, loop : rosetta.protocols.loops.Loop, cycles : int) -> NoneType   3. __init__(handle, rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, int, int) -> NoneType   doc   4. __init__(self : handle, kinmover_in : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover, loop_begin : int, loop_end : int, cycles : int) -> NoneType   5. __init__(handle, rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper) -> 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_closure.kinematic_closure.KinematicWrapper, pose : rosetta.core.pose.Pose) -> NoneType   re-applies KinematicMover with different pivots until success get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper) -> str respect_this_movemap(...) from builtins.PyCapsule respect_this_movemap(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper, mm : rosetta.core.kinematics.MoveMap) -> NoneType   this function derives the allowed_positions_ vector from mm and the loop begin/end Methods inherited from rosetta.protocols.moves.Mover: assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.moves.Mover, other : rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply clone(...) from builtins.PyCapsule clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Return a clone of the Mover object. create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class NeighborDependentTabooSamplingKinematicPerturber(BaseTabooPerturber)     Neighbor-dependent Taboo-sampling kinematic perturber (still samples randomly, but only within a given torsion bin; the Taboo sampler ensures that this torsion bin is varied in each iteration) that uses neighbor-dependent Ramachandran distributions (rama2b)     Amelie Stein     Mon May 21 11:39:26 PDT 2012     Method resolution order: NeighborDependentTabooSamplingKinematicPerturber BaseTabooPerturber KinematicPerturber builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, kinmover_in : rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. perturber_type(...) from builtins.PyCapsule perturber_type(rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber) -> str Methods inherited from BaseTabooPerturber: assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber,  : rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber) -> rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber clear_torsion_string_stack(...) from builtins.PyCapsule clear_torsion_string_stack(rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber) -> NoneType next_torsion_string(...) from builtins.PyCapsule next_torsion_string(rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber) -> rosetta.utility.vector0_core_conformation_ppo_torsion_bin num_strings(...) from builtins.PyCapsule num_strings(rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber) -> int perturb_chain(...) from builtins.PyCapsule perturb_chain(self : rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber, pose : rosetta.core.pose.Pose, torsions : rosetta.utility.vector1_double, bond_ang : rosetta.utility.vector1_double,  : rosetta.utility.vector1_double) -> NoneType set_pose_after_closure(...) from builtins.PyCapsule set_pose_after_closure(self : rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber, pose : rosetta.core.pose.Pose, torsions : rosetta.utility.vector1_double, bond_ang : rosetta.utility.vector1_double, bond_len : rosetta.utility.vector1_double, closure_successful : bool) -> NoneType set_vary_ca_bond_angles(...) from builtins.PyCapsule set_vary_ca_bond_angles(self : rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber, vary_ca_bond_angles : bool) -> NoneType Methods inherited from KinematicPerturber: get_movemap(...) from builtins.PyCapsule get_movemap(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.core.kinematics.MoveMap kinmover(...) from builtins.PyCapsule kinmover(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t max_sample_iterations(...) from builtins.PyCapsule max_sample_iterations(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> int perturber_exhausted(...) from builtins.PyCapsule perturber_exhausted(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> bool set_kinmover(...) from builtins.PyCapsule set_kinmover(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, kinmover : rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t) -> NoneType set_max_sample_iterations(...) from builtins.PyCapsule set_max_sample_iterations(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, sample_its : int) -> NoneType set_movemap(...) from builtins.PyCapsule set_movemap(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, mm : rosetta.core.kinematics.MoveMap) -> NoneType   class NeighborDependentTorsionSamplingKinematicPerturber(KinematicPerturber)     Amelie Stein     neighbor-dependent torsion sampling kinematic perturber -- uses rama2b for phi/psi lookup     Method resolution order: NeighborDependentTorsionSamplingKinematicPerturber KinematicPerturber builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, kinmover_in : rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. perturb_chain(...) from builtins.PyCapsule perturb_chain(self : rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber, pose : rosetta.core.pose.Pose, torsions : rosetta.utility.vector1_double, bond_ang : rosetta.utility.vector1_double,  : rosetta.utility.vector1_double) -> NoneType perturber_type(...) from builtins.PyCapsule perturber_type(rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber) -> str set_pose_after_closure(...) from builtins.PyCapsule set_pose_after_closure(self : rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber, pose : rosetta.core.pose.Pose, torsions : rosetta.utility.vector1_double, bond_ang : rosetta.utility.vector1_double, bond_len : rosetta.utility.vector1_double, closure_successful : bool) -> NoneType set_vary_ca_bond_angles(...) from builtins.PyCapsule set_vary_ca_bond_angles(self : rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber, vary_ca_bond_angles : bool) -> NoneType Methods inherited from KinematicPerturber: assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber,  : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber clear_torsion_string_stack(...) from builtins.PyCapsule clear_torsion_string_stack(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> NoneType get_movemap(...) from builtins.PyCapsule get_movemap(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.core.kinematics.MoveMap kinmover(...) from builtins.PyCapsule kinmover(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t max_sample_iterations(...) from builtins.PyCapsule max_sample_iterations(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> int perturber_exhausted(...) from builtins.PyCapsule perturber_exhausted(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> bool set_kinmover(...) from builtins.PyCapsule set_kinmover(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, kinmover : rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t) -> NoneType set_max_sample_iterations(...) from builtins.PyCapsule set_max_sample_iterations(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, sample_its : int) -> NoneType set_movemap(...) from builtins.PyCapsule set_movemap(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, mm : rosetta.core.kinematics.MoveMap) -> NoneType   class TabooSamplingKinematicPerturber(BaseTabooPerturber)     Taboo-sampling kinematic perturber (still samples randomly, but only within a specific torsion bin, and the Taboo sampler ensures that this torsion bin is varied in each iteration)     Amelie Stein     Method resolution order: TabooSamplingKinematicPerturber BaseTabooPerturber KinematicPerturber builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, kinmover_in : rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. perturber_type(...) from builtins.PyCapsule perturber_type(rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber) -> str Methods inherited from BaseTabooPerturber: assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber,  : rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber) -> rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber clear_torsion_string_stack(...) from builtins.PyCapsule clear_torsion_string_stack(rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber) -> NoneType next_torsion_string(...) from builtins.PyCapsule next_torsion_string(rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber) -> rosetta.utility.vector0_core_conformation_ppo_torsion_bin num_strings(...) from builtins.PyCapsule num_strings(rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber) -> int perturb_chain(...) from builtins.PyCapsule perturb_chain(self : rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber, pose : rosetta.core.pose.Pose, torsions : rosetta.utility.vector1_double, bond_ang : rosetta.utility.vector1_double,  : rosetta.utility.vector1_double) -> NoneType set_pose_after_closure(...) from builtins.PyCapsule set_pose_after_closure(self : rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber, pose : rosetta.core.pose.Pose, torsions : rosetta.utility.vector1_double, bond_ang : rosetta.utility.vector1_double, bond_len : rosetta.utility.vector1_double, closure_successful : bool) -> NoneType set_vary_ca_bond_angles(...) from builtins.PyCapsule set_vary_ca_bond_angles(self : rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber, vary_ca_bond_angles : bool) -> NoneType Methods inherited from KinematicPerturber: get_movemap(...) from builtins.PyCapsule get_movemap(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.core.kinematics.MoveMap kinmover(...) from builtins.PyCapsule kinmover(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t max_sample_iterations(...) from builtins.PyCapsule max_sample_iterations(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> int perturber_exhausted(...) from builtins.PyCapsule perturber_exhausted(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> bool set_kinmover(...) from builtins.PyCapsule set_kinmover(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, kinmover : rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t) -> NoneType set_max_sample_iterations(...) from builtins.PyCapsule set_max_sample_iterations(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, sample_its : int) -> NoneType set_movemap(...) from builtins.PyCapsule set_movemap(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, mm : rosetta.core.kinematics.MoveMap) -> NoneType   class TorsionRestrictedKinematicPerturber(KinematicPerturber)     torsion-restricted kinematic perturber (still samples randomly, but only within a given torsion bin)     Amelie Stein     Method resolution order: TorsionRestrictedKinematicPerturber KinematicPerturber builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, kinmover_in : rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t, torsion_bins : rosetta.utility.vector0_core_conformation_ppo_torsion_bin) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. perturb_chain(...) from builtins.PyCapsule perturb_chain(self : rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber, pose : rosetta.core.pose.Pose, torsions : rosetta.utility.vector1_double, bond_ang : rosetta.utility.vector1_double,  : rosetta.utility.vector1_double) -> NoneType perturber_type(...) from builtins.PyCapsule perturber_type(rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber) -> str set_pose_after_closure(...) from builtins.PyCapsule set_pose_after_closure(self : rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber, pose : rosetta.core.pose.Pose, torsions : rosetta.utility.vector1_double, bond_ang : rosetta.utility.vector1_double, bond_len : rosetta.utility.vector1_double, closure_successful : bool) -> NoneType set_vary_ca_bond_angles(...) from builtins.PyCapsule set_vary_ca_bond_angles(self : rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber, vary_ca_bond_angles : bool) -> NoneType Methods inherited from KinematicPerturber: assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber,  : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber clear_torsion_string_stack(...) from builtins.PyCapsule clear_torsion_string_stack(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> NoneType get_movemap(...) from builtins.PyCapsule get_movemap(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.core.kinematics.MoveMap kinmover(...) from builtins.PyCapsule kinmover(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t max_sample_iterations(...) from builtins.PyCapsule max_sample_iterations(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> int perturber_exhausted(...) from builtins.PyCapsule perturber_exhausted(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> bool set_kinmover(...) from builtins.PyCapsule set_kinmover(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, kinmover : rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t) -> NoneType set_max_sample_iterations(...) from builtins.PyCapsule set_max_sample_iterations(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, sample_its : int) -> NoneType set_movemap(...) from builtins.PyCapsule set_movemap(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, mm : rosetta.core.kinematics.MoveMap) -> NoneType   class TorsionSamplingKinematicPerturber(KinematicPerturber)     torsion sampling kinematic perturber     Method resolution order: TorsionSamplingKinematicPerturber KinematicPerturber builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, kinmover_in : rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. initialize_betaresidue_minima(...) from builtins.PyCapsule initialize_betaresidue_minima(self : rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber, philist : rosetta.utility.vector1_double, thetalist : rosetta.utility.vector1_double, psilist : rosetta.utility.vector1_double, mode : int) -> NoneType   Initialize positions of minima in the beta-amino acid Ramachandran cube. perturb_beta_residue(...) from builtins.PyCapsule perturb_beta_residue(self : rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber, phi : float, theta : float, psi : float, beta_residue_type : int) -> NoneType   Varies torsions of a beta-amino acid residue based on minimia in the beta-amino acid Ramachandran cube.  This randomly picks a minimum, then chooses phi/theta/psi values randomly in a Gaussian centered in that minimum. perturb_chain(...) from builtins.PyCapsule perturb_chain(self : rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber, pose : rosetta.core.pose.Pose, torsions : rosetta.utility.vector1_double, bond_ang : rosetta.utility.vector1_double,  : rosetta.utility.vector1_double) -> NoneType   varies torsions always and bond angles sometimes.  Currently torsion varying will respect a movemap if present; angles do NOT look for a movemap. perturber_type(...) from builtins.PyCapsule perturber_type(rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber) -> str set_pose_after_closure(...) from builtins.PyCapsule set_pose_after_closure(self : rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber, pose : rosetta.core.pose.Pose, torsions : rosetta.utility.vector1_double, bond_ang : rosetta.utility.vector1_double, bond_len : rosetta.utility.vector1_double, closure_successful : bool) -> NoneType set_vary_ca_bond_angles(...) from builtins.PyCapsule set_vary_ca_bond_angles(self : rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber, vary_ca_bond_angles : bool) -> NoneType Methods inherited from KinematicPerturber: assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber,  : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber clear_torsion_string_stack(...) from builtins.PyCapsule clear_torsion_string_stack(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> NoneType get_movemap(...) from builtins.PyCapsule get_movemap(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.core.kinematics.MoveMap kinmover(...) from builtins.PyCapsule kinmover(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t max_sample_iterations(...) from builtins.PyCapsule max_sample_iterations(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> int perturber_exhausted(...) from builtins.PyCapsule perturber_exhausted(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> bool set_kinmover(...) from builtins.PyCapsule set_kinmover(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, kinmover : rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t) -> NoneType set_max_sample_iterations(...) from builtins.PyCapsule set_max_sample_iterations(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, sample_its : int) -> NoneType set_movemap(...) from builtins.PyCapsule set_movemap(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, mm : rosetta.core.kinematics.MoveMap) -> NoneType   class TorsionSweepingKinematicPerturber(KinematicPerturber)     Here's some commentary on why the TorsionSweepingKinematicPerturber is Fun and Awesome to use!  Basically, you take the loop as given and search for solutions nearby.  Its purpose is not to produce large changes, but instead to produce small perturbations to find the bottom of the current energy well.  It's not meant to be used for the original KIC protocol, in which the pivots are changed regularly: you can't sweep through nonpivot torsion space if the pivots don't stay the same.     Method resolution order: TorsionSweepingKinematicPerturber KinematicPerturber 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_closure.kinematic_closure.TorsionSweepingKinematicPerturber) -> 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_closure.kinematic_closure.TorsionSweepingKinematicPerturber,  : rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber) -> rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber perturb_chain(...) from builtins.PyCapsule perturb_chain(self : rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber, pose : rosetta.core.pose.Pose, torsions : rosetta.utility.vector1_double, bond_ang : rosetta.utility.vector1_double,  : rosetta.utility.vector1_double) -> NoneType   movemap control NOT IMPLEMENTED in TorsionSweepingKP.  It is also NOT NEEDED because you can use set_nonpivot_res_to_sweep instead. perturber_exhausted(...) from builtins.PyCapsule perturber_exhausted(rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber) -> bool perturber_type(...) from builtins.PyCapsule perturber_type(rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber) -> str set_nonpivot_bb_torsion_id(...) from builtins.PyCapsule set_nonpivot_bb_torsion_id(self : rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber, bbtorids : rosetta.utility.vector1_unsigned_long) -> NoneType set_nonpivot_res_to_sweep(...) from builtins.PyCapsule set_nonpivot_res_to_sweep(self : rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber, resids : rosetta.utility.vector1_unsigned_long) -> NoneType set_sweep_nsteps(...) from builtins.PyCapsule set_sweep_nsteps(self : rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber, nsteps : rosetta.utility.vector1_unsigned_long) -> NoneType set_sweep_start_angle(...) from builtins.PyCapsule set_sweep_start_angle(self : rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber, angles_in_degrees : rosetta.utility.vector1_double) -> NoneType set_sweep_step_size(...) from builtins.PyCapsule set_sweep_step_size(self : rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber, angle_steps_in_degrees : rosetta.utility.vector1_double) -> NoneType Methods inherited from KinematicPerturber: clear_torsion_string_stack(...) from builtins.PyCapsule clear_torsion_string_stack(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> NoneType get_movemap(...) from builtins.PyCapsule get_movemap(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.core.kinematics.MoveMap kinmover(...) from builtins.PyCapsule kinmover(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t max_sample_iterations(...) from builtins.PyCapsule max_sample_iterations(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> int set_kinmover(...) from builtins.PyCapsule set_kinmover(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, kinmover : rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t) -> NoneType set_max_sample_iterations(...) from builtins.PyCapsule set_max_sample_iterations(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, sample_its : int) -> NoneType set_movemap(...) from builtins.PyCapsule set_movemap(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, mm : rosetta.core.kinematics.MoveMap) -> NoneType set_pose_after_closure(...) from builtins.PyCapsule set_pose_after_closure(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, pose : rosetta.core.pose.Pose, torsions : rosetta.utility.vector1_double,  : rosetta.utility.vector1_double,  : rosetta.utility.vector1_double,  : bool) -> NoneType   after the kinmover has closed the loop, the perturber needs  to put the solutions into the pose  note: the base class version of this function sets the torsions,  so any KinematicPerturber that only changes the torsions will not have  to implement this function   class VicinitySamplingKinematicPerturber(KinematicPerturber)     vicinity sampling kinematic perturber     Amelie Stein (just the refactoring)     Method resolution order: VicinitySamplingKinematicPerturber KinematicPerturber builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, kinmover_in : rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t) -> 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_closure.kinematic_closure.VicinitySamplingKinematicPerturber,  : rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber) -> rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber perturb_chain(...) from builtins.PyCapsule perturb_chain(self : rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber, pose : rosetta.core.pose.Pose, torsions : rosetta.utility.vector1_double, bond_ang : rosetta.utility.vector1_double,  : rosetta.utility.vector1_double) -> NoneType   varies torsions always and bond angles sometimes.  Currently torsion varying will respect a movemap if present; angles do NOT look for a movemap. -- note that the analytic closure and pivot selection currently do not respect movemaps though perturber_type(...) from builtins.PyCapsule perturber_type(rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber) -> str set_degree_vicinity(...) from builtins.PyCapsule set_degree_vicinity(self : rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber, degree_vicinity : float) -> NoneType set_pose_after_closure(...) from builtins.PyCapsule set_pose_after_closure(self : rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber, pose : rosetta.core.pose.Pose, torsions : rosetta.utility.vector1_double, bond_ang : rosetta.utility.vector1_double, bond_len : rosetta.utility.vector1_double, closure_successful : bool) -> NoneType set_vary_ca_bond_angles(...) from builtins.PyCapsule set_vary_ca_bond_angles(self : rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber, vary_ca_bond_angles : bool) -> NoneType Methods inherited from KinematicPerturber: clear_torsion_string_stack(...) from builtins.PyCapsule clear_torsion_string_stack(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> NoneType get_movemap(...) from builtins.PyCapsule get_movemap(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.core.kinematics.MoveMap kinmover(...) from builtins.PyCapsule kinmover(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t max_sample_iterations(...) from builtins.PyCapsule max_sample_iterations(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> int perturber_exhausted(...) from builtins.PyCapsule perturber_exhausted(rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber) -> bool set_kinmover(...) from builtins.PyCapsule set_kinmover(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, kinmover : rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t) -> NoneType set_max_sample_iterations(...) from builtins.PyCapsule set_max_sample_iterations(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, sample_its : int) -> NoneType set_movemap(...) from builtins.PyCapsule set_movemap(self : rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber, mm : rosetta.core.kinematics.MoveMap) -> NoneType