Bindings for protocols::stepwise::modeler namespace

Modules
		rosetta.protocols.stepwise.modeler.align rosetta.protocols.stepwise.modeler.movemap rosetta.protocols.stepwise.modeler.options rosetta.protocols.stepwise.modeler.packer rosetta.protocols.stepwise.modeler.polar_hydrogens rosetta.protocols.stepwise.modeler.precomputed rosetta.protocols.stepwise.modeler.protein rosetta.protocols.stepwise.modeler.rna rosetta.protocols.stepwise.modeler.working_parameters

Classes
		rosetta.protocols.moves.Mover(builtins.object) StepWiseMinimizer StepWiseModeler rosetta.protocols.moves.MoverForPoseList(rosetta.protocols.moves.Mover) StepWiseConnectionSampler   class StepWiseConnectionSampler(rosetta.protocols.moves.MoverForPoseList)       Method resolution order: StepWiseConnectionSampler rosetta.protocols.moves.MoverForPoseList rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, working_parameters_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> NoneType   2. __init__(handle, rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_residue_alternative_set(...) from builtins.PyCapsule add_residue_alternative_set(self : rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler, residue_alternative_set : rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeSet) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler, pose_to_visualize : rosetta.core.pose.Pose) -> NoneType get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler) -> str get_pose_list(...) from builtins.PyCapsule get_pose_list(rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler) -> rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t set_input_streams(...) from builtins.PyCapsule set_input_streams(self : rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler, input_streams : rosetta.utility.vector1_std_shared_ptr_protocols_stepwise_modeler_protein_InputStreamWithResidueInfo_t) -> NoneType set_master_packer(...) from builtins.PyCapsule set_master_packer(self : rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler, master_packer : rosetta.protocols.stepwise.modeler.packer.StepWiseMasterPacker) -> NoneType set_options(...) from builtins.PyCapsule set_options(self : rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler, options : protocols::stepwise::modeler::options::StepWiseModelerOptions) -> NoneType set_pose_list(...) from builtins.PyCapsule set_pose_list(self : rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler, pose_list : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) -> NoneType set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_user_input_VDW_bin_checker(...) from builtins.PyCapsule set_user_input_VDW_bin_checker(self : rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler, user_input_VDW_bin_checker : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker) -> NoneType Methods inherited from rosetta.protocols.moves.MoverForPoseList: assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.moves.MoverForPoseList,  : rosetta.protocols.moves.MoverForPoseList) -> rosetta.protocols.moves.MoverForPoseList 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 StepWiseMinimizer(rosetta.protocols.moves.Mover)       Method resolution order: StepWiseMinimizer rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, pose_list : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, working_parameters : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, options : protocols::stepwise::modeler::options::StepWiseModelerOptions, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   2. __init__(handle, rosetta.protocols.stepwise.modeler.StepWiseMinimizer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.stepwise.modeler.StepWiseMinimizer, pose : rosetta.core.pose.Pose) -> NoneType get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.stepwise.modeler.StepWiseMinimizer) -> str num_pose_minimize(...) from builtins.PyCapsule num_pose_minimize(rosetta.protocols.stepwise.modeler.StepWiseMinimizer) -> int pose_list(...) from builtins.PyCapsule pose_list(rosetta.protocols.stepwise.modeler.StepWiseMinimizer) -> rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.stepwise.modeler.StepWiseMinimizer, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_working_pack_res(...) from builtins.PyCapsule set_working_pack_res(self : rosetta.protocols.stepwise.modeler.StepWiseMinimizer, setting : rosetta.utility.vector1_unsigned_long) -> NoneType working_minimize_res(...) from builtins.PyCapsule working_minimize_res(rosetta.protocols.stepwise.modeler.StepWiseMinimizer) -> rosetta.utility.vector1_unsigned_long working_pack_res(...) from builtins.PyCapsule working_pack_res(rosetta.protocols.stepwise.modeler.StepWiseMinimizer) -> rosetta.utility.vector1_unsigned_long 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 StepWiseModeler(rosetta.protocols.moves.Mover)       Method resolution order: StepWiseModeler rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, moving_res : int, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   2. __init__(self : handle, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   3. __init__(handle, rosetta.protocols.stepwise.modeler.StepWiseModeler) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.stepwise.modeler.StepWiseModeler, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.stepwise.modeler.StepWiseModeler, src : rosetta.protocols.stepwise.modeler.StepWiseModeler) -> rosetta.protocols.stepwise.modeler.StepWiseModeler clone_modeler(...) from builtins.PyCapsule clone_modeler(rosetta.protocols.stepwise.modeler.StepWiseModeler) -> rosetta.protocols.stepwise.modeler.StepWiseModeler get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.stepwise.modeler.StepWiseModeler) -> str get_num_sampled(...) from builtins.PyCapsule get_num_sampled(rosetta.protocols.stepwise.modeler.StepWiseModeler) -> int options(...) from builtins.PyCapsule options(rosetta.protocols.stepwise.modeler.StepWiseModeler) -> rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions precomputed_library_mover(...) from builtins.PyCapsule precomputed_library_mover(rosetta.protocols.stepwise.modeler.StepWiseModeler) -> protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover scorefxn(...) from builtins.PyCapsule scorefxn(rosetta.protocols.stepwise.modeler.StepWiseModeler) -> rosetta.core.scoring.ScoreFunction set_figure_out_prepack_res(...) from builtins.PyCapsule set_figure_out_prepack_res(self : rosetta.protocols.stepwise.modeler.StepWiseModeler, setting : bool) -> NoneType set_input_streams(...) from builtins.PyCapsule set_input_streams(self : rosetta.protocols.stepwise.modeler.StepWiseModeler, input_streams : rosetta.utility.vector1_std_shared_ptr_protocols_stepwise_modeler_protein_InputStreamWithResidueInfo_t) -> NoneType set_moving_res_and_reset(...) from builtins.PyCapsule set_moving_res_and_reset(self : rosetta.protocols.stepwise.modeler.StepWiseModeler, moving_res : int) -> NoneType set_moving_res_list(...) from builtins.PyCapsule set_moving_res_list(self : rosetta.protocols.stepwise.modeler.StepWiseModeler, setting : rosetta.utility.vector1_unsigned_long) -> NoneType set_options(...) from builtins.PyCapsule set_options(self : rosetta.protocols.stepwise.modeler.StepWiseModeler, options : rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions) -> NoneType set_precomputed_library_mover(...) from builtins.PyCapsule set_precomputed_library_mover(self : rosetta.protocols.stepwise.modeler.StepWiseModeler, precomputed_library_mover : protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover) -> NoneType set_working_minimize_res(...) from builtins.PyCapsule set_working_minimize_res(self : rosetta.protocols.stepwise.modeler.StepWiseModeler, setting : rosetta.utility.vector1_unsigned_long) -> NoneType set_working_parameters(...) from builtins.PyCapsule set_working_parameters(self : rosetta.protocols.stepwise.modeler.StepWiseModeler, working_parameters : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> NoneType set_working_prepack_res(...) from builtins.PyCapsule set_working_prepack_res(self : rosetta.protocols.stepwise.modeler.StepWiseModeler, setting : rosetta.utility.vector1_unsigned_long) -> NoneType working_parameters(...) from builtins.PyCapsule working_parameters(rosetta.protocols.stepwise.modeler.StepWiseModeler) -> protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters 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

Functions
		add_to_pose_list(...) method of builtins.PyCapsule instance add_to_pose_list(pose_list : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, pose : rosetta.core.pose.Pose, pose_tag : str) -> NoneType check_for_input_domain(...) method of builtins.PyCapsule instance check_for_input_domain(*args, **kwargs) Overloaded function.   1. check_for_input_domain(pose : rosetta.core.pose.Pose, partition_res : rosetta.utility.vector1_unsigned_long) -> bool   2. check_for_input_domain(pose : rosetta.core.pose.Pose) -> bool check_jump_to_next_residue_in_chain(...) method of builtins.PyCapsule instance check_jump_to_next_residue_in_chain(*args, **kwargs) Overloaded function.   1. check_jump_to_next_residue_in_chain(pose : rosetta.core.pose.Pose, i : int, current_element : rosetta.utility.vector1_unsigned_long) -> int   2. check_jump_to_next_residue_in_chain(pose : rosetta.core.pose.Pose, i : int, current_element : rosetta.utility.vector1_unsigned_long, full_model_info : rosetta.core.pose.full_model_info.FullModelInfo) -> int   3. check_jump_to_next_residue_in_chain(pose : rosetta.core.pose.Pose, i : int, current_element : rosetta.utility.vector1_unsigned_long, res_list : rosetta.utility.vector1_unsigned_long, chains_in_full_model : rosetta.utility.vector1_unsigned_long) -> int check_jump_to_previous_residue_in_chain(...) method of builtins.PyCapsule instance check_jump_to_previous_residue_in_chain(*args, **kwargs) Overloaded function.   1. check_jump_to_previous_residue_in_chain(pose : rosetta.core.pose.Pose, i : int, current_element : rosetta.utility.vector1_unsigned_long) -> int   2. check_jump_to_previous_residue_in_chain(pose : rosetta.core.pose.Pose, i : int, current_element : rosetta.utility.vector1_unsigned_long, full_model_info : rosetta.core.pose.full_model_info.FullModelInfo) -> int   3. check_jump_to_previous_residue_in_chain(pose : rosetta.core.pose.Pose, i : int, current_element : rosetta.utility.vector1_unsigned_long, res_list : rosetta.utility.vector1_unsigned_long, chains_in_full_model : rosetta.utility.vector1_unsigned_long) -> int check_scorefxn_has_constraint_terms_if_pose_has_constraints(...) method of builtins.PyCapsule instance check_scorefxn_has_constraint_terms_if_pose_has_constraints(pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType constraint_set_slice(...) method of builtins.PyCapsule instance constraint_set_slice(cst_set : rosetta.core.scoring.constraints.ConstraintSet, slice_res : rosetta.utility.vector1_unsigned_long, pose : rosetta.core.pose.Pose, full_pose : rosetta.core.pose.Pose) -> rosetta.core.scoring.constraints.ConstraintSet definite_terminal_root(...) method of builtins.PyCapsule instance definite_terminal_root(pose : rosetta.core.pose.Pose, i : int) -> bool figure_out_moving_chain_break_res(...) method of builtins.PyCapsule instance figure_out_moving_chain_break_res(pose : rosetta.core.pose.Pose, mm : rosetta.core.kinematics.MoveMap) -> rosetta.utility.vector1_unsigned_long figure_out_moving_chain_breaks(...) method of builtins.PyCapsule instance figure_out_moving_chain_breaks(pose : rosetta.core.pose.Pose, moving_partition_res : rosetta.utility.vector1_unsigned_long, cutpoints_closed : rosetta.utility.vector1_unsigned_long, five_prime_chain_breaks : rosetta.utility.vector1_unsigned_long, three_prime_chain_breaks : rosetta.utility.vector1_unsigned_long, chain_break_gap_sizes : rosetta.utility.vector1_unsigned_long) -> NoneType figure_out_moving_cutpoints_closed(...) method of builtins.PyCapsule instance figure_out_moving_cutpoints_closed(pose : rosetta.core.pose.Pose, moving_partition_res : rosetta.utility.vector1_unsigned_long) -> rosetta.utility.vector1_unsigned_long figure_out_moving_cutpoints_closed_from_moving_res(...) method of builtins.PyCapsule instance figure_out_moving_cutpoints_closed_from_moving_res(*args, **kwargs) Overloaded function.   1. figure_out_moving_cutpoints_closed_from_moving_res(pose : rosetta.core.pose.Pose, moving_res : int) -> rosetta.utility.vector1_unsigned_long   2. figure_out_moving_cutpoints_closed_from_moving_res(pose : rosetta.core.pose.Pose, moving_res_list : rosetta.utility.vector1_unsigned_long) -> rosetta.utility.vector1_unsigned_long figure_out_moving_partition_res(...) method of builtins.PyCapsule instance figure_out_moving_partition_res(*args, **kwargs) Overloaded function.   1. figure_out_moving_partition_res(pose : rosetta.core.pose.Pose, moving_res : int) -> rosetta.utility.vector1_unsigned_long   2. figure_out_moving_partition_res(pose : rosetta.core.pose.Pose, moving_res_list : rosetta.utility.vector1_unsigned_long) -> rosetta.utility.vector1_unsigned_long figure_out_moving_partition_res_for_jump(...) method of builtins.PyCapsule instance figure_out_moving_partition_res_for_jump(pose : rosetta.core.pose.Pose, jump_nr : int) -> rosetta.utility.vector1_unsigned_long figure_out_moving_partition_res_for_suite(...) method of builtins.PyCapsule instance figure_out_moving_partition_res_for_suite(pose : rosetta.core.pose.Pose, moving_res : int, reference_res : int) -> rosetta.utility.vector1_unsigned_long figure_out_reference_res_for_suite(...) method of builtins.PyCapsule instance figure_out_reference_res_for_suite(pose : rosetta.core.pose.Pose, moving_res : int) -> int figure_out_root_and_moving_partition_res(...) method of builtins.PyCapsule instance figure_out_root_and_moving_partition_res(pose : rosetta.core.pose.Pose, moving_res : int, root_partition_res : rosetta.utility.vector1_unsigned_long, moving_partition_res : rosetta.utility.vector1_unsigned_long) -> NoneType figure_out_root_partition_res(...) method of builtins.PyCapsule instance figure_out_root_partition_res(pose : rosetta.core.pose.Pose, moving_res_list : rosetta.utility.vector1_unsigned_long) -> rosetta.utility.vector1_unsigned_long find_downstream_connection_res(...) method of builtins.PyCapsule instance find_downstream_connection_res(pose : rosetta.core.pose.Pose, moving_partition_res : rosetta.utility.vector1_unsigned_long) -> int find_jump_number_at_suite(...) method of builtins.PyCapsule instance find_jump_number_at_suite(fold_tree : rosetta.core.kinematics.FoldTree, moving_suite : int) -> int fix_protein_jump_atom(...) method of builtins.PyCapsule instance fix_protein_jump_atom(pose : rosetta.core.pose.Pose, res : int, atom_name : str) -> NoneType fix_up_jump_atoms(...) method of builtins.PyCapsule instance fix_up_jump_atoms(pose : rosetta.core.pose.Pose) -> NoneType fix_up_jump_atoms_and_residue_type_variants(...) method of builtins.PyCapsule instance fix_up_jump_atoms_and_residue_type_variants(pose_to_fix : rosetta.core.pose.Pose) -> NoneType fix_up_residue_type_variants(...) method of builtins.PyCapsule instance fix_up_residue_type_variants(pose : rosetta.core.pose.Pose) -> NoneType fix_up_residue_type_variants_at_strand_beginning(...) method of builtins.PyCapsule instance fix_up_residue_type_variants_at_strand_beginning(pose : rosetta.core.pose.Pose, res : int) -> NoneType fix_up_residue_type_variants_at_strand_end(...) method of builtins.PyCapsule instance fix_up_residue_type_variants_at_strand_end(pose : rosetta.core.pose.Pose, res : int) -> NoneType get_all_residues(...) method of builtins.PyCapsule instance get_all_residues(pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long get_all_working_moving_res(...) method of builtins.PyCapsule instance get_all_working_moving_res(working_parameters : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> rosetta.utility.vector1_unsigned_long get_cutpoint_closed(...) method of builtins.PyCapsule instance get_cutpoint_closed(pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long get_domain_boundary_res(...) method of builtins.PyCapsule instance get_domain_boundary_res(pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long get_domain_boundary_suites(...) method of builtins.PyCapsule instance get_domain_boundary_suites(pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long get_file_name(...) method of builtins.PyCapsule instance get_file_name(silent_file : str, tag : str) -> str get_minimize_scorefxn(...) method of builtins.PyCapsule instance get_minimize_scorefxn(pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, options : rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions) -> rosetta.core.scoring.ScoreFunction get_moving_res_including_domain_boundaries(...) method of builtins.PyCapsule instance get_moving_res_including_domain_boundaries(pose : rosetta.core.pose.Pose, moving_res_list : rosetta.utility.vector1_unsigned_long) -> rosetta.utility.vector1_unsigned_long get_partition_definition(...) method of builtins.PyCapsule instance get_partition_definition(pose : rosetta.core.pose.Pose, moving_suite : int) -> rosetta.utility.vector1_bool get_partition_definition_by_jump(...) method of builtins.PyCapsule instance get_partition_definition_by_jump(pose : rosetta.core.pose.Pose, jump_nr : int) -> rosetta.utility.vector1_bool get_unique_connection_res(...) method of builtins.PyCapsule instance get_unique_connection_res(pose : rosetta.core.pose.Pose, moving_partition_res : rosetta.utility.vector1_unsigned_long) -> int initialize_o2prime_pack_scorefxn(...) method of builtins.PyCapsule instance initialize_o2prime_pack_scorefxn(scorefxn : rosetta.core.scoring.ScoreFunction) -> rosetta.core.scoring.ScoreFunction initialize_pack_scorefxn(...) method of builtins.PyCapsule instance initialize_pack_scorefxn(sample_scorefxn : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> rosetta.core.scoring.ScoreFunction initialize_sample_scorefxn(...) method of builtins.PyCapsule instance initialize_sample_scorefxn(scorefxn : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, options : rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions) -> rosetta.core.scoring.ScoreFunction is_cutpoint_closed(...) method of builtins.PyCapsule instance is_cutpoint_closed(pose : rosetta.core.pose.Pose, seq_num : int) -> bool is_protein(...) method of builtins.PyCapsule instance is_protein(pose : rosetta.core.pose.Pose, moving_res_list : rosetta.utility.vector1_unsigned_long) -> bool look_for_unique_jump_to_moving_res(...) method of builtins.PyCapsule instance look_for_unique_jump_to_moving_res(fold_tree : rosetta.core.kinematics.FoldTree, i : int) -> int make_cut_at_moving_suite(...) method of builtins.PyCapsule instance make_cut_at_moving_suite(*args, **kwargs) Overloaded function.   1. make_cut_at_moving_suite(pose : rosetta.core.pose.Pose, moving_suite : int) -> int   2. make_cut_at_moving_suite(fold_tree : rosetta.core.kinematics.FoldTree, moving_suite : int) -> int make_variants_match(...) method of builtins.PyCapsule instance make_variants_match(pose : rosetta.core.pose.Pose, reference_pose : rosetta.core.pose.Pose, n : int, variant_type : rosetta.core.chemical.VariantType) -> NoneType merge_in_other_pose(...) method of builtins.PyCapsule instance merge_in_other_pose(pose : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, lower_merge_res : int, upper_merge_res : int, connect_residues_by_bond : bool) -> NoneType merge_in_other_pose_by_bond(...) method of builtins.PyCapsule instance merge_in_other_pose_by_bond(pose : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, merge_res : int) -> NoneType merge_in_other_pose_by_jump(...) method of builtins.PyCapsule instance merge_in_other_pose_by_jump(pose : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, lower_merge_res : int, upper_merge_res : int) -> NoneType merge_two_poses(...) method of builtins.PyCapsule instance merge_two_poses(*args, **kwargs) Overloaded function.   1. merge_two_poses(pose : rosetta.core.pose.Pose, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, working_res1 : rosetta.utility.vector1_unsigned_long, working_res2 : rosetta.utility.vector1_unsigned_long, lower_merge_res : int, upper_merge_res : int, connect_residues_by_bond : bool) -> rosetta.utility.vector1_unsigned_long   2. merge_two_poses(pose : rosetta.core.pose.Pose, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, working_res1 : rosetta.utility.vector1_unsigned_long, working_res2 : rosetta.utility.vector1_unsigned_long, lower_merge_res : int, upper_merge_res : int, connect_residues_by_bond : bool, fix_first_pose : bool) -> rosetta.utility.vector1_unsigned_long merge_two_poses_using_full_model_info(...) method of builtins.PyCapsule instance merge_two_poses_using_full_model_info(pose : rosetta.core.pose.Pose, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, lower_merge_res : int, upper_merge_res : int, connect_residues_by_bond : bool) -> rosetta.utility.vector1_unsigned_long merge_vectors(...) method of builtins.PyCapsule instance merge_vectors(vec1 : rosetta.utility.vector1_unsigned_long, vec2 : rosetta.utility.vector1_unsigned_long) -> rosetta.utility.vector1_unsigned_long remove_silent_file_if_it_exists(...) method of builtins.PyCapsule instance remove_silent_file_if_it_exists(silent_file : str) -> NoneType reroot(...) method of builtins.PyCapsule instance reroot(pose : rosetta.core.pose.Pose, root_partition_res : rosetta.utility.vector1_unsigned_long, res_list : rosetta.utility.vector1_unsigned_long, preferred_root_res : rosetta.utility.vector1_unsigned_long, fixed_domain_map : rosetta.utility.vector1_unsigned_long, cutpoint_open_in_full_model : rosetta.utility.vector1_unsigned_long, working_res : rosetta.utility.vector1_unsigned_long) -> NoneType reroot_based_on_full_model_info(...) method of builtins.PyCapsule instance reroot_based_on_full_model_info(*args, **kwargs) Overloaded function.   1. reroot_based_on_full_model_info(pose : rosetta.core.pose.Pose) -> NoneType   2. reroot_based_on_full_model_info(pose : rosetta.core.pose.Pose, root_partition_res : rosetta.utility.vector1_unsigned_long) -> NoneType revise_root_and_moving_res(...) method of builtins.PyCapsule instance revise_root_and_moving_res(pose : rosetta.core.pose.Pose, moving_res : int) -> bool revise_root_and_moving_res_list(...) method of builtins.PyCapsule instance revise_root_and_moving_res_list(pose : rosetta.core.pose.Pose, moving_res_list : rosetta.utility.vector1_unsigned_long) -> bool slice(...) method of builtins.PyCapsule instance slice(sliced_out_pose : rosetta.core.pose.Pose, pose : rosetta.core.pose.Pose, slice_res : rosetta.utility.vector1_unsigned_long) -> NoneType slice_out_pose(...) method of builtins.PyCapsule instance slice_out_pose(pose : rosetta.core.pose.Pose, sliced_out_pose : rosetta.core.pose.Pose, residues_to_delete : rosetta.utility.vector1_unsigned_long) -> NoneType split_pose(...) method of builtins.PyCapsule instance split_pose(*args, **kwargs) Overloaded function.   1. split_pose(pose : rosetta.core.pose.Pose, moving_res : int, reference_res : int) -> int   2. split_pose(pose : rosetta.core.pose.Pose, moving_res_list : rosetta.utility.vector1_unsigned_long) -> NoneType stepwise_addable_pose_residue(...) method of builtins.PyCapsule instance stepwise_addable_pose_residue(n : int, pose : rosetta.core.pose.Pose) -> bool stepwise_addable_residue(...) method of builtins.PyCapsule instance stepwise_addable_residue(n : int, non_standard_residue_map : rosetta.std.map_unsigned_long_std_string) -> bool switch_focus_among_poses_randomly(...) method of builtins.PyCapsule instance switch_focus_among_poses_randomly(*args, **kwargs) Overloaded function.   1. switch_focus_among_poses_randomly(pose : rosetta.core.pose.Pose) -> bool   2. switch_focus_among_poses_randomly(pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction) -> bool   3. switch_focus_among_poses_randomly(pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, force_switch : bool) -> bool switch_focus_to_other_pose(...) method of builtins.PyCapsule instance switch_focus_to_other_pose(*args, **kwargs) Overloaded function.   1. switch_focus_to_other_pose(pose : rosetta.core.pose.Pose, focus_pose_idx : int) -> NoneType   2. switch_focus_to_other_pose(pose : rosetta.core.pose.Pose, focus_pose_idx : int, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType virtualize_side_chains(...) method of builtins.PyCapsule instance virtualize_side_chains(pose : rosetta.core.pose.Pose) -> NoneType