Bindings for protocols::magnesium namespace

Classes
		builtins.object SampleGrid rosetta.protocols.moves.Mover(builtins.object) MgHydrater MgMonteCarlo MgOrbitalFrameFinder MgScanner MgWaterHydrogenPacker rosetta.protocols.moves.MoverForPoseList(rosetta.protocols.moves.Mover) MgMinimizer   class MgHydrater(rosetta.protocols.moves.Mover)       Method resolution order: MgHydrater rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, mg_res_list : rosetta.utility.vector1_unsigned_long) -> NoneType   3. __init__(handle, rosetta.protocols.magnesium.MgHydrater) -> 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.magnesium.MgHydrater, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.magnesium.MgHydrater,  : rosetta.protocols.magnesium.MgHydrater) -> rosetta.protocols.magnesium.MgHydrater excise_mini_pose(...) from builtins.PyCapsule excise_mini_pose(rosetta.protocols.magnesium.MgHydrater) -> bool get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.magnesium.MgHydrater) -> str set_excise_mini_pose(...) from builtins.PyCapsule set_excise_mini_pose(self : rosetta.protocols.magnesium.MgHydrater, setting : bool) -> NoneType set_use_fast_frame_heuristic(...) from builtins.PyCapsule set_use_fast_frame_heuristic(self : rosetta.protocols.magnesium.MgHydrater, setting : bool) -> NoneType set_use_virtual_waters_as_placeholders(...) from builtins.PyCapsule set_use_virtual_waters_as_placeholders(self : rosetta.protocols.magnesium.MgHydrater, setting : bool) -> NoneType set_verbose(...) from builtins.PyCapsule set_verbose(self : rosetta.protocols.magnesium.MgHydrater, setting : bool) -> NoneType use_fast_frame_heuristic(...) from builtins.PyCapsule use_fast_frame_heuristic(rosetta.protocols.magnesium.MgHydrater) -> bool use_virtual_waters_as_placeholders(...) from builtins.PyCapsule use_virtual_waters_as_placeholders(rosetta.protocols.magnesium.MgHydrater) -> bool verbose(...) from builtins.PyCapsule verbose(rosetta.protocols.magnesium.MgHydrater) -> bool 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 MgMinimizer(rosetta.protocols.moves.MoverForPoseList)       Method resolution order: MgMinimizer rosetta.protocols.moves.MoverForPoseList rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.magnesium.MgMinimizer) -> 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.magnesium.MgMinimizer, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.magnesium.MgMinimizer,  : rosetta.protocols.magnesium.MgMinimizer) -> rosetta.protocols.magnesium.MgMinimizer get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.magnesium.MgMinimizer) -> str mg_coord_cst_dist(...) from builtins.PyCapsule mg_coord_cst_dist(rosetta.protocols.magnesium.MgMinimizer) -> float mg_res(...) from builtins.PyCapsule mg_res(rosetta.protocols.magnesium.MgMinimizer) -> rosetta.utility.vector1_unsigned_long minimize_scorefxn(...) from builtins.PyCapsule minimize_scorefxn(rosetta.protocols.magnesium.MgMinimizer) -> rosetta.core.scoring.ScoreFunction set_mg_coord_cst_dist(...) from builtins.PyCapsule set_mg_coord_cst_dist(self : rosetta.protocols.magnesium.MgMinimizer, setting : float) -> NoneType set_mg_res(...) from builtins.PyCapsule set_mg_res(self : rosetta.protocols.magnesium.MgMinimizer, setting : rosetta.utility.vector1_unsigned_long) -> NoneType set_minimize_scorefxn(...) from builtins.PyCapsule set_minimize_scorefxn(self : rosetta.protocols.magnesium.MgMinimizer, setting : rosetta.core.scoring.ScoreFunction) -> 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 MgMonteCarlo(rosetta.protocols.moves.Mover)       Method resolution order: MgMonteCarlo rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.magnesium.MgMonteCarlo) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_delete_frequency(...) from builtins.PyCapsule add_delete_frequency(rosetta.protocols.magnesium.MgMonteCarlo) -> float apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.magnesium.MgMonteCarlo, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.magnesium.MgMonteCarlo,  : rosetta.protocols.magnesium.MgMonteCarlo) -> rosetta.protocols.magnesium.MgMonteCarlo cycles(...) from builtins.PyCapsule cycles(rosetta.protocols.magnesium.MgMonteCarlo) -> int get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.magnesium.MgMonteCarlo) -> str output_pdb(...) from builtins.PyCapsule output_pdb(rosetta.protocols.magnesium.MgMonteCarlo) -> bool set_add_delete_frequency(...) from builtins.PyCapsule set_add_delete_frequency(self : rosetta.protocols.magnesium.MgMonteCarlo, setting : float) -> NoneType set_cycles(...) from builtins.PyCapsule set_cycles(self : rosetta.protocols.magnesium.MgMonteCarlo, setting : int) -> NoneType set_output_pdb(...) from builtins.PyCapsule set_output_pdb(self : rosetta.protocols.magnesium.MgMonteCarlo, setting : bool) -> NoneType set_temperature(...) from builtins.PyCapsule set_temperature(self : rosetta.protocols.magnesium.MgMonteCarlo, setting : float) -> NoneType temperature(...) from builtins.PyCapsule temperature(rosetta.protocols.magnesium.MgMonteCarlo) -> float 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 MgOrbitalFrameFinder(rosetta.protocols.moves.Mover)       Method resolution order: MgOrbitalFrameFinder rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.magnesium.MgOrbitalFrameFinder) -> 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.magnesium.MgOrbitalFrameFinder, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.magnesium.MgOrbitalFrameFinder,  : rosetta.protocols.magnesium.MgOrbitalFrameFinder) -> rosetta.protocols.magnesium.MgOrbitalFrameFinder get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.magnesium.MgOrbitalFrameFinder) -> str 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 MgScanner(rosetta.protocols.moves.Mover)       Method resolution order: MgScanner rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.magnesium.MgScanner) -> 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.magnesium.MgScanner, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.magnesium.MgScanner,  : rosetta.protocols.magnesium.MgScanner) -> rosetta.protocols.magnesium.MgScanner get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.magnesium.MgScanner) -> str hydrate(...) from builtins.PyCapsule hydrate(rosetta.protocols.magnesium.MgScanner) -> bool input_scan_res(...) from builtins.PyCapsule input_scan_res(rosetta.protocols.magnesium.MgScanner) -> rosetta.utility.vector1_unsigned_long integration_test(...) from builtins.PyCapsule integration_test(rosetta.protocols.magnesium.MgScanner) -> bool minimize(...) from builtins.PyCapsule minimize(rosetta.protocols.magnesium.MgScanner) -> bool minimize_during_scoring(...) from builtins.PyCapsule minimize_during_scoring(rosetta.protocols.magnesium.MgScanner) -> bool minimize_mg_coord_constraint_distance(...) from builtins.PyCapsule minimize_mg_coord_constraint_distance(rosetta.protocols.magnesium.MgScanner) -> float output_pdb(...) from builtins.PyCapsule output_pdb(rosetta.protocols.magnesium.MgScanner) -> str score_cut(...) from builtins.PyCapsule score_cut(rosetta.protocols.magnesium.MgScanner) -> float score_cut_PDB(...) from builtins.PyCapsule score_cut_PDB(rosetta.protocols.magnesium.MgScanner) -> float scorefxn(...) from builtins.PyCapsule scorefxn(rosetta.protocols.magnesium.MgScanner) -> rosetta.core.scoring.ScoreFunction set_hydrate(...) from builtins.PyCapsule set_hydrate(self : rosetta.protocols.magnesium.MgScanner, setting : bool) -> NoneType set_input_scan_res(...) from builtins.PyCapsule set_input_scan_res(self : rosetta.protocols.magnesium.MgScanner, setting : rosetta.utility.vector1_unsigned_long) -> NoneType set_integration_test(...) from builtins.PyCapsule set_integration_test(self : rosetta.protocols.magnesium.MgScanner, setting : bool) -> NoneType set_minimize(...) from builtins.PyCapsule set_minimize(self : rosetta.protocols.magnesium.MgScanner, setting : bool) -> NoneType set_minimize_during_scoring(...) from builtins.PyCapsule set_minimize_during_scoring(self : rosetta.protocols.magnesium.MgScanner, setting : bool) -> NoneType set_minimize_mg_coord_constraint_distance(...) from builtins.PyCapsule set_minimize_mg_coord_constraint_distance(self : rosetta.protocols.magnesium.MgScanner, setting : float) -> NoneType set_output_pdb(...) from builtins.PyCapsule set_output_pdb(self : rosetta.protocols.magnesium.MgScanner, setting : str) -> NoneType set_score_cut(...) from builtins.PyCapsule set_score_cut(self : rosetta.protocols.magnesium.MgScanner, setting : float) -> NoneType set_score_cut_PDB(...) from builtins.PyCapsule set_score_cut_PDB(self : rosetta.protocols.magnesium.MgScanner, setting : float) -> NoneType set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.magnesium.MgScanner, setting : rosetta.core.scoring.ScoreFunction) -> NoneType set_silent_file(...) from builtins.PyCapsule set_silent_file(self : rosetta.protocols.magnesium.MgScanner, setting : str) -> NoneType set_tether_to_closest_res(...) from builtins.PyCapsule set_tether_to_closest_res(self : rosetta.protocols.magnesium.MgScanner, setting : bool) -> NoneType set_xyz_step(...) from builtins.PyCapsule set_xyz_step(self : rosetta.protocols.magnesium.MgScanner, setting : float) -> NoneType silent_file(...) from builtins.PyCapsule silent_file(rosetta.protocols.magnesium.MgScanner) -> str tether_to_closest_res(...) from builtins.PyCapsule tether_to_closest_res(rosetta.protocols.magnesium.MgScanner) -> bool xyz_step(...) from builtins.PyCapsule xyz_step(rosetta.protocols.magnesium.MgScanner) -> float 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 MgWaterHydrogenPacker(rosetta.protocols.moves.Mover)       Method resolution order: MgWaterHydrogenPacker rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, mg_res_list : rosetta.utility.vector1_unsigned_long) -> NoneType   3. __init__(handle, rosetta.protocols.magnesium.MgWaterHydrogenPacker) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. apply(...) from builtins.PyCapsule apply(*args, **kwargs) Overloaded function.   1. apply(self : rosetta.protocols.magnesium.MgWaterHydrogenPacker, pose : rosetta.core.pose.Pose) -> NoneType   2. apply(self : rosetta.protocols.magnesium.MgWaterHydrogenPacker, pose : rosetta.core.pose.Pose, mg_water : (int, int)) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.magnesium.MgWaterHydrogenPacker,  : rosetta.protocols.magnesium.MgWaterHydrogenPacker) -> rosetta.protocols.magnesium.MgWaterHydrogenPacker excise_mini_pose(...) from builtins.PyCapsule excise_mini_pose(rosetta.protocols.magnesium.MgWaterHydrogenPacker) -> bool get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.magnesium.MgWaterHydrogenPacker) -> str remove_waters_except_mg_bound(...) from builtins.PyCapsule remove_waters_except_mg_bound(self : rosetta.protocols.magnesium.MgWaterHydrogenPacker, pose : rosetta.core.pose.Pose) -> NoneType set_excise_mini_pose(...) from builtins.PyCapsule set_excise_mini_pose(self : rosetta.protocols.magnesium.MgWaterHydrogenPacker, setting : bool) -> NoneType set_use_fast_heuristic(...) from builtins.PyCapsule set_use_fast_heuristic(self : rosetta.protocols.magnesium.MgWaterHydrogenPacker, setting : bool) -> NoneType use_fast_heuristic(...) from builtins.PyCapsule use_fast_heuristic(rosetta.protocols.magnesium.MgWaterHydrogenPacker) -> bool 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 SampleGrid(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.magnesium.SampleGrid, pose : rosetta.core.pose.Pose) -> NoneType   2. __init__(self : rosetta.protocols.magnesium.SampleGrid,  : rosetta.protocols.magnesium.SampleGrid) -> 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.magnesium.SampleGrid,  : rosetta.protocols.magnesium.SampleGrid) -> rosetta.protocols.magnesium.SampleGrid get_mg_positions(...) from builtins.PyCapsule get_mg_positions(self : rosetta.protocols.magnesium.SampleGrid, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_numeric_xyzVector_double_t input_scan_res(...) from builtins.PyCapsule input_scan_res(rosetta.protocols.magnesium.SampleGrid) -> rosetta.utility.vector1_unsigned_long set_input_scan_res(...) from builtins.PyCapsule set_input_scan_res(self : rosetta.protocols.magnesium.SampleGrid, setting : rosetta.utility.vector1_unsigned_long) -> NoneType set_tether_to_closest_res(...) from builtins.PyCapsule set_tether_to_closest_res(self : rosetta.protocols.magnesium.SampleGrid, setting : bool) -> NoneType set_xyz_step(...) from builtins.PyCapsule set_xyz_step(self : rosetta.protocols.magnesium.SampleGrid, setting : float) -> NoneType tether_to_closest_res(...) from builtins.PyCapsule tether_to_closest_res(rosetta.protocols.magnesium.SampleGrid) -> bool xmax(...) from builtins.PyCapsule xmax(rosetta.protocols.magnesium.SampleGrid) -> float xmin(...) from builtins.PyCapsule xmin(rosetta.protocols.magnesium.SampleGrid) -> float xyz_step(...) from builtins.PyCapsule xyz_step(rosetta.protocols.magnesium.SampleGrid) -> float ymax(...) from builtins.PyCapsule ymax(rosetta.protocols.magnesium.SampleGrid) -> float ymin(...) from builtins.PyCapsule ymin(rosetta.protocols.magnesium.SampleGrid) -> float zmax(...) from builtins.PyCapsule zmax(rosetta.protocols.magnesium.SampleGrid) -> float zmin(...) from builtins.PyCapsule zmin(rosetta.protocols.magnesium.SampleGrid) -> float

Functions
		add_single_magnesium(...) method of builtins.PyCapsule instance add_single_magnesium(pose : rosetta.core.pose.Pose) -> NoneType append_mg_bound_water(...) method of builtins.PyCapsule instance append_mg_bound_water(pose : rosetta.core.pose.Pose, rsd : rosetta.core.conformation.Residue, mg_res : int) -> int define_mg_water_map(...) method of builtins.PyCapsule instance define_mg_water_map(pose : rosetta.core.pose.Pose) -> rosetta.std.map_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t filter_acceptor_ligands(...) method of builtins.PyCapsule instance filter_acceptor_ligands(pose : rosetta.core.pose.Pose, ligands : rosetta.utility.vector1_core_id_AtomID) -> rosetta.utility.vector1_core_id_AtomID find_bound_waters_that_are_daughters_in_fold_tree(...) method of builtins.PyCapsule instance find_bound_waters_that_are_daughters_in_fold_tree(pose : rosetta.core.pose.Pose, mg_res : int) -> rosetta.utility.vector1_unsigned_long fixup_magnesiums(...) method of builtins.PyCapsule instance fixup_magnesiums(pose : rosetta.core.pose.Pose) -> NoneType get_closest_non_hoh_contact(...) method of builtins.PyCapsule instance get_closest_non_hoh_contact(*args, **kwargs) Overloaded function.   1. get_closest_non_hoh_contact(pose : rosetta.core.pose.Pose, i : int) -> rosetta.core.id.AtomID   2. get_closest_non_hoh_contact(pose : rosetta.core.pose.Pose, i : int, exclude_rsd : str) -> rosetta.core.id.AtomID get_hydration_stats(...) method of builtins.PyCapsule instance get_hydration_stats(pose : rosetta.core.pose.Pose, reference_pose : rosetta.core.pose.Pose, pdb_mg_res_list_in : rosetta.utility.vector1_unsigned_long, outfile : str) -> NoneType get_mg_ligands(...) method of builtins.PyCapsule instance get_mg_ligands(*args, **kwargs) Overloaded function.   1. get_mg_ligands(pose : rosetta.core.pose.Pose, i : int) -> rosetta.utility.vector1_core_id_AtomID   2. get_mg_ligands(pose : rosetta.core.pose.Pose, i : int, filter_for_acceptors : bool) -> rosetta.utility.vector1_core_id_AtomID   3. get_mg_ligands(pose : rosetta.core.pose.Pose, i : int, filter_for_acceptors : bool, exclude_virtual_waters : bool) -> rosetta.utility.vector1_core_id_AtomID get_mg_res(...) method of builtins.PyCapsule instance get_mg_res(pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long get_mg_rsd(...) method of builtins.PyCapsule instance get_mg_rsd() -> rosetta.core.conformation.Residue get_mg_scorefxn(...) method of builtins.PyCapsule instance get_mg_scorefxn() -> rosetta.core.scoring.ScoreFunction get_mg_water_pairs(...) method of builtins.PyCapsule instance get_mg_water_pairs(*args, **kwargs) Overloaded function.   1. get_mg_water_pairs(pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t   2. get_mg_water_pairs(pose : rosetta.core.pose.Pose, exclude_virtual_waters : bool) -> rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t   3. get_mg_water_pairs(pose : rosetta.core.pose.Pose, mg_res : rosetta.utility.vector1_unsigned_long) -> rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t   4. get_mg_water_pairs(pose : rosetta.core.pose.Pose, mg_res : rosetta.utility.vector1_unsigned_long, exclude_virtual_waters : bool) -> rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t get_octahedral_uniform_rotation_sampler(...) method of builtins.PyCapsule instance get_octahedral_uniform_rotation_sampler(*args, **kwargs) Overloaded function.   1. get_octahedral_uniform_rotation_sampler() -> rosetta.numeric.UniformRotationSampler   2. get_octahedral_uniform_rotation_sampler(rotstep : float) -> rosetta.numeric.UniformRotationSampler   3. get_octahedral_uniform_rotation_sampler(rotstep : float, remove_redundant : bool) -> rosetta.numeric.UniformRotationSampler get_useful_HOH_coords(...) method of builtins.PyCapsule instance get_useful_HOH_coords(Oc : rosetta.numeric.xyzVector_double_t, OH1c : rosetta.numeric.xyzVector_double_t, OH2c : rosetta.numeric.xyzVector_double_t, residue_set : rosetta.core.chemical.ResidueTypeSet) -> rosetta.core.conformation.Residue get_water_res(...) method of builtins.PyCapsule instance get_water_res(pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long get_water_uniform_rotation_sampler(...) method of builtins.PyCapsule instance get_water_uniform_rotation_sampler() -> rosetta.numeric.UniformRotationSampler hydrate_magnesiums(...) method of builtins.PyCapsule instance hydrate_magnesiums(*args, **kwargs) Overloaded function.   1. hydrate_magnesiums(pose : rosetta.core.pose.Pose) -> NoneType   2. hydrate_magnesiums(pose : rosetta.core.pose.Pose, use_virtual_waters_as_placeholders : bool) -> NoneType   3. hydrate_magnesiums(pose : rosetta.core.pose.Pose, use_virtual_waters_as_placeholders : bool, test_all_mg_hydration_frames : bool) -> NoneType instantiate_water_at_octahedral_vertex(...) method of builtins.PyCapsule instance instantiate_water_at_octahedral_vertex(*args, **kwargs) Overloaded function.   1. instantiate_water_at_octahedral_vertex(pose : rosetta.core.pose.Pose, mg_res : int, n : int) -> int   2. instantiate_water_at_octahedral_vertex(pose : rosetta.core.pose.Pose, mg_res : int, n : int, hoh_distance : float) -> int   3. instantiate_water_at_octahedral_vertex(pose : rosetta.core.pose.Pose, mg_res : int, n : int, hoh_distance : float, replace_residue : bool) -> int   4. instantiate_water_at_octahedral_vertex(pose : rosetta.core.pose.Pose, mg_res : int, n : int, hoh_distance : float, replace_residue : bool, virtual_water : bool) -> int minimize_magnesium_and_hydration_shell(...) method of builtins.PyCapsule instance minimize_magnesium_and_hydration_shell(*args, **kwargs) Overloaded function.   1. minimize_magnesium_and_hydration_shell(pose : rosetta.core.pose.Pose, mg_res : rosetta.utility.vector1_unsigned_long) -> NoneType   2. minimize_magnesium_and_hydration_shell(pose : rosetta.core.pose.Pose, mg_res : rosetta.utility.vector1_unsigned_long, minimize_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   3. minimize_magnesium_and_hydration_shell(pose : rosetta.core.pose.Pose, mg_res : rosetta.utility.vector1_unsigned_long, minimize_scorefxn : rosetta.core.scoring.ScoreFunction, mg_coord_cst_dist : float) -> NoneType   4. minimize_magnesium_and_hydration_shell(pose : rosetta.core.pose.Pose, pose_list : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, mg_res : rosetta.utility.vector1_unsigned_long) -> NoneType   5. minimize_magnesium_and_hydration_shell(pose : rosetta.core.pose.Pose, pose_list : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, mg_res : rosetta.utility.vector1_unsigned_long, minimize_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   6. minimize_magnesium_and_hydration_shell(pose : rosetta.core.pose.Pose, pose_list : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, mg_res : rosetta.utility.vector1_unsigned_long, minimize_scorefxn : rosetta.core.scoring.ScoreFunction, mg_coord_cst_dist : float) -> NoneType pdbslice(...) method of builtins.PyCapsule instance pdbslice(*args, **kwargs) Overloaded function.   1. pdbslice(pose : rosetta.core.pose.Pose, center_res : int) -> rosetta.utility.vector1_unsigned_long   2. pdbslice(pose : rosetta.core.pose.Pose, center_res : int, distance_cutoff : float) -> rosetta.utility.vector1_unsigned_long remove_mg_bound_waters(...) method of builtins.PyCapsule instance remove_mg_bound_waters(*args, **kwargs) Overloaded function.   1. remove_mg_bound_waters(pose : rosetta.core.pose.Pose, mg_res : rosetta.utility.vector1_unsigned_long) -> NoneType   2. remove_mg_bound_waters(pose : rosetta.core.pose.Pose, mg_res : rosetta.utility.vector1_unsigned_long, leave_other_waters : bool) -> NoneType remove_waters_except_mg_bound(...) method of builtins.PyCapsule instance remove_waters_except_mg_bound(pose : rosetta.core.pose.Pose, mg_water_pairs : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> NoneType strip_out_magnesiums(...) method of builtins.PyCapsule instance strip_out_magnesiums(pose : rosetta.core.pose.Pose) -> NoneType update_jump_atoms_for_mg_bound_water(...) method of builtins.PyCapsule instance update_jump_atoms_for_mg_bound_water(pose : rosetta.core.pose.Pose, n : int) -> NoneType update_mg_hoh_fold_tree(...) method of builtins.PyCapsule instance update_mg_hoh_fold_tree(pose : rosetta.core.pose.Pose) -> NoneType update_numbers_in_pdb_info(...) method of builtins.PyCapsule instance update_numbers_in_pdb_info(*args, **kwargs) Overloaded function.   1. update_numbers_in_pdb_info(pose : rosetta.core.pose.Pose) -> NoneType   2. update_numbers_in_pdb_info(pose : rosetta.core.pose.Pose, reset_waters : bool) -> NoneType