Bindings for protocols::forge::remodel namespace

Classes
		builtins.object LineObject RemodelData RemodelWorkingSet ResidueVicinityInfo Segment rosetta.core.pack.task.operation.TaskOperation(builtins.object) RemodelRotamerLinks rosetta.core.pack.task.operation.TaskOperationCreator(builtins.object) RemodelRotamerLinksCreator rosetta.protocols.moves.Mover(builtins.object) RemodelAccumulator RemodelConstraintGenerator GenericRemodelConstraintGenerator ResidueVicinityRCG RemodelDesignMover RemodelGlobalFrame RemodelLigandHandler RemodelLoopMover RemodelMover rosetta.protocols.moves.MoverCreator(builtins.object) RemodelMoverCreator ResidueVicinityCstGeneratorCreator rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO(builtins.object) RemodelEnzdesCstModule rosetta.utility.excn.EXCN_Base(builtins.object) EXCN_RemoveCstsFailed   class EXCN_RemoveCstsFailed(rosetta.utility.excn.EXCN_Base)       Method resolution order: EXCN_RemoveCstsFailed rosetta.utility.excn.EXCN_Base builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.forge.remodel.EXCN_RemoveCstsFailed,  : rosetta.protocols.forge.remodel.EXCN_RemoveCstsFailed) -> rosetta.protocols.forge.remodel.EXCN_RemoveCstsFailed Methods inherited from rosetta.utility.excn.EXCN_Base: __str__(...) from builtins.PyCapsule __str__(rosetta.utility.excn.EXCN_Base) -> str msg(...) from builtins.PyCapsule msg(rosetta.utility.excn.EXCN_Base) -> str   class GenericRemodelConstraintGenerator(RemodelConstraintGenerator)     generic remodel constraint generator for use with arbitrary ConstraintGenerators     Method resolution order: GenericRemodelConstraintGenerator RemodelConstraintGenerator rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, id : str, cg : rosetta.protocols.constraint_generator.ConstraintGenerator) -> NoneType   2. __init__(handle, rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator) -> 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.forge.remodel.GenericRemodelConstraintGenerator,  : rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator) -> rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator) -> rosetta.protocols.moves.Mover generate_remodel_constraints(...) from builtins.PyCapsule generate_remodel_constraints(self : rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator, pose : rosetta.core.pose.Pose) -> NoneType get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator) -> str Methods inherited from RemodelConstraintGenerator: add_remodel_constraints_to_pose(...) from builtins.PyCapsule add_remodel_constraints_to_pose(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator, pose : rosetta.core.pose.Pose) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator, pose : rosetta.core.pose.Pose) -> NoneType   generates constraints and adds them to the pose constraints(...) from builtins.PyCapsule constraints(rosetta.protocols.forge.remodel.RemodelConstraintGenerator) -> rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t id(...) from builtins.PyCapsule id(rosetta.protocols.forge.remodel.RemodelConstraintGenerator) -> str init(...) from builtins.PyCapsule init(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator,  : rosetta.core.pose.Pose) -> NoneType   Pose-specific setup routines go here lookup_stored_constraints(...) from builtins.PyCapsule lookup_stored_constraints(id : str) -> rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t remove_remodel_constraints_from_pose(...) from builtins.PyCapsule remove_remodel_constraints_from_pose(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator, pose : rosetta.core.pose.Pose) -> NoneType seqmap(...) from builtins.PyCapsule seqmap(rosetta.protocols.forge.remodel.RemodelConstraintGenerator) -> rosetta.core.id.SequenceMapping set_id(...) from builtins.PyCapsule set_id(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator, id : str) -> NoneType set_seqmap(...) from builtins.PyCapsule set_seqmap(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator, seqmap : rosetta.core.id.SequenceMapping) -> NoneType set_vlb(...) from builtins.PyCapsule set_vlb(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator, vlb : rosetta.std.weak_ptr_protocols_forge_components_VarLengthBuild_t) -> NoneType vlb(...) from builtins.PyCapsule vlb(rosetta.protocols.forge.remodel.RemodelConstraintGenerator) -> rosetta.std.weak_ptr_protocols_forge_components_VarLengthBuild_t Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class LineObject(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.forge.remodel.LineObject) -> NoneType   2. __init__(self : rosetta.protocols.forge.remodel.LineObject,  : rosetta.protocols.forge.remodel.LineObject) -> 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.forge.remodel.LineObject,  : rosetta.protocols.forge.remodel.LineObject) -> rosetta.protocols.forge.remodel.LineObject Data descriptors defined here: aminoAcidList constraint_definition design_type has_constraints has_ncaa index isDesignable ncaaList original_index resname sstype   class RemodelAccumulator(rosetta.protocols.moves.Mover)       Method resolution order: RemodelAccumulator 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, working_model : rosetta.protocols.forge.remodel.RemodelWorkingSet) -> NoneType   3. __init__(handle, rosetta.protocols.forge.remodel.RemodelAccumulator) -> 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.forge.remodel.RemodelAccumulator, pose : rosetta.core.pose.Pose) -> NoneType   2. apply(self : rosetta.protocols.forge.remodel.RemodelAccumulator, pose : rosetta.core.pose.Pose, score : float) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.forge.remodel.RemodelAccumulator,  : rosetta.protocols.forge.remodel.RemodelAccumulator) -> rosetta.protocols.forge.remodel.RemodelAccumulator clear(...) from builtins.PyCapsule clear(rosetta.protocols.forge.remodel.RemodelAccumulator) -> NoneType clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.remodel.RemodelAccumulator) -> rosetta.protocols.moves.Mover cluster_loop(...) from builtins.PyCapsule cluster_loop(rosetta.protocols.forge.remodel.RemodelAccumulator) -> NoneType cluster_pose(...) from builtins.PyCapsule cluster_pose(rosetta.protocols.forge.remodel.RemodelAccumulator) -> NoneType cluster_switch(...) from builtins.PyCapsule cluster_switch(rosetta.protocols.forge.remodel.RemodelAccumulator) -> bool clustered_best_poses(...) from builtins.PyCapsule clustered_best_poses(rosetta.protocols.forge.remodel.RemodelAccumulator) -> rosetta.std.vector_std_shared_ptr_core_pose_Pose_t clustered_top_poses(...) from builtins.PyCapsule clustered_top_poses(self : rosetta.protocols.forge.remodel.RemodelAccumulator, count : int) -> rosetta.std.vector_std_shared_ptr_core_pose_Pose_t contents_in_pose_store(...) from builtins.PyCapsule contents_in_pose_store(rosetta.protocols.forge.remodel.RemodelAccumulator) -> rosetta.std.vector_std_shared_ptr_core_pose_Pose_t fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.forge.remodel.RemodelAccumulator) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.forge.remodel.RemodelAccumulator) -> str keep_top_pose(...) from builtins.PyCapsule keep_top_pose(self : rosetta.protocols.forge.remodel.RemodelAccumulator, num_to_keep : int) -> NoneType pop(...) from builtins.PyCapsule pop(rosetta.protocols.forge.remodel.RemodelAccumulator) -> rosetta.core.pose.Pose recover_checkpoint(...) from builtins.PyCapsule recover_checkpoint(rosetta.protocols.forge.remodel.RemodelAccumulator) -> int run_cluster(...) from builtins.PyCapsule run_cluster(rosetta.protocols.forge.remodel.RemodelAccumulator) -> NoneType shrink_cluster(...) from builtins.PyCapsule shrink_cluster(self : rosetta.protocols.forge.remodel.RemodelAccumulator, num_top : int) -> NoneType size(...) from builtins.PyCapsule size(rosetta.protocols.forge.remodel.RemodelAccumulator) -> int write_checkpoint(...) from builtins.PyCapsule write_checkpoint(self : rosetta.protocols.forge.remodel.RemodelAccumulator, progress_point : int) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class RemodelConstraintGenerator(rosetta.protocols.moves.Mover)     pure virtual base class     Method resolution order: RemodelConstraintGenerator rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.forge.remodel.RemodelConstraintGenerator) -> NoneType   2. __init__(rosetta.protocols.forge.remodel.RemodelConstraintGenerator, rosetta.protocols.forge.remodel.RemodelConstraintGenerator) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_remodel_constraints_to_pose(...) from builtins.PyCapsule add_remodel_constraints_to_pose(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator, pose : rosetta.core.pose.Pose) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator, pose : rosetta.core.pose.Pose) -> NoneType   generates constraints and adds them to the pose assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator,  : rosetta.protocols.forge.remodel.RemodelConstraintGenerator) -> rosetta.protocols.forge.remodel.RemodelConstraintGenerator constraints(...) from builtins.PyCapsule constraints(rosetta.protocols.forge.remodel.RemodelConstraintGenerator) -> rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t generate_remodel_constraints(...) from builtins.PyCapsule generate_remodel_constraints(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator, pose : rosetta.core.pose.Pose) -> NoneType id(...) from builtins.PyCapsule id(rosetta.protocols.forge.remodel.RemodelConstraintGenerator) -> str init(...) from builtins.PyCapsule init(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator,  : rosetta.core.pose.Pose) -> NoneType   Pose-specific setup routines go here lookup_stored_constraints(...) from builtins.PyCapsule lookup_stored_constraints(id : str) -> rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t remove_remodel_constraints_from_pose(...) from builtins.PyCapsule remove_remodel_constraints_from_pose(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator, pose : rosetta.core.pose.Pose) -> NoneType seqmap(...) from builtins.PyCapsule seqmap(rosetta.protocols.forge.remodel.RemodelConstraintGenerator) -> rosetta.core.id.SequenceMapping set_id(...) from builtins.PyCapsule set_id(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator, id : str) -> NoneType set_seqmap(...) from builtins.PyCapsule set_seqmap(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator, seqmap : rosetta.core.id.SequenceMapping) -> NoneType set_vlb(...) from builtins.PyCapsule set_vlb(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator, vlb : rosetta.std.weak_ptr_protocols_forge_components_VarLengthBuild_t) -> NoneType vlb(...) from builtins.PyCapsule vlb(rosetta.protocols.forge.remodel.RemodelConstraintGenerator) -> rosetta.std.weak_ptr_protocols_forge_components_VarLengthBuild_t 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_name(...) from builtins.PyCapsule get_name(rosetta.protocols.moves.Mover) -> str   Each derived class must specify its name.  The class name. 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 RemodelData(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.forge.remodel.RemodelData) -> NoneType   2. __init__(self : rosetta.protocols.forge.remodel.RemodelData,  : rosetta.protocols.forge.remodel.RemodelData) -> 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.forge.remodel.RemodelData,  : rosetta.protocols.forge.remodel.RemodelData) -> rosetta.protocols.forge.remodel.RemodelData collectInsertionPose(...) from builtins.PyCapsule collectInsertionPose(rosetta.protocols.forge.remodel.RemodelData) -> NoneType getLoopsToBuildFromBlueprint(...) from builtins.PyCapsule getLoopsToBuildFromBlueprint(self : rosetta.protocols.forge.remodel.RemodelData, text_blueprint : str) -> NoneType getLoopsToBuildFromFile(...) from builtins.PyCapsule getLoopsToBuildFromFile(self : rosetta.protocols.forge.remodel.RemodelData, filename : str) -> NoneType splitString(...) from builtins.PyCapsule splitString(self : rosetta.protocols.forge.remodel.RemodelData, str : str, delim : str, results : rosetta.std.vector_std_string) -> NoneType translateDSSP_ABEGO(...) from builtins.PyCapsule translateDSSP_ABEGO(self : rosetta.protocols.forge.remodel.RemodelData, ss : str, abego : str) -> NoneType updateWithDsspAssignment(...) from builtins.PyCapsule updateWithDsspAssignment(self : rosetta.protocols.forge.remodel.RemodelData, dsspSS : ObjexxFCL::FArray1D<char>) -> NoneType Data descriptors defined here: abego auto_design blueprint design_mode design_neighbor disulfLandingRange disulfMobileRange dssp_updated_ss has_design_info_ insertPose insertionSS insertionSize loops_to_build natro_movemap_ parsed_string_for_resfile pdb_start pdb_stop sequence ss total_chain_break_score   class RemodelDesignMover(rosetta.protocols.moves.Mover)       Method resolution order: RemodelDesignMover 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, remodel_data : rosetta.protocols.forge.remodel.RemodelData, working_model : rosetta.protocols.forge.remodel.RemodelWorkingSet, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType   3. __init__(handle, rosetta.protocols.forge.remodel.RemodelDesignMover) -> 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.forge.remodel.RemodelDesignMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.forge.remodel.RemodelDesignMover,  : rosetta.protocols.forge.remodel.RemodelDesignMover) -> rosetta.protocols.forge.remodel.RemodelDesignMover check_state(...) from builtins.PyCapsule check_state(rosetta.protocols.forge.remodel.RemodelDesignMover) -> bool clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.remodel.RemodelDesignMover) -> rosetta.protocols.moves.Mover find_disulfides_in_the_neighborhood(...) from builtins.PyCapsule find_disulfides_in_the_neighborhood(self : rosetta.protocols.forge.remodel.RemodelDesignMover, pose : rosetta.core.pose.Pose, disulf_partners : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, match_rt_limit : float, rosetta_scripts_min_loop : int, rosetta_scripts_include_current_ds : bool, rosetta_scripts_keep_current_ds : bool, relax_bb_for_disulf : bool, use_match_rt : bool, use_disulf_fa_score : bool, disulf_fa_max : float) -> bool fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.forge.remodel.RemodelDesignMover) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.forge.remodel.RemodelDesignMover) -> str make_disulfide(...) from builtins.PyCapsule make_disulfide(self : rosetta.protocols.forge.remodel.RemodelDesignMover, pose : rosetta.core.pose.Pose, disulf_partners : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, mm : rosetta.core.kinematics.MoveMap) -> NoneType make_disulfide_fast(...) from builtins.PyCapsule make_disulfide_fast(self : rosetta.protocols.forge.remodel.RemodelDesignMover, pose : rosetta.core.pose.Pose, disulf_partners : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> NoneType mode1_1_packertask(...) from builtins.PyCapsule mode1_1_packertask(self : rosetta.protocols.forge.remodel.RemodelDesignMover, pose : rosetta.core.pose.Pose) -> NoneType mode1_packertask(...) from builtins.PyCapsule mode1_packertask(self : rosetta.protocols.forge.remodel.RemodelDesignMover, pose : rosetta.core.pose.Pose) -> NoneType mode2_packertask(...) from builtins.PyCapsule mode2_packertask(self : rosetta.protocols.forge.remodel.RemodelDesignMover, pose : rosetta.core.pose.Pose) -> NoneType mode3_packertask(...) from builtins.PyCapsule mode3_packertask(self : rosetta.protocols.forge.remodel.RemodelDesignMover, pose : rosetta.core.pose.Pose) -> NoneType mode4_packertask(...) from builtins.PyCapsule mode4_packertask(self : rosetta.protocols.forge.remodel.RemodelDesignMover, pose : rosetta.core.pose.Pose) -> NoneType mode5_packertask(...) from builtins.PyCapsule mode5_packertask(self : rosetta.protocols.forge.remodel.RemodelDesignMover, pose : rosetta.core.pose.Pose) -> NoneType mode6_packertask(...) from builtins.PyCapsule mode6_packertask(self : rosetta.protocols.forge.remodel.RemodelDesignMover, pose : rosetta.core.pose.Pose) -> NoneType reduce_task(...) from builtins.PyCapsule reduce_task(self : rosetta.protocols.forge.remodel.RemodelDesignMover, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask, core : bool, boundary : bool, surface : bool) -> NoneType scorefunction(...) from builtins.PyCapsule scorefunction(self : rosetta.protocols.forge.remodel.RemodelDesignMover, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_state(...) from builtins.PyCapsule set_state(self : rosetta.protocols.forge.remodel.RemodelDesignMover, state_tag : str) -> NoneType task(...) from builtins.PyCapsule task(rosetta.protocols.forge.remodel.RemodelDesignMover) -> rosetta.core.pack.task.PackerTask Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class RemodelEnzdesCstModule(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO)       Method resolution order: RemodelEnzdesCstModule rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.forge.remodel.RemodelEnzdesCstModule, external_data : rosetta.protocols.forge.remodel.RemodelData) -> NoneType   2. __init__(self : rosetta.protocols.forge.remodel.RemodelEnzdesCstModule,  : rosetta.protocols.forge.remodel.RemodelEnzdesCstModule) -> 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.forge.remodel.RemodelEnzdesCstModule, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.forge.remodel.RemodelEnzdesCstModule,  : rosetta.protocols.forge.remodel.RemodelEnzdesCstModule) -> rosetta.protocols.forge.remodel.RemodelEnzdesCstModule blueprint_cst_definition(...) from builtins.PyCapsule blueprint_cst_definition(self : rosetta.protocols.forge.remodel.RemodelEnzdesCstModule, pose : rosetta.core.pose.Pose) -> NoneType enable_constraint_scoreterms(...) from builtins.PyCapsule enable_constraint_scoreterms(self : rosetta.protocols.forge.remodel.RemodelEnzdesCstModule, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType use_all_blocks(...) from builtins.PyCapsule use_all_blocks(rosetta.protocols.forge.remodel.RemodelEnzdesCstModule) -> NoneType use_backbone_only_blocks(...) from builtins.PyCapsule use_backbone_only_blocks(rosetta.protocols.forge.remodel.RemodelEnzdesCstModule) -> NoneType Methods inherited from rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO: add_constraints_to_pose(...) from builtins.PyCapsule add_constraints_to_pose(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, scofx : rosetta.core.scoring.ScoreFunction, accept_blocks_missing_header : bool) -> NoneType add_constraints_to_pose_for_block_without_clearing_and_header_processing(...) from builtins.PyCapsule add_constraints_to_pose_for_block_without_clearing_and_header_processing(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, scofx : rosetta.core.scoring.ScoreFunction, cst_block : int) -> NoneType   BE CAREFUL when using this function, it generates constraints      without clearing the internal data structures and reading in      the information in the pdb REMARKs      if you're unsure use the above one add_pregenerated_constraints_to_pose(...) from builtins.PyCapsule add_pregenerated_constraints_to_pose(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, scofx : rosetta.core.scoring.ScoreFunction) -> NoneType   convenience function that will add constraints to the pose if they have      been previously generated. BE CAREFUL when using this function, it relies on the      pose having the same residue types at the same constrained positions as in the pose      that was originally used to generate the constraints. If in doubt, it's safer to      regenerate the constraints before adding (i.e. use the above add_constraints_to_pose      function.) allowed_res_name3_at_position(...) from builtins.PyCapsule allowed_res_name3_at_position(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, seqpos : int) -> rosetta.utility.vector1_std_string clear_active_pose_constraints_for_block(...) from builtins.PyCapsule clear_active_pose_constraints_for_block(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, cst_block : int) -> NoneType contains_position(...) from builtins.PyCapsule contains_position(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, seqpos : int) -> bool   are constraints specified for this position? enz_cst_params(...) from builtins.PyCapsule enz_cst_params(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, block : int) -> protocols::toolbox::match_enzdes_util::EnzConstraintParameters enz_cst_params_missing_in_pose(...) from builtins.PyCapsule enz_cst_params_missing_in_pose(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintParameters_t enz_cst_params_size(...) from builtins.PyCapsule enz_cst_params_size(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> int get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO   self pointers   2. get_self_ptr(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintIO_t   2. get_self_weak_ptr(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> rosetta.std.weak_ptr_protocols_toolbox_match_enzdes_util_EnzConstraintIO_t is_backbone_only_cst(...) from builtins.PyCapsule is_backbone_only_cst(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, seqpos : int) -> bool   are the constraints specified at this position  mediated through backbone interactions only? mcfi_list(...) from builtins.PyCapsule mcfi_list(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, block : int) -> protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList mcfi_lists_size(...) from builtins.PyCapsule mcfi_lists_size(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> int num_mcfi_lists(...) from builtins.PyCapsule num_mcfi_lists(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> int ordered_constrained_positions(...) from builtins.PyCapsule ordered_constrained_positions(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long process_pdb_header(...) from builtins.PyCapsule process_pdb_header(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, accept_missing_blocks : bool) -> NoneType read_enzyme_cstfile(...) from builtins.PyCapsule read_enzyme_cstfile(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, fname : str) -> NoneType remap_resid(...) from builtins.PyCapsule remap_resid(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, smap : rosetta.core.id.SequenceMapping) -> NoneType   changing the constrained residues if the sequence length changes remove_constraints_from_pose(...) from builtins.PyCapsule remove_constraints_from_pose(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, keep_covalent : bool, fail_on_constraints_missing : bool) -> NoneType remove_constraints_from_pose_for_block(...) from builtins.PyCapsule remove_constraints_from_pose_for_block(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, cst_block : int, fail_on_constraints_missing : bool) -> NoneType remove_position_from_template_res(...) from builtins.PyCapsule remove_position_from_template_res(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, pos : int) -> NoneType remove_position_from_template_res_for_block(...) from builtins.PyCapsule remove_position_from_template_res_for_block(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, pos : int, cst_block : int) -> NoneType set_external_position_for_resA_in_parameter_block(...) from builtins.PyCapsule set_external_position_for_resA_in_parameter_block(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, cst_block : int, respos : int) -> NoneType set_external_position_for_resB_in_parameter_block(...) from builtins.PyCapsule set_external_position_for_resB_in_parameter_block(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, cst_block : int, respos : int) -> NoneType set_position_for_missing_res_in_parameter_block(...) from builtins.PyCapsule set_position_for_missing_res_in_parameter_block(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, cst_block : int, respos : int) -> NoneType show_cst_definitions(...) from builtins.PyCapsule show_cst_definitions(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> NoneType target_downstream_res(...) from builtins.PyCapsule target_downstream_res(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t update_pdb_remarks_for_backbone_params(...) from builtins.PyCapsule update_pdb_remarks_for_backbone_params(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose) -> NoneType   class RemodelGlobalFrame(rosetta.protocols.moves.Mover)       Method resolution order: RemodelGlobalFrame 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, remodel_data : rosetta.protocols.forge.remodel.RemodelData, working_model : rosetta.protocols.forge.remodel.RemodelWorkingSet, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType   3. __init__(self : handle, segment_size : int) -> NoneType   4. __init__(handle, rosetta.protocols.forge.remodel.RemodelGlobalFrame) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. align_segment(...) from builtins.PyCapsule align_segment(self : rosetta.protocols.forge.remodel.RemodelGlobalFrame, pose : rosetta.core.pose.Pose) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.forge.remodel.RemodelGlobalFrame, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.forge.remodel.RemodelGlobalFrame,  : rosetta.protocols.forge.remodel.RemodelGlobalFrame) -> rosetta.protocols.forge.remodel.RemodelGlobalFrame clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.remodel.RemodelGlobalFrame) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.forge.remodel.RemodelGlobalFrame) -> rosetta.protocols.moves.Mover get_helical_params(...) from builtins.PyCapsule get_helical_params(self : rosetta.protocols.forge.remodel.RemodelGlobalFrame, pose : rosetta.core.pose.Pose) -> NoneType get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.forge.remodel.RemodelGlobalFrame) -> str identity_matrix(...) from builtins.PyCapsule identity_matrix(self : rosetta.protocols.forge.remodel.RemodelGlobalFrame, R : rosetta.numeric.xyzMatrix_double_t) -> NoneType omega(...) from builtins.PyCapsule omega(rosetta.protocols.forge.remodel.RemodelGlobalFrame) -> float radius(...) from builtins.PyCapsule radius(rosetta.protocols.forge.remodel.RemodelGlobalFrame) -> float restore_original_cst(...) from builtins.PyCapsule restore_original_cst(self : rosetta.protocols.forge.remodel.RemodelGlobalFrame, pose : rosetta.core.pose.Pose) -> NoneType rise(...) from builtins.PyCapsule rise(rosetta.protocols.forge.remodel.RemodelGlobalFrame) -> float scorefunction(...) from builtins.PyCapsule scorefunction(self : rosetta.protocols.forge.remodel.RemodelGlobalFrame, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_native_cst_set(...) from builtins.PyCapsule set_native_cst_set(*args, **kwargs) Overloaded function.   1. set_native_cst_set(self : rosetta.protocols.forge.remodel.RemodelGlobalFrame, cst_set : rosetta.core.scoring.constraints.ConstraintSet) -> NoneType   2. set_native_cst_set(self : rosetta.protocols.forge.remodel.RemodelGlobalFrame, pose : rosetta.core.pose.Pose) -> NoneType set_segment_size(...) from builtins.PyCapsule set_segment_size(self : rosetta.protocols.forge.remodel.RemodelGlobalFrame, segment_size : int) -> NoneType setup_CM_helical_constraint(...) from builtins.PyCapsule setup_CM_helical_constraint(self : rosetta.protocols.forge.remodel.RemodelGlobalFrame, pose : rosetta.core.pose.Pose) -> NoneType setup_helical_constraint(...) from builtins.PyCapsule setup_helical_constraint(self : rosetta.protocols.forge.remodel.RemodelGlobalFrame, pose : rosetta.core.pose.Pose) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class RemodelLigandHandler(rosetta.protocols.moves.Mover)       Method resolution order: RemodelLigandHandler 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.forge.remodel.RemodelLigandHandler) -> 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.forge.remodel.RemodelLigandHandler, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.forge.remodel.RemodelLigandHandler,  : rosetta.protocols.forge.remodel.RemodelLigandHandler) -> rosetta.protocols.forge.remodel.RemodelLigandHandler clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.remodel.RemodelLigandHandler) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.forge.remodel.RemodelLigandHandler) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.forge.remodel.RemodelLigandHandler) -> str minimize(...) from builtins.PyCapsule minimize(self : rosetta.protocols.forge.remodel.RemodelLigandHandler, pose : rosetta.core.pose.Pose) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class RemodelLoopMover(rosetta.protocols.moves.Mover)     Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++.     Method resolution order: RemodelLoopMover rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, loops : rosetta.protocols.loops.Loops) -> NoneType   3. __init__(handle, rosetta.protocols.forge.remodel.RemodelLoopMover) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_fragments(...) from builtins.PyCapsule add_fragments(self : rosetta.protocols.forge.remodel.RemodelLoopMover, fragset : rosetta.core.fragment.FragSet) -> NoneType   add a fragment set add_loop(...) from builtins.PyCapsule add_loop(self : rosetta.protocols.forge.remodel.RemodelLoopMover, loop : rosetta.protocols.loops.Loop) -> NoneType   add a loop to model allowed_closure_attempts(...) from builtins.PyCapsule allowed_closure_attempts(*args, **kwargs) Overloaded function.   1. allowed_closure_attempts(rosetta.protocols.forge.remodel.RemodelLoopMover) -> int   the allowed number of overall closure attempts before apply() exits   (default 3)   2. allowed_closure_attempts(self : rosetta.protocols.forge.remodel.RemodelLoopMover, attempts : int) -> NoneType   the allowed number of overall closure attempts before apply() exits apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.forge.remodel.RemodelLoopMover, pose : rosetta.core.pose.Pose) -> NoneType   apply defined moves to given Pose      Sets protocols::moves::MS_SUCCESS upon successful closure of   all loops, otherwise sets protocols::moves::FAIL_RETRY. boost_closure_cycles(...) from builtins.PyCapsule boost_closure_cycles(*args, **kwargs) Overloaded function.   1. boost_closure_cycles(rosetta.protocols.forge.remodel.RemodelLoopMover) -> int   the maximum number of possible lockdown closure cycles to perform   (default 30)   2. boost_closure_cycles(self : rosetta.protocols.forge.remodel.RemodelLoopMover, cycles : int) -> NoneType   the maximum number of possible lockdown closure cycles to perform clear_fragments(...) from builtins.PyCapsule clear_fragments(rosetta.protocols.forge.remodel.RemodelLoopMover) -> NoneType   clear all fragment sets clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.remodel.RemodelLoopMover) -> rosetta.protocols.moves.Mover   clone this object false_movemap(...) from builtins.PyCapsule false_movemap(*args, **kwargs) Overloaded function.   1. false_movemap(rosetta.protocols.forge.remodel.RemodelLoopMover) -> rosetta.core.kinematics.MoveMap   get the false movemap      All movemaps are generated with respect to this movemap.   Any explicit False settings within this movemap will be retained in all   descendant movemaps.   2. false_movemap(self : rosetta.protocols.forge.remodel.RemodelLoopMover, movemap : rosetta.core.kinematics.MoveMap) -> NoneType   set the false movemap to use      All movemaps are generated with respect to this movemap.   Any explicit False settings within this movemap will be retained in all   descendant movemaps. fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.forge.remodel.RemodelLoopMover) -> rosetta.protocols.moves.Mover   create this type of object get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.forge.remodel.RemodelLoopMover) -> str independent_cycles(...) from builtins.PyCapsule independent_cycles(*args, **kwargs) Overloaded function.   1. independent_cycles(rosetta.protocols.forge.remodel.RemodelLoopMover) -> int   the number of independent closure cycles to perform (default 8)   2. independent_cycles(self : rosetta.protocols.forge.remodel.RemodelLoopMover, cycles : int) -> NoneType   the number of independent closure cycles to perform loophash_cycles(...) from builtins.PyCapsule loophash_cycles(*args, **kwargs) Overloaded function.   1. loophash_cycles(rosetta.protocols.forge.remodel.RemodelLoopMover) -> int   the number of loophash closure cycles to perform (default 8)   2. loophash_cycles(self : rosetta.protocols.forge.remodel.RemodelLoopMover, cycles : int) -> NoneType   the number of loophash closure cycles to perform loops(...) from builtins.PyCapsule loops(*args, **kwargs) Overloaded function.   1. loops(rosetta.protocols.forge.remodel.RemodelLoopMover) -> rosetta.protocols.loops.Loops   the loops to model   2. loops(self : rosetta.protocols.forge.remodel.RemodelLoopMover, loops : rosetta.protocols.loops.Loops) -> NoneType   set the loops to model max_linear_chainbreak(...) from builtins.PyCapsule max_linear_chainbreak(*args, **kwargs) Overloaded function.   1. max_linear_chainbreak(rosetta.protocols.forge.remodel.RemodelLoopMover) -> float   if linear chainbreak is <= this value, loop is considered closed   (default 0.07)   2. max_linear_chainbreak(self : rosetta.protocols.forge.remodel.RemodelLoopMover, val : float) -> NoneType   if linear chainbreak is <= this value, loop is considered closed randomize_loops(...) from builtins.PyCapsule randomize_loops(*args, **kwargs) Overloaded function.   1. randomize_loops(rosetta.protocols.forge.remodel.RemodelLoopMover) -> bool   randomize loops prior to running main protocol? (default true)   2. randomize_loops(self : rosetta.protocols.forge.remodel.RemodelLoopMover, flag : bool) -> NoneType   randomize loops prior to running main protocol? randomize_stage(...) from builtins.PyCapsule randomize_stage(self : rosetta.protocols.forge.remodel.RemodelLoopMover, pose : rosetta.core.pose.Pose) -> NoneType   randomize loops 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 remodelData(...) from builtins.PyCapsule remodelData(self : rosetta.protocols.forge.remodel.RemodelLoopMover, remodel_data : rosetta.protocols.forge.remodel.RemodelData) -> NoneType   adds the remodel data to thei remodelLoopMover object repeat_generation_with_additional_residue(...) from builtins.PyCapsule repeat_generation_with_additional_residue(self : rosetta.protocols.forge.remodel.RemodelLoopMover, pose : rosetta.core.pose.Pose, repeat_pose : rosetta.core.pose.Pose) -> NoneType repeat_propagation(...) from builtins.PyCapsule repeat_propagation(self : rosetta.protocols.forge.remodel.RemodelLoopMover, pose : rosetta.core.pose.Pose, repeat_pose : rosetta.core.pose.Pose, repeat_number : int) -> NoneType repeat_sync(...) from builtins.PyCapsule repeat_sync(self : rosetta.protocols.forge.remodel.RemodelLoopMover, repeat_pose : rosetta.core.pose.Pose, repeat_number : int) -> NoneType scorefunction(...) from builtins.PyCapsule scorefunction(*args, **kwargs) Overloaded function.   1. scorefunction(rosetta.protocols.forge.remodel.RemodelLoopMover) -> rosetta.core.scoring.ScoreFunction   the ScoreFunction to use during modeling;   2. scorefunction(self : rosetta.protocols.forge.remodel.RemodelLoopMover, sfx : rosetta.core.scoring.ScoreFunction) -> NoneType   the ScoreFunction to use during modeling set_keep_input_foldtree(...) from builtins.PyCapsule set_keep_input_foldtree(self : rosetta.protocols.forge.remodel.RemodelLoopMover, setting : bool) -> NoneType set_param_from_options(...) from builtins.PyCapsule set_param_from_options(rosetta.protocols.forge.remodel.RemodelLoopMover) -> NoneType set_repeat_tail_length(...) from builtins.PyCapsule set_repeat_tail_length(self : rosetta.protocols.forge.remodel.RemodelLoopMover, length : int) -> NoneType set_seal_foldtree(...) from builtins.PyCapsule set_seal_foldtree(self : rosetta.protocols.forge.remodel.RemodelLoopMover, setting : bool) -> NoneType set_user_provided_movers(...) from builtins.PyCapsule set_user_provided_movers(self : rosetta.protocols.forge.remodel.RemodelLoopMover, movers : rosetta.utility.vector1_std_shared_ptr_protocols_moves_Mover_t) -> NoneType simultaneous_cycles(...) from builtins.PyCapsule simultaneous_cycles(*args, **kwargs) Overloaded function.   1. simultaneous_cycles(rosetta.protocols.forge.remodel.RemodelLoopMover) -> int   the number of simultaneous closure cycles to perform (default 2)   2. simultaneous_cycles(self : rosetta.protocols.forge.remodel.RemodelLoopMover, cycles : int) -> NoneType   the number of simultaneous closure cycles to perform temperature(...) from builtins.PyCapsule temperature(*args, **kwargs) Overloaded function.   1. temperature(rosetta.protocols.forge.remodel.RemodelLoopMover) -> float   temperature for mc ( default 2.0 )   2. temperature(self : rosetta.protocols.forge.remodel.RemodelLoopMover, temp : float) -> NoneType   temperature for mc total_standard_cycles(...) from builtins.PyCapsule total_standard_cycles(rosetta.protocols.forge.remodel.RemodelLoopMover) -> int   the total number of "standard" (equal to simul + independent)   to perform user_provided_movers_apply_cycle(...) from builtins.PyCapsule user_provided_movers_apply_cycle(self : rosetta.protocols.forge.remodel.RemodelLoopMover, cycle : int) -> NoneType 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 create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. 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 RemodelMover(rosetta.protocols.moves.Mover)       Method resolution order: RemodelMover 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.forge.remodel.RemodelMover) -> 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.forge.remodel.RemodelMover, pose : rosetta.core.pose.Pose) -> NoneType   apply defined moves to given Pose centroid_loop_mover_str(...) from builtins.PyCapsule centroid_loop_mover_str(self : rosetta.protocols.forge.remodel.RemodelMover, loop_mover_str : str) -> NoneType   the loop mover string to use during centroid build      set to either a string the create_loop_mover() LoopMoverFactory   recognizes or the "RemodelLoopMover" centroid_scorefunction(...) from builtins.PyCapsule centroid_scorefunction(*args, **kwargs) Overloaded function.   1. centroid_scorefunction(rosetta.protocols.forge.remodel.RemodelMover) -> rosetta.core.scoring.ScoreFunction   the centroid level score function, default "remodel_cen"   2. centroid_scorefunction(self : rosetta.protocols.forge.remodel.RemodelMover, sfx : rosetta.core.scoring.ScoreFunction) -> NoneType   set the centroid level score function   3. centroid_scorefunction(self : rosetta.protocols.forge.remodel.RemodelMover, sfx : rosetta.core.scoring.ScoreFunction) -> NoneType   set the centroid level score function clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.remodel.RemodelMover) -> rosetta.protocols.moves.Mover   clone this object confirm_sequence(...) from builtins.PyCapsule confirm_sequence(self : rosetta.protocols.forge.remodel.RemodelMover, pose : rosetta.core.pose.Pose) -> bool dr_cycles(...) from builtins.PyCapsule dr_cycles(self : rosetta.protocols.forge.remodel.RemodelMover, cycles : int) -> NoneType   set the number of design-refine cycles to perform      set this to 0 to skip design-refine fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.forge.remodel.RemodelMover) -> rosetta.protocols.moves.Mover   create this type of object fullatom_scorefunction(...) from builtins.PyCapsule fullatom_scorefunction(*args, **kwargs) Overloaded function.   1. fullatom_scorefunction(rosetta.protocols.forge.remodel.RemodelMover) -> rosetta.core.scoring.ScoreFunction   the full-atom level score function   2. fullatom_scorefunction(self : rosetta.protocols.forge.remodel.RemodelMover, sfx : rosetta.core.scoring.ScoreFunction) -> NoneType   set the full-atom level score function   3. fullatom_scorefunction(self : rosetta.protocols.forge.remodel.RemodelMover, sfx : rosetta.core.scoring.ScoreFunction) -> NoneType   set the full-atom level score function get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.forge.remodel.RemodelMover) -> str loops_buns_polar_calc_name(...) from builtins.PyCapsule loops_buns_polar_calc_name() -> str   the name for the loops' buried unsatisfied polars   calculator max_linear_chainbreak(...) from builtins.PyCapsule max_linear_chainbreak(self : rosetta.protocols.forge.remodel.RemodelMover, threshold : float) -> NoneType   the maximum allowed linear chainbreak neighborhood_buns_polar_calc_name(...) from builtins.PyCapsule neighborhood_buns_polar_calc_name() -> str   the name for the loops' neighborhood buried unsatisfied polars   calculator neighborhood_calc_name(...) from builtins.PyCapsule neighborhood_calc_name() -> str   the name for the loops' neighborhood calculator redesign_loop_neighborhood(...) from builtins.PyCapsule redesign_loop_neighborhood(self : rosetta.protocols.forge.remodel.RemodelMover, flag : bool) -> NoneType   redesign the neighborhood around the loop?  if false, then just   repacks during the design phase 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 create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class RemodelMoverCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: RemodelMoverCreator rosetta.protocols.moves.MoverCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.forge.remodel.RemodelMoverCreator,  : rosetta.protocols.forge.remodel.RemodelMoverCreator) -> rosetta.protocols.forge.remodel.RemodelMoverCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.forge.remodel.RemodelMoverCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.forge.remodel.RemodelMoverCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class RemodelRotamerLinks(rosetta.core.pack.task.operation.TaskOperation)       Method resolution order: RemodelRotamerLinks rosetta.core.pack.task.operation.TaskOperation builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.forge.remodel.RemodelRotamerLinks, pose : rosetta.core.pose.Pose, ptask : rosetta.core.pack.task.PackerTask) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.forge.remodel.RemodelRotamerLinks,  : rosetta.protocols.forge.remodel.RemodelRotamerLinks) -> rosetta.protocols.forge.remodel.RemodelRotamerLinks clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.remodel.RemodelRotamerLinks) -> rosetta.core.pack.task.operation.TaskOperation keyname(...) from builtins.PyCapsule keyname() -> str parse_tag(...) from builtins.PyCapsule parse_tag(self : rosetta.protocols.forge.remodel.RemodelRotamerLinks,  : rosetta.utility.tag.Tag,  : rosetta.basic.datacache.DataMap) -> NoneType provide_xml_schema(...) from builtins.PyCapsule provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType   class RemodelRotamerLinksCreator(rosetta.core.pack.task.operation.TaskOperationCreator)       Method resolution order: RemodelRotamerLinksCreator rosetta.core.pack.task.operation.TaskOperationCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.forge.remodel.RemodelRotamerLinksCreator,  : rosetta.protocols.forge.remodel.RemodelRotamerLinksCreator) -> rosetta.protocols.forge.remodel.RemodelRotamerLinksCreator create_task_operation(...) from builtins.PyCapsule create_task_operation(rosetta.protocols.forge.remodel.RemodelRotamerLinksCreator) -> rosetta.core.pack.task.operation.TaskOperation keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.forge.remodel.RemodelRotamerLinksCreator) -> str provide_xml_schema(...) from builtins.PyCapsule provide_xml_schema(self : rosetta.protocols.forge.remodel.RemodelRotamerLinksCreator, xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType   class RemodelWorkingSet(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.forge.remodel.RemodelWorkingSet) -> NoneType   2. __init__(self : rosetta.protocols.forge.remodel.RemodelWorkingSet, rval : rosetta.protocols.forge.remodel.RemodelWorkingSet) -> 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.forge.remodel.RemodelWorkingSet, rval : rosetta.protocols.forge.remodel.RemodelWorkingSet) -> rosetta.protocols.forge.remodel.RemodelWorkingSet manualPackerTaskGen(...) from builtins.PyCapsule manualPackerTaskGen(self : rosetta.protocols.forge.remodel.RemodelWorkingSet, built_pose : rosetta.core.pose.Pose, data : rosetta.protocols.forge.remodel.RemodelData) -> NoneType workingSetGen(...) from builtins.PyCapsule workingSetGen(self : rosetta.protocols.forge.remodel.RemodelWorkingSet, input_pose : rosetta.core.pose.Pose, data : rosetta.protocols.forge.remodel.RemodelData) -> NoneType Data descriptors defined here: aa abego begin buildDisulfide copy_begin copy_end design_matrix disulfide_cutpoint disulfide_jump_points disulfide_ss end hasInsertion insertionEndIndex insertionStartIndex loops manager rvjump_pose safe_root_ sequence src_begin src_end ss task translate_index   class ResidueVicinityCstGeneratorCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: ResidueVicinityCstGeneratorCreator rosetta.protocols.moves.MoverCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.forge.remodel.ResidueVicinityCstGeneratorCreator,  : rosetta.protocols.forge.remodel.ResidueVicinityCstGeneratorCreator) -> rosetta.protocols.forge.remodel.ResidueVicinityCstGeneratorCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.forge.remodel.ResidueVicinityCstGeneratorCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.forge.remodel.ResidueVicinityCstGeneratorCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class ResidueVicinityInfo(builtins.object)     small helper class for the ResidueVicinityRCG     Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.protocols.forge.remodel.ResidueVicinityInfo, old_seqpos : int, residue_atoms : rosetta.utility.vector1_unsigned_long, loopres_atoms : rosetta.utility.vector1_unsigned_long, desired_remodelres_in_vicinity : int) -> 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.forge.remodel.ResidueVicinityInfo,  : rosetta.protocols.forge.remodel.ResidueVicinityInfo) -> rosetta.protocols.forge.remodel.ResidueVicinityInfo desired_remodelres_in_vicinity(...) from builtins.PyCapsule desired_remodelres_in_vicinity(rosetta.protocols.forge.remodel.ResidueVicinityInfo) -> int dis(...) from builtins.PyCapsule dis(rosetta.protocols.forge.remodel.ResidueVicinityInfo) -> rosetta.core.scoring.func.Func loop_ang(...) from builtins.PyCapsule loop_ang(rosetta.protocols.forge.remodel.ResidueVicinityInfo) -> rosetta.core.scoring.func.Func loop_dih(...) from builtins.PyCapsule loop_dih(rosetta.protocols.forge.remodel.ResidueVicinityInfo) -> rosetta.core.scoring.func.Func loopres_atoms(...) from builtins.PyCapsule loopres_atoms(rosetta.protocols.forge.remodel.ResidueVicinityInfo) -> rosetta.utility.vector1_unsigned_long loopres_base2_atoms(...) from builtins.PyCapsule loopres_base2_atoms(rosetta.protocols.forge.remodel.ResidueVicinityInfo) -> rosetta.utility.vector1_unsigned_long loopres_base_atoms(...) from builtins.PyCapsule loopres_base_atoms(rosetta.protocols.forge.remodel.ResidueVicinityInfo) -> rosetta.utility.vector1_unsigned_long lt_dih(...) from builtins.PyCapsule lt_dih(rosetta.protocols.forge.remodel.ResidueVicinityInfo) -> rosetta.core.scoring.func.Func old_seqpos(...) from builtins.PyCapsule old_seqpos(rosetta.protocols.forge.remodel.ResidueVicinityInfo) -> int residue_atoms(...) from builtins.PyCapsule residue_atoms(rosetta.protocols.forge.remodel.ResidueVicinityInfo) -> rosetta.utility.vector1_unsigned_long residue_base2_atoms(...) from builtins.PyCapsule residue_base2_atoms(rosetta.protocols.forge.remodel.ResidueVicinityInfo) -> rosetta.utility.vector1_unsigned_long residue_base_atoms(...) from builtins.PyCapsule residue_base_atoms(rosetta.protocols.forge.remodel.ResidueVicinityInfo) -> rosetta.utility.vector1_unsigned_long set_dis(...) from builtins.PyCapsule set_dis(self : rosetta.protocols.forge.remodel.ResidueVicinityInfo, dis : rosetta.core.scoring.func.Func) -> NoneType set_loop_ang(...) from builtins.PyCapsule set_loop_ang(self : rosetta.protocols.forge.remodel.ResidueVicinityInfo, loop_ang : rosetta.core.scoring.func.Func) -> NoneType set_loop_dih(...) from builtins.PyCapsule set_loop_dih(self : rosetta.protocols.forge.remodel.ResidueVicinityInfo, loop_dih : rosetta.core.scoring.func.Func) -> NoneType set_loopres_base2_atoms(...) from builtins.PyCapsule set_loopres_base2_atoms(self : rosetta.protocols.forge.remodel.ResidueVicinityInfo, loopres_base2_atoms : rosetta.utility.vector1_unsigned_long) -> NoneType set_loopres_base_atoms(...) from builtins.PyCapsule set_loopres_base_atoms(self : rosetta.protocols.forge.remodel.ResidueVicinityInfo, loopres_base_atoms : rosetta.utility.vector1_unsigned_long) -> NoneType set_lt_dih(...) from builtins.PyCapsule set_lt_dih(self : rosetta.protocols.forge.remodel.ResidueVicinityInfo, lt_dih : rosetta.core.scoring.func.Func) -> NoneType set_residue_base2_atoms(...) from builtins.PyCapsule set_residue_base2_atoms(self : rosetta.protocols.forge.remodel.ResidueVicinityInfo, residue_base2_atoms : rosetta.utility.vector1_unsigned_long) -> NoneType set_residue_base_atoms(...) from builtins.PyCapsule set_residue_base_atoms(self : rosetta.protocols.forge.remodel.ResidueVicinityInfo, residue_base_atoms : rosetta.utility.vector1_unsigned_long) -> NoneType set_targ_ang(...) from builtins.PyCapsule set_targ_ang(self : rosetta.protocols.forge.remodel.ResidueVicinityInfo, targ_ang : rosetta.core.scoring.func.Func) -> NoneType set_targ_dih(...) from builtins.PyCapsule set_targ_dih(self : rosetta.protocols.forge.remodel.ResidueVicinityInfo, targ_dih : rosetta.core.scoring.func.Func) -> NoneType targ_ang(...) from builtins.PyCapsule targ_ang(rosetta.protocols.forge.remodel.ResidueVicinityInfo) -> rosetta.core.scoring.func.Func targ_dih(...) from builtins.PyCapsule targ_dih(rosetta.protocols.forge.remodel.ResidueVicinityInfo) -> rosetta.core.scoring.func.Func   class ResidueVicinityRCG(RemodelConstraintGenerator)     a RemodelConstraintGenerator that creates AmbiguousMultiConstraints for all positions     in the remodeled loop to the desired positions, such that during remodeling, the remodeled     region will be driven towards the vicinity of these residues     Method resolution order: ResidueVicinityRCG RemodelConstraintGenerator 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.forge.remodel.ResidueVicinityRCG) -> NoneType   3. __init__(self : handle, lstart : int, lstop : int, rv_infos : rosetta.utility.vector1_std_shared_ptr_protocols_forge_remodel_ResidueVicinityInfo_t) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_rv_info(...) from builtins.PyCapsule add_rv_info(self : rosetta.protocols.forge.remodel.ResidueVicinityRCG, rv_info : rosetta.protocols.forge.remodel.ResidueVicinityInfo) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.forge.remodel.ResidueVicinityRCG,  : rosetta.protocols.forge.remodel.ResidueVicinityRCG) -> rosetta.protocols.forge.remodel.ResidueVicinityRCG clear_rv_infos(...) from builtins.PyCapsule clear_rv_infos(rosetta.protocols.forge.remodel.ResidueVicinityRCG) -> NoneType clone(...) from builtins.PyCapsule clone(rosetta.protocols.forge.remodel.ResidueVicinityRCG) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.forge.remodel.ResidueVicinityRCG) -> rosetta.protocols.moves.Mover generate_remodel_constraints(...) from builtins.PyCapsule generate_remodel_constraints(self : rosetta.protocols.forge.remodel.ResidueVicinityRCG, pose : rosetta.core.pose.Pose) -> NoneType get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.forge.remodel.ResidueVicinityRCG) -> str lstart(...) from builtins.PyCapsule lstart(self : rosetta.protocols.forge.remodel.ResidueVicinityRCG, lstart : int) -> NoneType lstop(...) from builtins.PyCapsule lstop(self : rosetta.protocols.forge.remodel.ResidueVicinityRCG, lstop : int) -> NoneType set_rv_infos(...) from builtins.PyCapsule set_rv_infos(self : rosetta.protocols.forge.remodel.ResidueVicinityRCG, rv_infos : rosetta.utility.vector1_std_shared_ptr_protocols_forge_remodel_ResidueVicinityInfo_t) -> NoneType Methods inherited from RemodelConstraintGenerator: add_remodel_constraints_to_pose(...) from builtins.PyCapsule add_remodel_constraints_to_pose(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator, pose : rosetta.core.pose.Pose) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator, pose : rosetta.core.pose.Pose) -> NoneType   generates constraints and adds them to the pose constraints(...) from builtins.PyCapsule constraints(rosetta.protocols.forge.remodel.RemodelConstraintGenerator) -> rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t id(...) from builtins.PyCapsule id(rosetta.protocols.forge.remodel.RemodelConstraintGenerator) -> str init(...) from builtins.PyCapsule init(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator,  : rosetta.core.pose.Pose) -> NoneType   Pose-specific setup routines go here lookup_stored_constraints(...) from builtins.PyCapsule lookup_stored_constraints(id : str) -> rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t remove_remodel_constraints_from_pose(...) from builtins.PyCapsule remove_remodel_constraints_from_pose(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator, pose : rosetta.core.pose.Pose) -> NoneType seqmap(...) from builtins.PyCapsule seqmap(rosetta.protocols.forge.remodel.RemodelConstraintGenerator) -> rosetta.core.id.SequenceMapping set_id(...) from builtins.PyCapsule set_id(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator, id : str) -> NoneType set_seqmap(...) from builtins.PyCapsule set_seqmap(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator, seqmap : rosetta.core.id.SequenceMapping) -> NoneType set_vlb(...) from builtins.PyCapsule set_vlb(self : rosetta.protocols.forge.remodel.RemodelConstraintGenerator, vlb : rosetta.std.weak_ptr_protocols_forge_components_VarLengthBuild_t) -> NoneType vlb(...) from builtins.PyCapsule vlb(rosetta.protocols.forge.remodel.RemodelConstraintGenerator) -> rosetta.std.weak_ptr_protocols_forge_components_VarLengthBuild_t Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class Segment(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.forge.remodel.Segment) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Data descriptors defined here: residues