Bindings for protocols::sewing namespace

Modules
		rosetta.protocols.sewing.sampling rosetta.protocols.sewing.scoring

Classes
		builtins.object Assembly ContinuousAssembly DisembodiedAssembly AssemblyFactory Basis HashResult HashValue Hasher Model SewAtom SewResidue SewSegment move_type rosetta.core.graph.Edge(builtins.object) HashEdge rosetta.core.graph.Graph(builtins.object) SewGraph rosetta.core.graph.Node(builtins.object) ModelNode rosetta.core.pack.task.operation.TaskOperation(builtins.object) ReadNativeRotamersFile ReadRepeatNativeRotamersFile rosetta.core.pack.task.operation.TaskOperationCreator(builtins.object) ReadNativeRotamersFileCreator ReadRepeatNativeRotamersFileCreator rosetta.protocols.moves.Mover(builtins.object) AddStartnodeFragments AssemblyConstraintsMover AssemblyMover EnumerateAssemblyMover GivenPathAssemblyMover GreedyAssemblyMover MonteCarloAssemblyMover AppendAssemblyMover RepeatAssemblyMover rosetta.protocols.moves.MoverCreator(builtins.object) AddStartnodeFragmentsCreator AppendAssemblyMoverCreator AssemblyConstraintsMoverCreator EnumerateAssemblyMoverCreator GivenPathAssemblyMoverCreator GreedyAssemblyMoverCreator MonteCarloAssemblyMoverCreator RepeatAssemblyMoverCreator rosetta.std.binary_function_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_bool_t(builtins.object) basis_pair_equal_to rosetta.std.binary_function_utility_fixedsizearray1_int_3_utility_fixedsizearray1_int_3_bool_t(builtins.object) coord_equal_to rosetta.std.unary_function_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_unsigned_long_t(builtins.object) basis_pair_hash rosetta.std.unary_function_utility_fixedsizearray1_int_3_unsigned_long_t(builtins.object) coord_hash rosetta.utility.vector1_protocols_sewing_SewSegment(builtins.object) SegmentGraph   class AddStartnodeFragments(rosetta.protocols.moves.Mover)       Method resolution order: AddStartnodeFragments 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.sewing.AddStartnodeFragments) -> 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.sewing.AddStartnodeFragments, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.sewing.AddStartnodeFragments,  : rosetta.protocols.sewing.AddStartnodeFragments) -> rosetta.protocols.sewing.AddStartnodeFragments clone(...) from builtins.PyCapsule clone(rosetta.protocols.sewing.AddStartnodeFragments) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.sewing.AddStartnodeFragments) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.sewing.AddStartnodeFragments) -> str Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply 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 AddStartnodeFragmentsCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: AddStartnodeFragmentsCreator 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.sewing.AddStartnodeFragmentsCreator,  : rosetta.protocols.sewing.AddStartnodeFragmentsCreator) -> rosetta.protocols.sewing.AddStartnodeFragmentsCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.sewing.AddStartnodeFragmentsCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.sewing.AddStartnodeFragmentsCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class AppendAssemblyMover(MonteCarloAssemblyMover)       Method resolution order: AppendAssemblyMover MonteCarloAssemblyMover AssemblyMover 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.sewing.AppendAssemblyMover) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_starting_model(...) from builtins.PyCapsule add_starting_model(self : rosetta.protocols.sewing.AppendAssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> NoneType   The starting node for the Assembly from the append mover will always be the input PDB apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.sewing.AppendAssemblyMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.sewing.AppendAssemblyMover,  : rosetta.protocols.sewing.AppendAssemblyMover) -> rosetta.protocols.sewing.AppendAssemblyMover clone(...) from builtins.PyCapsule clone(rosetta.protocols.sewing.AppendAssemblyMover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.sewing.AppendAssemblyMover) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.sewing.AppendAssemblyMover) -> str hash_pdb_model(...) from builtins.PyCapsule hash_pdb_model(self : rosetta.protocols.sewing.AppendAssemblyMover, pdb_model : rosetta.protocols.sewing.Model) -> NoneType refine_assembly(...) from builtins.PyCapsule refine_assembly(self : rosetta.protocols.sewing.AppendAssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose Methods inherited from MonteCarloAssemblyMover: generate_assembly(...) from builtins.PyCapsule generate_assembly(rosetta.protocols.sewing.MonteCarloAssemblyMover) -> rosetta.protocols.sewing.Assembly Methods inherited from AssemblyMover: append_movie_frame(...) from builtins.PyCapsule append_movie_frame(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, cycle : int) -> NoneType follow_random_edge_from_node(...) from builtins.PyCapsule follow_random_edge_from_node(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, reference_node : rosetta.protocols.sewing.ModelNode) -> bool get_centroid_pose(...) from builtins.PyCapsule get_centroid_pose(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose get_fullatom_pose(...) from builtins.PyCapsule get_fullatom_pose(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose output_stats(...) from builtins.PyCapsule output_stats(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose, indicator_whether_from_MonteCarloAssemblyMover_or_ExhaustiveAssemblyMover : str) -> NoneType   add several outputs to the score file Pose can't be const due to scoring. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.sewing.AssemblyMover) -> bool Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply 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. 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 AppendAssemblyMoverCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: AppendAssemblyMoverCreator 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.sewing.AppendAssemblyMoverCreator,  : rosetta.protocols.sewing.AppendAssemblyMoverCreator) -> rosetta.protocols.sewing.AppendAssemblyMoverCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.sewing.AppendAssemblyMoverCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.sewing.AppendAssemblyMoverCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class Assembly(builtins.object)     An Assembly is a collection of SewSegments. Assemblies are created using the geometric "compatibility" data generated by the Hasher.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.sewing.Assembly) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.sewing.Assembly) -> str add_loop_segment(...) from builtins.PyCapsule add_loop_segment(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop, segment : int) -> NoneType add_model(...) from builtins.PyCapsule add_model(*args, **kwargs) Overloaded function.   1. add_model(self : rosetta.protocols.sewing.Assembly, graph : rosetta.protocols.sewing.SewGraph, model : rosetta.protocols.sewing.Model) -> NoneType   Add a model to the Assembly. Only used for first node and special cases.   2. add_model(self : rosetta.protocols.sewing.Assembly, graph : rosetta.protocols.sewing.SewGraph, model : rosetta.protocols.sewing.Model, available : bool) -> NoneType   Add a model to the Assembly. Only used for first node and special cases. align_model(...) from builtins.PyCapsule align_model(self : rosetta.protocols.sewing.Assembly, mobile_model : rosetta.protocols.sewing.Model, atom_alignments : rosetta.std.map_core_id_AtomID_core_id_AtomID, reference_model_id : int) -> NoneType all_segments(...) from builtins.PyCapsule all_segments(rosetta.protocols.sewing.Assembly) -> rosetta.utility.vector1_utility_vector1_protocols_sewing_SewSegment_std_allocator_protocols_sewing_SewSegment_t append_model(...) from builtins.PyCapsule append_model(self : rosetta.protocols.sewing.Assembly, model : rosetta.protocols.sewing.Model, edge_score : ((rosetta.protocols.sewing.Basis, rosetta.protocols.sewing.Basis), rosetta.protocols.sewing.HashResult)) -> NoneType   append the given model to the end of the assembly append_segments(...) from builtins.PyCapsule append_segments(self : rosetta.protocols.sewing.Assembly, segments : rosetta.utility.vector1_protocols_sewing_SewSegment) -> NoneType   append the segments to the given assembly. This should be used very infrequently. The normal way to add segments is to follow an edge assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.sewing.Assembly,  : rosetta.protocols.sewing.Assembly) -> rosetta.protocols.sewing.Assembly atom_map_from_score_result(...) from builtins.PyCapsule atom_map_from_score_result(self : rosetta.protocols.sewing.Assembly, alignment_scores : ((rosetta.protocols.sewing.Basis, rosetta.protocols.sewing.Basis), rosetta.protocols.sewing.HashResult)) -> rosetta.std.map_core_id_AtomID_core_id_AtomID clone(...) from builtins.PyCapsule clone(rosetta.protocols.sewing.Assembly) -> rosetta.protocols.sewing.Assembly create_chimera_segment(...) from builtins.PyCapsule create_chimera_segment(self : rosetta.protocols.sewing.Assembly, reference_segment : rosetta.protocols.sewing.SewSegment, mobile_segment : rosetta.protocols.sewing.SewSegment, atom_map : rosetta.std.map_core_id_AtomID_core_id_AtomID, reference_is_nter : bool) -> rosetta.protocols.sewing.SewSegment delete_segments(...) from builtins.PyCapsule delete_segments(self : rosetta.protocols.sewing.Assembly, seg_index : int) -> NoneType   delete segments at the given index. This should be used very infrequently disconnected_segments(...) from builtins.PyCapsule disconnected_segments(rosetta.protocols.sewing.Assembly) -> rosetta.utility.vector1_unsigned_long ending_node(...) from builtins.PyCapsule ending_node(rosetta.protocols.sewing.Assembly) -> rosetta.protocols.sewing.ModelNode find_possible_orders(...) from builtins.PyCapsule find_possible_orders(self : rosetta.protocols.sewing.Assembly, max_loop_distance : float) -> rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t follow_edge(...) from builtins.PyCapsule follow_edge(self : rosetta.protocols.sewing.Assembly, graph : rosetta.protocols.sewing.SewGraph, edge : rosetta.protocols.sewing.HashEdge, source_index : int) -> NoneType get_model_segments(...) from builtins.PyCapsule get_model_segments(self : rosetta.protocols.sewing.Assembly, model_id : int) -> rosetta.utility.vector1_protocols_sewing_SewSegment get_next_reference_node(...) from builtins.PyCapsule get_next_reference_node(self : rosetta.protocols.sewing.Assembly, graph : rosetta.protocols.sewing.SewGraph) -> int   Pick which model to use as the reference model for the next node additon get_partner(...) from builtins.PyCapsule get_partner(rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose get_score_result(...) from builtins.PyCapsule get_score_result(self : rosetta.protocols.sewing.Assembly, model_1_node : rosetta.protocols.sewing.ModelNode, cur_edge : rosetta.protocols.sewing.HashEdge, graph : rosetta.protocols.sewing.SewGraph) -> ((rosetta.protocols.sewing.Basis, rosetta.protocols.sewing.Basis), rosetta.protocols.sewing.HashResult) map_residues(...) from builtins.PyCapsule map_residues(self : rosetta.protocols.sewing.Assembly, reference_model_id : int, mobile_model : rosetta.protocols.sewing.Model, atom_alignments : rosetta.std.map_core_id_AtomID_core_id_AtomID) -> NoneType   create mappings between SewResidues in the Assembly that map to the same pose number model_ids(...) from builtins.PyCapsule model_ids(rosetta.protocols.sewing.Assembly) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t native_positions(...) from builtins.PyCapsule native_positions(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t natives_select(...) from builtins.PyCapsule natives_select(*args, **kwargs) Overloaded function.   1. natives_select(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose) -> str   print pymol selection of "native" positions   2. natives_select(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose, object_name : str) -> str   print pymol selection of "native" positions path(...) from builtins.PyCapsule path(rosetta.protocols.sewing.Assembly) -> rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t percent_native(...) from builtins.PyCapsule percent_native(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose) -> float   count the amount of 'native' residues retained in the pose pose_loop_anchors(...) from builtins.PyCapsule pose_loop_anchors(rosetta.protocols.sewing.Assembly) -> rosetta.utility.vector1_unsigned_long pose_num(...) from builtins.PyCapsule pose_num(self : rosetta.protocols.sewing.Assembly, model_id : int, resnum : int) -> int prepare_for_packing(...) from builtins.PyCapsule prepare_for_packing(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose, task_factory : rosetta.core.pack.task.TaskFactory, base_native_bonus : float, neighbor_cutoff : int) -> NoneType   Update the task factory such that the 'native' rotamers are added to the rotamer set, and the native residues are favored regenerate_model(...) from builtins.PyCapsule regenerate_model(self : rosetta.protocols.sewing.Assembly, model_id : int) -> rosetta.protocols.sewing.Model reorder(...) from builtins.PyCapsule reorder(self : rosetta.protocols.sewing.Assembly, new_order : rosetta.utility.vector1_unsigned_long) -> NoneType reorder_randomly(...) from builtins.PyCapsule reorder_randomly(self : rosetta.protocols.sewing.Assembly, max_loop_distance : float) -> bool   reorder segments in a random fashion that satisfies the maximum loop distance cutoff If this is not possible then return false, otherwise true segments(...) from builtins.PyCapsule segments(rosetta.protocols.sewing.Assembly) -> rosetta.utility.vector1_protocols_sewing_SewSegment set_partner(...) from builtins.PyCapsule set_partner(self : rosetta.protocols.sewing.Assembly, partner_pose : rosetta.core.pose.Pose) -> NoneType starting_node(...) from builtins.PyCapsule starting_node(rosetta.protocols.sewing.Assembly) -> rosetta.protocols.sewing.ModelNode string_blosum(...) from builtins.PyCapsule string_blosum(self : rosetta.protocols.sewing.Assembly, blosum_history : rosetta.utility.vector1_std_pair_double_unsigned_long_t) -> str string_path(...) from builtins.PyCapsule string_path(rosetta.protocols.sewing.Assembly) -> str to_multichain_pose(...) from builtins.PyCapsule to_multichain_pose(self : rosetta.protocols.sewing.Assembly, residue_type_set : str) -> rosetta.core.pose.Pose to_pose(...) from builtins.PyCapsule to_pose(*args, **kwargs) Overloaded function.   1. to_pose(self : rosetta.protocols.sewing.Assembly, residue_type_set : str) -> rosetta.core.pose.Pose   2. to_pose(self : rosetta.protocols.sewing.Assembly, residue_type_set : str, create_cuts : bool) -> rosetta.core.pose.Pose total_residue(...) from builtins.PyCapsule total_residue(rosetta.protocols.sewing.Assembly) -> int update_coords_from_pose(...) from builtins.PyCapsule update_coords_from_pose(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose) -> NoneType Data descriptors defined here: blosum_history_   class AssemblyConstraintsMover(rosetta.protocols.moves.Mover)     ///////////AssemblyConstraintsMover/////////////////     Method resolution order: AssemblyConstraintsMover 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.sewing.AssemblyConstraintsMover) -> 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.sewing.AssemblyConstraintsMover, pose : rosetta.core.pose.Pose) -> NoneType apply_repeat(...) from builtins.PyCapsule apply_repeat(self : rosetta.protocols.sewing.AssemblyConstraintsMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.sewing.AssemblyConstraintsMover,  : rosetta.protocols.sewing.AssemblyConstraintsMover) -> rosetta.protocols.sewing.AssemblyConstraintsMover base_native_bonus(...) from builtins.PyCapsule base_native_bonus(self : rosetta.protocols.sewing.AssemblyConstraintsMover, base_native_bonus : float) -> NoneType clone(...) from builtins.PyCapsule clone(rosetta.protocols.sewing.AssemblyConstraintsMover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.sewing.AssemblyConstraintsMover) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.sewing.AssemblyConstraintsMover) -> str neighbor_cutoff(...) from builtins.PyCapsule neighbor_cutoff(self : rosetta.protocols.sewing.AssemblyConstraintsMover, neighbor_cutoff : float) -> 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 AssemblyConstraintsMoverCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: AssemblyConstraintsMoverCreator 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.sewing.AssemblyConstraintsMoverCreator,  : rosetta.protocols.sewing.AssemblyConstraintsMoverCreator) -> rosetta.protocols.sewing.AssemblyConstraintsMoverCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.sewing.AssemblyConstraintsMoverCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.sewing.AssemblyConstraintsMoverCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class AssemblyFactory(builtins.object)     An Assembly is a collection of SewSegments. Assemblies are created using the geometric "compatibility" data generated by the Hasher.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.sewing.AssemblyFactory) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. create_assembly(...) from builtins.PyCapsule create_assembly(assembly_name : str) -> rosetta.protocols.sewing.Assembly   class AssemblyMover(rosetta.protocols.moves.Mover)       Method resolution order: AssemblyMover rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.sewing.AssemblyMover) -> NoneType   2. __init__(rosetta.protocols.sewing.AssemblyMover, rosetta.protocols.sewing.AssemblyMover) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_starting_model(...) from builtins.PyCapsule add_starting_model(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> NoneType append_movie_frame(...) from builtins.PyCapsule append_movie_frame(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, cycle : int) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.sewing.AssemblyMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.sewing.AssemblyMover,  : rosetta.protocols.sewing.AssemblyMover) -> rosetta.protocols.sewing.AssemblyMover follow_random_edge_from_node(...) from builtins.PyCapsule follow_random_edge_from_node(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, reference_node : rosetta.protocols.sewing.ModelNode) -> bool generate_assembly(...) from builtins.PyCapsule generate_assembly(rosetta.protocols.sewing.AssemblyMover) -> rosetta.protocols.sewing.Assembly get_centroid_pose(...) from builtins.PyCapsule get_centroid_pose(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose get_fullatom_pose(...) from builtins.PyCapsule get_fullatom_pose(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.sewing.AssemblyMover) -> str output_stats(...) from builtins.PyCapsule output_stats(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose, indicator_whether_from_MonteCarloAssemblyMover_or_ExhaustiveAssemblyMover : str) -> NoneType   add several outputs to the score file Pose can't be const due to scoring. refine_assembly(...) from builtins.PyCapsule refine_assembly(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.sewing.AssemblyMover) -> bool Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply clone(...) from builtins.PyCapsule clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Return a clone of the Mover object. create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. 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 Basis(builtins.object)     //////////////////////// HashMap for score results ///////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.sewing.Basis) -> NoneType   2. __init__(self : rosetta.protocols.sewing.Basis, model_id_temp : int, resnum_temp : int) -> NoneType   3. __init__(self : rosetta.protocols.sewing.Basis,  : rosetta.protocols.sewing.Basis) -> 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.sewing.Basis,  : rosetta.protocols.sewing.Basis) -> rosetta.protocols.sewing.Basis Data descriptors defined here: model_id resnum   class ContinuousAssembly(Assembly)     An Assembly is a collection of SewSegments. Assemblies are created using the geometric "compatibility" data generated by the Hasher.     Method resolution order: ContinuousAssembly Assembly 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. append_model(...) from builtins.PyCapsule append_model(self : rosetta.protocols.sewing.ContinuousAssembly, model : rosetta.protocols.sewing.Model, edge_score : ((rosetta.protocols.sewing.Basis, rosetta.protocols.sewing.Basis), rosetta.protocols.sewing.HashResult)) -> NoneType   Needs to be implemented. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.sewing.ContinuousAssembly,  : rosetta.protocols.sewing.ContinuousAssembly) -> rosetta.protocols.sewing.ContinuousAssembly clone(...) from builtins.PyCapsule clone(rosetta.protocols.sewing.ContinuousAssembly) -> rosetta.protocols.sewing.Assembly Methods inherited from Assembly: __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.sewing.Assembly) -> str add_loop_segment(...) from builtins.PyCapsule add_loop_segment(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop, segment : int) -> NoneType add_model(...) from builtins.PyCapsule add_model(*args, **kwargs) Overloaded function.   1. add_model(self : rosetta.protocols.sewing.Assembly, graph : rosetta.protocols.sewing.SewGraph, model : rosetta.protocols.sewing.Model) -> NoneType   Add a model to the Assembly. Only used for first node and special cases.   2. add_model(self : rosetta.protocols.sewing.Assembly, graph : rosetta.protocols.sewing.SewGraph, model : rosetta.protocols.sewing.Model, available : bool) -> NoneType   Add a model to the Assembly. Only used for first node and special cases. align_model(...) from builtins.PyCapsule align_model(self : rosetta.protocols.sewing.Assembly, mobile_model : rosetta.protocols.sewing.Model, atom_alignments : rosetta.std.map_core_id_AtomID_core_id_AtomID, reference_model_id : int) -> NoneType all_segments(...) from builtins.PyCapsule all_segments(rosetta.protocols.sewing.Assembly) -> rosetta.utility.vector1_utility_vector1_protocols_sewing_SewSegment_std_allocator_protocols_sewing_SewSegment_t append_segments(...) from builtins.PyCapsule append_segments(self : rosetta.protocols.sewing.Assembly, segments : rosetta.utility.vector1_protocols_sewing_SewSegment) -> NoneType   append the segments to the given assembly. This should be used very infrequently. The normal way to add segments is to follow an edge atom_map_from_score_result(...) from builtins.PyCapsule atom_map_from_score_result(self : rosetta.protocols.sewing.Assembly, alignment_scores : ((rosetta.protocols.sewing.Basis, rosetta.protocols.sewing.Basis), rosetta.protocols.sewing.HashResult)) -> rosetta.std.map_core_id_AtomID_core_id_AtomID create_chimera_segment(...) from builtins.PyCapsule create_chimera_segment(self : rosetta.protocols.sewing.Assembly, reference_segment : rosetta.protocols.sewing.SewSegment, mobile_segment : rosetta.protocols.sewing.SewSegment, atom_map : rosetta.std.map_core_id_AtomID_core_id_AtomID, reference_is_nter : bool) -> rosetta.protocols.sewing.SewSegment delete_segments(...) from builtins.PyCapsule delete_segments(self : rosetta.protocols.sewing.Assembly, seg_index : int) -> NoneType   delete segments at the given index. This should be used very infrequently disconnected_segments(...) from builtins.PyCapsule disconnected_segments(rosetta.protocols.sewing.Assembly) -> rosetta.utility.vector1_unsigned_long ending_node(...) from builtins.PyCapsule ending_node(rosetta.protocols.sewing.Assembly) -> rosetta.protocols.sewing.ModelNode find_possible_orders(...) from builtins.PyCapsule find_possible_orders(self : rosetta.protocols.sewing.Assembly, max_loop_distance : float) -> rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t follow_edge(...) from builtins.PyCapsule follow_edge(self : rosetta.protocols.sewing.Assembly, graph : rosetta.protocols.sewing.SewGraph, edge : rosetta.protocols.sewing.HashEdge, source_index : int) -> NoneType get_model_segments(...) from builtins.PyCapsule get_model_segments(self : rosetta.protocols.sewing.Assembly, model_id : int) -> rosetta.utility.vector1_protocols_sewing_SewSegment get_next_reference_node(...) from builtins.PyCapsule get_next_reference_node(self : rosetta.protocols.sewing.Assembly, graph : rosetta.protocols.sewing.SewGraph) -> int   Pick which model to use as the reference model for the next node additon get_partner(...) from builtins.PyCapsule get_partner(rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose get_score_result(...) from builtins.PyCapsule get_score_result(self : rosetta.protocols.sewing.Assembly, model_1_node : rosetta.protocols.sewing.ModelNode, cur_edge : rosetta.protocols.sewing.HashEdge, graph : rosetta.protocols.sewing.SewGraph) -> ((rosetta.protocols.sewing.Basis, rosetta.protocols.sewing.Basis), rosetta.protocols.sewing.HashResult) map_residues(...) from builtins.PyCapsule map_residues(self : rosetta.protocols.sewing.Assembly, reference_model_id : int, mobile_model : rosetta.protocols.sewing.Model, atom_alignments : rosetta.std.map_core_id_AtomID_core_id_AtomID) -> NoneType   create mappings between SewResidues in the Assembly that map to the same pose number model_ids(...) from builtins.PyCapsule model_ids(rosetta.protocols.sewing.Assembly) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t native_positions(...) from builtins.PyCapsule native_positions(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t natives_select(...) from builtins.PyCapsule natives_select(*args, **kwargs) Overloaded function.   1. natives_select(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose) -> str   print pymol selection of "native" positions   2. natives_select(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose, object_name : str) -> str   print pymol selection of "native" positions path(...) from builtins.PyCapsule path(rosetta.protocols.sewing.Assembly) -> rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t percent_native(...) from builtins.PyCapsule percent_native(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose) -> float   count the amount of 'native' residues retained in the pose pose_loop_anchors(...) from builtins.PyCapsule pose_loop_anchors(rosetta.protocols.sewing.Assembly) -> rosetta.utility.vector1_unsigned_long pose_num(...) from builtins.PyCapsule pose_num(self : rosetta.protocols.sewing.Assembly, model_id : int, resnum : int) -> int prepare_for_packing(...) from builtins.PyCapsule prepare_for_packing(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose, task_factory : rosetta.core.pack.task.TaskFactory, base_native_bonus : float, neighbor_cutoff : int) -> NoneType   Update the task factory such that the 'native' rotamers are added to the rotamer set, and the native residues are favored regenerate_model(...) from builtins.PyCapsule regenerate_model(self : rosetta.protocols.sewing.Assembly, model_id : int) -> rosetta.protocols.sewing.Model reorder(...) from builtins.PyCapsule reorder(self : rosetta.protocols.sewing.Assembly, new_order : rosetta.utility.vector1_unsigned_long) -> NoneType reorder_randomly(...) from builtins.PyCapsule reorder_randomly(self : rosetta.protocols.sewing.Assembly, max_loop_distance : float) -> bool   reorder segments in a random fashion that satisfies the maximum loop distance cutoff If this is not possible then return false, otherwise true segments(...) from builtins.PyCapsule segments(rosetta.protocols.sewing.Assembly) -> rosetta.utility.vector1_protocols_sewing_SewSegment set_partner(...) from builtins.PyCapsule set_partner(self : rosetta.protocols.sewing.Assembly, partner_pose : rosetta.core.pose.Pose) -> NoneType starting_node(...) from builtins.PyCapsule starting_node(rosetta.protocols.sewing.Assembly) -> rosetta.protocols.sewing.ModelNode string_blosum(...) from builtins.PyCapsule string_blosum(self : rosetta.protocols.sewing.Assembly, blosum_history : rosetta.utility.vector1_std_pair_double_unsigned_long_t) -> str string_path(...) from builtins.PyCapsule string_path(rosetta.protocols.sewing.Assembly) -> str to_multichain_pose(...) from builtins.PyCapsule to_multichain_pose(self : rosetta.protocols.sewing.Assembly, residue_type_set : str) -> rosetta.core.pose.Pose to_pose(...) from builtins.PyCapsule to_pose(*args, **kwargs) Overloaded function.   1. to_pose(self : rosetta.protocols.sewing.Assembly, residue_type_set : str) -> rosetta.core.pose.Pose   2. to_pose(self : rosetta.protocols.sewing.Assembly, residue_type_set : str, create_cuts : bool) -> rosetta.core.pose.Pose total_residue(...) from builtins.PyCapsule total_residue(rosetta.protocols.sewing.Assembly) -> int update_coords_from_pose(...) from builtins.PyCapsule update_coords_from_pose(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose) -> NoneType Data descriptors inherited from Assembly: blosum_history_   class DisembodiedAssembly(Assembly)     An Assembly is a collection of SewSegments. Assemblies are created using the geometric "compatibility" data generated by the Hasher.     Method resolution order: DisembodiedAssembly Assembly 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. append_model(...) from builtins.PyCapsule append_model(self : rosetta.protocols.sewing.DisembodiedAssembly, model : rosetta.protocols.sewing.Model, edge_score : ((rosetta.protocols.sewing.Basis, rosetta.protocols.sewing.Basis), rosetta.protocols.sewing.HashResult)) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.sewing.DisembodiedAssembly,  : rosetta.protocols.sewing.DisembodiedAssembly) -> rosetta.protocols.sewing.DisembodiedAssembly clone(...) from builtins.PyCapsule clone(rosetta.protocols.sewing.DisembodiedAssembly) -> rosetta.protocols.sewing.Assembly Methods inherited from Assembly: __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.sewing.Assembly) -> str add_loop_segment(...) from builtins.PyCapsule add_loop_segment(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose, loop : rosetta.protocols.loops.Loop, segment : int) -> NoneType add_model(...) from builtins.PyCapsule add_model(*args, **kwargs) Overloaded function.   1. add_model(self : rosetta.protocols.sewing.Assembly, graph : rosetta.protocols.sewing.SewGraph, model : rosetta.protocols.sewing.Model) -> NoneType   Add a model to the Assembly. Only used for first node and special cases.   2. add_model(self : rosetta.protocols.sewing.Assembly, graph : rosetta.protocols.sewing.SewGraph, model : rosetta.protocols.sewing.Model, available : bool) -> NoneType   Add a model to the Assembly. Only used for first node and special cases. align_model(...) from builtins.PyCapsule align_model(self : rosetta.protocols.sewing.Assembly, mobile_model : rosetta.protocols.sewing.Model, atom_alignments : rosetta.std.map_core_id_AtomID_core_id_AtomID, reference_model_id : int) -> NoneType all_segments(...) from builtins.PyCapsule all_segments(rosetta.protocols.sewing.Assembly) -> rosetta.utility.vector1_utility_vector1_protocols_sewing_SewSegment_std_allocator_protocols_sewing_SewSegment_t append_segments(...) from builtins.PyCapsule append_segments(self : rosetta.protocols.sewing.Assembly, segments : rosetta.utility.vector1_protocols_sewing_SewSegment) -> NoneType   append the segments to the given assembly. This should be used very infrequently. The normal way to add segments is to follow an edge atom_map_from_score_result(...) from builtins.PyCapsule atom_map_from_score_result(self : rosetta.protocols.sewing.Assembly, alignment_scores : ((rosetta.protocols.sewing.Basis, rosetta.protocols.sewing.Basis), rosetta.protocols.sewing.HashResult)) -> rosetta.std.map_core_id_AtomID_core_id_AtomID create_chimera_segment(...) from builtins.PyCapsule create_chimera_segment(self : rosetta.protocols.sewing.Assembly, reference_segment : rosetta.protocols.sewing.SewSegment, mobile_segment : rosetta.protocols.sewing.SewSegment, atom_map : rosetta.std.map_core_id_AtomID_core_id_AtomID, reference_is_nter : bool) -> rosetta.protocols.sewing.SewSegment delete_segments(...) from builtins.PyCapsule delete_segments(self : rosetta.protocols.sewing.Assembly, seg_index : int) -> NoneType   delete segments at the given index. This should be used very infrequently disconnected_segments(...) from builtins.PyCapsule disconnected_segments(rosetta.protocols.sewing.Assembly) -> rosetta.utility.vector1_unsigned_long ending_node(...) from builtins.PyCapsule ending_node(rosetta.protocols.sewing.Assembly) -> rosetta.protocols.sewing.ModelNode find_possible_orders(...) from builtins.PyCapsule find_possible_orders(self : rosetta.protocols.sewing.Assembly, max_loop_distance : float) -> rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t follow_edge(...) from builtins.PyCapsule follow_edge(self : rosetta.protocols.sewing.Assembly, graph : rosetta.protocols.sewing.SewGraph, edge : rosetta.protocols.sewing.HashEdge, source_index : int) -> NoneType get_model_segments(...) from builtins.PyCapsule get_model_segments(self : rosetta.protocols.sewing.Assembly, model_id : int) -> rosetta.utility.vector1_protocols_sewing_SewSegment get_next_reference_node(...) from builtins.PyCapsule get_next_reference_node(self : rosetta.protocols.sewing.Assembly, graph : rosetta.protocols.sewing.SewGraph) -> int   Pick which model to use as the reference model for the next node additon get_partner(...) from builtins.PyCapsule get_partner(rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose get_score_result(...) from builtins.PyCapsule get_score_result(self : rosetta.protocols.sewing.Assembly, model_1_node : rosetta.protocols.sewing.ModelNode, cur_edge : rosetta.protocols.sewing.HashEdge, graph : rosetta.protocols.sewing.SewGraph) -> ((rosetta.protocols.sewing.Basis, rosetta.protocols.sewing.Basis), rosetta.protocols.sewing.HashResult) map_residues(...) from builtins.PyCapsule map_residues(self : rosetta.protocols.sewing.Assembly, reference_model_id : int, mobile_model : rosetta.protocols.sewing.Model, atom_alignments : rosetta.std.map_core_id_AtomID_core_id_AtomID) -> NoneType   create mappings between SewResidues in the Assembly that map to the same pose number model_ids(...) from builtins.PyCapsule model_ids(rosetta.protocols.sewing.Assembly) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t native_positions(...) from builtins.PyCapsule native_positions(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t natives_select(...) from builtins.PyCapsule natives_select(*args, **kwargs) Overloaded function.   1. natives_select(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose) -> str   print pymol selection of "native" positions   2. natives_select(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose, object_name : str) -> str   print pymol selection of "native" positions path(...) from builtins.PyCapsule path(rosetta.protocols.sewing.Assembly) -> rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t percent_native(...) from builtins.PyCapsule percent_native(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose) -> float   count the amount of 'native' residues retained in the pose pose_loop_anchors(...) from builtins.PyCapsule pose_loop_anchors(rosetta.protocols.sewing.Assembly) -> rosetta.utility.vector1_unsigned_long pose_num(...) from builtins.PyCapsule pose_num(self : rosetta.protocols.sewing.Assembly, model_id : int, resnum : int) -> int prepare_for_packing(...) from builtins.PyCapsule prepare_for_packing(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose, task_factory : rosetta.core.pack.task.TaskFactory, base_native_bonus : float, neighbor_cutoff : int) -> NoneType   Update the task factory such that the 'native' rotamers are added to the rotamer set, and the native residues are favored regenerate_model(...) from builtins.PyCapsule regenerate_model(self : rosetta.protocols.sewing.Assembly, model_id : int) -> rosetta.protocols.sewing.Model reorder(...) from builtins.PyCapsule reorder(self : rosetta.protocols.sewing.Assembly, new_order : rosetta.utility.vector1_unsigned_long) -> NoneType reorder_randomly(...) from builtins.PyCapsule reorder_randomly(self : rosetta.protocols.sewing.Assembly, max_loop_distance : float) -> bool   reorder segments in a random fashion that satisfies the maximum loop distance cutoff If this is not possible then return false, otherwise true segments(...) from builtins.PyCapsule segments(rosetta.protocols.sewing.Assembly) -> rosetta.utility.vector1_protocols_sewing_SewSegment set_partner(...) from builtins.PyCapsule set_partner(self : rosetta.protocols.sewing.Assembly, partner_pose : rosetta.core.pose.Pose) -> NoneType starting_node(...) from builtins.PyCapsule starting_node(rosetta.protocols.sewing.Assembly) -> rosetta.protocols.sewing.ModelNode string_blosum(...) from builtins.PyCapsule string_blosum(self : rosetta.protocols.sewing.Assembly, blosum_history : rosetta.utility.vector1_std_pair_double_unsigned_long_t) -> str string_path(...) from builtins.PyCapsule string_path(rosetta.protocols.sewing.Assembly) -> str to_multichain_pose(...) from builtins.PyCapsule to_multichain_pose(self : rosetta.protocols.sewing.Assembly, residue_type_set : str) -> rosetta.core.pose.Pose to_pose(...) from builtins.PyCapsule to_pose(*args, **kwargs) Overloaded function.   1. to_pose(self : rosetta.protocols.sewing.Assembly, residue_type_set : str) -> rosetta.core.pose.Pose   2. to_pose(self : rosetta.protocols.sewing.Assembly, residue_type_set : str, create_cuts : bool) -> rosetta.core.pose.Pose total_residue(...) from builtins.PyCapsule total_residue(rosetta.protocols.sewing.Assembly) -> int update_coords_from_pose(...) from builtins.PyCapsule update_coords_from_pose(self : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose) -> NoneType Data descriptors inherited from Assembly: blosum_history_   class EnumerateAssemblyMover(AssemblyMover)       Method resolution order: EnumerateAssemblyMover AssemblyMover 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.sewing.EnumerateAssemblyMover) -> 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.sewing.EnumerateAssemblyMover,  : rosetta.protocols.sewing.EnumerateAssemblyMover) -> rosetta.protocols.sewing.EnumerateAssemblyMover clone(...) from builtins.PyCapsule clone(rosetta.protocols.sewing.EnumerateAssemblyMover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.sewing.EnumerateAssemblyMover) -> rosetta.protocols.moves.Mover generate_assembly(...) from builtins.PyCapsule generate_assembly(rosetta.protocols.sewing.EnumerateAssemblyMover) -> rosetta.protocols.sewing.Assembly get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.sewing.EnumerateAssemblyMover) -> str Methods inherited from AssemblyMover: add_starting_model(...) from builtins.PyCapsule add_starting_model(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> NoneType append_movie_frame(...) from builtins.PyCapsule append_movie_frame(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, cycle : int) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.sewing.AssemblyMover, pose : rosetta.core.pose.Pose) -> NoneType follow_random_edge_from_node(...) from builtins.PyCapsule follow_random_edge_from_node(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, reference_node : rosetta.protocols.sewing.ModelNode) -> bool get_centroid_pose(...) from builtins.PyCapsule get_centroid_pose(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose get_fullatom_pose(...) from builtins.PyCapsule get_fullatom_pose(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose output_stats(...) from builtins.PyCapsule output_stats(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose, indicator_whether_from_MonteCarloAssemblyMover_or_ExhaustiveAssemblyMover : str) -> NoneType   add several outputs to the score file Pose can't be const due to scoring. refine_assembly(...) from builtins.PyCapsule refine_assembly(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.sewing.AssemblyMover) -> bool Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply 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. 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 EnumerateAssemblyMoverCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: EnumerateAssemblyMoverCreator 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.sewing.EnumerateAssemblyMoverCreator,  : rosetta.protocols.sewing.EnumerateAssemblyMoverCreator) -> rosetta.protocols.sewing.EnumerateAssemblyMoverCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.sewing.EnumerateAssemblyMoverCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.sewing.EnumerateAssemblyMoverCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class GivenPathAssemblyMover(AssemblyMover)       Method resolution order: GivenPathAssemblyMover AssemblyMover 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.sewing.GivenPathAssemblyMover) -> 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.sewing.GivenPathAssemblyMover,  : rosetta.protocols.sewing.GivenPathAssemblyMover) -> rosetta.protocols.sewing.GivenPathAssemblyMover clone(...) from builtins.PyCapsule clone(rosetta.protocols.sewing.GivenPathAssemblyMover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.sewing.GivenPathAssemblyMover) -> rosetta.protocols.moves.Mover generate_assembly(...) from builtins.PyCapsule generate_assembly(rosetta.protocols.sewing.GivenPathAssemblyMover) -> rosetta.protocols.sewing.Assembly get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.sewing.GivenPathAssemblyMover) -> str Methods inherited from AssemblyMover: add_starting_model(...) from builtins.PyCapsule add_starting_model(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> NoneType append_movie_frame(...) from builtins.PyCapsule append_movie_frame(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, cycle : int) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.sewing.AssemblyMover, pose : rosetta.core.pose.Pose) -> NoneType follow_random_edge_from_node(...) from builtins.PyCapsule follow_random_edge_from_node(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, reference_node : rosetta.protocols.sewing.ModelNode) -> bool get_centroid_pose(...) from builtins.PyCapsule get_centroid_pose(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose get_fullatom_pose(...) from builtins.PyCapsule get_fullatom_pose(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose output_stats(...) from builtins.PyCapsule output_stats(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose, indicator_whether_from_MonteCarloAssemblyMover_or_ExhaustiveAssemblyMover : str) -> NoneType   add several outputs to the score file Pose can't be const due to scoring. refine_assembly(...) from builtins.PyCapsule refine_assembly(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.sewing.AssemblyMover) -> bool Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply 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. 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 GivenPathAssemblyMoverCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: GivenPathAssemblyMoverCreator 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.sewing.GivenPathAssemblyMoverCreator,  : rosetta.protocols.sewing.GivenPathAssemblyMoverCreator) -> rosetta.protocols.sewing.GivenPathAssemblyMoverCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.sewing.GivenPathAssemblyMoverCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.sewing.GivenPathAssemblyMoverCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class GreedyAssemblyMover(AssemblyMover)       Method resolution order: GreedyAssemblyMover AssemblyMover 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.sewing.GreedyAssemblyMover) -> 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.sewing.GreedyAssemblyMover,  : rosetta.protocols.sewing.GreedyAssemblyMover) -> rosetta.protocols.sewing.GreedyAssemblyMover clone(...) from builtins.PyCapsule clone(rosetta.protocols.sewing.GreedyAssemblyMover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.sewing.GreedyAssemblyMover) -> rosetta.protocols.moves.Mover generate_assembly(...) from builtins.PyCapsule generate_assembly(rosetta.protocols.sewing.GreedyAssemblyMover) -> rosetta.protocols.sewing.Assembly get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.sewing.GreedyAssemblyMover) -> str Methods inherited from AssemblyMover: add_starting_model(...) from builtins.PyCapsule add_starting_model(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> NoneType append_movie_frame(...) from builtins.PyCapsule append_movie_frame(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, cycle : int) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.sewing.AssemblyMover, pose : rosetta.core.pose.Pose) -> NoneType follow_random_edge_from_node(...) from builtins.PyCapsule follow_random_edge_from_node(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, reference_node : rosetta.protocols.sewing.ModelNode) -> bool get_centroid_pose(...) from builtins.PyCapsule get_centroid_pose(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose get_fullatom_pose(...) from builtins.PyCapsule get_fullatom_pose(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose output_stats(...) from builtins.PyCapsule output_stats(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose, indicator_whether_from_MonteCarloAssemblyMover_or_ExhaustiveAssemblyMover : str) -> NoneType   add several outputs to the score file Pose can't be const due to scoring. refine_assembly(...) from builtins.PyCapsule refine_assembly(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.sewing.AssemblyMover) -> bool Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply 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. 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 GreedyAssemblyMoverCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: GreedyAssemblyMoverCreator 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.sewing.GreedyAssemblyMoverCreator,  : rosetta.protocols.sewing.GreedyAssemblyMoverCreator) -> rosetta.protocols.sewing.GreedyAssemblyMoverCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.sewing.GreedyAssemblyMoverCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.sewing.GreedyAssemblyMoverCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class HashEdge(rosetta.core.graph.Edge)     /////////////////////////////////////////////////////////////////////////////////////// ////////////////////////////   Edge Class   /////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////     Method resolution order: HashEdge rosetta.core.graph.Edge builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : protocols::sewing::SewGraph, n1 : int, n2 : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.sewing.HashEdge) -> str basis_pair(...) from builtins.PyCapsule basis_pair(*args, **kwargs) Overloaded function.   1. basis_pair(self : rosetta.protocols.sewing.HashEdge, basis_pair : (rosetta.protocols.sewing.Basis, rosetta.protocols.sewing.Basis)) -> NoneType   2. basis_pair(rosetta.protocols.sewing.HashEdge) -> (rosetta.protocols.sewing.Basis, rosetta.protocols.sewing.Basis) model_resnum(...) from builtins.PyCapsule model_resnum(self : rosetta.protocols.sewing.HashEdge, model_id : int) -> int Methods inherited from rosetta.core.graph.Edge: copy_from(...) from builtins.PyCapsule copy_from(self : rosetta.core.graph.Edge, source : rosetta.core.graph.Edge) -> NoneType   copy-from for use in Graph::operator= and copy ctors count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.graph.Edge) -> int   how much memory is dynamically allocated by this edge -- must be recursively invoked  by a derived class. count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.graph.Edge) -> int   how much memory is statically allocated by this edge get_first_node_ind(...) from builtins.PyCapsule get_first_node_ind(rosetta.core.graph.Edge) -> int   returns the index of the lower node get_other_ind(...) from builtins.PyCapsule get_other_ind(self : rosetta.core.graph.Edge, node_index : int) -> int   returns the index of the one node given the index of the other.  node_index must be one of the two nodes that this edge is incident upon. get_other_node(...) from builtins.PyCapsule get_other_node(*args, **kwargs) Overloaded function.   1. get_other_node(self : rosetta.core.graph.Edge, node_index : int) -> rosetta.core.graph.Node   returns a const pointer to one node given the index of the other.  node_index must be one of the two nodes that this edge is incident upon.   2. get_other_node(self : rosetta.core.graph.Edge, node_index : int) -> rosetta.core.graph.Node   returns a non-const pointer to one node given the index of the other.  node_index must be one of the two nodes that this edge is incident upon. get_second_node_ind(...) from builtins.PyCapsule get_second_node_ind(rosetta.core.graph.Edge) -> int   returns the index of the upper node is_loop(...) from builtins.PyCapsule is_loop(rosetta.core.graph.Edge) -> bool   Is this edge a loop? In Pseudographs, loop edges are incident twice on a single vertex. same_edge(...) from builtins.PyCapsule same_edge(self : rosetta.core.graph.Edge, node1 : int, node2 : int) -> bool   Is this the same edge as another edge (node1,node2)?  Note:  this graph does not work for multi-graphs.  Edges must be unique. set_pos_in_owners_list(...) from builtins.PyCapsule set_pos_in_owners_list(self : rosetta.core.graph.Edge, edge_iterator : rosetta.core.graph.EdgeListIterator) -> NoneType   called only by class Graph, this function gives the Edge the data it needs  to later delete itself from its owner's edge list in constant time.   class HashResult(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.sewing.HashResult) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Data descriptors defined here: clash_count segment_match_counts segment_matches   class HashValue(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.sewing.HashValue) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Data descriptors defined here: atomno basis_resnum model_id resnum segment_id   class Hasher(builtins.object)     //////////////////////// End HashMap for score results ///////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.sewing.Hasher) -> 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.sewing.Hasher,  : rosetta.protocols.sewing.Hasher) -> rosetta.protocols.sewing.Hasher generate_key(...) from builtins.PyCapsule generate_key(self : rosetta.protocols.sewing.Hasher, atom : rosetta.protocols.sewing.SewAtom) -> rosetta.utility.fixedsizearray1_int_3_t   Create the HashKey from a SewAtom hash_model(...) from builtins.PyCapsule hash_model(self : rosetta.protocols.sewing.Hasher, transformed_model : rosetta.protocols.sewing.Model, basis_residue : rosetta.protocols.sewing.SewResidue) -> NoneType   Hash the transformed residues into the HashMap insert(...) from builtins.PyCapsule insert(self : rosetta.protocols.sewing.Hasher, model : rosetta.protocols.sewing.Model) -> NoneType   Insert this model into the hash table read_from_disk(...) from builtins.PyCapsule read_from_disk(self : rosetta.protocols.sewing.Hasher, filename : str) -> NoneType   Populate the hash table from one on disk. remove_connection_inconsistencies(...) from builtins.PyCapsule remove_connection_inconsistencies(self : rosetta.protocols.sewing.Hasher, models : rosetta.std.map_int_protocols_sewing_Model, scores : rosetta.std.map_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_t_protocols_sewing_HashResult) -> NoneType   remove edges between segments that both have 'next' or 'previous' segments remove_duplicates(...) from builtins.PyCapsule remove_duplicates(self : rosetta.protocols.sewing.Hasher, scores : rosetta.std.map_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_t_protocols_sewing_HashResult) -> rosetta.std.map_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_t_protocols_sewing_HashResult   keep only best scoring alignment between two models score(...) from builtins.PyCapsule score(*args, **kwargs) Overloaded function.   1. score(self : rosetta.protocols.sewing.Hasher, model : rosetta.protocols.sewing.Model, num_segment_matches : int, min_segment_score : int, max_clash_score : int, score_segments : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, store_atoms : bool, box_length : int) -> rosetta.std.map_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_t_protocols_sewing_HashResult   2. score(self : rosetta.protocols.sewing.Hasher, model : rosetta.protocols.sewing.Model, num_segment_matches : int, min_segment_score : int, max_clash_score : int, store_atoms : bool, box_length : int) -> rosetta.std.map_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_t_protocols_sewing_HashResult   Score the given model against the models in the hash table score_basis(...) from builtins.PyCapsule score_basis(self : rosetta.protocols.sewing.Hasher, alignment_scores : rosetta.std.map_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_t_protocols_sewing_HashResult, transformed_model : rosetta.protocols.sewing.Model, basis_residue : rosetta.protocols.sewing.SewResidue, store_atoms : bool) -> NoneType score_basis_125(...) from builtins.PyCapsule score_basis_125(self : rosetta.protocols.sewing.Hasher, alignment_scores : rosetta.std.map_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_t_protocols_sewing_HashResult, transformed_model : rosetta.protocols.sewing.Model, basis_residue : rosetta.protocols.sewing.SewResidue, store_atoms : bool) -> NoneType score_one(...) from builtins.PyCapsule score_one(self : rosetta.protocols.sewing.Hasher, m1 : rosetta.protocols.sewing.Model, m1_basis : rosetta.protocols.sewing.SewResidue, m2 : rosetta.protocols.sewing.Model, m2_basis : rosetta.protocols.sewing.SewResidue, box_length : int) -> ((rosetta.protocols.sewing.Basis, rosetta.protocols.sewing.Basis), rosetta.protocols.sewing.HashResult) transform_model(...) from builtins.PyCapsule transform_model(self : rosetta.protocols.sewing.Hasher, model : rosetta.protocols.sewing.Model, basis_residue : rosetta.protocols.sewing.SewResidue) -> rosetta.protocols.sewing.Model   Transform all features to the local coordinate frame of the basis set trim_scores(...) from builtins.PyCapsule trim_scores(self : rosetta.protocols.sewing.Hasher, scores : rosetta.std.map_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_t_protocols_sewing_HashResult, num_segment_matches : int, min_segment_score : int, max_clash_score : int) -> NoneType   Trim the ScoreResults to remove weak hits write_to_disk(...) from builtins.PyCapsule write_to_disk(self : rosetta.protocols.sewing.Hasher, filename : str) -> NoneType   Serialize hash table to disk   class Model(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.sewing.Model) -> NoneType   2. __init__(self : rosetta.protocols.sewing.Model,  : rosetta.protocols.sewing.Model) -> 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.sewing.Model,  : rosetta.protocols.sewing.Model) -> rosetta.protocols.sewing.Model get_residue(...) from builtins.PyCapsule get_residue(self : rosetta.protocols.sewing.Model, resnum : int) -> rosetta.protocols.sewing.SewResidue pose_number(...) from builtins.PyCapsule pose_number(self : rosetta.protocols.sewing.Model, resnum : int) -> int   get the corresponding pose resnum from the segment_ids(...) from builtins.PyCapsule segment_ids(rosetta.protocols.sewing.Model) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   return the set of segment ids for this model to_pose_from_db(...) from builtins.PyCapsule to_pose_from_db(rosetta.protocols.sewing.Model) -> rosetta.core.pose.Pose   create a pose for this model from the database trim_db_pose(...) from builtins.PyCapsule trim_db_pose(self : rosetta.protocols.sewing.Model, pose : rosetta.core.pose.Pose) -> NoneType   trim the given pose to include only model residues Data descriptors defined here: distance_ hoist_angle_degrees_ meridian_angle_degrees_ model_id_ packing_angle_degrees_ pdb_code_ segments_ structure_id_   class ModelNode(rosetta.core.graph.Node)     /////////////////////////////////////////////////////////////////////////////////////// ////////////////////////////   Node Class   /////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////     Method resolution order: ModelNode rosetta.core.graph.Node builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.graph.Graph, index : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.sewing.ModelNode) -> str copy_from(...) from builtins.PyCapsule copy_from(self : rosetta.protocols.sewing.ModelNode, source : rosetta.core.graph.Node) -> NoneType model(...) from builtins.PyCapsule model(*args, **kwargs) Overloaded function.   1. model(rosetta.protocols.sewing.ModelNode) -> rosetta.protocols.sewing.Model   2. model(self : rosetta.protocols.sewing.ModelNode, model : rosetta.protocols.sewing.Model) -> NoneType segment_ids(...) from builtins.PyCapsule segment_ids(*args, **kwargs) Overloaded function.   1. segment_ids(rosetta.protocols.sewing.ModelNode) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   2. segment_ids(self : rosetta.protocols.sewing.ModelNode, segment_ids : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType Methods inherited from rosetta.core.graph.Node: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.graph.Node, edge_ptr : core::graph::Edge,  : rosetta.core.graph.EdgeListIterator) -> NoneType   adds edge pointer to edge list; returns an iterator to the new  list element const_edge_list_begin(...) from builtins.PyCapsule const_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of its edge list const_edge_list_end(...) from builtins.PyCapsule const_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of its edge list const_lower_edge_list_begin(...) from builtins.PyCapsule const_lower_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of its lower-edge list const_lower_edge_list_end(...) from builtins.PyCapsule const_lower_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of its lower-edge list const_upper_edge_list_begin(...) from builtins.PyCapsule const_upper_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of its upper-edge list const_upper_edge_list_end(...) from builtins.PyCapsule const_upper_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of its upper-edge list count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.graph.Node) -> int   memory accounting scheme count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.graph.Node) -> int   memory accounting scheme drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.graph.Node) -> NoneType   deletes all edges incident upon this node drop_edge(...) from builtins.PyCapsule drop_edge(self : rosetta.core.graph.Node, edge_iterator : rosetta.core.graph.EdgeListIterator) -> NoneType   removes an edge iterator from the node's edge list.  Only called by Edge class. edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of its edge list edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of its edge list find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.graph.Node, other_node_index : int) -> core::graph::Edge   a "slow" (linear) search for an edge.   2. find_edge(self : rosetta.core.graph.Node, other_node_index : int) -> core::graph::Edge get_node_index(...) from builtins.PyCapsule get_node_index(rosetta.core.graph.Node) -> int   the index for this node get_num_edges_to_larger_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_larger_indexed_nodes(rosetta.core.graph.Node) -> int   the number of upper neighbors -- which "self" neighborness is counted if a loop edge  is present get_num_edges_to_smaller_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_smaller_indexed_nodes(rosetta.core.graph.Node) -> int   the number of lower neighbors loop_incident(...) from builtins.PyCapsule loop_incident(rosetta.core.graph.Node) -> bool   NOTE TO SELF: remove loop support lower_edge_list_begin(...) from builtins.PyCapsule lower_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of its lower-edge list lower_edge_list_end(...) from builtins.PyCapsule lower_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of its lower-edge list num_edges(...) from builtins.PyCapsule num_edges(rosetta.core.graph.Node) -> int   the number of edges incident on this node, which may include a loop edge num_neighbors_counting_self(...) from builtins.PyCapsule num_neighbors_counting_self(rosetta.core.graph.Node) -> int   the number of neighbors counting "self" as a neighbor. num_neighbors_counting_self_static(...) from builtins.PyCapsule num_neighbors_counting_self_static(rosetta.core.graph.Node) -> int   the number of neighbors counting "self" as neighbor. Defaults to  num_neighbors_counting_self() but can be set to other values as well.  Useful in calculation of symmetrical structures. print(...) from builtins.PyCapsule print(rosetta.core.graph.Node) -> NoneType   send summaray data about this node to the screen set_num_neighbors_counting_self_static(...) from builtins.PyCapsule set_num_neighbors_counting_self_static(self : rosetta.core.graph.Node, neighbor : int) -> NoneType   manually change the number of neighbors for a Node. Used  for symmetry scoring upper_edge_list_begin(...) from builtins.PyCapsule upper_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of its upper-edge list upper_edge_list_end(...) from builtins.PyCapsule upper_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of its upper-edge list   class MonteCarloAssemblyMover(AssemblyMover)       Method resolution order: MonteCarloAssemblyMover AssemblyMover 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.sewing.MonteCarloAssemblyMover) -> 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.sewing.MonteCarloAssemblyMover,  : rosetta.protocols.sewing.MonteCarloAssemblyMover) -> rosetta.protocols.sewing.MonteCarloAssemblyMover clone(...) from builtins.PyCapsule clone(rosetta.protocols.sewing.MonteCarloAssemblyMover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.sewing.MonteCarloAssemblyMover) -> rosetta.protocols.moves.Mover generate_assembly(...) from builtins.PyCapsule generate_assembly(rosetta.protocols.sewing.MonteCarloAssemblyMover) -> rosetta.protocols.sewing.Assembly get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.sewing.MonteCarloAssemblyMover) -> str Methods inherited from AssemblyMover: add_starting_model(...) from builtins.PyCapsule add_starting_model(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> NoneType append_movie_frame(...) from builtins.PyCapsule append_movie_frame(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, cycle : int) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.sewing.AssemblyMover, pose : rosetta.core.pose.Pose) -> NoneType follow_random_edge_from_node(...) from builtins.PyCapsule follow_random_edge_from_node(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, reference_node : rosetta.protocols.sewing.ModelNode) -> bool get_centroid_pose(...) from builtins.PyCapsule get_centroid_pose(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose get_fullatom_pose(...) from builtins.PyCapsule get_fullatom_pose(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose output_stats(...) from builtins.PyCapsule output_stats(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose, indicator_whether_from_MonteCarloAssemblyMover_or_ExhaustiveAssemblyMover : str) -> NoneType   add several outputs to the score file Pose can't be const due to scoring. refine_assembly(...) from builtins.PyCapsule refine_assembly(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.sewing.AssemblyMover) -> bool Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply 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. 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 MonteCarloAssemblyMoverCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: MonteCarloAssemblyMoverCreator 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.sewing.MonteCarloAssemblyMoverCreator,  : rosetta.protocols.sewing.MonteCarloAssemblyMoverCreator) -> rosetta.protocols.sewing.MonteCarloAssemblyMoverCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.sewing.MonteCarloAssemblyMoverCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.sewing.MonteCarloAssemblyMoverCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class ReadNativeRotamersFile(rosetta.core.pack.task.operation.TaskOperation)     ///////////ReadNativeRotamersFile/////////////////     Method resolution order: ReadNativeRotamersFile 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.sewing.ReadNativeRotamersFile,  : rosetta.core.pose.Pose,  : rosetta.core.pack.task.PackerTask) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.sewing.ReadNativeRotamersFile,  : rosetta.protocols.sewing.ReadNativeRotamersFile) -> rosetta.protocols.sewing.ReadNativeRotamersFile clone(...) from builtins.PyCapsule clone(rosetta.protocols.sewing.ReadNativeRotamersFile) -> rosetta.core.pack.task.operation.TaskOperation keyname(...) from builtins.PyCapsule keyname(*args, **kwargs) Overloaded function.   1. keyname() -> str   2. keyname() -> str parse_tag(...) from builtins.PyCapsule parse_tag(self : rosetta.protocols.sewing.ReadNativeRotamersFile,  : rosetta.utility.tag.Tag,  : rosetta.basic.datacache.DataMap) -> NoneType provide_xml_schema(...) from builtins.PyCapsule provide_xml_schema(*args, **kwargs) Overloaded function.   1. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType   2. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType   class ReadNativeRotamersFileCreator(rosetta.core.pack.task.operation.TaskOperationCreator)       Method resolution order: ReadNativeRotamersFileCreator 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.sewing.ReadNativeRotamersFileCreator,  : rosetta.protocols.sewing.ReadNativeRotamersFileCreator) -> rosetta.protocols.sewing.ReadNativeRotamersFileCreator create_task_operation(...) from builtins.PyCapsule create_task_operation(rosetta.protocols.sewing.ReadNativeRotamersFileCreator) -> rosetta.core.pack.task.operation.TaskOperation keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.sewing.ReadNativeRotamersFileCreator) -> str provide_xml_schema(...) from builtins.PyCapsule provide_xml_schema(self : rosetta.protocols.sewing.ReadNativeRotamersFileCreator, xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType   class ReadRepeatNativeRotamersFile(ReadNativeRotamersFile)     ///////////ReadRepeatNativeRotamersFile/////////////////     Method resolution order: ReadRepeatNativeRotamersFile ReadNativeRotamersFile 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.sewing.ReadRepeatNativeRotamersFile,  : rosetta.core.pose.Pose,  : rosetta.core.pack.task.PackerTask) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.sewing.ReadRepeatNativeRotamersFile,  : rosetta.protocols.sewing.ReadRepeatNativeRotamersFile) -> rosetta.protocols.sewing.ReadRepeatNativeRotamersFile clone(...) from builtins.PyCapsule clone(rosetta.protocols.sewing.ReadRepeatNativeRotamersFile) -> rosetta.core.pack.task.operation.TaskOperation keyname(...) from builtins.PyCapsule keyname(*args, **kwargs) Overloaded function.   1. keyname() -> str   2. keyname() -> str provide_xml_schema(...) from builtins.PyCapsule provide_xml_schema(*args, **kwargs) Overloaded function.   1. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType   2. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType Data descriptors defined here: parent Methods inherited from ReadNativeRotamersFile: parse_tag(...) from builtins.PyCapsule parse_tag(self : rosetta.protocols.sewing.ReadNativeRotamersFile,  : rosetta.utility.tag.Tag,  : rosetta.basic.datacache.DataMap) -> NoneType   class ReadRepeatNativeRotamersFileCreator(rosetta.core.pack.task.operation.TaskOperationCreator)       Method resolution order: ReadRepeatNativeRotamersFileCreator 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.sewing.ReadRepeatNativeRotamersFileCreator,  : rosetta.protocols.sewing.ReadRepeatNativeRotamersFileCreator) -> rosetta.protocols.sewing.ReadRepeatNativeRotamersFileCreator create_task_operation(...) from builtins.PyCapsule create_task_operation(rosetta.protocols.sewing.ReadRepeatNativeRotamersFileCreator) -> rosetta.core.pack.task.operation.TaskOperation keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.sewing.ReadRepeatNativeRotamersFileCreator) -> str provide_xml_schema(...) from builtins.PyCapsule provide_xml_schema(self : rosetta.protocols.sewing.ReadRepeatNativeRotamersFileCreator, xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType   class RepeatAssemblyMover(AssemblyMover)       Method resolution order: RepeatAssemblyMover AssemblyMover 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.sewing.RepeatAssemblyMover) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_repeats(...) from builtins.PyCapsule add_repeats(self : rosetta.protocols.sewing.RepeatAssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.sewing.RepeatAssemblyMover,  : rosetta.protocols.sewing.RepeatAssemblyMover) -> rosetta.protocols.sewing.RepeatAssemblyMover clone(...) from builtins.PyCapsule clone(rosetta.protocols.sewing.RepeatAssemblyMover) -> rosetta.protocols.moves.Mover dfs_cycle_finder(...) from builtins.PyCapsule dfs_cycle_finder(self : rosetta.protocols.sewing.RepeatAssemblyMover, reference_node : rosetta.protocols.sewing.ModelNode, visited_nodes : rosetta.utility.vector1_const_protocols_sewing_ModelNode_*, assembly : rosetta.protocols.sewing.Assembly) -> (bool, rosetta.protocols.sewing.Assembly) fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.sewing.RepeatAssemblyMover) -> rosetta.protocols.moves.Mover generate_assembly(...) from builtins.PyCapsule generate_assembly(rosetta.protocols.sewing.RepeatAssemblyMover) -> rosetta.protocols.sewing.Assembly get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.sewing.RepeatAssemblyMover) -> str get_segment_coords(...) from builtins.PyCapsule get_segment_coords(self : rosetta.protocols.sewing.RepeatAssemblyMover, segment : rosetta.protocols.sewing.SewSegment) -> rosetta.utility.vector1_numeric_xyzVector_double_t output_base_stats(...) from builtins.PyCapsule output_base_stats(self : rosetta.protocols.sewing.RepeatAssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> NoneType   adds single repeat unit data to score file refine_assembly(...) from builtins.PyCapsule refine_assembly(self : rosetta.protocols.sewing.RepeatAssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose transform_segment_coords(...) from builtins.PyCapsule transform_segment_coords(self : rosetta.protocols.sewing.RepeatAssemblyMover, segment : rosetta.protocols.sewing.SewSegment, transformer : rosetta.numeric.xyzTransform_double_t, com : rosetta.numeric.xyzVector_float_t, n_transformations : int) -> NoneType Methods inherited from AssemblyMover: add_starting_model(...) from builtins.PyCapsule add_starting_model(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> NoneType append_movie_frame(...) from builtins.PyCapsule append_movie_frame(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, cycle : int) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.sewing.AssemblyMover, pose : rosetta.core.pose.Pose) -> NoneType follow_random_edge_from_node(...) from builtins.PyCapsule follow_random_edge_from_node(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, reference_node : rosetta.protocols.sewing.ModelNode) -> bool get_centroid_pose(...) from builtins.PyCapsule get_centroid_pose(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose get_fullatom_pose(...) from builtins.PyCapsule get_fullatom_pose(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly) -> rosetta.core.pose.Pose output_stats(...) from builtins.PyCapsule output_stats(self : rosetta.protocols.sewing.AssemblyMover, assembly : rosetta.protocols.sewing.Assembly, pose : rosetta.core.pose.Pose, indicator_whether_from_MonteCarloAssemblyMover_or_ExhaustiveAssemblyMover : str) -> NoneType   add several outputs to the score file Pose can't be const due to scoring. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.sewing.AssemblyMover) -> bool Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply 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. 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 RepeatAssemblyMoverCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: RepeatAssemblyMoverCreator 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.sewing.RepeatAssemblyMoverCreator,  : rosetta.protocols.sewing.RepeatAssemblyMoverCreator) -> rosetta.protocols.sewing.RepeatAssemblyMoverCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.sewing.RepeatAssemblyMoverCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.sewing.RepeatAssemblyMoverCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class SegmentGraph(rosetta.utility.vector1_protocols_sewing_SewSegment)     Simple wrapper around a vector1 of SewSegments, which maintains connection information.     Method resolution order: SegmentGraph rosetta.utility.vector1_protocols_sewing_SewSegment builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.sewing.SegmentGraph,  : rosetta.protocols.sewing.SegmentGraph) -> NoneType   2. __init__(rosetta.protocols.sewing.SegmentGraph) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_connection(...) from builtins.PyCapsule add_connection(self : rosetta.protocols.sewing.SegmentGraph, i : int, j : int) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.sewing.SegmentGraph,  : rosetta.protocols.sewing.SegmentGraph) -> rosetta.protocols.sewing.SegmentGraph c_segment(...) from builtins.PyCapsule c_segment(self : rosetta.protocols.sewing.SegmentGraph, ind : int) -> int clear_connections(...) from builtins.PyCapsule clear_connections(rosetta.protocols.sewing.SegmentGraph) -> NoneType forward_connections(...) from builtins.PyCapsule forward_connections(rosetta.protocols.sewing.SegmentGraph) -> rosetta.std.map_unsigned_long_unsigned_long has_next(...) from builtins.PyCapsule has_next(self : rosetta.protocols.sewing.SegmentGraph, ind : int) -> bool has_previous(...) from builtins.PyCapsule has_previous(self : rosetta.protocols.sewing.SegmentGraph, ind : int) -> bool insert_connected_segment(...) from builtins.PyCapsule insert_connected_segment(self : rosetta.protocols.sewing.SegmentGraph, segment : rosetta.protocols.sewing.SewSegment, ind : int) -> NoneType n_segment(...) from builtins.PyCapsule n_segment(self : rosetta.protocols.sewing.SegmentGraph, ind : int) -> int next(...) from builtins.PyCapsule next(self : rosetta.protocols.sewing.SegmentGraph, ind : int) -> int previous(...) from builtins.PyCapsule previous(self : rosetta.protocols.sewing.SegmentGraph, ind : int) -> int reorder(...) from builtins.PyCapsule reorder(self : rosetta.protocols.sewing.SegmentGraph, new_order : rosetta.utility.vector1_unsigned_long) -> NoneType reverse_connections(...) from builtins.PyCapsule reverse_connections(rosetta.protocols.sewing.SegmentGraph) -> rosetta.std.map_unsigned_long_unsigned_long Methods inherited from rosetta.utility.vector1_protocols_sewing_SewSegment: __bool__(...) from builtins.PyCapsule __bool__(rosetta.utility.vector1_protocols_sewing_SewSegment) -> bool   Check whether the list is nonempty __getitem__(...) from builtins.PyCapsule __getitem__(rosetta.utility.vector1_protocols_sewing_SewSegment, int) -> protocols::sewing::SewSegment __iter__(...) from builtins.PyCapsule __iter__(rosetta.utility.vector1_protocols_sewing_SewSegment) -> iterator __len__(...) from builtins.PyCapsule __len__(rosetta.utility.vector1_protocols_sewing_SewSegment) -> int __setitem__(...) from builtins.PyCapsule __setitem__(rosetta.utility.vector1_protocols_sewing_SewSegment, int, protocols::sewing::SewSegment) -> NoneType append(...) from builtins.PyCapsule append(rosetta.utility.vector1_protocols_sewing_SewSegment, protocols::sewing::SewSegment) -> NoneType   adds an element to the end back(...) from builtins.PyCapsule back(rosetta.utility.vector1_protocols_sewing_SewSegment) -> protocols::sewing::SewSegment   access the last element capacity(...) from builtins.PyCapsule capacity(std::vector<protocols::sewing::SewSegment, std::allocator<protocols::sewing::SewSegment> >) -> int   returns the number of elements that can be held in currently allocated storage clear(...) from builtins.PyCapsule clear(std::vector<protocols::sewing::SewSegment, std::allocator<protocols::sewing::SewSegment> >) -> NoneType   clears the contents erase(...) from builtins.PyCapsule erase(rosetta.utility.vector1_protocols_sewing_SewSegment, int) -> NoneType   erases element at index extend = _vector_extend_func(vec, othervec) # Vector compatibility: Adding 'extend' to all utility.vector* functions front(...) from builtins.PyCapsule front(rosetta.utility.vector1_protocols_sewing_SewSegment) -> protocols::sewing::SewSegment   access the first element l(...) from builtins.PyCapsule l(rosetta.utility.vector1_protocols_sewing_SewSegment) -> int   lower index max_size(...) from builtins.PyCapsule max_size(std::vector<protocols::sewing::SewSegment, std::allocator<protocols::sewing::SewSegment> >) -> int   returns the maximum possible number of elements pop(...) from builtins.PyCapsule pop(*args, **kwargs) Overloaded function.   1. pop(rosetta.utility.vector1_protocols_sewing_SewSegment) -> protocols::sewing::SewSegment   remove and return last item   2. pop(rosetta.utility.vector1_protocols_sewing_SewSegment, int) -> protocols::sewing::SewSegment   remove and return item at index reserve(...) from builtins.PyCapsule reserve(std::vector<protocols::sewing::SewSegment, std::allocator<protocols::sewing::SewSegment> >, int) -> NoneType   reserves storage resize(...) from builtins.PyCapsule resize(rosetta.utility.vector1_protocols_sewing_SewSegment, int) -> NoneType   changes the number of elements stored shrink_to_fit(...) from builtins.PyCapsule shrink_to_fit(std::vector<protocols::sewing::SewSegment, std::allocator<protocols::sewing::SewSegment> >) -> NoneType   reduces memory usage by freeing unused memory u(...) from builtins.PyCapsule u(rosetta.utility.vector1_protocols_sewing_SewSegment) -> int   upper index   class SewAtom(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.sewing.SewAtom) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Data descriptors defined here: atomno_ coords_   class SewGraph(rosetta.core.graph.Graph)     /////////////////////////////////////////////////////////////////////////////////////// ////////////////////////   SewGraph Class   /////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////     Method resolution order: SewGraph rosetta.core.graph.Graph builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.sewing.SewGraph) -> NoneType   3. __init__(self : handle, models : rosetta.std.map_int_protocols_sewing_Model, segment_matches_per_edge : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_all_model_edges_from_binary(...) from builtins.PyCapsule add_all_model_edges_from_binary(self : rosetta.protocols.sewing.SewGraph, filename : str, model_id : int) -> NoneType add_edges_from_binary(...) from builtins.PyCapsule add_edges_from_binary(self : rosetta.protocols.sewing.SewGraph, filename : str, node_id : int) -> NoneType add_special_edges(...) from builtins.PyCapsule add_special_edges(rosetta.protocols.sewing.SewGraph) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.sewing.SewGraph,  : rosetta.protocols.sewing.SewGraph) -> rosetta.protocols.sewing.SewGraph create_new_edge(...) from builtins.PyCapsule create_new_edge(self : rosetta.protocols.sewing.SewGraph, index1 : int, index2 : int) -> rosetta.core.graph.Edge   Factory method for edge creation create_new_node(...) from builtins.PyCapsule create_new_node(self : rosetta.protocols.sewing.SewGraph, index : int) -> rosetta.core.graph.Node   Factory method for node creation delete_edge(...) from builtins.PyCapsule delete_edge(self : rosetta.protocols.sewing.SewGraph, edge : rosetta.core.graph.Edge) -> NoneType find_hash_edge(...) from builtins.PyCapsule find_hash_edge(*args, **kwargs) Overloaded function.   1. find_hash_edge(self : rosetta.protocols.sewing.SewGraph, n1 : int, n2 : int) -> rosetta.protocols.sewing.HashEdge   2. find_hash_edge(self : rosetta.protocols.sewing.SewGraph, n1 : int, n2 : int) -> rosetta.protocols.sewing.HashEdge generate_binary_score_file(...) from builtins.PyCapsule generate_binary_score_file(self : rosetta.protocols.sewing.SewGraph, score_filename : str, binary_filename : str) -> NoneType get_model_node(...) from builtins.PyCapsule get_model_node(*args, **kwargs) Overloaded function.   1. get_model_node(self : rosetta.protocols.sewing.SewGraph, n : int) -> rosetta.protocols.sewing.ModelNode   2. get_model_node(self : rosetta.protocols.sewing.SewGraph, model_id : int, segment_ids : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> rosetta.protocols.sewing.ModelNode get_node_indices_from_model_id(...) from builtins.PyCapsule get_node_indices_from_model_id(self : rosetta.protocols.sewing.SewGraph, model_id : int) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t get_random_node(...) from builtins.PyCapsule get_random_node(rosetta.protocols.sewing.SewGraph) -> rosetta.protocols.sewing.ModelNode   get a random node from the graph get_random_node_with_edges(...) from builtins.PyCapsule get_random_node_with_edges(rosetta.protocols.sewing.SewGraph) -> rosetta.protocols.sewing.ModelNode   get a random node involved in at least one edge from the graph report_binary_stats(...) from builtins.PyCapsule report_binary_stats(self : rosetta.protocols.sewing.SewGraph, models : rosetta.std.map_int_protocols_sewing_Model, filename : str) -> NoneType set_special_edges(...) from builtins.PyCapsule set_special_edges(self : rosetta.protocols.sewing.SewGraph, scores : rosetta.std.map_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_t_protocols_sewing_HashResult) -> NoneType Methods inherited from rosetta.core.graph.Graph: add_edge(...) from builtins.PyCapsule add_edge(*args, **kwargs) Overloaded function.   1. add_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   add an edge between two vertices.  Invokes "create_edge" from the derived class.  Returns a pointer to the edge after its been added, allowing the calling function  to immediately set data for this edge.   2. add_edge(self : rosetta.core.graph.Graph, example_edge : rosetta.core.graph.Edge) -> rosetta.core.graph.Edge   add an edge to this graph copying the data from an edge in another graph.  Returns a pointer to the edge after its been added, allowing the calling function  to immediately set data for this edge. all_pairs_shortest_paths(...) from builtins.PyCapsule all_pairs_shortest_paths(rosetta.core.graph.Graph) -> ObjexxFCL::FArray2D<int>   O(V^3).  Computes all pairs shortest paths using Warshall's algorithm  and writes all the path distances to the two-dimensional table. const_edge_list_begin(...) from builtins.PyCapsule const_edge_list_begin(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex const_edge_list_end(...) from builtins.PyCapsule const_edge_list_end(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex copy_connectivity(...) from builtins.PyCapsule copy_connectivity(self : rosetta.core.graph.Graph, source : rosetta.core.graph.Graph) -> NoneType   copy the edge connectivity from a source graph with a potentially  unknown type. drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.graph.Graph) -> NoneType   delete all the edges present in the graph drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.graph.Graph, node : int) -> NoneType   delete all the edges for a single vertex in the graph edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   returns a pointer to the edge connecting nodes node1 and node2, if that edge exists  in the graph, o.w. returns 0.  Focuses the graph on this edge for fast subsequent retrieval.   2. find_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   returns a const pointer to the edge connecting nodes node1 and node2, if that edge exists  in the graph, o.w. returns 0.  Focuses the graph on this edge for fast subsequent retrieval. focused_edge(...) from builtins.PyCapsule focused_edge(*args, **kwargs) Overloaded function.   1. focused_edge(rosetta.core.graph.Graph) -> rosetta.core.graph.Edge   returns a pointer to the focused edge   2. focused_edge(rosetta.core.graph.Graph) -> rosetta.core.graph.Edge   returns a const-pointer to the focused edge getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.graph.Graph) -> int   returns a count of all the memory used by every vertex and edge in a graph  by invoking the polymorphic count_static_memory and count_dynamic_memory of each  (possibly derived) node and edge object as well as for the (possibly derived) graph  class. get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> bool   is an edge already present in the graph? O(V) worst case.  O(1) iff all vertices have O(1) edges get_node(...) from builtins.PyCapsule get_node(*args, **kwargs) Overloaded function.   1. get_node(self : rosetta.core.graph.Graph, index : int) -> rosetta.core.graph.Node   2. get_node(self : rosetta.core.graph.Graph, index : int) -> rosetta.core.graph.Node get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.core.graph.Graph) -> rosetta.core.graph.Graph   self pointers   2. get_self_ptr(rosetta.core.graph.Graph) -> rosetta.core.graph.Graph num_edges(...) from builtins.PyCapsule num_edges(rosetta.core.graph.Graph) -> int num_nodes(...) from builtins.PyCapsule num_nodes(rosetta.core.graph.Graph) -> int   the number of nodes in the graph print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.graph.Graph) -> NoneType   send summary information to the screen for all vertices in the graph set_num_nodes(...) from builtins.PyCapsule set_num_nodes(self : rosetta.core.graph.Graph, num_nodes : int) -> NoneType   set the number of nodes in the graph -- deletes any existing edges in the graph   class SewResidue(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.sewing.SewResidue) -> NoneType   2. __init__(self : rosetta.protocols.sewing.SewResidue,  : rosetta.protocols.sewing.SewResidue) -> 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.sewing.SewResidue,  : rosetta.protocols.sewing.SewResidue) -> rosetta.protocols.sewing.SewResidue Data descriptors defined here: basis_atoms_ chi_angles_ matched_residues_ num_neighbors_ residue_type_ resnum_   class SewSegment(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.sewing.SewSegment) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Data descriptors defined here: chimera_ dssp_ hash_ model_id_ residues_ segment_id_   class basis_pair_equal_to(rosetta.std.binary_function_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_bool_t)       Method resolution order: basis_pair_equal_to rosetta.std.binary_function_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_bool_t builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.protocols.sewing.basis_pair_equal_to, bp1 : (rosetta.protocols.sewing.Basis, rosetta.protocols.sewing.Basis), bp2 : (rosetta.protocols.sewing.Basis, rosetta.protocols.sewing.Basis)) -> bool __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.sewing.basis_pair_equal_to) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Methods inherited from rosetta.std.binary_function_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_bool_t: assign(...) from builtins.PyCapsule assign(self : rosetta.std.binary_function_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_bool_t,  : rosetta.std.binary_function_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_bool_t) -> rosetta.std.binary_function_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_bool_t   class basis_pair_hash(rosetta.std.unary_function_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_unsigned_long_t)       Method resolution order: basis_pair_hash rosetta.std.unary_function_std_pair_protocols_sewing_Basis_protocols_sewing_Basis_unsigned_long_t builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.protocols.sewing.basis_pair_hash, basis_pair : (rosetta.protocols.sewing.Basis, rosetta.protocols.sewing.Basis)) -> int __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.sewing.basis_pair_hash) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature.   class coord_equal_to(rosetta.std.binary_function_utility_fixedsizearray1_int_3_utility_fixedsizearray1_int_3_bool_t)       Method resolution order: coord_equal_to rosetta.std.binary_function_utility_fixedsizearray1_int_3_utility_fixedsizearray1_int_3_bool_t builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.protocols.sewing.coord_equal_to, key1 : rosetta.utility.fixedsizearray1_int_3_t, key2 : rosetta.utility.fixedsizearray1_int_3_t) -> bool __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.sewing.coord_equal_to) -> NoneType   2. __init__(self : rosetta.protocols.sewing.coord_equal_to,  : rosetta.protocols.sewing.coord_equal_to) -> 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.sewing.coord_equal_to,  : rosetta.protocols.sewing.coord_equal_to) -> rosetta.protocols.sewing.coord_equal_to   class coord_hash(rosetta.std.unary_function_utility_fixedsizearray1_int_3_unsigned_long_t)       Method resolution order: coord_hash rosetta.std.unary_function_utility_fixedsizearray1_int_3_unsigned_long_t builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.protocols.sewing.coord_hash, key : rosetta.utility.fixedsizearray1_int_3_t) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.sewing.coord_hash) -> NoneType   2. __init__(self : rosetta.protocols.sewing.coord_hash,  : rosetta.protocols.sewing.coord_hash) -> 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.sewing.coord_hash,  : rosetta.protocols.sewing.coord_hash) -> rosetta.protocols.sewing.coord_hash   class move_type(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.protocols.sewing.move_type, rosetta.protocols.sewing.move_type) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.protocols.sewing.move_type) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.sewing.move_type, int) -> NoneType   2. __init__(rosetta.protocols.sewing.move_type, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.protocols.sewing.move_type) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.protocols.sewing.move_type, rosetta.protocols.sewing.move_type) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.protocols.sewing.move_type) -> str Data and other attributes defined here: ADD_EDGE = move_type.ADD_EDGE DELETE_EDGE = move_type.DELETE_EDGE SWITCH_EDGE = move_type.SWITCH_EDGE