Bindings for protocols::loophash namespace

Classes
		builtins.object BBData BBExtraData BackboneDB BackboneSegment LeapIndex LegacyLeapIndex LocalInserter LocalInserter_SimpleMin LoopHashMap LoopHashSampler rosetta.basic.resource_manager.ResourceLoader(builtins.object) LoopHashLibraryLoader rosetta.basic.resource_manager.ResourceLoaderCreator(builtins.object) LoopHashLibraryLoaderCreator rosetta.basic.resource_manager.ResourceOptions(builtins.object) LoopHashLibraryOptions rosetta.basic.resource_manager.ResourceOptionsCreator(builtins.object) LoopHashLibraryOptionsCreator rosetta.protocols.moves.Mover(builtins.object) FastGapMover LoopHashDiversifier LoopHashLibrary LoopHashMoverWrapper LoopHashRelaxProtocol Mover_LoopHashRefine rosetta.protocols.moves.MoverCreator(builtins.object) LoopHashDiversifierCreator LoopHashMoverWrapperCreator rosetta.protocols.wum.MPI_WorkUnitManager(rosetta.protocols.wum.WorkUnitManager) MPI_LoopHashRefine MPI_LoopHashRefine_Emperor MPI_LoopHashRefine_Master rosetta.protocols.wum.WorkUnit_SilentStructStore(rosetta.protocols.wum.WorkUnitBase) WorkUnit_LoopHash rosetta.utility.excn.EXCN_Msg_Exception(rosetta.utility.excn.EXCN_Exception) EXCN_DB_IO_Failed EXCN_Invalid_Hashmap EXCN_No_Extra_Data_To_Write EXCN_Wrong_DB_Format EXCN_bbdb_Merge_Failed   class BBData(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.loophash.BBData) -> NoneType   2. __init__(self : rosetta.protocols.loophash.BBData,  : rosetta.protocols.loophash.BBData) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Data descriptors defined here: angles extra_key   class BBExtraData(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.loophash.BBExtraData,  : rosetta.protocols.loophash.BBExtraData) -> NoneType   2. __init__(rosetta.protocols.loophash.BBExtraData) -> 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.loophash.BBExtraData,  : rosetta.protocols.loophash.BBExtraData) -> rosetta.protocols.loophash.BBExtraData Data descriptors defined here: pdb_id rotamer_id sequence   class BackboneDB(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.loophash.BackboneDB) -> NoneType   2. __init__(self : rosetta.protocols.loophash.BackboneDB,  : rosetta.protocols.loophash.BackboneDB) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_extra_data(...) from builtins.PyCapsule add_extra_data(self : rosetta.protocols.loophash.BackboneDB, extra : rosetta.protocols.loophash.BBExtraData) -> NoneType add_pose(...) from builtins.PyCapsule add_pose(*args, **kwargs) Overloaded function.   1. add_pose(self : rosetta.protocols.loophash.BackboneDB, pose : rosetta.core.pose.Pose, nres : int, offset : int) -> NoneType   2. add_pose(self : rosetta.protocols.loophash.BackboneDB, pose : rosetta.core.pose.Pose, nres : int, offset : int, chunk : rosetta.protocols.frag_picker.VallChunk) -> NoneType add_protein(...) from builtins.PyCapsule add_protein(self : rosetta.protocols.loophash.BackboneDB, new_protein : rosetta.protocols.loophash.BBData) -> NoneType angle(...) from builtins.PyCapsule angle(self : rosetta.protocols.loophash.BackboneDB, index : int, offset : int) -> float assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loophash.BackboneDB,  : rosetta.protocols.loophash.BackboneDB) -> rosetta.protocols.loophash.BackboneDB extra_size(...) from builtins.PyCapsule extra_size(rosetta.protocols.loophash.BackboneDB) -> int get_backbone_segment(...) from builtins.PyCapsule get_backbone_segment(self : rosetta.protocols.loophash.BackboneDB, index : int, offset : int, len : int, bs : rosetta.protocols.loophash.BackboneSegment) -> NoneType get_extra_data(...) from builtins.PyCapsule get_extra_data(self : rosetta.protocols.loophash.BackboneDB, index : int, extra : rosetta.protocols.loophash.BBExtraData) -> NoneType get_mem_foot_print(...) from builtins.PyCapsule get_mem_foot_print(rosetta.protocols.loophash.BackboneDB) -> int get_protein(...) from builtins.PyCapsule get_protein(self : rosetta.protocols.loophash.BackboneDB, index : int, protein : rosetta.protocols.loophash.BBData) -> NoneType read_db(...) from builtins.PyCapsule read_db(self : rosetta.protocols.loophash.BackboneDB, filename : str, load_extra : bool) -> NoneType read_homologs(...) from builtins.PyCapsule read_homologs(rosetta.protocols.loophash.BackboneDB) -> NoneType read_legacydb(...) from builtins.PyCapsule read_legacydb(self : rosetta.protocols.loophash.BackboneDB, filename : str) -> NoneType size(...) from builtins.PyCapsule size(rosetta.protocols.loophash.BackboneDB) -> int write_db(...) from builtins.PyCapsule write_db(self : rosetta.protocols.loophash.BackboneDB, filename : str) -> NoneType   class BackboneSegment(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.protocols.loophash.BackboneSegment, bs1 : rosetta.protocols.loophash.BackboneSegment) -> bool __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.loophash.BackboneSegment) -> NoneType   2. __init__(self : rosetta.protocols.loophash.BackboneSegment, phi : rosetta.std.vector_double, psi : rosetta.std.vector_double, omega : rosetta.std.vector_double) -> NoneType __ne__(...) from builtins.PyCapsule __ne__(self : rosetta.protocols.loophash.BackboneSegment, other : rosetta.protocols.loophash.BackboneSegment) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. apply_to_pose(...) from builtins.PyCapsule apply_to_pose(*args, **kwargs) Overloaded function.   1. apply_to_pose(self : rosetta.protocols.loophash.BackboneSegment, pose : rosetta.core.pose.Pose, ir : int) -> NoneType   2. apply_to_pose(self : rosetta.protocols.loophash.BackboneSegment, pose : rosetta.core.pose.Pose, ir : int, cut : bool) -> NoneType compare(...) from builtins.PyCapsule compare(self : rosetta.protocols.loophash.BackboneSegment, bs1 : rosetta.protocols.loophash.BackboneSegment, tolerance : float) -> bool get_mem_foot_print(...) from builtins.PyCapsule get_mem_foot_print(rosetta.protocols.loophash.BackboneSegment) -> int length(...) from builtins.PyCapsule length(rosetta.protocols.loophash.BackboneSegment) -> int omega(...) from builtins.PyCapsule omega(rosetta.protocols.loophash.BackboneSegment) -> rosetta.std.vector_double phi(...) from builtins.PyCapsule phi(rosetta.protocols.loophash.BackboneSegment) -> rosetta.std.vector_double print(...) from builtins.PyCapsule print(rosetta.protocols.loophash.BackboneSegment) -> NoneType psi(...) from builtins.PyCapsule psi(rosetta.protocols.loophash.BackboneSegment) -> rosetta.std.vector_double read_from_pose(...) from builtins.PyCapsule read_from_pose(self : rosetta.protocols.loophash.BackboneSegment, pose : rosetta.core.pose.Pose, ir : int, length : int) -> NoneType   class EXCN_DB_IO_Failed(rosetta.utility.excn.EXCN_Msg_Exception)       Method resolution order: EXCN_DB_IO_Failed rosetta.utility.excn.EXCN_Msg_Exception rosetta.utility.excn.EXCN_Exception rosetta.utility.excn.EXCN_Base builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, filename : str, action : str) -> NoneType   2. __init__(handle, rosetta.protocols.loophash.EXCN_DB_IO_Failed) -> 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.loophash.EXCN_DB_IO_Failed,  : rosetta.protocols.loophash.EXCN_DB_IO_Failed) -> rosetta.protocols.loophash.EXCN_DB_IO_Failed Methods inherited from rosetta.utility.excn.EXCN_Msg_Exception: add_msg(...) from builtins.PyCapsule add_msg(self : rosetta.utility.excn.EXCN_Msg_Exception, str : str) -> NoneType msg(...) from builtins.PyCapsule msg(rosetta.utility.excn.EXCN_Msg_Exception) -> str Methods inherited from rosetta.utility.excn.EXCN_Base: __str__(...) from builtins.PyCapsule __str__(rosetta.utility.excn.EXCN_Base) -> str   class EXCN_Invalid_Hashmap(rosetta.utility.excn.EXCN_Msg_Exception)       Method resolution order: EXCN_Invalid_Hashmap rosetta.utility.excn.EXCN_Msg_Exception rosetta.utility.excn.EXCN_Exception rosetta.utility.excn.EXCN_Base builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, size : int) -> NoneType   2. __init__(handle, rosetta.protocols.loophash.EXCN_Invalid_Hashmap) -> 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.loophash.EXCN_Invalid_Hashmap,  : rosetta.protocols.loophash.EXCN_Invalid_Hashmap) -> rosetta.protocols.loophash.EXCN_Invalid_Hashmap Methods inherited from rosetta.utility.excn.EXCN_Msg_Exception: add_msg(...) from builtins.PyCapsule add_msg(self : rosetta.utility.excn.EXCN_Msg_Exception, str : str) -> NoneType msg(...) from builtins.PyCapsule msg(rosetta.utility.excn.EXCN_Msg_Exception) -> str Methods inherited from rosetta.utility.excn.EXCN_Base: __str__(...) from builtins.PyCapsule __str__(rosetta.utility.excn.EXCN_Base) -> str   class EXCN_No_Extra_Data_To_Write(rosetta.utility.excn.EXCN_Msg_Exception)       Method resolution order: EXCN_No_Extra_Data_To_Write rosetta.utility.excn.EXCN_Msg_Exception rosetta.utility.excn.EXCN_Exception rosetta.utility.excn.EXCN_Base builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.loophash.EXCN_No_Extra_Data_To_Write) -> 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.loophash.EXCN_No_Extra_Data_To_Write,  : rosetta.protocols.loophash.EXCN_No_Extra_Data_To_Write) -> rosetta.protocols.loophash.EXCN_No_Extra_Data_To_Write Methods inherited from rosetta.utility.excn.EXCN_Msg_Exception: add_msg(...) from builtins.PyCapsule add_msg(self : rosetta.utility.excn.EXCN_Msg_Exception, str : str) -> NoneType msg(...) from builtins.PyCapsule msg(rosetta.utility.excn.EXCN_Msg_Exception) -> str Methods inherited from rosetta.utility.excn.EXCN_Base: __str__(...) from builtins.PyCapsule __str__(rosetta.utility.excn.EXCN_Base) -> str   class EXCN_Wrong_DB_Format(rosetta.utility.excn.EXCN_Msg_Exception)       Method resolution order: EXCN_Wrong_DB_Format rosetta.utility.excn.EXCN_Msg_Exception rosetta.utility.excn.EXCN_Exception rosetta.utility.excn.EXCN_Base builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, filename : str) -> NoneType   2. __init__(handle, rosetta.protocols.loophash.EXCN_Wrong_DB_Format) -> 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.loophash.EXCN_Wrong_DB_Format,  : rosetta.protocols.loophash.EXCN_Wrong_DB_Format) -> rosetta.protocols.loophash.EXCN_Wrong_DB_Format Methods inherited from rosetta.utility.excn.EXCN_Msg_Exception: add_msg(...) from builtins.PyCapsule add_msg(self : rosetta.utility.excn.EXCN_Msg_Exception, str : str) -> NoneType msg(...) from builtins.PyCapsule msg(rosetta.utility.excn.EXCN_Msg_Exception) -> str Methods inherited from rosetta.utility.excn.EXCN_Base: __str__(...) from builtins.PyCapsule __str__(rosetta.utility.excn.EXCN_Base) -> str   class EXCN_bbdb_Merge_Failed(rosetta.utility.excn.EXCN_Msg_Exception)       Method resolution order: EXCN_bbdb_Merge_Failed rosetta.utility.excn.EXCN_Msg_Exception rosetta.utility.excn.EXCN_Exception rosetta.utility.excn.EXCN_Base builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, reason : str) -> NoneType   2. __init__(self : handle,  : bool,  : bool) -> NoneType   3. __init__(handle, rosetta.protocols.loophash.EXCN_bbdb_Merge_Failed) -> 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.loophash.EXCN_bbdb_Merge_Failed,  : rosetta.protocols.loophash.EXCN_bbdb_Merge_Failed) -> rosetta.protocols.loophash.EXCN_bbdb_Merge_Failed Methods inherited from rosetta.utility.excn.EXCN_Msg_Exception: add_msg(...) from builtins.PyCapsule add_msg(self : rosetta.utility.excn.EXCN_Msg_Exception, str : str) -> NoneType msg(...) from builtins.PyCapsule msg(rosetta.utility.excn.EXCN_Msg_Exception) -> str Methods inherited from rosetta.utility.excn.EXCN_Base: __str__(...) from builtins.PyCapsule __str__(rosetta.utility.excn.EXCN_Base) -> str   class FastGapMover(rosetta.protocols.moves.Mover)     Mover class for closing gaps. This Mover checks for any gaps using residue residue distances Then eats back at the chain surrounding it until loophash finds a fragment that fits in the space without changing the rest of pose too much.     Method resolution order: FastGapMover 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.loophash.FastGapMover) -> 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.loophash.FastGapMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loophash.FastGapMover,  : rosetta.protocols.loophash.FastGapMover) -> rosetta.protocols.loophash.FastGapMover clone(...) from builtins.PyCapsule clone(rosetta.protocols.loophash.FastGapMover) -> rosetta.protocols.moves.Mover   clone has to be overridden only if clone invocation is expected. fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.loophash.FastGapMover) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.loophash.FastGapMover) -> str max_rms(...) from builtins.PyCapsule max_rms(self : rosetta.protocols.loophash.FastGapMover, setting : float) -> rosetta.protocols.loophash.FastGapMover min_rms(...) from builtins.PyCapsule min_rms(self : rosetta.protocols.loophash.FastGapMover, setting : float) -> rosetta.protocols.loophash.FastGapMover non_ideal(...) from builtins.PyCapsule non_ideal(self : rosetta.protocols.loophash.FastGapMover, setting : bool) -> rosetta.protocols.loophash.FastGapMover 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 LeapIndex(builtins.object)     The LeapIndex stores information about a particular Leap. It hold the oroiginal high precision rigid body transform  and an Index to a Backbone Database (BackboneDB) that has the actual phi psi angles. THe storage of the precise RT takes a lot of space and may be deprecated at some point, since once it is hashed, it is rarely needed and can be recomputed if it is. Note that the length of the loop is not stored either, this is again done for saving memory, as huge lists of Leaps are typically created all with the same length. THe length is stored and handled by the owner of LeapIndex list. The LeapIndex does not store the actual backbone coordinates of the Leap. It merely contains an index (the BackboneIndex) which refers to a serial store of backbone triples (phi,psi, omega) which are stored somewhere else in a BackboneDB. THis is improtant to save memory storage since multiple Leaps cna share the same backbone triple and redundant storage would be hugely wasteful.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.loophash.LeapIndex) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Data descriptors defined here: index key offset   class LegacyLeapIndex(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.loophash.LegacyLeapIndex) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Data descriptors defined here: ba rotx roty rotz vecx vecy vecz   class LocalInserter(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.loophash.LocalInserter) -> NoneType   2. __init__(rosetta.protocols.loophash.LocalInserter, rosetta.protocols.loophash.LocalInserter) -> 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.loophash.LocalInserter,  : rosetta.protocols.loophash.LocalInserter) -> rosetta.protocols.loophash.LocalInserter make_local_bb_change(...) from builtins.PyCapsule make_local_bb_change(self : rosetta.protocols.loophash.LocalInserter, start_pose : rosetta.core.pose.Pose, original_pose : rosetta.core.pose.Pose, new_bs : rosetta.protocols.loophash.BackboneSegment, res_pos : int) -> float make_local_bb_change_close_gaps(...) from builtins.PyCapsule make_local_bb_change_close_gaps(self : rosetta.protocols.loophash.LocalInserter, start_pose : rosetta.core.pose.Pose, original_pose : rosetta.core.pose.Pose, new_bs : rosetta.protocols.loophash.BackboneSegment, res_pos : int) -> float make_local_bb_change_include_cut(...) from builtins.PyCapsule make_local_bb_change_include_cut(self : rosetta.protocols.loophash.LocalInserter, start_pose : rosetta.core.pose.Pose, original_pose : rosetta.core.pose.Pose, new_bs : rosetta.protocols.loophash.BackboneSegment, res_pos : int) -> float   class LocalInserter_SimpleMin(LocalInserter)       Method resolution order: LocalInserter_SimpleMin LocalInserter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.loophash.LocalInserter_SimpleMin) -> 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.loophash.LocalInserter_SimpleMin,  : rosetta.protocols.loophash.LocalInserter_SimpleMin) -> rosetta.protocols.loophash.LocalInserter_SimpleMin make_local_bb_change(...) from builtins.PyCapsule make_local_bb_change(self : rosetta.protocols.loophash.LocalInserter_SimpleMin, start_pose : rosetta.core.pose.Pose, original_pose : rosetta.core.pose.Pose, new_bs : rosetta.protocols.loophash.BackboneSegment, res_pos : int) -> float make_local_bb_change_close_gaps(...) from builtins.PyCapsule make_local_bb_change_close_gaps(self : rosetta.protocols.loophash.LocalInserter_SimpleMin, start_pose : rosetta.core.pose.Pose, original_pose : rosetta.core.pose.Pose, new_bs : rosetta.protocols.loophash.BackboneSegment, res_pos : int) -> float make_local_bb_change_include_cut(...) from builtins.PyCapsule make_local_bb_change_include_cut(self : rosetta.protocols.loophash.LocalInserter_SimpleMin, start_pose : rosetta.core.pose.Pose, original_pose : rosetta.core.pose.Pose, new_bs : rosetta.protocols.loophash.BackboneSegment, res_pos : int) -> float scorefxn_cen_cst(...) from builtins.PyCapsule scorefxn_cen_cst(self : rosetta.protocols.loophash.LocalInserter_SimpleMin, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   set the score function for the second round of minimization during a loophash insert scorefxn_rama_cst(...) from builtins.PyCapsule scorefxn_rama_cst(self : rosetta.protocols.loophash.LocalInserter_SimpleMin, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   set the score function for the first round of minimization during a loophash insert   class LoopHashDiversifier(rosetta.protocols.moves.Mover)       Method resolution order: LoopHashDiversifier rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, library : rosetta.protocols.loophash.LoopHashLibrary, min_inter_ss_bbrms : float, max_inter_ss_bbrms : float, min_intra_ss_bbrms : float, max_intra_ss_bbrms : float, min_rms : float, max_rms : float, start_res : int, stop_res : int, window_size : int, max_radius : int, max_struct : int, num_iterations : int, num_try_div : int, diversify_loop_only : bool, ideal : bool, filter_by_phipsi : bool, cenfilter : rosetta.protocols.filters.Filter, ranking_cenfilter : rosetta.protocols.filters.Filter, scorefxn_cen_cst : rosetta.core.scoring.ScoreFunction, scorefxn_rama_cst : rosetta.core.scoring.ScoreFunction) -> NoneType   3. __init__(handle, rosetta.protocols.loophash.LoopHashDiversifier) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_loop_size(...) from builtins.PyCapsule add_loop_size(self : rosetta.protocols.loophash.LoopHashDiversifier, loop_size : int) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.loophash.LoopHashDiversifier, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loophash.LoopHashDiversifier,  : rosetta.protocols.loophash.LoopHashDiversifier) -> rosetta.protocols.loophash.LoopHashDiversifier cenfilter(...) from builtins.PyCapsule cenfilter(self : rosetta.protocols.loophash.LoopHashDiversifier, cenfilter : rosetta.protocols.filters.Filter) -> NoneType clone(...) from builtins.PyCapsule clone(rosetta.protocols.loophash.LoopHashDiversifier) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.loophash.LoopHashDiversifier) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.loophash.LoopHashDiversifier) -> str loop_sizes(...) from builtins.PyCapsule loop_sizes(rosetta.protocols.loophash.LoopHashDiversifier) -> rosetta.utility.vector1_unsigned_long max_inter_ss_bbrms(...) from builtins.PyCapsule max_inter_ss_bbrms(*args, **kwargs) Overloaded function.   1. max_inter_ss_bbrms(rosetta.protocols.loophash.LoopHashDiversifier) -> float   2. max_inter_ss_bbrms(self : rosetta.protocols.loophash.LoopHashDiversifier, max_inter_ss_bbrms : float) -> NoneType max_intra_ss_bbrms(...) from builtins.PyCapsule max_intra_ss_bbrms(*args, **kwargs) Overloaded function.   1. max_intra_ss_bbrms(rosetta.protocols.loophash.LoopHashDiversifier) -> float   2. max_intra_ss_bbrms(self : rosetta.protocols.loophash.LoopHashDiversifier, max_intra_ss_bbrms : float) -> NoneType max_rms(...) from builtins.PyCapsule max_rms(*args, **kwargs) Overloaded function.   1. max_rms(rosetta.protocols.loophash.LoopHashDiversifier) -> float   2. max_rms(self : rosetta.protocols.loophash.LoopHashDiversifier, max_rms : float) -> NoneType min_inter_ss_bbrms(...) from builtins.PyCapsule min_inter_ss_bbrms(*args, **kwargs) Overloaded function.   1. min_inter_ss_bbrms(rosetta.protocols.loophash.LoopHashDiversifier) -> float   2. min_inter_ss_bbrms(self : rosetta.protocols.loophash.LoopHashDiversifier, min_inter_ss_bbrms : float) -> NoneType min_intra_ss_bbrms(...) from builtins.PyCapsule min_intra_ss_bbrms(*args, **kwargs) Overloaded function.   1. min_intra_ss_bbrms(rosetta.protocols.loophash.LoopHashDiversifier) -> float   2. min_intra_ss_bbrms(self : rosetta.protocols.loophash.LoopHashDiversifier, min_intra_ss_bbrms : float) -> NoneType min_rms(...) from builtins.PyCapsule min_rms(*args, **kwargs) Overloaded function.   1. min_rms(rosetta.protocols.loophash.LoopHashDiversifier) -> float   2. min_rms(self : rosetta.protocols.loophash.LoopHashDiversifier, min_rms : float) -> NoneType num_iterations(...) from builtins.PyCapsule num_iterations(*args, **kwargs) Overloaded function.   1. num_iterations(rosetta.protocols.loophash.LoopHashDiversifier) -> int   2. num_iterations(self : rosetta.protocols.loophash.LoopHashDiversifier, num_iterations : int) -> NoneType num_try_div(...) from builtins.PyCapsule num_try_div(*args, **kwargs) Overloaded function.   1. num_try_div(rosetta.protocols.loophash.LoopHashDiversifier) -> int   2. num_try_div(self : rosetta.protocols.loophash.LoopHashDiversifier, num_try_div : int) -> NoneType ranking_cenfilter(...) from builtins.PyCapsule ranking_cenfilter(*args, **kwargs) Overloaded function.   1. ranking_cenfilter(self : rosetta.protocols.loophash.LoopHashDiversifier, filter : rosetta.protocols.filters.Filter) -> NoneType   2. ranking_cenfilter(rosetta.protocols.loophash.LoopHashDiversifier) -> rosetta.protocols.filters.Filter 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 LoopHashDiversifierCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: LoopHashDiversifierCreator 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.loophash.LoopHashDiversifierCreator,  : rosetta.protocols.loophash.LoopHashDiversifierCreator) -> rosetta.protocols.loophash.LoopHashDiversifierCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.loophash.LoopHashDiversifierCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.loophash.LoopHashDiversifierCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class LoopHashLibrary(rosetta.protocols.moves.Mover)       Method resolution order: LoopHashLibrary rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   doc   2. __init__(handle, rosetta.utility.vector1_unsigned_long) -> NoneType   doc   3. __init__(handle, rosetta.utility.vector1_unsigned_long, int) -> NoneType   doc   4. __init__(self : handle, init_sizes : rosetta.utility.vector1_unsigned_long, num_partitions : int, assigned_num : int) -> NoneType   5. __init__(handle, rosetta.protocols.loophash.LoopHashLibrary) -> 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.loophash.LoopHashLibrary, pose : rosetta.core.pose.Pose) -> NoneType apply_random(...) from builtins.PyCapsule apply_random(self : rosetta.protocols.loophash.LoopHashLibrary, pose : rosetta.core.pose.Pose, fir : int, fjr : int, min_rms : float, max_rms : float) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loophash.LoopHashLibrary,  : rosetta.protocols.loophash.LoopHashLibrary) -> rosetta.protocols.loophash.LoopHashLibrary backbone_database(...) from builtins.PyCapsule backbone_database(rosetta.protocols.loophash.LoopHashLibrary) -> rosetta.protocols.loophash.BackboneDB clone(...) from builtins.PyCapsule clone(rosetta.protocols.loophash.LoopHashLibrary) -> rosetta.protocols.moves.Mover create_db(...) from builtins.PyCapsule create_db(rosetta.protocols.loophash.LoopHashLibrary) -> NoneType delete_db(...) from builtins.PyCapsule delete_db(rosetta.protocols.loophash.LoopHashLibrary) -> NoneType extract_data_from_pose(...) from builtins.PyCapsule extract_data_from_pose(*args, **kwargs) Overloaded function.   1. extract_data_from_pose(self : rosetta.protocols.loophash.LoopHashLibrary, pose : rosetta.core.pose.Pose, nres : int) -> NoneType   2. extract_data_from_pose(self : rosetta.protocols.loophash.LoopHashLibrary, pose : rosetta.core.pose.Pose, nres : int, chunk : rosetta.protocols.frag_picker.VallChunk) -> NoneType   3. extract_data_from_pose(self : rosetta.protocols.loophash.LoopHashLibrary, pose : rosetta.core.pose.Pose) -> NoneType fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.loophash.LoopHashLibrary) -> rosetta.protocols.moves.Mover get_all(...) from builtins.PyCapsule get_all(*args, **kwargs) Overloaded function.   1. get_all(self : rosetta.protocols.loophash.LoopHashLibrary, pose : rosetta.core.pose.Pose, lib_structs : rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType   2. get_all(self : rosetta.protocols.loophash.LoopHashLibrary, pose : rosetta.core.pose.Pose, lib_structs : rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t, start_res : int) -> NoneType   3. get_all(self : rosetta.protocols.loophash.LoopHashLibrary, pose : rosetta.core.pose.Pose, lib_structs : rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t, start_res : int, stop_res : int) -> NoneType   4. get_all(self : rosetta.protocols.loophash.LoopHashLibrary, pose : rosetta.core.pose.Pose, lib_structs : rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t, start_res : int, stop_res : int, min_bbrms : float) -> NoneType   5. get_all(self : rosetta.protocols.loophash.LoopHashLibrary, pose : rosetta.core.pose.Pose, lib_structs : rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t, start_res : int, stop_res : int, min_bbrms : float, max_bbrms : float) -> NoneType   6. get_all(self : rosetta.protocols.loophash.LoopHashLibrary, pose : rosetta.core.pose.Pose, lib_structs : rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t, start_res : int, stop_res : int, min_bbrms : float, max_bbrms : float, min_rms : float) -> NoneType   7. get_all(self : rosetta.protocols.loophash.LoopHashLibrary, pose : rosetta.core.pose.Pose, lib_structs : rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t, start_res : int, stop_res : int, min_bbrms : float, max_bbrms : float, min_rms : float, max_rms : float) -> NoneType get_extra(...) from builtins.PyCapsule get_extra(rosetta.protocols.loophash.LoopHashLibrary) -> bool get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.loophash.LoopHashLibrary) -> str gethash(...) from builtins.PyCapsule gethash(self : rosetta.protocols.loophash.LoopHashLibrary, size : int) -> rosetta.protocols.loophash.LoopHashMap graft_loop(...) from builtins.PyCapsule graft_loop(self : rosetta.protocols.loophash.LoopHashLibrary, src_pose : rosetta.core.pose.Pose, tgt_pose : rosetta.core.pose.Pose, myloop : rosetta.protocols.loops.Loop) -> NoneType hash_sizes(...) from builtins.PyCapsule hash_sizes(rosetta.protocols.loophash.LoopHashLibrary) -> rosetta.std.vector_unsigned_long load_db(...) from builtins.PyCapsule load_db(rosetta.protocols.loophash.LoopHashLibrary) -> NoneType load_mergeddb(...) from builtins.PyCapsule load_mergeddb(rosetta.protocols.loophash.LoopHashLibrary) -> NoneType loopdb_range(...) from builtins.PyCapsule loopdb_range(rosetta.protocols.loophash.LoopHashLibrary) -> (int, int) mem_foot_print(...) from builtins.PyCapsule mem_foot_print(rosetta.protocols.loophash.LoopHashLibrary) -> NoneType merge(...) from builtins.PyCapsule merge(self : rosetta.protocols.loophash.LoopHashLibrary, second_lib : rosetta.protocols.loophash.LoopHashLibrary, rms_cutoffs : rosetta.utility.vector1_double) -> NoneType merge_bbdb(...) from builtins.PyCapsule merge_bbdb(self : rosetta.protocols.loophash.LoopHashLibrary, second_bbdb : rosetta.protocols.loophash.BackboneDB, index_offset : int) -> bool save_db(...) from builtins.PyCapsule save_db(rosetta.protocols.loophash.LoopHashLibrary) -> NoneType set_create_db(...) from builtins.PyCapsule set_create_db(*args, **kwargs) Overloaded function.   1. set_create_db(rosetta.protocols.loophash.LoopHashLibrary) -> NoneType   2. set_create_db(self : rosetta.protocols.loophash.LoopHashLibrary, setting : bool) -> NoneType set_db_path(...) from builtins.PyCapsule set_db_path(self : rosetta.protocols.loophash.LoopHashLibrary, setting : str) -> NoneType set_default_score_functions(...) from builtins.PyCapsule set_default_score_functions(rosetta.protocols.loophash.LoopHashLibrary) -> NoneType setup_hash_maps(...) from builtins.PyCapsule setup_hash_maps(rosetta.protocols.loophash.LoopHashLibrary) -> NoneType sort(...) from builtins.PyCapsule sort(rosetta.protocols.loophash.LoopHashLibrary) -> NoneType test_loop_sample(...) from builtins.PyCapsule test_loop_sample(self : rosetta.protocols.loophash.LoopHashLibrary, pose : rosetta.core.pose.Pose, nres : int) -> NoneType test_saving_library(...) from builtins.PyCapsule test_saving_library(self : rosetta.protocols.loophash.LoopHashLibrary,  : rosetta.core.pose.Pose, ir : int, deposit : bool) -> 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. 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 LoopHashLibraryLoader(rosetta.basic.resource_manager.ResourceLoader)     %LoopHashLibraryLoader constructs a LoopHashLibrary instance from data provided by the %ResourceManager.     The %LoopHashLibraryLoader is given a LoopHashLibraryOptions containing a %vector of loop lengths from the ResourceManager.  This information is then used to produce a LoopHashLibraryOP to return to the protocol.     Method resolution order: LoopHashLibraryLoader rosetta.basic.resource_manager.ResourceLoader 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.loophash.LoopHashLibraryLoader,  : rosetta.protocols.loophash.LoopHashLibraryLoader) -> rosetta.protocols.loophash.LoopHashLibraryLoader default_options(...) from builtins.PyCapsule default_options(rosetta.protocols.loophash.LoopHashLibraryLoader) -> rosetta.basic.resource_manager.ResourceOptions   Return a ResourceOptionsOP with the default set of options.   class LoopHashLibraryLoaderCreator(rosetta.basic.resource_manager.ResourceLoaderCreator)     %LoopHashLibraryLoaderCreator allows the ResourceLoaderFactory to create a LoopHashLibraryLoader instance.     The LoopHashLibraryLoader class can be constructed from the string "LoopHashLibrary", which enables a user to specify that this type of %resource is required for a particular %job in their XML input file.     Method resolution order: LoopHashLibraryLoaderCreator rosetta.basic.resource_manager.ResourceLoaderCreator 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.loophash.LoopHashLibraryLoaderCreator,  : rosetta.protocols.loophash.LoopHashLibraryLoaderCreator) -> rosetta.protocols.loophash.LoopHashLibraryLoaderCreator create_resource_loader(...) from builtins.PyCapsule create_resource_loader(rosetta.protocols.loophash.LoopHashLibraryLoaderCreator) -> rosetta.basic.resource_manager.ResourceLoader   Return a up-casted owning pointer (ResourceLoaderOP) to the resource loader. loader_type(...) from builtins.PyCapsule loader_type(rosetta.protocols.loophash.LoopHashLibraryLoaderCreator) -> str   Return the string identifier for the associated ResourceLoader (LoopHashLibrary).   class LoopHashLibraryOptions(rosetta.basic.resource_manager.ResourceOptions)     %LoopHashLibraryOptions encapsulates the options associated with LoopHashLibrary %resources.     These options are read in from a resource definition file and each LoopHashLibrary resource has a corresponding %LoopHashLibraryOptions instance.     Method resolution order: LoopHashLibraryOptions rosetta.basic.resource_manager.ResourceOptions builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.loophash.LoopHashLibraryOptions) -> 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.loophash.LoopHashLibraryOptions,  : rosetta.protocols.loophash.LoopHashLibraryOptions) -> rosetta.protocols.loophash.LoopHashLibraryOptions loop_sizes(...) from builtins.PyCapsule loop_sizes(*args, **kwargs) Overloaded function.   1. loop_sizes(rosetta.protocols.loophash.LoopHashLibraryOptions) -> rosetta.utility.vector1_unsigned_long   Return a %vector of loop sizes that will be used to construct a LoopHashLibrary.   2. loop_sizes(self : rosetta.protocols.loophash.LoopHashLibraryOptions, loop_sizes : rosetta.utility.vector1_unsigned_long) -> NoneType   Set the loop sizes that will be used to construct a LoopHashLibrary to a %vector of loop lengths. parse_my_tag(...) from builtins.PyCapsule parse_my_tag(self : rosetta.protocols.loophash.LoopHashLibraryOptions, tag : rosetta.utility.tag.Tag) -> NoneType   Read the configuration of the LoopHashLibrary %resource from the tag generated from the resource definition  file. type(...) from builtins.PyCapsule type(rosetta.protocols.loophash.LoopHashLibraryOptions) -> str   Return the name of this class (LoopHashLibraryOptions). Methods inherited from rosetta.basic.resource_manager.ResourceOptions: __str__(...) from builtins.PyCapsule __str__(rosetta.basic.resource_manager.ResourceOptions) -> str name(...) from builtins.PyCapsule name(*args, **kwargs) Overloaded function.   1. name(rosetta.basic.resource_manager.ResourceOptions) -> str   A name given to a particular ResourceOptions instance.  This function allows for better error message delivery.   2. name(self : rosetta.basic.resource_manager.ResourceOptions, setting : str) -> NoneType   Set the name for this %ResoureOptions instance.   class LoopHashLibraryOptionsCreator(rosetta.basic.resource_manager.ResourceOptionsCreator)     %LoopHashLibraryOptionsCreator allows the ResourceLoaderFactory to create a LoopHashLibraryOptions instance.     The LoopHashLibraryOptions class can be constructed from the string "LoopHashLibraryOptions", which enables a user to configure a LoopHashLibrary %resource in his/her resource definitions file.     Method resolution order: LoopHashLibraryOptionsCreator rosetta.basic.resource_manager.ResourceOptionsCreator 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.loophash.LoopHashLibraryOptionsCreator,  : rosetta.protocols.loophash.LoopHashLibraryOptionsCreator) -> rosetta.protocols.loophash.LoopHashLibraryOptionsCreator create_options(...) from builtins.PyCapsule create_options(rosetta.protocols.loophash.LoopHashLibraryOptionsCreator) -> rosetta.basic.resource_manager.ResourceOptions   Return a up-casted owning pointer (ResourceOptionsOP) to the resource options. options_type(...) from builtins.PyCapsule options_type(rosetta.protocols.loophash.LoopHashLibraryOptionsCreator) -> str   Return the string identifier for the associated ResourceOptions (LoopHashLibraryOptions).   class LoopHashMap(builtins.object)     the loop hash map stores LeapIndexes and a hashmap to access those LeapIndexes quickly by their 6D coordinates.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.loophash.LoopHashMap) -> NoneType   doc   2. __init__(self : rosetta.protocols.loophash.LoopHashMap, loop_size : int) -> NoneType   3. __init__(self : rosetta.protocols.loophash.LoopHashMap, other : rosetta.protocols.loophash.LoopHashMap) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_leap(...) from builtins.PyCapsule add_leap(*args, **kwargs) Overloaded function.   1. add_leap(self : rosetta.protocols.loophash.LoopHashMap, leap_index : rosetta.protocols.loophash.LeapIndex, transform : rosetta.utility.fixedsizearray1_double_6_t) -> NoneType   Add a leap/loop to the HashMap   2. add_leap(self : rosetta.protocols.loophash.LoopHashMap, leap_index : rosetta.protocols.loophash.LeapIndex, key : int) -> NoneType   Add a leap/loop to the HashMap with a key, skipping hashing add_legacyleap(...) from builtins.PyCapsule add_legacyleap(self : rosetta.protocols.loophash.LoopHashMap, legacyleap_index : rosetta.protocols.loophash.LegacyLeapIndex) -> NoneType   Add an legacy leap/loop to the HashMap assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loophash.LoopHashMap, other : rosetta.protocols.loophash.LoopHashMap) -> rosetta.protocols.loophash.LoopHashMap get_loop_size(...) from builtins.PyCapsule get_loop_size(rosetta.protocols.loophash.LoopHashMap) -> int   Query the loopsize of this LoopHashMap get_peptide(...) from builtins.PyCapsule get_peptide(self : rosetta.protocols.loophash.LoopHashMap, index : int) -> rosetta.protocols.loophash.LeapIndex   Obtain an index to a given peptide saved lookup(...) from builtins.PyCapsule lookup(*args, **kwargs) Overloaded function.   1. lookup(self : rosetta.protocols.loophash.LoopHashMap, transform : rosetta.utility.fixedsizearray1_double_6_t, result : rosetta.std.vector_unsigned_long) -> NoneType   Append to a bucket of vectors in the appropriate bin, lookup by transform   2. lookup(self : rosetta.protocols.loophash.LoopHashMap, index : int, result : rosetta.std.vector_unsigned_long) -> NoneType   Append to a bucket of vectors in the appropriate bin, lookup by bin index  Using core::Size instead of boost::uinst64_t lookup_withkey(...) from builtins.PyCapsule lookup_withkey(self : rosetta.protocols.loophash.LoopHashMap, key : int, result : rosetta.std.vector_unsigned_long) -> NoneType   Return a vector of loops with equal keys  given a key mem_foot_print(...) from builtins.PyCapsule mem_foot_print(rosetta.protocols.loophash.LoopHashMap) -> NoneType   Return the memory usage of this class n_loops(...) from builtins.PyCapsule n_loops(rosetta.protocols.loophash.LoopHashMap) -> int radial_count(...) from builtins.PyCapsule radial_count(self : rosetta.protocols.loophash.LoopHashMap, radius : int, center : rosetta.utility.fixedsizearray1_double_6_t) -> int   count hits in the appropriate bin, radial lookup by transform radial_lookup(...) from builtins.PyCapsule radial_lookup(self : rosetta.protocols.loophash.LoopHashMap, radius : int, transform : rosetta.utility.fixedsizearray1_double_6_t, result : rosetta.std.vector_unsigned_long) -> NoneType   Append to a bucket of vectors in the appropriate bin, radial lookup by transform radial_lookup_withkey(...) from builtins.PyCapsule radial_lookup_withkey(self : rosetta.protocols.loophash.LoopHashMap, key : int, radius : int, result : rosetta.std.vector_unsigned_long) -> NoneType   Return a vector of loops with equal keys  given a key read_db(...) from builtins.PyCapsule read_db(*args, **kwargs) Overloaded function.   1. read_db(self : rosetta.protocols.loophash.LoopHashMap, filename : str, loopdb_range : (int, int), homolog_index : rosetta.std.map_unsigned_long_bool) -> NoneType   Basic IO functionality - allows reading and writing text states to/from disk   2. read_db(self : rosetta.protocols.loophash.LoopHashMap, filename : str) -> NoneType read_legacydb(...) from builtins.PyCapsule read_legacydb(self : rosetta.protocols.loophash.LoopHashMap, filename : str) -> NoneType   Reads legacy binary dbs return_key(...) from builtins.PyCapsule return_key(self : rosetta.protocols.loophash.LoopHashMap, bb_index : int) -> int   Returns a hashmap key given a member of a bucket  Don't think boost implements this, have to manually look it up sort(...) from builtins.PyCapsule sort(rosetta.protocols.loophash.LoopHashMap) -> NoneType   Sorts the loopdb_ by leap_index.index write_db(...) from builtins.PyCapsule write_db(self : rosetta.protocols.loophash.LoopHashMap, filename : str) -> NoneType   Basic IO functionality - allows reading and writing text states to/from disk   class LoopHashMoverWrapper(rosetta.protocols.moves.Mover)       Method resolution order: LoopHashMoverWrapper 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.loophash.LoopHashMoverWrapper) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_loop_size(...) from builtins.PyCapsule add_loop_size(self : rosetta.protocols.loophash.LoopHashMoverWrapper, loop_size : int) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.loophash.LoopHashMoverWrapper, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loophash.LoopHashMoverWrapper,  : rosetta.protocols.loophash.LoopHashMoverWrapper) -> rosetta.protocols.loophash.LoopHashMoverWrapper cenfilter(...) from builtins.PyCapsule cenfilter(self : rosetta.protocols.loophash.LoopHashMoverWrapper, cenfilter : rosetta.protocols.filters.Filter) -> NoneType clone(...) from builtins.PyCapsule clone(rosetta.protocols.loophash.LoopHashMoverWrapper) -> rosetta.protocols.moves.Mover fafilter(...) from builtins.PyCapsule fafilter(self : rosetta.protocols.loophash.LoopHashMoverWrapper, fafilter : rosetta.protocols.filters.Filter) -> NoneType fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.loophash.LoopHashMoverWrapper) -> rosetta.protocols.moves.Mover get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.loophash.LoopHashMoverWrapper) -> rosetta.core.pose.Pose get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.loophash.LoopHashMoverWrapper) -> str loop_sizes(...) from builtins.PyCapsule loop_sizes(rosetta.protocols.loophash.LoopHashMoverWrapper) -> rosetta.utility.vector1_unsigned_long max_bbrms(...) from builtins.PyCapsule max_bbrms(*args, **kwargs) Overloaded function.   1. max_bbrms(rosetta.protocols.loophash.LoopHashMoverWrapper) -> float   2. max_bbrms(self : rosetta.protocols.loophash.LoopHashMoverWrapper, max_bbrms : float) -> NoneType max_nstruct(...) from builtins.PyCapsule max_nstruct(*args, **kwargs) Overloaded function.   1. max_nstruct(rosetta.protocols.loophash.LoopHashMoverWrapper) -> int   2. max_nstruct(self : rosetta.protocols.loophash.LoopHashMoverWrapper, max_nstruct : int) -> NoneType max_rms(...) from builtins.PyCapsule max_rms(*args, **kwargs) Overloaded function.   1. max_rms(rosetta.protocols.loophash.LoopHashMoverWrapper) -> float   2. max_rms(self : rosetta.protocols.loophash.LoopHashMoverWrapper, max_rms : float) -> NoneType min_bbrms(...) from builtins.PyCapsule min_bbrms(*args, **kwargs) Overloaded function.   1. min_bbrms(rosetta.protocols.loophash.LoopHashMoverWrapper) -> float   2. min_bbrms(self : rosetta.protocols.loophash.LoopHashMoverWrapper, min_bbrms : float) -> NoneType min_rms(...) from builtins.PyCapsule min_rms(*args, **kwargs) Overloaded function.   1. min_rms(rosetta.protocols.loophash.LoopHashMoverWrapper) -> float   2. min_rms(self : rosetta.protocols.loophash.LoopHashMoverWrapper, min_rms : float) -> NoneType ranking_cenfilter(...) from builtins.PyCapsule ranking_cenfilter(*args, **kwargs) Overloaded function.   1. ranking_cenfilter(self : rosetta.protocols.loophash.LoopHashMoverWrapper, filter : rosetta.protocols.filters.Filter) -> NoneType   2. ranking_cenfilter(rosetta.protocols.loophash.LoopHashMoverWrapper) -> rosetta.protocols.filters.Filter ranking_fafilter(...) from builtins.PyCapsule ranking_fafilter(self : rosetta.protocols.loophash.LoopHashMoverWrapper, ranking_fafilter : rosetta.protocols.filters.Filter) -> NoneType relax_mover(...) from builtins.PyCapsule relax_mover(self : rosetta.protocols.loophash.LoopHashMoverWrapper, relax_mover : rosetta.protocols.relax.FastRelax) -> 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_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 LoopHashMoverWrapperCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: LoopHashMoverWrapperCreator 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.loophash.LoopHashMoverWrapperCreator,  : rosetta.protocols.loophash.LoopHashMoverWrapperCreator) -> rosetta.protocols.loophash.LoopHashMoverWrapperCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.loophash.LoopHashMoverWrapperCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.loophash.LoopHashMoverWrapperCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class LoopHashRelaxProtocol(rosetta.protocols.moves.Mover)       Method resolution order: LoopHashRelaxProtocol rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, library : rosetta.protocols.loophash.LoopHashLibrary) -> NoneType   2. __init__(handle, rosetta.protocols.loophash.LoopHashRelaxProtocol) -> 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.loophash.LoopHashRelaxProtocol, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loophash.LoopHashRelaxProtocol,  : rosetta.protocols.loophash.LoopHashRelaxProtocol) -> rosetta.protocols.loophash.LoopHashRelaxProtocol clone(...) from builtins.PyCapsule clone(rosetta.protocols.loophash.LoopHashRelaxProtocol) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.loophash.LoopHashRelaxProtocol) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.loophash.LoopHashRelaxProtocol) -> str manual_call(...) from builtins.PyCapsule manual_call(self : rosetta.protocols.loophash.LoopHashRelaxProtocol, pose : rosetta.core.pose.Pose) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class LoopHashSampler(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.protocols.loophash.LoopHashSampler, library : protocols::loophash::LoopHashLibrary, inserter : protocols::loophash::LocalInserter) -> 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.loophash.LoopHashSampler,  : rosetta.protocols.loophash.LoopHashSampler) -> rosetta.protocols.loophash.LoopHashSampler build_structures(...) from builtins.PyCapsule build_structures(self : rosetta.protocols.loophash.LoopHashSampler, start_pose : rosetta.core.pose.Pose, lib_structs : rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType   create a set of structures for a the given range of residues and other parameters stored int his class. close_gaps(...) from builtins.PyCapsule close_gaps(self : rosetta.protocols.loophash.LoopHashSampler, start_pose : rosetta.core.pose.Pose, lib_structs : rosetta.std.vector_core_pose_Pose, loop_size : int) -> NoneType   create a set of structures with closed gaps get_filter_by_phipsi(...) from builtins.PyCapsule get_filter_by_phipsi(rosetta.protocols.loophash.LoopHashSampler) -> bool get_max_bbrms(...) from builtins.PyCapsule get_max_bbrms(rosetta.protocols.loophash.LoopHashSampler) -> float get_max_nstruct(...) from builtins.PyCapsule get_max_nstruct(rosetta.protocols.loophash.LoopHashSampler) -> int get_max_rms(...) from builtins.PyCapsule get_max_rms(rosetta.protocols.loophash.LoopHashSampler) -> float get_min_bbrms(...) from builtins.PyCapsule get_min_bbrms(rosetta.protocols.loophash.LoopHashSampler) -> float get_min_rms(...) from builtins.PyCapsule get_min_rms(rosetta.protocols.loophash.LoopHashSampler) -> float get_start_res(...) from builtins.PyCapsule get_start_res(rosetta.protocols.loophash.LoopHashSampler) -> int get_stop_res(...) from builtins.PyCapsule get_stop_res(rosetta.protocols.loophash.LoopHashSampler) -> int set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.loophash.LoopHashSampler) -> NoneType set_filter_by_phipsi(...) from builtins.PyCapsule set_filter_by_phipsi(self : rosetta.protocols.loophash.LoopHashSampler, value : bool) -> NoneType set_max_bbrms(...) from builtins.PyCapsule set_max_bbrms(self : rosetta.protocols.loophash.LoopHashSampler, value : float) -> NoneType set_max_nstruct(...) from builtins.PyCapsule set_max_nstruct(self : rosetta.protocols.loophash.LoopHashSampler, value : int) -> NoneType set_max_radius(...) from builtins.PyCapsule set_max_radius(self : rosetta.protocols.loophash.LoopHashSampler, value : int) -> NoneType set_max_rms(...) from builtins.PyCapsule set_max_rms(self : rosetta.protocols.loophash.LoopHashSampler, value : float) -> NoneType set_max_struct(...) from builtins.PyCapsule set_max_struct(self : rosetta.protocols.loophash.LoopHashSampler, value : int) -> NoneType set_max_struct_per_radius(...) from builtins.PyCapsule set_max_struct_per_radius(self : rosetta.protocols.loophash.LoopHashSampler, value : int) -> NoneType set_min_bbrms(...) from builtins.PyCapsule set_min_bbrms(self : rosetta.protocols.loophash.LoopHashSampler, value : float) -> NoneType set_min_rms(...) from builtins.PyCapsule set_min_rms(self : rosetta.protocols.loophash.LoopHashSampler, value : float) -> NoneType set_nonideal(...) from builtins.PyCapsule set_nonideal(self : rosetta.protocols.loophash.LoopHashSampler, value : bool) -> NoneType set_start_res(...) from builtins.PyCapsule set_start_res(self : rosetta.protocols.loophash.LoopHashSampler, value : int) -> NoneType set_stop_res(...) from builtins.PyCapsule set_stop_res(self : rosetta.protocols.loophash.LoopHashSampler, value : int) -> NoneType use_prefiltering(...) from builtins.PyCapsule use_prefiltering(self : rosetta.protocols.loophash.LoopHashSampler, score_filt : rosetta.core.scoring.ScoreFunction, nstruct : int) -> NoneType   class MPI_LoopHashRefine(rosetta.protocols.wum.MPI_WorkUnitManager)       Method resolution order: MPI_LoopHashRefine rosetta.protocols.wum.MPI_WorkUnitManager rosetta.protocols.wum.WorkUnitManager builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.loophash.MPI_LoopHashRefine, machine_letter : str) -> NoneType   2. __init__(rosetta.protocols.loophash.MPI_LoopHashRefine, rosetta.protocols.loophash.MPI_LoopHashRefine) -> 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.loophash.MPI_LoopHashRefine,  : rosetta.protocols.loophash.MPI_LoopHashRefine) -> rosetta.protocols.loophash.MPI_LoopHashRefine set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.loophash.MPI_LoopHashRefine) -> NoneType Methods inherited from rosetta.protocols.wum.MPI_WorkUnitManager: go(...) from builtins.PyCapsule go(rosetta.protocols.wum.MPI_WorkUnitManager) -> NoneType Methods inherited from rosetta.protocols.wum.WorkUnitManager: inbound(...) from builtins.PyCapsule inbound(*args, **kwargs) Overloaded function.   1. inbound(rosetta.protocols.wum.WorkUnitManager) -> rosetta.protocols.wum.WorkUnitQueue   2. inbound(rosetta.protocols.wum.WorkUnitManager) -> rosetta.protocols.wum.WorkUnitQueue outbound(...) from builtins.PyCapsule outbound(*args, **kwargs) Overloaded function.   1. outbound(rosetta.protocols.wum.WorkUnitManager) -> rosetta.protocols.wum.WorkUnitQueue   2. outbound(rosetta.protocols.wum.WorkUnitManager) -> rosetta.protocols.wum.WorkUnitQueue register_work_units(...) from builtins.PyCapsule register_work_units(self : rosetta.protocols.wum.WorkUnitManager, work_unit_list : rosetta.protocols.wum.WorkUnitList) -> NoneType   class MPI_LoopHashRefine_Emperor(MPI_LoopHashRefine)       Method resolution order: MPI_LoopHashRefine_Emperor MPI_LoopHashRefine rosetta.protocols.wum.MPI_WorkUnitManager rosetta.protocols.wum.WorkUnitManager builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.loophash.MPI_LoopHashRefine_Emperor) -> 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.loophash.MPI_LoopHashRefine_Emperor,  : rosetta.protocols.loophash.MPI_LoopHashRefine_Emperor) -> rosetta.protocols.loophash.MPI_LoopHashRefine_Emperor go(...) from builtins.PyCapsule go(rosetta.protocols.loophash.MPI_LoopHashRefine_Emperor) -> NoneType set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.loophash.MPI_LoopHashRefine_Emperor) -> NoneType Methods inherited from rosetta.protocols.wum.WorkUnitManager: inbound(...) from builtins.PyCapsule inbound(*args, **kwargs) Overloaded function.   1. inbound(rosetta.protocols.wum.WorkUnitManager) -> rosetta.protocols.wum.WorkUnitQueue   2. inbound(rosetta.protocols.wum.WorkUnitManager) -> rosetta.protocols.wum.WorkUnitQueue outbound(...) from builtins.PyCapsule outbound(*args, **kwargs) Overloaded function.   1. outbound(rosetta.protocols.wum.WorkUnitManager) -> rosetta.protocols.wum.WorkUnitQueue   2. outbound(rosetta.protocols.wum.WorkUnitManager) -> rosetta.protocols.wum.WorkUnitQueue register_work_units(...) from builtins.PyCapsule register_work_units(self : rosetta.protocols.wum.WorkUnitManager, work_unit_list : rosetta.protocols.wum.WorkUnitList) -> NoneType   class MPI_LoopHashRefine_Master(MPI_LoopHashRefine)       Method resolution order: MPI_LoopHashRefine_Master MPI_LoopHashRefine rosetta.protocols.wum.MPI_WorkUnitManager rosetta.protocols.wum.WorkUnitManager builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, my_emperor : int, master_rank : int) -> NoneType   2. __init__(handle, rosetta.protocols.loophash.MPI_LoopHashRefine_Master) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. go(...) from builtins.PyCapsule go(rosetta.protocols.loophash.MPI_LoopHashRefine_Master) -> NoneType set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.loophash.MPI_LoopHashRefine_Master) -> NoneType Methods inherited from MPI_LoopHashRefine: assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loophash.MPI_LoopHashRefine,  : rosetta.protocols.loophash.MPI_LoopHashRefine) -> rosetta.protocols.loophash.MPI_LoopHashRefine Methods inherited from rosetta.protocols.wum.WorkUnitManager: inbound(...) from builtins.PyCapsule inbound(*args, **kwargs) Overloaded function.   1. inbound(rosetta.protocols.wum.WorkUnitManager) -> rosetta.protocols.wum.WorkUnitQueue   2. inbound(rosetta.protocols.wum.WorkUnitManager) -> rosetta.protocols.wum.WorkUnitQueue outbound(...) from builtins.PyCapsule outbound(*args, **kwargs) Overloaded function.   1. outbound(rosetta.protocols.wum.WorkUnitManager) -> rosetta.protocols.wum.WorkUnitQueue   2. outbound(rosetta.protocols.wum.WorkUnitManager) -> rosetta.protocols.wum.WorkUnitQueue register_work_units(...) from builtins.PyCapsule register_work_units(self : rosetta.protocols.wum.WorkUnitManager, work_unit_list : rosetta.protocols.wum.WorkUnitList) -> NoneType   class Mover_LoopHashRefine(rosetta.protocols.moves.Mover)       Method resolution order: Mover_LoopHashRefine rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, library : rosetta.protocols.loophash.LoopHashLibrary) -> NoneType   2. __init__(handle, rosetta.protocols.loophash.Mover_LoopHashRefine) -> 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.loophash.Mover_LoopHashRefine, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loophash.Mover_LoopHashRefine,  : rosetta.protocols.loophash.Mover_LoopHashRefine) -> rosetta.protocols.loophash.Mover_LoopHashRefine clone(...) from builtins.PyCapsule clone(rosetta.protocols.loophash.Mover_LoopHashRefine) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.loophash.Mover_LoopHashRefine) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.loophash.Mover_LoopHashRefine) -> 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 WorkUnit_LoopHash(rosetta.protocols.wum.WorkUnit_SilentStructStore)       Method resolution order: WorkUnit_LoopHash rosetta.protocols.wum.WorkUnit_SilentStructStore rosetta.protocols.wum.WorkUnitBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   doc   2. __init__(handle, int) -> NoneType   doc   3. __init__(handle, int, int) -> NoneType   doc   4. __init__(self : handle, start_ir : int, end_ir : int, ssid : int) -> NoneType   5. __init__(handle, rosetta.protocols.loophash.WorkUnit_LoopHash) -> 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.loophash.WorkUnit_LoopHash,  : rosetta.protocols.loophash.WorkUnit_LoopHash) -> rosetta.protocols.loophash.WorkUnit_LoopHash clone(...) from builtins.PyCapsule clone(rosetta.protocols.loophash.WorkUnit_LoopHash) -> rosetta.protocols.wum.WorkUnitBase init_from_cmd(...) from builtins.PyCapsule init_from_cmd(self : rosetta.protocols.loophash.WorkUnit_LoopHash, mpi_rank : int) -> NoneType run(...) from builtins.PyCapsule run(rosetta.protocols.loophash.WorkUnit_LoopHash) -> NoneType set_end(...) from builtins.PyCapsule set_end(self : rosetta.protocols.loophash.WorkUnit_LoopHash, end_ir : int) -> NoneType set_ssid(...) from builtins.PyCapsule set_ssid(self : rosetta.protocols.loophash.WorkUnit_LoopHash, ssid : int) -> NoneType set_start(...) from builtins.PyCapsule set_start(self : rosetta.protocols.loophash.WorkUnit_LoopHash, start_ir : int) -> NoneType Methods inherited from rosetta.protocols.wum.WorkUnit_SilentStructStore: decoys(...) from builtins.PyCapsule decoys(*args, **kwargs) Overloaded function.   1. decoys(rosetta.protocols.wum.WorkUnit_SilentStructStore) -> rosetta.protocols.wum.SilentStructStore   Accessor for decoy store   2. decoys(rosetta.protocols.wum.WorkUnit_SilentStructStore) -> rosetta.protocols.wum.SilentStructStore   Accessor for decoy store deserialize(...) from builtins.PyCapsule deserialize(rosetta.protocols.wum.WorkUnit_SilentStructStore) -> NoneType   Make ready for working serialize(...) from builtins.PyCapsule serialize(rosetta.protocols.wum.WorkUnit_SilentStructStore) -> NoneType   write decoys into serial data store overwritinge whatever was there before. It basically syncs the silent struct store with the derial data Methods inherited from rosetta.protocols.wum.WorkUnitBase: add_blacklist(...) from builtins.PyCapsule add_blacklist(self : rosetta.protocols.wum.WorkUnitBase, mpi_rank : int) -> NoneType   Adds to the blacklist clear_blacklist(...) from builtins.PyCapsule clear_blacklist(rosetta.protocols.wum.WorkUnitBase) -> NoneType   Erases the blacklist clear_serial_data(...) from builtins.PyCapsule clear_serial_data(rosetta.protocols.wum.WorkUnitBase) -> NoneType   Remove all data, make sure that the memory is also cleared, hence the cals to reserve extra_data_1(...) from builtins.PyCapsule extra_data_1(rosetta.protocols.wum.WorkUnitBase) -> int   Accessor to the extra_data_1 and 3 field of the header extra_data_2(...) from builtins.PyCapsule extra_data_2(rosetta.protocols.wum.WorkUnitBase) -> int extra_data_3(...) from builtins.PyCapsule extra_data_3(rosetta.protocols.wum.WorkUnitBase) -> int get_options(...) from builtins.PyCapsule get_options(rosetta.protocols.wum.WorkUnitBase) -> str   Optain the options string from the header get_run_time(...) from builtins.PyCapsule get_run_time(rosetta.protocols.wum.WorkUnitBase) -> int   Returns the differrence between unix start and stop times get_wu_type(...) from builtins.PyCapsule get_wu_type(rosetta.protocols.wum.WorkUnitBase) -> str   Accessor to header structure, return the WorkUnit Type id(...) from builtins.PyCapsule id(rosetta.protocols.wum.WorkUnitBase) -> int   Accessor to the ID of the WorkUnit in_blacklist(...) from builtins.PyCapsule in_blacklist(self : rosetta.protocols.wum.WorkUnitBase, mpi_rank : int) -> bool   Finds in blacklist, true if is, false if it isn't last_received_from(...) from builtins.PyCapsule last_received_from(rosetta.protocols.wum.WorkUnitBase) -> int mem_footprint(...) from builtins.PyCapsule mem_footprint(rosetta.protocols.wum.WorkUnitBase) -> int   Return the memory usage of this WorkUnit set_extra_data_1(...) from builtins.PyCapsule set_extra_data_1(self : rosetta.protocols.wum.WorkUnitBase, value : int) -> NoneType set_extra_data_2(...) from builtins.PyCapsule set_extra_data_2(self : rosetta.protocols.wum.WorkUnitBase, value : int) -> NoneType set_extra_data_3(...) from builtins.PyCapsule set_extra_data_3(self : rosetta.protocols.wum.WorkUnitBase, value : int) -> NoneType set_options(...) from builtins.PyCapsule set_options(self : rosetta.protocols.wum.WorkUnitBase, text : str) -> NoneType   Accesor to the "options" text field set_wu_type(...) from builtins.PyCapsule set_wu_type(self : rosetta.protocols.wum.WorkUnitBase, text : str) -> NoneType   Accessor to header structure, sets the WorkUnit Type

Functions
		RealAngleToShort(...) method of builtins.PyCapsule instance RealAngleToShort(angle : float) -> int ShortToRealAngle(...) method of builtins.PyCapsule instance ShortToRealAngle(angle : int) -> float get_rmsd(...) method of builtins.PyCapsule instance get_rmsd(bs1 : rosetta.protocols.loophash.BackboneSegment, bs2 : rosetta.protocols.loophash.BackboneSegment) -> float get_rt_over_leap(...) method of builtins.PyCapsule instance get_rt_over_leap(orig_pose : rosetta.core.pose.Pose, ir : int, jr : int, rt_6 : rosetta.utility.fixedsizearray1_double_6_t) -> bool   This takes a pose and two residue positions and determines the rigid body transform of the Leap described by those two residues.         Returns true is successful or false if something went haywire and one should just ignore this loop (this can happen at the ends) get_rt_over_leap_fast(...) method of builtins.PyCapsule instance get_rt_over_leap_fast(pose : rosetta.core.pose.Pose, ir : int, jr : int, rt_6 : rosetta.utility.fixedsizearray1_double_6_t) -> bool   This takes a pose and two residue positions and determines the rigid body transform of the Leap described by those two residues         Returns true is successful or false if something went haywire and one should just ignore this loop (this can happen at the ends)        THe difference between this and the get_rt_over_leap function is that this version doesnt make a copy of the pose which makes it faster.      However this means that the pose passed cannot be a const pose, even though the function restores the fold tree afterwards.. get_rt_over_leap_without_foldtree_bs(...) method of builtins.PyCapsule instance get_rt_over_leap_without_foldtree_bs(pose : rosetta.core.pose.Pose, ir : int, jr : int, rt_6 : rosetta.utility.fixedsizearray1_double_6_t) -> bool   This takes a pose and two residue positions and determines the rigid body transform of the Leap described by those two residues. loophash_main(...) method of builtins.PyCapsule instance loophash_main() -> int