Bindings for protocols::matdes namespace

Classes
		builtins.object MatDesPointMutationCalculator rosetta.core.pack.task.operation.TaskOperation(builtins.object) BuildingBlockInterfaceOperation rosetta.core.pack.task.operation.TaskOperationCreator(builtins.object) BuildingBlockInterfaceOperationCreator rosetta.protocols.filters.Filter(builtins.object) ClashCheckFilter GetRBDOFValues InterfacePackingFilter OligomericAverageDegreeFilter SymUnsatHbondFilter rosetta.protocols.filters.FilterCreator(builtins.object) ClashCheckFilterCreator GetRBDOFValuesCreator InterfacePackingFilterCreator OligomericAverageDegreeFilterCreator SymUnsatHbondFilterCreator rosetta.protocols.moves.Mover(builtins.object) ExtractSubposeMover MatDesGreedyOptMutationMover SchemePlaceMotifsMover SymDofMover rosetta.protocols.moves.MoverCreator(builtins.object) ExtractSubposeMoverCreator MatDesGreedyOptMutationMoverCreator SchemePlaceMotifsMoverCreator SymDofMoverCreator rosetta.utility.SingletonBase_protocols_matdes_SymDofMoverSampler_t(builtins.object) SymDofMoverSampler   class BuildingBlockInterfaceOperation(rosetta.core.pack.task.operation.TaskOperation)       Method resolution order: BuildingBlockInterfaceOperation rosetta.core.pack.task.operation.TaskOperation 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, str) -> NoneType   doc   4. __init__(handle, int, str, float) -> NoneType   doc   5. __init__(handle, int, str, float, float) -> NoneType   doc   6. __init__(handle, int, str, float, float, float) -> NoneType   doc   7. __init__(handle, int, str, float, float, float, bool) -> NoneType   doc   8. __init__(handle, int, str, float, float, float, bool, bool) -> NoneType   doc   9. __init__(self : handle, nsub_bblock : int, sym_dof_names : str, contact_dist : float, bblock_dist : float, fa_rep_cut : float, filter_intrabb : bool, intrabb_only : bool, multicomponent : bool) -> NoneType   10. __init__(handle, rosetta.protocols.matdes.BuildingBlockInterfaceOperation) -> 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.matdes.BuildingBlockInterfaceOperation,  : rosetta.core.pose.Pose,  : rosetta.core.pack.task.PackerTask) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.matdes.BuildingBlockInterfaceOperation,  : rosetta.protocols.matdes.BuildingBlockInterfaceOperation) -> rosetta.protocols.matdes.BuildingBlockInterfaceOperation clone(...) from builtins.PyCapsule clone(rosetta.protocols.matdes.BuildingBlockInterfaceOperation) -> rosetta.core.pack.task.operation.TaskOperation keyname(...) from builtins.PyCapsule keyname() -> str parse_tag(...) from builtins.PyCapsule parse_tag(self : rosetta.protocols.matdes.BuildingBlockInterfaceOperation, tag : rosetta.utility.tag.Tag,  : rosetta.basic.datacache.DataMap) -> NoneType provide_xml_schema(...) from builtins.PyCapsule provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType   class BuildingBlockInterfaceOperationCreator(rosetta.core.pack.task.operation.TaskOperationCreator)       Method resolution order: BuildingBlockInterfaceOperationCreator rosetta.core.pack.task.operation.TaskOperationCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.matdes.BuildingBlockInterfaceOperationCreator,  : rosetta.protocols.matdes.BuildingBlockInterfaceOperationCreator) -> rosetta.protocols.matdes.BuildingBlockInterfaceOperationCreator create_task_operation(...) from builtins.PyCapsule create_task_operation(rosetta.protocols.matdes.BuildingBlockInterfaceOperationCreator) -> rosetta.core.pack.task.operation.TaskOperation keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.matdes.BuildingBlockInterfaceOperationCreator) -> str provide_xml_schema(...) from builtins.PyCapsule provide_xml_schema(self : rosetta.protocols.matdes.BuildingBlockInterfaceOperationCreator, xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType   class ClashCheckFilter(rosetta.protocols.filters.Filter)       Method resolution order: ClashCheckFilter rosetta.protocols.filters.Filter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, task_factory : rosetta.core.pack.task.TaskFactory, c : float, s : str, n : int, t : int, v : bool, w : bool) -> NoneType   3. __init__(handle, rosetta.protocols.matdes.ClashCheckFilter) -> 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.matdes.ClashCheckFilter, pose : rosetta.core.pose.Pose) -> bool clash_dist(...) from builtins.PyCapsule clash_dist(*args, **kwargs) Overloaded function.   1. clash_dist(self : rosetta.protocols.matdes.ClashCheckFilter, c : float) -> NoneType   2. clash_dist(rosetta.protocols.matdes.ClashCheckFilter) -> float clone(...) from builtins.PyCapsule clone(rosetta.protocols.matdes.ClashCheckFilter) -> rosetta.protocols.filters.Filter compute(...) from builtins.PyCapsule compute(self : rosetta.protocols.matdes.ClashCheckFilter, pose : rosetta.core.pose.Pose, v : bool, w : bool) -> int   calc oligomeric AverageDegree fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.matdes.ClashCheckFilter) -> rosetta.protocols.filters.Filter name(...) from builtins.PyCapsule name(rosetta.protocols.matdes.ClashCheckFilter) -> str nsub_bblock(...) from builtins.PyCapsule nsub_bblock(*args, **kwargs) Overloaded function.   1. nsub_bblock(self : rosetta.protocols.matdes.ClashCheckFilter, n : int) -> NoneType   2. nsub_bblock(rosetta.protocols.matdes.ClashCheckFilter) -> int report_sm(...) from builtins.PyCapsule report_sm(self : rosetta.protocols.matdes.ClashCheckFilter, pose : rosetta.core.pose.Pose) -> float sym_dof_names(...) from builtins.PyCapsule sym_dof_names(*args, **kwargs) Overloaded function.   1. sym_dof_names(self : rosetta.protocols.matdes.ClashCheckFilter, s : str) -> NoneType   2. sym_dof_names(rosetta.protocols.matdes.ClashCheckFilter) -> str task_factory(...) from builtins.PyCapsule task_factory(*args, **kwargs) Overloaded function.   1. task_factory(self : rosetta.protocols.matdes.ClashCheckFilter, task_factory : rosetta.core.pack.task.TaskFactory) -> NoneType   2. task_factory(rosetta.protocols.matdes.ClashCheckFilter) -> rosetta.core.pack.task.TaskFactory threshold(...) from builtins.PyCapsule threshold(*args, **kwargs) Overloaded function.   1. threshold(self : rosetta.protocols.matdes.ClashCheckFilter, t : int) -> NoneType   2. threshold(rosetta.protocols.matdes.ClashCheckFilter) -> int verbose(...) from builtins.PyCapsule verbose(*args, **kwargs) Overloaded function.   1. verbose(self : rosetta.protocols.matdes.ClashCheckFilter, v : bool) -> NoneType   2. verbose(rosetta.protocols.matdes.ClashCheckFilter) -> bool write(...) from builtins.PyCapsule write(*args, **kwargs) Overloaded function.   1. write(self : rosetta.protocols.matdes.ClashCheckFilter, w : bool) -> NoneType   2. write(rosetta.protocols.matdes.ClashCheckFilter) -> bool write_pymol_string_to_pdb(...) from builtins.PyCapsule write_pymol_string_to_pdb(self : rosetta.protocols.matdes.ClashCheckFilter, pymol_selection : str) -> NoneType write_to_pdb(...) from builtins.PyCapsule write_to_pdb(self : rosetta.protocols.matdes.ClashCheckFilter, pose : rosetta.core.pose.Pose, residue_name : str, residue : int, atom_name : str) -> NoneType Methods inherited from rosetta.protocols.filters.Filter: clear(...) from builtins.PyCapsule clear(rosetta.protocols.filters.Filter) -> NoneType   used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.filters.Filter) -> str get_user_defined_name(...) from builtins.PyCapsule get_user_defined_name(rosetta.protocols.filters.Filter) -> str score(...) from builtins.PyCapsule score(self : rosetta.protocols.filters.Filter, pose : rosetta.core.pose.Pose) -> float set_user_defined_name(...) from builtins.PyCapsule set_user_defined_name(self : rosetta.protocols.filters.Filter, name : str) -> NoneType   class ClashCheckFilterCreator(rosetta.protocols.filters.FilterCreator)       Method resolution order: ClashCheckFilterCreator rosetta.protocols.filters.FilterCreator 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.matdes.ClashCheckFilterCreator,  : rosetta.protocols.matdes.ClashCheckFilterCreator) -> rosetta.protocols.matdes.ClashCheckFilterCreator create_filter(...) from builtins.PyCapsule create_filter(rosetta.protocols.matdes.ClashCheckFilterCreator) -> rosetta.protocols.filters.Filter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.matdes.ClashCheckFilterCreator) -> str   class ExtractSubposeMover(rosetta.protocols.moves.Mover)       Method resolution order: ExtractSubposeMover 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.matdes.ExtractSubposeMover) -> 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.matdes.ExtractSubposeMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.matdes.ExtractSubposeMover,  : rosetta.protocols.matdes.ExtractSubposeMover) -> rosetta.protocols.matdes.ExtractSubposeMover clone(...) from builtins.PyCapsule clone(rosetta.protocols.matdes.ExtractSubposeMover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.matdes.ExtractSubposeMover) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.matdes.ExtractSubposeMover) -> 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 ExtractSubposeMoverCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: ExtractSubposeMoverCreator 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.matdes.ExtractSubposeMoverCreator,  : rosetta.protocols.matdes.ExtractSubposeMoverCreator) -> rosetta.protocols.matdes.ExtractSubposeMoverCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.matdes.ExtractSubposeMoverCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.matdes.ExtractSubposeMoverCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class GetRBDOFValues(rosetta.protocols.filters.Filter)     WARNING WARNING WARNING THIS CLASS USES THE THREAD UNSAFE SymDofMoverSampler AND MAKES ANY PROTOCOL THAT USES THIS CLASS THREAD UNSAFE.     Method resolution order: GetRBDOFValues rosetta.protocols.filters.Filter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, jump : int, dof_name : str, verb : bool, ax : str, disp : bool, ang : bool, init_d : float, init_a : float, get_init : bool) -> NoneType   3. __init__(handle, rosetta.protocols.matdes.GetRBDOFValues) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. angle(...) from builtins.PyCapsule angle(*args, **kwargs) Overloaded function.   1. angle(self : rosetta.protocols.matdes.GetRBDOFValues, ang : bool) -> NoneType   2. angle(rosetta.protocols.matdes.GetRBDOFValues) -> bool apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.matdes.GetRBDOFValues, pose : rosetta.core.pose.Pose) -> bool axis(...) from builtins.PyCapsule axis(*args, **kwargs) Overloaded function.   1. axis(self : rosetta.protocols.matdes.GetRBDOFValues, ax : str) -> NoneType   2. axis(rosetta.protocols.matdes.GetRBDOFValues) -> str clone(...) from builtins.PyCapsule clone(rosetta.protocols.matdes.GetRBDOFValues) -> rosetta.protocols.filters.Filter compute(...) from builtins.PyCapsule compute(self : rosetta.protocols.matdes.GetRBDOFValues, pose : rosetta.core.pose.Pose, verb : bool, dof_name : str, jump : int, ax : str, disp : bool, ang : bool, init_d : float, init_a : float, get_init : bool) -> float   get the translation and rotation for a user specified jump fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.matdes.GetRBDOFValues) -> rosetta.protocols.filters.Filter get_init_value(...) from builtins.PyCapsule get_init_value(*args, **kwargs) Overloaded function.   1. get_init_value(self : rosetta.protocols.matdes.GetRBDOFValues, get_init : bool) -> NoneType   2. get_init_value(rosetta.protocols.matdes.GetRBDOFValues) -> bool init_angle(...) from builtins.PyCapsule init_angle(*args, **kwargs) Overloaded function.   1. init_angle(self : rosetta.protocols.matdes.GetRBDOFValues, init_a : float) -> NoneType   2. init_angle(rosetta.protocols.matdes.GetRBDOFValues) -> float init_disp(...) from builtins.PyCapsule init_disp(*args, **kwargs) Overloaded function.   1. init_disp(self : rosetta.protocols.matdes.GetRBDOFValues, init_d : float) -> NoneType   2. init_disp(rosetta.protocols.matdes.GetRBDOFValues) -> float jump_id(...) from builtins.PyCapsule jump_id(*args, **kwargs) Overloaded function.   1. jump_id(self : rosetta.protocols.matdes.GetRBDOFValues, jump : int) -> NoneType   2. jump_id(rosetta.protocols.matdes.GetRBDOFValues) -> int name(...) from builtins.PyCapsule name(rosetta.protocols.matdes.GetRBDOFValues) -> str radial_disp(...) from builtins.PyCapsule radial_disp(*args, **kwargs) Overloaded function.   1. radial_disp(self : rosetta.protocols.matdes.GetRBDOFValues, disp : bool) -> NoneType   2. radial_disp(rosetta.protocols.matdes.GetRBDOFValues) -> bool report_sm(...) from builtins.PyCapsule report_sm(self : rosetta.protocols.matdes.GetRBDOFValues, pose : rosetta.core.pose.Pose) -> float sym_dof_name(...) from builtins.PyCapsule sym_dof_name(*args, **kwargs) Overloaded function.   1. sym_dof_name(self : rosetta.protocols.matdes.GetRBDOFValues, dof_name : str) -> NoneType   2. sym_dof_name(rosetta.protocols.matdes.GetRBDOFValues) -> str verbose(...) from builtins.PyCapsule verbose(*args, **kwargs) Overloaded function.   1. verbose(self : rosetta.protocols.matdes.GetRBDOFValues, verb : bool) -> NoneType   2. verbose(rosetta.protocols.matdes.GetRBDOFValues) -> bool Methods inherited from rosetta.protocols.filters.Filter: clear(...) from builtins.PyCapsule clear(rosetta.protocols.filters.Filter) -> NoneType   used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.filters.Filter) -> str get_user_defined_name(...) from builtins.PyCapsule get_user_defined_name(rosetta.protocols.filters.Filter) -> str score(...) from builtins.PyCapsule score(self : rosetta.protocols.filters.Filter, pose : rosetta.core.pose.Pose) -> float set_user_defined_name(...) from builtins.PyCapsule set_user_defined_name(self : rosetta.protocols.filters.Filter, name : str) -> NoneType   class GetRBDOFValuesCreator(rosetta.protocols.filters.FilterCreator)       Method resolution order: GetRBDOFValuesCreator rosetta.protocols.filters.FilterCreator 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.matdes.GetRBDOFValuesCreator,  : rosetta.protocols.matdes.GetRBDOFValuesCreator) -> rosetta.protocols.matdes.GetRBDOFValuesCreator create_filter(...) from builtins.PyCapsule create_filter(rosetta.protocols.matdes.GetRBDOFValuesCreator) -> rosetta.protocols.filters.Filter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.matdes.GetRBDOFValuesCreator) -> str   class InterfacePackingFilter(rosetta.protocols.filters.Filter)       Method resolution order: InterfacePackingFilter rosetta.protocols.filters.Filter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.matdes.InterfacePackingFilter) -> 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.matdes.InterfacePackingFilter, pose : rosetta.core.pose.Pose) -> bool clone(...) from builtins.PyCapsule clone(rosetta.protocols.matdes.InterfacePackingFilter) -> rosetta.protocols.filters.Filter compute(...) from builtins.PyCapsule compute(self : rosetta.protocols.matdes.InterfacePackingFilter, pose : rosetta.core.pose.Pose) -> float contact_dist(...) from builtins.PyCapsule contact_dist(*args, **kwargs) Overloaded function.   1. contact_dist(rosetta.protocols.matdes.InterfacePackingFilter) -> float   2. contact_dist(self : rosetta.protocols.matdes.InterfacePackingFilter, c : float) -> NoneType distance_cutoff(...) from builtins.PyCapsule distance_cutoff(*args, **kwargs) Overloaded function.   1. distance_cutoff(rosetta.protocols.matdes.InterfacePackingFilter) -> float   2. distance_cutoff(self : rosetta.protocols.matdes.InterfacePackingFilter, d : float) -> NoneType fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.matdes.InterfacePackingFilter) -> rosetta.protocols.filters.Filter lower_threshold(...) from builtins.PyCapsule lower_threshold(*args, **kwargs) Overloaded function.   1. lower_threshold(rosetta.protocols.matdes.InterfacePackingFilter) -> float   2. lower_threshold(self : rosetta.protocols.matdes.InterfacePackingFilter, l : float) -> NoneType multicomp(...) from builtins.PyCapsule multicomp(*args, **kwargs) Overloaded function.   1. multicomp(rosetta.protocols.matdes.InterfacePackingFilter) -> bool   2. multicomp(self : rosetta.protocols.matdes.InterfacePackingFilter, multicomp : bool) -> NoneType report_sm(...) from builtins.PyCapsule report_sm(self : rosetta.protocols.matdes.InterfacePackingFilter, pose : rosetta.core.pose.Pose) -> float sym_dof_names(...) from builtins.PyCapsule sym_dof_names(*args, **kwargs) Overloaded function.   1. sym_dof_names(rosetta.protocols.matdes.InterfacePackingFilter) -> str   2. sym_dof_names(self : rosetta.protocols.matdes.InterfacePackingFilter, s : str) -> NoneType upper_threshold(...) from builtins.PyCapsule upper_threshold(*args, **kwargs) Overloaded function.   1. upper_threshold(rosetta.protocols.matdes.InterfacePackingFilter) -> float   2. upper_threshold(self : rosetta.protocols.matdes.InterfacePackingFilter, u : float) -> NoneType Methods inherited from rosetta.protocols.filters.Filter: clear(...) from builtins.PyCapsule clear(rosetta.protocols.filters.Filter) -> NoneType   used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.filters.Filter) -> str get_user_defined_name(...) from builtins.PyCapsule get_user_defined_name(rosetta.protocols.filters.Filter) -> str name(...) from builtins.PyCapsule name(rosetta.protocols.filters.Filter) -> str score(...) from builtins.PyCapsule score(self : rosetta.protocols.filters.Filter, pose : rosetta.core.pose.Pose) -> float set_user_defined_name(...) from builtins.PyCapsule set_user_defined_name(self : rosetta.protocols.filters.Filter, name : str) -> NoneType   class InterfacePackingFilterCreator(rosetta.protocols.filters.FilterCreator)       Method resolution order: InterfacePackingFilterCreator rosetta.protocols.filters.FilterCreator 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.matdes.InterfacePackingFilterCreator,  : rosetta.protocols.matdes.InterfacePackingFilterCreator) -> rosetta.protocols.matdes.InterfacePackingFilterCreator create_filter(...) from builtins.PyCapsule create_filter(rosetta.protocols.matdes.InterfacePackingFilterCreator) -> rosetta.protocols.filters.Filter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.matdes.InterfacePackingFilterCreator) -> str   class MatDesGreedyOptMutationMover(rosetta.protocols.moves.Mover)       Method resolution order: MatDesGreedyOptMutationMover 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.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t, rosetta.utility.vector1_std_pair_std_string_double_t, rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t, rosetta.utility.vector1_std_string, rosetta.utility.vector1_double) -> NoneType   doc   3. __init__(handle, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t, rosetta.utility.vector1_std_pair_std_string_double_t, rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t, rosetta.utility.vector1_std_string, rosetta.utility.vector1_double, bool) -> NoneType   doc   4. __init__(handle, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t, rosetta.utility.vector1_std_pair_std_string_double_t, rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t, rosetta.utility.vector1_std_string, rosetta.utility.vector1_double, bool, bool) -> NoneType   doc   5. __init__(handle, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t, rosetta.utility.vector1_std_pair_std_string_double_t, rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t, rosetta.utility.vector1_std_string, rosetta.utility.vector1_double, bool, bool, bool) -> NoneType   doc   6. __init__(handle, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t, rosetta.utility.vector1_std_pair_std_string_double_t, rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t, rosetta.utility.vector1_std_string, rosetta.utility.vector1_double, bool, bool, bool, bool) -> NoneType   doc   7. __init__(handle, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t, rosetta.utility.vector1_std_pair_std_string_double_t, rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t, rosetta.utility.vector1_std_string, rosetta.utility.vector1_double, bool, bool, bool, bool, bool) -> NoneType   doc   8. __init__(handle, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t, rosetta.utility.vector1_std_pair_std_string_double_t, rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t, rosetta.utility.vector1_std_string, rosetta.utility.vector1_double, bool, bool, bool, bool, bool, bool) -> NoneType   doc   9. __init__(handle, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t, rosetta.utility.vector1_std_pair_std_string_double_t, rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t, rosetta.utility.vector1_std_string, rosetta.utility.vector1_double, bool, bool, bool, bool, bool, bool, bool) -> NoneType   doc   10. __init__(handle, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t, rosetta.utility.vector1_std_pair_std_string_double_t, rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t, rosetta.utility.vector1_std_string, rosetta.utility.vector1_double, bool, bool, bool, bool, bool, bool, bool, bool) -> NoneType   doc   11. __init__(handle, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t, rosetta.utility.vector1_std_pair_std_string_double_t, rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t, rosetta.utility.vector1_std_string, rosetta.utility.vector1_double, bool, bool, bool, bool, bool, bool, bool, bool, bool) -> NoneType   doc   12. __init__(handle, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t, rosetta.utility.vector1_std_pair_std_string_double_t, rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t, rosetta.utility.vector1_std_string, rosetta.utility.vector1_double, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) -> NoneType   doc   13. __init__(handle, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t, rosetta.utility.vector1_std_pair_std_string_double_t, rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t, rosetta.utility.vector1_std_string, rosetta.utility.vector1_double, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) -> NoneType   doc   14. __init__(self : handle, task_factory : rosetta.core.pack.task.TaskFactory, scorefxn : rosetta.core.scoring.ScoreFunction, relax_mover : rosetta.protocols.moves.Mover, filters : rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t, filter_thresholds : rosetta.utility.vector1_std_pair_std_string_double_t, set_task_for_filters : rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t, sample_types : rosetta.utility.vector1_std_string, filter_deltas : rosetta.utility.vector1_double, dump_pdb : bool, dump_table : bool, parallel : bool, stop_before_condition : bool, skip_best_check : bool, rtmin : bool, shuffle_order : bool, diversify : bool, incl_nonopt : bool, force_natro : bool, keep_trying : bool, stopping_condition : rosetta.protocols.filters.Filter) -> NoneType   15. __init__(handle, rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_filter(...) from builtins.PyCapsule add_filter(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover,  : rosetta.protocols.filters.Filter, sample_type : str, filter_delta : float) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover,  : rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> rosetta.protocols.matdes.MatDesGreedyOptMutationMover calc_pfront_poses_filter_ranks(...) from builtins.PyCapsule calc_pfront_poses_filter_ranks(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> NoneType clear_cached_data(...) from builtins.PyCapsule clear_cached_data(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> NoneType clone(...) from builtins.PyCapsule clone(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> rosetta.protocols.moves.Mover delta_filters(...) from builtins.PyCapsule delta_filters(*args, **kwargs) Overloaded function.   1. delta_filters(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_DeltaFilter_t   2. delta_filters(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, d : rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_DeltaFilter_t) -> NoneType diversify(...) from builtins.PyCapsule diversify(*args, **kwargs) Overloaded function.   1. diversify(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool   2. diversify(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, b : bool) -> NoneType dump_pdb(...) from builtins.PyCapsule dump_pdb(*args, **kwargs) Overloaded function.   1. dump_pdb(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool   2. dump_pdb(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, dump_pdb : bool) -> NoneType dump_scoring_table(...) from builtins.PyCapsule dump_scoring_table(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, filename : str, ref_pose : rosetta.core.pose.Pose) -> NoneType dump_table(...) from builtins.PyCapsule dump_table(*args, **kwargs) Overloaded function.   1. dump_table(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool   2. dump_table(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, dump_table : bool) -> NoneType filter_deltas(...) from builtins.PyCapsule filter_deltas(*args, **kwargs) Overloaded function.   1. filter_deltas(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> rosetta.utility.vector1_double   2. filter_deltas(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, filter_deltas : rosetta.utility.vector1_double) -> NoneType filter_pareto_opt_poses(...) from builtins.PyCapsule filter_pareto_opt_poses(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> NoneType filter_seqpos_pareto_opt_ptmuts(...) from builtins.PyCapsule filter_seqpos_pareto_opt_ptmuts(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> NoneType filter_thresholds(...) from builtins.PyCapsule filter_thresholds(*args, **kwargs) Overloaded function.   1. filter_thresholds(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> rosetta.utility.vector1_std_pair_std_string_double_t   2. filter_thresholds(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, filter_thresholds : rosetta.utility.vector1_std_pair_std_string_double_t) -> NoneType filters(...) from builtins.PyCapsule filters(*args, **kwargs) Overloaded function.   1. filters(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t   2. filters(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, filters : rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t) -> NoneType force_natro(...) from builtins.PyCapsule force_natro(*args, **kwargs) Overloaded function.   1. force_natro(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool   2. force_natro(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, f : bool) -> NoneType force_natro_for_stored_task_names(...) from builtins.PyCapsule force_natro_for_stored_task_names(*args, **kwargs) Overloaded function.   1. force_natro_for_stored_task_names(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> rosetta.utility.vector1_std_string   2. force_natro_for_stored_task_names(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, force_natro_for_stored_task_names : rosetta.utility.vector1_std_string) -> NoneType fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> str incl_nonopt(...) from builtins.PyCapsule incl_nonopt(*args, **kwargs) Overloaded function.   1. incl_nonopt(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool   2. incl_nonopt(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, b : bool) -> NoneType keep_trying(...) from builtins.PyCapsule keep_trying(*args, **kwargs) Overloaded function.   1. keep_trying(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool   2. keep_trying(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, k : bool) -> NoneType parallel(...) from builtins.PyCapsule parallel(*args, **kwargs) Overloaded function.   1. parallel(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool   2. parallel(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, parallel : bool) -> NoneType pose_coords_are_same(...) from builtins.PyCapsule pose_coords_are_same(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose) -> bool reference_pose(...) from builtins.PyCapsule reference_pose(*args, **kwargs) Overloaded function.   1. reference_pose(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> rosetta.core.pose.Pose   2. reference_pose(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, reference_pose : rosetta.core.pose.Pose) -> NoneType relax_mover(...) from builtins.PyCapsule relax_mover(*args, **kwargs) Overloaded function.   1. relax_mover(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> rosetta.protocols.moves.Mover   2. relax_mover(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, relax_mover : rosetta.protocols.moves.Mover) -> NoneType reset_delta_filter_baselines(...) from builtins.PyCapsule reset_delta_filter_baselines(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, pose : rosetta.core.pose.Pose) -> NoneType rtmin(...) from builtins.PyCapsule rtmin(*args, **kwargs) Overloaded function.   1. rtmin(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool   2. rtmin(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, b : bool) -> NoneType sample_types(...) from builtins.PyCapsule sample_types(*args, **kwargs) Overloaded function.   1. sample_types(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> rosetta.utility.vector1_std_string   2. sample_types(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, sample_types : rosetta.utility.vector1_std_string) -> NoneType scorefxn(...) from builtins.PyCapsule scorefxn(*args, **kwargs) Overloaded function.   1. scorefxn(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> rosetta.core.scoring.ScoreFunction   2. scorefxn(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_task_for_filters(...) from builtins.PyCapsule set_task_for_filters(*args, **kwargs) Overloaded function.   1. set_task_for_filters(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t   2. set_task_for_filters(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, set_task_for_filters : rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t) -> NoneType shuffle_order(...) from builtins.PyCapsule shuffle_order(*args, **kwargs) Overloaded function.   1. shuffle_order(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool   2. shuffle_order(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, b : bool) -> NoneType skip_best_check(...) from builtins.PyCapsule skip_best_check(*args, **kwargs) Overloaded function.   1. skip_best_check(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool   2. skip_best_check(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, skip_best_check : bool) -> NoneType stop_before_condition(...) from builtins.PyCapsule stop_before_condition(*args, **kwargs) Overloaded function.   1. stop_before_condition(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool   2. stop_before_condition(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, stop_before_condition : bool) -> NoneType stopping_condition(...) from builtins.PyCapsule stopping_condition(*args, **kwargs) Overloaded function.   1. stopping_condition(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, f : rosetta.protocols.filters.Filter) -> NoneType   2. stopping_condition(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> rosetta.protocols.filters.Filter task_factory(...) from builtins.PyCapsule task_factory(*args, **kwargs) Overloaded function.   1. task_factory(rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> rosetta.core.pack.task.TaskFactory   2. task_factory(self : rosetta.protocols.matdes.MatDesGreedyOptMutationMover, task_factory : rosetta.core.pack.task.TaskFactory) -> 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 MatDesGreedyOptMutationMoverCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: MatDesGreedyOptMutationMoverCreator 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.matdes.MatDesGreedyOptMutationMoverCreator,  : rosetta.protocols.matdes.MatDesGreedyOptMutationMoverCreator) -> rosetta.protocols.matdes.MatDesGreedyOptMutationMoverCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.matdes.MatDesGreedyOptMutationMoverCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.matdes.MatDesGreedyOptMutationMoverCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class MatDesPointMutationCalculator(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.matdes.MatDesPointMutationCalculator) -> NoneType   2. __init__(rosetta.protocols.matdes.MatDesPointMutationCalculator, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t, rosetta.utility.vector1_std_pair_std_string_double_t, rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t, rosetta.utility.vector1_std_string) -> NoneType   doc   3. __init__(rosetta.protocols.matdes.MatDesPointMutationCalculator, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t, rosetta.utility.vector1_std_pair_std_string_double_t, rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t, rosetta.utility.vector1_std_string, bool) -> NoneType   doc   4. __init__(rosetta.protocols.matdes.MatDesPointMutationCalculator, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t, rosetta.utility.vector1_std_pair_std_string_double_t, rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t, rosetta.utility.vector1_std_string, bool, bool) -> NoneType   doc   5. __init__(rosetta.protocols.matdes.MatDesPointMutationCalculator, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t, rosetta.utility.vector1_std_pair_std_string_double_t, rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t, rosetta.utility.vector1_std_string, bool, bool, bool) -> NoneType   doc   6. __init__(rosetta.protocols.matdes.MatDesPointMutationCalculator, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t, rosetta.utility.vector1_std_pair_std_string_double_t, rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t, rosetta.utility.vector1_std_string, bool, bool, bool, float) -> NoneType   doc   7. __init__(rosetta.protocols.matdes.MatDesPointMutationCalculator, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t, rosetta.utility.vector1_std_pair_std_string_double_t, rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t, rosetta.utility.vector1_std_string, bool, bool, bool, float, float) -> NoneType   doc   8. __init__(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, task_factory : rosetta.core.pack.task.TaskFactory, scorefxn : rosetta.core.scoring.ScoreFunction, relax_mover : rosetta.protocols.moves.Mover, filters : rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t, filter_thresholds : rosetta.utility.vector1_std_pair_std_string_double_t, set_task_for_filters : rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t, sample_types : rosetta.utility.vector1_std_string, dump_pdb : bool, rtmin : bool, parallel : bool, design_shell : float, repack_shell : float, force_natro : bool) -> NoneType   9. __init__(rosetta.protocols.matdes.MatDesPointMutationCalculator, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.protocols.filters.Filter, (str, float), protocols::simple_filters::TaskAwareScoreTypeFilter) -> NoneType   doc   10. __init__(rosetta.protocols.matdes.MatDesPointMutationCalculator, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.protocols.filters.Filter, (str, float), protocols::simple_filters::TaskAwareScoreTypeFilter, str) -> NoneType   doc   11. __init__(rosetta.protocols.matdes.MatDesPointMutationCalculator, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.protocols.filters.Filter, (str, float), protocols::simple_filters::TaskAwareScoreTypeFilter, str, bool) -> NoneType   doc   12. __init__(rosetta.protocols.matdes.MatDesPointMutationCalculator, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.protocols.filters.Filter, (str, float), protocols::simple_filters::TaskAwareScoreTypeFilter, str, bool, bool) -> NoneType   doc   13. __init__(rosetta.protocols.matdes.MatDesPointMutationCalculator, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.protocols.filters.Filter, (str, float), protocols::simple_filters::TaskAwareScoreTypeFilter, str, bool, bool, bool) -> NoneType   doc   14. __init__(rosetta.protocols.matdes.MatDesPointMutationCalculator, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.protocols.filters.Filter, (str, float), protocols::simple_filters::TaskAwareScoreTypeFilter, str, bool, bool, bool, float) -> NoneType   doc   15. __init__(rosetta.protocols.matdes.MatDesPointMutationCalculator, rosetta.core.pack.task.TaskFactory, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, rosetta.protocols.filters.Filter, (str, float), protocols::simple_filters::TaskAwareScoreTypeFilter, str, bool, bool, bool, float, float) -> NoneType   doc   16. __init__(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, task_factory : rosetta.core.pack.task.TaskFactory, scorefxn : rosetta.core.scoring.ScoreFunction, relax_mover : rosetta.protocols.moves.Mover, filter : rosetta.protocols.filters.Filter, filter_threshold : (str, float), set_task_for_filter : protocols::simple_filters::TaskAwareScoreTypeFilter, sample_type : str, dump_pdb : bool, rtmin : bool, parallel : bool, design_shell : float, repack_shell : float, force_natro : bool) -> 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.matdes.MatDesPointMutationCalculator,  : rosetta.protocols.matdes.MatDesPointMutationCalculator) -> rosetta.protocols.matdes.MatDesPointMutationCalculator calc_point_mut_filters(...) from builtins.PyCapsule calc_point_mut_filters(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, start_pose : rosetta.core.pose.Pose, seqpos_aa_vals_vec : rosetta.utility.vector1_std_pair_unsigned_long_utility_vector1_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_std_allocator_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_t) -> NoneType clone(...) from builtins.PyCapsule clone(rosetta.protocols.matdes.MatDesPointMutationCalculator) -> rosetta.protocols.matdes.MatDesPointMutationCalculator dump_pdb(...) from builtins.PyCapsule dump_pdb(*args, **kwargs) Overloaded function.   1. dump_pdb(rosetta.protocols.matdes.MatDesPointMutationCalculator) -> bool   2. dump_pdb(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, dump_pdb : bool) -> NoneType eval_filters(...) from builtins.PyCapsule eval_filters(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, pose : rosetta.core.pose.Pose, filter_pass : bool, vals : rosetta.utility.vector1_double, always_eval : bool) -> NoneType filter_thresholds(...) from builtins.PyCapsule filter_thresholds(*args, **kwargs) Overloaded function.   1. filter_thresholds(rosetta.protocols.matdes.MatDesPointMutationCalculator) -> rosetta.utility.vector1_std_pair_std_string_double_t   2. filter_thresholds(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, filter_thresholds : rosetta.utility.vector1_std_pair_std_string_double_t) -> NoneType filters(...) from builtins.PyCapsule filters(*args, **kwargs) Overloaded function.   1. filters(rosetta.protocols.matdes.MatDesPointMutationCalculator) -> rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t   2. filters(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, filters : rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t) -> NoneType force_natro(...) from builtins.PyCapsule force_natro(*args, **kwargs) Overloaded function.   1. force_natro(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, force_natro : bool) -> NoneType   2. force_natro(rosetta.protocols.matdes.MatDesPointMutationCalculator) -> bool mutate_and_relax(...) from builtins.PyCapsule mutate_and_relax(*args, **kwargs) Overloaded function.   1. mutate_and_relax(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, pose : rosetta.core.pose.Pose, resi : int, target_aa : rosetta.core.chemical.AA) -> NoneType   2. mutate_and_relax(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, pose : rosetta.core.pose.Pose, resi : int, target_aa : rosetta.core.chemical.AA, green_packer : protocols::simple_moves::GreenPacker) -> NoneType new_tasks(...) from builtins.PyCapsule new_tasks(*args, **kwargs) Overloaded function.   1. new_tasks(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, new_tasks : rosetta.utility.vector1_std_shared_ptr_core_pack_task_PackerTask_t) -> NoneType   2. new_tasks(rosetta.protocols.matdes.MatDesPointMutationCalculator) -> rosetta.utility.vector1_std_shared_ptr_core_pack_task_PackerTask_t parallel(...) from builtins.PyCapsule parallel(*args, **kwargs) Overloaded function.   1. parallel(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, r : bool) -> NoneType   2. parallel(rosetta.protocols.matdes.MatDesPointMutationCalculator) -> bool reference_pose(...) from builtins.PyCapsule reference_pose(*args, **kwargs) Overloaded function.   1. reference_pose(rosetta.protocols.matdes.MatDesPointMutationCalculator) -> rosetta.core.pose.Pose   2. reference_pose(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, reference_pose : rosetta.core.pose.Pose) -> NoneType relax_mover(...) from builtins.PyCapsule relax_mover(*args, **kwargs) Overloaded function.   1. relax_mover(rosetta.protocols.matdes.MatDesPointMutationCalculator) -> rosetta.protocols.moves.Mover   2. relax_mover(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, relax_mover : rosetta.protocols.moves.Mover) -> NoneType rtmin(...) from builtins.PyCapsule rtmin(*args, **kwargs) Overloaded function.   1. rtmin(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, r : bool) -> NoneType   2. rtmin(rosetta.protocols.matdes.MatDesPointMutationCalculator) -> bool sample_types(...) from builtins.PyCapsule sample_types(*args, **kwargs) Overloaded function.   1. sample_types(rosetta.protocols.matdes.MatDesPointMutationCalculator) -> rosetta.utility.vector1_std_string   2. sample_types(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, sample_types : rosetta.utility.vector1_std_string) -> NoneType scorefxn(...) from builtins.PyCapsule scorefxn(*args, **kwargs) Overloaded function.   1. scorefxn(rosetta.protocols.matdes.MatDesPointMutationCalculator) -> rosetta.core.scoring.ScoreFunction   2. scorefxn(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_design_shell(...) from builtins.PyCapsule set_design_shell(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, dz_shell : float) -> NoneType set_repack_shell(...) from builtins.PyCapsule set_repack_shell(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, rp_shell : float) -> NoneType set_task_for_filters(...) from builtins.PyCapsule set_task_for_filters(*args, **kwargs) Overloaded function.   1. set_task_for_filters(rosetta.protocols.matdes.MatDesPointMutationCalculator) -> rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t   2. set_task_for_filters(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, set_task_for_filters : rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t) -> NoneType stored_task_names(...) from builtins.PyCapsule stored_task_names(*args, **kwargs) Overloaded function.   1. stored_task_names(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, stored_task_names : rosetta.utility.vector1_std_string) -> NoneType   2. stored_task_names(rosetta.protocols.matdes.MatDesPointMutationCalculator) -> rosetta.utility.vector1_std_string task_factory(...) from builtins.PyCapsule task_factory(*args, **kwargs) Overloaded function.   1. task_factory(rosetta.protocols.matdes.MatDesPointMutationCalculator) -> rosetta.core.pack.task.TaskFactory   2. task_factory(self : rosetta.protocols.matdes.MatDesPointMutationCalculator, task_factory : rosetta.core.pack.task.TaskFactory) -> NoneType   class OligomericAverageDegreeFilter(rosetta.protocols.filters.Filter)       Method resolution order: OligomericAverageDegreeFilter rosetta.protocols.filters.Filter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, task_factory : rosetta.core.pack.task.TaskFactory, t : float, d : float, jump_set : bool, jump : int, dof_names : str, mcomp : bool) -> NoneType   3. __init__(handle, rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> 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.matdes.OligomericAverageDegreeFilter, pose : rosetta.core.pose.Pose) -> bool clone(...) from builtins.PyCapsule clone(rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> rosetta.protocols.filters.Filter compute(...) from builtins.PyCapsule compute(self : rosetta.protocols.matdes.OligomericAverageDegreeFilter, pose : rosetta.core.pose.Pose, verbose : bool, write : bool) -> float   calc oligomeric AverageDegree distance_threshold(...) from builtins.PyCapsule distance_threshold(*args, **kwargs) Overloaded function.   1. distance_threshold(self : rosetta.protocols.matdes.OligomericAverageDegreeFilter, d : float) -> NoneType   2. distance_threshold(rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> float fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> rosetta.protocols.filters.Filter jump_id(...) from builtins.PyCapsule jump_id(*args, **kwargs) Overloaded function.   1. jump_id(self : rosetta.protocols.matdes.OligomericAverageDegreeFilter, jump : int) -> NoneType   2. jump_id(rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> int jump_set(...) from builtins.PyCapsule jump_set(*args, **kwargs) Overloaded function.   1. jump_set(self : rosetta.protocols.matdes.OligomericAverageDegreeFilter, jump_set : bool) -> NoneType   2. jump_set(rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> bool multicomp(...) from builtins.PyCapsule multicomp(*args, **kwargs) Overloaded function.   1. multicomp(self : rosetta.protocols.matdes.OligomericAverageDegreeFilter, multicomp : bool) -> NoneType   2. multicomp(rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> bool name(...) from builtins.PyCapsule name(rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> str report_sm(...) from builtins.PyCapsule report_sm(self : rosetta.protocols.matdes.OligomericAverageDegreeFilter, pose : rosetta.core.pose.Pose) -> float sym_dof_names(...) from builtins.PyCapsule sym_dof_names(*args, **kwargs) Overloaded function.   1. sym_dof_names(self : rosetta.protocols.matdes.OligomericAverageDegreeFilter, dof_names : str) -> NoneType   2. sym_dof_names(rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> str task_factory(...) from builtins.PyCapsule task_factory(*args, **kwargs) Overloaded function.   1. task_factory(self : rosetta.protocols.matdes.OligomericAverageDegreeFilter, task_factory : rosetta.core.pack.task.TaskFactory) -> NoneType   2. task_factory(rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> rosetta.core.pack.task.TaskFactory threshold(...) from builtins.PyCapsule threshold(*args, **kwargs) Overloaded function.   1. threshold(self : rosetta.protocols.matdes.OligomericAverageDegreeFilter, t : float) -> NoneType   2. threshold(rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> float verbose(...) from builtins.PyCapsule verbose(*args, **kwargs) Overloaded function.   1. verbose(self : rosetta.protocols.matdes.OligomericAverageDegreeFilter, verb : bool) -> NoneType   2. verbose(rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> bool write2pdb(...) from builtins.PyCapsule write2pdb(*args, **kwargs) Overloaded function.   1. write2pdb(self : rosetta.protocols.matdes.OligomericAverageDegreeFilter, write : bool) -> NoneType   2. write2pdb(rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> bool write_to_pdb(...) from builtins.PyCapsule write_to_pdb(self : rosetta.protocols.matdes.OligomericAverageDegreeFilter, pose : rosetta.core.pose.Pose, residue : int, residue_name : str, neighbors : int) -> NoneType Methods inherited from rosetta.protocols.filters.Filter: clear(...) from builtins.PyCapsule clear(rosetta.protocols.filters.Filter) -> NoneType   used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.filters.Filter) -> str get_user_defined_name(...) from builtins.PyCapsule get_user_defined_name(rosetta.protocols.filters.Filter) -> str score(...) from builtins.PyCapsule score(self : rosetta.protocols.filters.Filter, pose : rosetta.core.pose.Pose) -> float set_user_defined_name(...) from builtins.PyCapsule set_user_defined_name(self : rosetta.protocols.filters.Filter, name : str) -> NoneType   class OligomericAverageDegreeFilterCreator(rosetta.protocols.filters.FilterCreator)       Method resolution order: OligomericAverageDegreeFilterCreator rosetta.protocols.filters.FilterCreator 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.matdes.OligomericAverageDegreeFilterCreator,  : rosetta.protocols.matdes.OligomericAverageDegreeFilterCreator) -> rosetta.protocols.matdes.OligomericAverageDegreeFilterCreator create_filter(...) from builtins.PyCapsule create_filter(rosetta.protocols.matdes.OligomericAverageDegreeFilterCreator) -> rosetta.protocols.filters.Filter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.matdes.OligomericAverageDegreeFilterCreator) -> str   class SchemePlaceMotifsMover(rosetta.protocols.moves.Mover)       Method resolution order: SchemePlaceMotifsMover 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.matdes.SchemePlaceMotifsMover) -> 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.matdes.SchemePlaceMotifsMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.matdes.SchemePlaceMotifsMover,  : rosetta.protocols.matdes.SchemePlaceMotifsMover) -> rosetta.protocols.matdes.SchemePlaceMotifsMover clone(...) from builtins.PyCapsule clone(rosetta.protocols.matdes.SchemePlaceMotifsMover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.matdes.SchemePlaceMotifsMover) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.matdes.SchemePlaceMotifsMover) -> 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 SchemePlaceMotifsMoverCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: SchemePlaceMotifsMoverCreator 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.matdes.SchemePlaceMotifsMoverCreator,  : rosetta.protocols.matdes.SchemePlaceMotifsMoverCreator) -> rosetta.protocols.matdes.SchemePlaceMotifsMoverCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.matdes.SchemePlaceMotifsMoverCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.matdes.SchemePlaceMotifsMoverCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class SymDofMover(rosetta.protocols.moves.Mover)     WARNING WARNING WARNING THIS IS A THREAD-UNSAFE CLASS SINCE IT USES THE SymDofMoverSampler, A NON-CONSTANT SINGLETON.  ANY PROTOCOL THAT RELIES ON THIS MOVER IS THREAD-UNSAFE.     Method resolution order: SymDofMover 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.matdes.SymDofMover) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_components_to_pose_if_necessary(...) from builtins.PyCapsule add_components_to_pose_if_necessary(self : rosetta.protocols.matdes.SymDofMover, pose : rosetta.core.pose.Pose) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.matdes.SymDofMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.matdes.SymDofMover,  : rosetta.protocols.matdes.SymDofMover) -> rosetta.protocols.matdes.SymDofMover clone(...) from builtins.PyCapsule clone(rosetta.protocols.matdes.SymDofMover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.matdes.SymDofMover) -> rosetta.protocols.moves.Mover   create this type of object get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.matdes.SymDofMover) -> 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 SymDofMoverCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: SymDofMoverCreator 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.matdes.SymDofMoverCreator,  : rosetta.protocols.matdes.SymDofMoverCreator) -> rosetta.protocols.matdes.SymDofMoverCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.matdes.SymDofMoverCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.matdes.SymDofMoverCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class SymDofMoverSampler(rosetta.utility.SingletonBase_protocols_matdes_SymDofMoverSampler_t)     WARNING WARNING WARNING THIS SINGLETON CLASS HOLDS NON-CONST, JOB SPECIFIC DATA AND MAKES EVERY CLASS THAT USES THIS DATA THREAD UNSAFE.  THIS IS NOT HOW SINGLETONS SHOULD BE USED.     Method resolution order: SymDofMoverSampler rosetta.utility.SingletonBase_protocols_matdes_SymDofMoverSampler_t builtins.object Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. get_angle_diffs(...) from builtins.PyCapsule get_angle_diffs(rosetta.protocols.matdes.SymDofMoverSampler) -> rosetta.utility.vector1_double get_angles(...) from builtins.PyCapsule get_angles(rosetta.protocols.matdes.SymDofMoverSampler) -> rosetta.utility.vector1_double get_radial_disp_diffs(...) from builtins.PyCapsule get_radial_disp_diffs(rosetta.protocols.matdes.SymDofMoverSampler) -> rosetta.utility.vector1_double get_radial_disps(...) from builtins.PyCapsule get_radial_disps(rosetta.protocols.matdes.SymDofMoverSampler) -> rosetta.utility.vector1_double get_sym_dof_names(...) from builtins.PyCapsule get_sym_dof_names(rosetta.protocols.matdes.SymDofMoverSampler) -> rosetta.utility.vector1_std_string set_angle_ranges(...) from builtins.PyCapsule set_angle_ranges(self : rosetta.protocols.matdes.SymDofMoverSampler, angles_range_min : rosetta.utility.vector1_double, angles_range_max : rosetta.utility.vector1_double, angle_steps : rosetta.utility.vector1_double) -> NoneType set_angles(...) from builtins.PyCapsule set_angles(self : rosetta.protocols.matdes.SymDofMoverSampler, angles : rosetta.utility.vector1_double) -> NoneType set_radial_disp_ranges(...) from builtins.PyCapsule set_radial_disp_ranges(self : rosetta.protocols.matdes.SymDofMoverSampler, radial_disps_range_min : rosetta.utility.vector1_double, radial_disps_range_max : rosetta.utility.vector1_double, radial_disp_steps : rosetta.utility.vector1_double) -> NoneType set_radial_disps(...) from builtins.PyCapsule set_radial_disps(self : rosetta.protocols.matdes.SymDofMoverSampler, radial_disps : rosetta.utility.vector1_double) -> NoneType set_sym_dof_names(...) from builtins.PyCapsule set_sym_dof_names(self : rosetta.protocols.matdes.SymDofMoverSampler, sym_dof_names : rosetta.utility.vector1_std_string) -> NoneType step(...) from builtins.PyCapsule step(rosetta.protocols.matdes.SymDofMoverSampler) -> NoneType Methods inherited from rosetta.utility.SingletonBase_protocols_matdes_SymDofMoverSampler_t: get_instance(...) from builtins.PyCapsule get_instance() -> protocols::matdes::SymDofMoverSampler   class SymUnsatHbondFilter(rosetta.protocols.filters.Filter)     filters based on an upper bound # of buried unsatisfied polar residues     Method resolution order: SymUnsatHbondFilter rosetta.protocols.filters.Filter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, upper_cutoff : int, jump : int, sym_dofs : str, verb : bool, write : bool, mode : str, compare_to_ref : bool, reference_pose : rosetta.core.pose.Pose) -> NoneType   3. __init__(handle, rosetta.protocols.matdes.SymUnsatHbondFilter) -> 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.matdes.SymUnsatHbondFilter, pose : rosetta.core.pose.Pose) -> bool clone(...) from builtins.PyCapsule clone(rosetta.protocols.matdes.SymUnsatHbondFilter) -> rosetta.protocols.filters.Filter compare_to_ref(...) from builtins.PyCapsule compare_to_ref(*args, **kwargs) Overloaded function.   1. compare_to_ref(self : rosetta.protocols.matdes.SymUnsatHbondFilter, compare_to_ref : bool) -> NoneType   2. compare_to_ref(rosetta.protocols.matdes.SymUnsatHbondFilter) -> bool compute(...) from builtins.PyCapsule compute(self : rosetta.protocols.matdes.SymUnsatHbondFilter, pose : rosetta.core.pose.Pose, verb : bool, write : bool) -> float fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.matdes.SymUnsatHbondFilter) -> rosetta.protocols.filters.Filter jump_num(...) from builtins.PyCapsule jump_num(*args, **kwargs) Overloaded function.   1. jump_num(self : rosetta.protocols.matdes.SymUnsatHbondFilter, jump : int) -> NoneType   2. jump_num(rosetta.protocols.matdes.SymUnsatHbondFilter) -> int mode(...) from builtins.PyCapsule mode(*args, **kwargs) Overloaded function.   1. mode(self : rosetta.protocols.matdes.SymUnsatHbondFilter, mode : str) -> NoneType   2. mode(rosetta.protocols.matdes.SymUnsatHbondFilter) -> str name(...) from builtins.PyCapsule name(rosetta.protocols.matdes.SymUnsatHbondFilter) -> str reference_pose(...) from builtins.PyCapsule reference_pose(*args, **kwargs) Overloaded function.   1. reference_pose(self : rosetta.protocols.matdes.SymUnsatHbondFilter, reference_pose : rosetta.core.pose.Pose) -> NoneType   2. reference_pose(rosetta.protocols.matdes.SymUnsatHbondFilter) -> rosetta.core.pose.Pose report_sm(...) from builtins.PyCapsule report_sm(self : rosetta.protocols.matdes.SymUnsatHbondFilter, pose : rosetta.core.pose.Pose) -> float sym_dof_names(...) from builtins.PyCapsule sym_dof_names(*args, **kwargs) Overloaded function.   1. sym_dof_names(self : rosetta.protocols.matdes.SymUnsatHbondFilter, sym_dofs : str) -> NoneType   2. sym_dof_names(rosetta.protocols.matdes.SymUnsatHbondFilter) -> str upper_threshold(...) from builtins.PyCapsule upper_threshold(*args, **kwargs) Overloaded function.   1. upper_threshold(self : rosetta.protocols.matdes.SymUnsatHbondFilter, upper_cutoff : int) -> NoneType   2. upper_threshold(rosetta.protocols.matdes.SymUnsatHbondFilter) -> int verbose(...) from builtins.PyCapsule verbose(*args, **kwargs) Overloaded function.   1. verbose(self : rosetta.protocols.matdes.SymUnsatHbondFilter, verb : bool) -> NoneType   2. verbose(rosetta.protocols.matdes.SymUnsatHbondFilter) -> bool write2pdb(...) from builtins.PyCapsule write2pdb(*args, **kwargs) Overloaded function.   1. write2pdb(self : rosetta.protocols.matdes.SymUnsatHbondFilter, write : bool) -> NoneType   2. write2pdb(rosetta.protocols.matdes.SymUnsatHbondFilter) -> bool write_pymol_string_to_pdb(...) from builtins.PyCapsule write_pymol_string_to_pdb(self : rosetta.protocols.matdes.SymUnsatHbondFilter, pymol_selection : str) -> NoneType write_to_pdb(...) from builtins.PyCapsule write_to_pdb(self : rosetta.protocols.matdes.SymUnsatHbondFilter, pose : rosetta.core.pose.Pose, mode : str, residue_name : str, residue : int, atom_name : str) -> NoneType Methods inherited from rosetta.protocols.filters.Filter: clear(...) from builtins.PyCapsule clear(rosetta.protocols.filters.Filter) -> NoneType   used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.filters.Filter) -> str get_user_defined_name(...) from builtins.PyCapsule get_user_defined_name(rosetta.protocols.filters.Filter) -> str score(...) from builtins.PyCapsule score(self : rosetta.protocols.filters.Filter, pose : rosetta.core.pose.Pose) -> float set_user_defined_name(...) from builtins.PyCapsule set_user_defined_name(self : rosetta.protocols.filters.Filter, name : str) -> NoneType   class SymUnsatHbondFilterCreator(rosetta.protocols.filters.FilterCreator)       Method resolution order: SymUnsatHbondFilterCreator rosetta.protocols.filters.FilterCreator 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.matdes.SymUnsatHbondFilterCreator,  : rosetta.protocols.matdes.SymUnsatHbondFilterCreator) -> rosetta.protocols.matdes.SymUnsatHbondFilterCreator create_filter(...) from builtins.PyCapsule create_filter(rosetta.protocols.matdes.SymUnsatHbondFilterCreator) -> rosetta.protocols.filters.Filter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.matdes.SymUnsatHbondFilterCreator) -> str