Bindings for protocols::nonlocal namespace

Classes
		builtins.object Chunk Policy SmoothPolicy UniformPolicy PolicyFactory Region TreeBuilder SimpleTreeBuilder StarTreeBuilder TreeBuilderFactory rosetta.protocols.moves.Mover(builtins.object) BiasedFragmentMover HelixRotate SheetTranslate SingleFragmentMover rosetta.protocols.moves.MoverCreator(builtins.object) SingleFragmentMoverCreator   class BiasedFragmentMover(rosetta.protocols.moves.Mover)     User-specified, per-residue sampling probabilities allow fine grained control over the simulation.     Method resolution order: BiasedFragmentMover rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, policy : rosetta.protocols.nonlocal.Policy, probs : rosetta.utility.vector1_double) -> NoneType   2. __init__(handle, rosetta.protocols.nonlocal.BiasedFragmentMover) -> 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.nonlocal.BiasedFragmentMover, pose : rosetta.core.pose.Pose) -> NoneType   Inserts a single fragment into pose.    Insertion position is chosen in a biased manner using the per-residue  probabilities provided in the constructor. The decision on which fragment  to insert from the fragment library is delegated to the policy specified  in the constructor.    Respects the underlying kinematics of the system. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.nonlocal.BiasedFragmentMover,  : rosetta.protocols.nonlocal.BiasedFragmentMover) -> rosetta.protocols.nonlocal.BiasedFragmentMover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.nonlocal.BiasedFragmentMover) -> str   Returns the name of this mover Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply clone(...) from builtins.PyCapsule clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Return a clone of the Mover object. create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class Chunk(builtins.object)     region of sequence and knowledge of how to sample insertion positions from it according to an underlying distribution. Certain residues within the region may not be movable. Current behavior mimics but improves upon existing end-biased selection.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.nonlocal.Chunk, region : rosetta.protocols.nonlocal.Region, movable : rosetta.core.kinematics.MoveMap) -> NoneType   2. __init__(self : rosetta.protocols.nonlocal.Chunk, other : rosetta.protocols.nonlocal.Chunk) -> 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.nonlocal.Chunk, other : rosetta.protocols.nonlocal.Chunk) -> rosetta.protocols.nonlocal.Chunk   Assignment operator choose(...) from builtins.PyCapsule choose(rosetta.protocols.nonlocal.Chunk) -> int   Chooses an allowable insertion position on [start, stop] according  to the probability distribution is_movable(...) from builtins.PyCapsule is_movable(rosetta.protocols.nonlocal.Chunk) -> bool   Returns true if at least one position on [start(), stop()] is movable length(...) from builtins.PyCapsule length(rosetta.protocols.nonlocal.Chunk) -> int   Returns the length of this region start(...) from builtins.PyCapsule start(rosetta.protocols.nonlocal.Chunk) -> int   Lower boundary of this chunk stop(...) from builtins.PyCapsule stop(rosetta.protocols.nonlocal.Chunk) -> int   Upper boundary of this chunk valid(...) from builtins.PyCapsule valid(rosetta.protocols.nonlocal.Chunk) -> bool   Returns true if there is at least one valid insertion position in  the closed region [start(), stop()], false otherwise.   class HelixRotate(rosetta.protocols.moves.Mover)     axis defined by its first and last residues. Makes no assumptions about the kinematics of the system.   TODO(cmiles) Improved handling of kinked helices     Method resolution order: HelixRotate rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, helix : rosetta.protocols.loops.Loop, degrees : float) -> NoneType   3. __init__(handle, rosetta.protocols.nonlocal.HelixRotate) -> 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.nonlocal.HelixRotate, pose : rosetta.core.pose.Pose) -> NoneType   Rotates the helix by the specified number of degrees assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.nonlocal.HelixRotate,  : rosetta.protocols.nonlocal.HelixRotate) -> rosetta.protocols.nonlocal.HelixRotate clone(...) from builtins.PyCapsule clone(rosetta.protocols.nonlocal.HelixRotate) -> rosetta.protocols.moves.Mover   Creates a new instance with the copy constructor fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.nonlocal.HelixRotate) -> rosetta.protocols.moves.Mover   Creates a new instance with the default constructor get_degrees(...) from builtins.PyCapsule get_degrees(rosetta.protocols.nonlocal.HelixRotate) -> float   Returns the number of degrees to rotate the helix get_helix(...) from builtins.PyCapsule get_helix(rosetta.protocols.nonlocal.HelixRotate) -> rosetta.protocols.loops.Loop   Returns the helix to be modified get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.nonlocal.HelixRotate) -> str   Returns the protocol's name set_degrees(...) from builtins.PyCapsule set_degrees(self : rosetta.protocols.nonlocal.HelixRotate, degrees : float) -> NoneType   Updates the number of degrees to rotate the helix set_helix(...) from builtins.PyCapsule set_helix(self : rosetta.protocols.nonlocal.HelixRotate, helix : rosetta.protocols.loops.Loop) -> NoneType   Updates the helix to be modified 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 Policy(builtins.object)     fragment from set of possibilities. This class is based on the observation that fragment insertion methods differ primarily in the manner in which they choose from among a set of possibilities.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.nonlocal.Policy, fragments : rosetta.core.fragment.FragSet) -> NoneType   2. __init__(rosetta.protocols.nonlocal.Policy, rosetta.protocols.nonlocal.Policy) -> 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.nonlocal.Policy,  : rosetta.protocols.nonlocal.Policy) -> rosetta.protocols.nonlocal.Policy choose(...) from builtins.PyCapsule choose(self : rosetta.protocols.nonlocal.Policy, frame : rosetta.core.fragment.Frame, pose : rosetta.core.pose.Pose) -> int   Selects a single fragment from a set of possibilities given the  current status of the pose. fragments(...) from builtins.PyCapsule fragments(rosetta.protocols.nonlocal.Policy) -> rosetta.core.fragment.FragSet   class PolicyFactory(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.nonlocal.PolicyFactory) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. get_policy(...) from builtins.PyCapsule get_policy(*args, **kwargs) Overloaded function.   1. get_policy(policy_name : str, fragments : rosetta.core.fragment.FragSet) -> rosetta.protocols.nonlocal.Policy   If a valid policy name was provided, returns a Policy object of the  given type, exits otherwise. The resulting instance is constructed with a  copy of the given set of fragments, which may be optionally filtered by  rank (see num_fragments).   2. get_policy(policy_name : str, fragments : rosetta.core.fragment.FragSet, num_fragments : int) -> rosetta.protocols.nonlocal.Policy   If a valid policy name was provided, returns a Policy object of the  given type, exits otherwise. The resulting instance is constructed with a  copy of the given set of fragments, which may be optionally filtered by  rank (see num_fragments).   class Region(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.protocols.nonlocal.Region, start_pos : int, stop_pos : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.nonlocal.Region,  : rosetta.protocols.nonlocal.Region) -> rosetta.protocols.nonlocal.Region decreasing(...) from builtins.PyCapsule decreasing(rosetta.protocols.nonlocal.Region) -> bool   Returns true if stop <= start, false otherwise increasing(...) from builtins.PyCapsule increasing(rosetta.protocols.nonlocal.Region) -> bool   Returns true if start <= stop, false otherwise length(...) from builtins.PyCapsule length(rosetta.protocols.nonlocal.Region) -> int   Returns the length of this region. Makes no assumption about  directionality. That is, Region(3,5).length() == Region(5,3).length().  O(1) start(...) from builtins.PyCapsule start(rosetta.protocols.nonlocal.Region) -> int   Returns the starting position of this region  O(1) stop(...) from builtins.PyCapsule stop(rosetta.protocols.nonlocal.Region) -> int   Returns the stopping position of this region  O(1)   class SheetTranslate(rosetta.protocols.moves.Mover)     the axis defined by its first and last residues. Makes no assumptions about the kinematics of the system.   TODO(cmiles) Consider having the user define the axis of translation. TODO(cmiles) Improved handling of curved sheets     Method resolution order: SheetTranslate rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, sheet : rosetta.protocols.loops.Loop, distance_ang : float) -> NoneType   3. __init__(handle, rosetta.protocols.nonlocal.SheetTranslate) -> 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.nonlocal.SheetTranslate, pose : rosetta.core.pose.Pose) -> NoneType   Translates the sheet by the specified distance (in Angstroms) assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.nonlocal.SheetTranslate,  : rosetta.protocols.nonlocal.SheetTranslate) -> rosetta.protocols.nonlocal.SheetTranslate clone(...) from builtins.PyCapsule clone(rosetta.protocols.nonlocal.SheetTranslate) -> rosetta.protocols.moves.Mover   Creates a new instance with the copy constructor fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.nonlocal.SheetTranslate) -> rosetta.protocols.moves.Mover   Creates a new instance with the default constructor get_distance(...) from builtins.PyCapsule get_distance(rosetta.protocols.nonlocal.SheetTranslate) -> float   Returns the distance (in Angstroms) to translate the sheet get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.nonlocal.SheetTranslate) -> str   Returns the protocol's name get_sheet(...) from builtins.PyCapsule get_sheet(rosetta.protocols.nonlocal.SheetTranslate) -> rosetta.protocols.loops.Loop   Returns the sheet to be modified set_distance(...) from builtins.PyCapsule set_distance(self : rosetta.protocols.nonlocal.SheetTranslate, distance_ang : float) -> NoneType   Updates the distance (in Angstroms) to translate the sheet set_sheet(...) from builtins.PyCapsule set_sheet(self : rosetta.protocols.nonlocal.SheetTranslate, sheet : rosetta.protocols.loops.Loop) -> NoneType   Updates the sheet to be modified 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 SimpleTreeBuilder(TreeBuilder)       Method resolution order: SimpleTreeBuilder TreeBuilder 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.nonlocal.SimpleTreeBuilder,  : rosetta.protocols.nonlocal.SimpleTreeBuilder) -> rosetta.protocols.nonlocal.SimpleTreeBuilder set_up(...) from builtins.PyCapsule set_up(self : rosetta.protocols.nonlocal.SimpleTreeBuilder, chunks : rosetta.protocols.loops.Loops, pose : rosetta.core.pose.Pose) -> NoneType Methods inherited from TreeBuilder: tear_down(...) from builtins.PyCapsule tear_down(self : rosetta.protocols.nonlocal.TreeBuilder,  : rosetta.core.pose.Pose) -> NoneType   Reverts any modifications to <pose> introduced in preceding calls  to set_up(). Only subclasses that introduce modifications are responsible  for overriding this method.   class SingleFragmentMover(rosetta.protocols.moves.Mover)       Method resolution order: SingleFragmentMover rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, fragments : rosetta.core.fragment.FragSet, movable : rosetta.core.kinematics.MoveMap) -> NoneType   3. __init__(self : handle, fragments : rosetta.core.fragment.FragSet, movable : rosetta.core.kinematics.MoveMap, policy : rosetta.protocols.nonlocal.Policy) -> NoneType   4. __init__(handle, rosetta.protocols.nonlocal.SingleFragmentMover) -> 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.nonlocal.SingleFragmentMover, pose : rosetta.core.pose.Pose) -> NoneType   Performs a single fragment insertion on <pose>, drawn from the set  of fragments specified in the constructor. Respects the underlying  kinematics of the system, as determined by the Pose's FoldTree and the  user-specified MoveMap. Fragment insertions will only occur in allowable  regions of the pose. No moves will span jumps in the FoldTree.    Assumptions:    - <pose> has been instantiated (i.e. constructed from sequence or an      alternate source) elsewhere    - <pose>'s FoldTree is valid    - <pose> is centroid-level (warning if full-atom)    - The combination of FoldTree and MoveMap provide an unambiguous      definition of what's movable and what's not assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.nonlocal.SingleFragmentMover,  : rosetta.protocols.nonlocal.SingleFragmentMover) -> rosetta.protocols.nonlocal.SingleFragmentMover clone(...) from builtins.PyCapsule clone(rosetta.protocols.nonlocal.SingleFragmentMover) -> rosetta.protocols.moves.Mover   Creates a new instance using the copy constructor fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.nonlocal.SingleFragmentMover) -> rosetta.protocols.moves.Mover   Creates a new instance using the default constructor get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.nonlocal.SingleFragmentMover) -> str   Returns the name of this mover valid(...) from builtins.PyCapsule valid(rosetta.protocols.nonlocal.SingleFragmentMover) -> bool   Returns true if this instance is in a usable state, false otherwise 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 SingleFragmentMoverCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: SingleFragmentMoverCreator 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.nonlocal.SingleFragmentMoverCreator,  : rosetta.protocols.nonlocal.SingleFragmentMoverCreator) -> rosetta.protocols.nonlocal.SingleFragmentMoverCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.nonlocal.SingleFragmentMoverCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.nonlocal.SingleFragmentMoverCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class SmoothPolicy(Policy)     that, when applied to the pose, minimizes total distortion ("smooth move").     Method resolution order: SmoothPolicy Policy builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, fragments : rosetta.core.fragment.FragSet) -> NoneType   2. __init__(handle, rosetta.protocols.nonlocal.SmoothPolicy) -> 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.nonlocal.SmoothPolicy,  : rosetta.protocols.nonlocal.SmoothPolicy) -> rosetta.protocols.nonlocal.SmoothPolicy choose(...) from builtins.PyCapsule choose(self : rosetta.protocols.nonlocal.SmoothPolicy, frame : rosetta.core.fragment.Frame,  : rosetta.core.pose.Pose) -> int   Given the current state of <pose>, selects the fragment in <frame>  that minimizes overall distortion Methods inherited from Policy: fragments(...) from builtins.PyCapsule fragments(rosetta.protocols.nonlocal.Policy) -> rosetta.core.fragment.FragSet   class StarTreeBuilder(TreeBuilder)       Method resolution order: StarTreeBuilder TreeBuilder 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.nonlocal.StarTreeBuilder,  : rosetta.protocols.nonlocal.StarTreeBuilder) -> rosetta.protocols.nonlocal.StarTreeBuilder set_up(...) from builtins.PyCapsule set_up(self : rosetta.protocols.nonlocal.StarTreeBuilder, chunks : rosetta.protocols.loops.Loops, pose : rosetta.core.pose.Pose) -> NoneType   Constructs a star fold tree by placing a virtual residue at  <chunks> center of mass and adding jumps from it to a stochastically  chosen anchor residue in each chunk. Cutpoints are added on chunk  boundaries.    Important: chunks must be sorted in increasing order of start position.  The simplest way to achieve this is a call to Loops::sequential_order().    Additionally, every residue in pose must belong to one and only one chunk. tear_down(...) from builtins.PyCapsule tear_down(self : rosetta.protocols.nonlocal.StarTreeBuilder, pose : rosetta.core.pose.Pose) -> NoneType   Removes the virtual residue added to <pose> in calls to set_up()   class TreeBuilder(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.nonlocal.TreeBuilder) -> 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.nonlocal.TreeBuilder,  : rosetta.protocols.nonlocal.TreeBuilder) -> rosetta.protocols.nonlocal.TreeBuilder set_up(...) from builtins.PyCapsule set_up(self : rosetta.protocols.nonlocal.TreeBuilder, chunks : rosetta.protocols.loops.Loops, pose : rosetta.core.pose.Pose) -> NoneType   Programmatically constructs a FoldTree, updating <pose>. tear_down(...) from builtins.PyCapsule tear_down(self : rosetta.protocols.nonlocal.TreeBuilder,  : rosetta.core.pose.Pose) -> NoneType   Reverts any modifications to <pose> introduced in preceding calls  to set_up(). Only subclasses that introduce modifications are responsible  for overriding this method.   class TreeBuilderFactory(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.nonlocal.TreeBuilderFactory) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. get_builder(...) from builtins.PyCapsule get_builder(builder_name : str) -> rosetta.protocols.nonlocal.TreeBuilder   class UniformPolicy(Policy)     possible fragments at a given position.     Method resolution order: UniformPolicy Policy builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, fragments : rosetta.core.fragment.FragSet) -> 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.nonlocal.UniformPolicy,  : rosetta.protocols.nonlocal.UniformPolicy) -> rosetta.protocols.nonlocal.UniformPolicy choose(...) from builtins.PyCapsule choose(self : rosetta.protocols.nonlocal.UniformPolicy, frame : rosetta.core.fragment.Frame,  : rosetta.core.pose.Pose) -> int   Selects uniformly among the set of possible fragments in <frame> Methods inherited from Policy: fragments(...) from builtins.PyCapsule fragments(rosetta.protocols.nonlocal.Policy) -> rosetta.core.fragment.FragSet

Functions
		chunks_by_CA_CA_distance(...) method of builtins.PyCapsule instance chunks_by_CA_CA_distance(*args, **kwargs) Overloaded function.   1. chunks_by_CA_CA_distance(pose : rosetta.core.pose.Pose, chunks : rosetta.protocols.loops.Loops) -> NoneType   Computes the distance between consecutive CA atoms. If the distance exceeds  a user-specified threshold, creates a new chunk and adds it to <chunks>. CA-CA  distance threshold is retrieved from the option system (rigid::max_ca_ca_dist).   2. chunks_by_CA_CA_distance(pose : rosetta.core.pose.Pose, chunks : rosetta.protocols.loops.Loops, threshold : float) -> NoneType   Computes the distance between consecutive CA atoms. If the distance exceeds  <threshold>, creates a new chunk and adds it to <chunks>. combine_and_trim(...) method of builtins.PyCapsule instance combine_and_trim(min_chunk_sz : int, num_residues : int, aligned_regions : rosetta.protocols.loops.Loops, unaligned_regions : rosetta.protocols.loops.Loops) -> rosetta.protocols.loops.Loops   Combine aligned and unaligned regions, limit size of final loop current_job(...) method of builtins.PyCapsule instance current_job() -> rosetta.protocols.comparative_modeling.ThreadingJob   Retrieves the current job from the JobDistributor decompose(...) method of builtins.PyCapsule instance decompose(min_chunk_sz : int, max_chunk_sz : int, loop : rosetta.protocols.loops.Loop, pieces : rosetta.utility.vector1_protocols_loops_Loop) -> NoneType   Recursively decomposes <loop> into a series of <pieces>, each having  length less than or equal to <max_length>. emit_intermediate(...) method of builtins.PyCapsule instance emit_intermediate(pose : rosetta.core.pose.Pose, file : str) -> NoneType   If -abinitio:debug is enabled, writes <pose> to <file>. find_regions_with_minimum_size(...) method of builtins.PyCapsule instance find_regions_with_minimum_size(alignment : rosetta.core.sequence.SequenceAlignment, unaligned_region_min_sz : int, aligned_regions : rosetta.protocols.loops.Loops, unaligned_regions : rosetta.protocols.loops.Loops) -> NoneType get_per_residue_score(...) method of builtins.PyCapsule instance get_per_residue_score(rsd_idx : int, scoretype : rosetta.core.scoring.ScoreType, pose : rosetta.core.pose.Pose) -> float   Returns the unweighted score of the ScoreType for the given residue. Assumes that the Pose has recently been scored by ScoreFunction with non-zero weight for the ScoreType. limit_chunk_size(...) method of builtins.PyCapsule instance limit_chunk_size(min_chunk_sz : int, max_chunk_sz : int, regions : rosetta.protocols.loops.Loops) -> NoneType   Best-effort attempt to limit the length of a chunk by recursively  decomposing <regions> such that min_chunk_sz <= |chunk| <= max_chunk_sz.