Bindings for protocols::loops::loop_closure::ccd namespace

Classes
		builtins.object ChainDirection LoopClosure ShortLoopClosure RamaCheckBase RamaCheck1B RamaCheck2B SecondaryStructureType rosetta.protocols.moves.Mover(builtins.object) CCDLoopClosureMover SlidingWindowLoopClosure WidthFirstSlidingWindowLoopClosure FASelectSlidingWindowLoopClosure rosetta.protocols.moves.MoverCreator(builtins.object) CCDLoopClosureMoverCreator   class CCDLoopClosureMover(rosetta.protocols.moves.Mover)     Close a loop (protein or otherwise) using bi-directional Cyclic Coordinate Descent     This class was initially a wrapper for fast_ccd_loop_closure(), an exposed method in ccd_closure.cc. Before using this mover:  1) Set a proper foldtree - usually a regular loop foldtree is used. (see protocols::loops::foldtree_from_loops)  2) Add cutpoint variants to the loop cutpoint   The original description of the CCD algorithm in relation to protein loop closure can be found here:  Canutescu AA, Dunbrack RL Jr: Cyclic coordinate descent: a robotics algorithm for protein loop closure.  Protein Sci 2003, 12:963-972.     Method resolution order: CCDLoopClosureMover 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.loops.loop_closure.ccd.CCDLoopClosureMover) -> NoneType   3. __init__(self : handle, loop : rosetta.protocols.loops.Loop) -> NoneType   4. __init__(self : handle, loop : rosetta.protocols.loops.Loop, mm : rosetta.core.kinematics.MoveMap) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> str actual_cycles(...) from builtins.PyCapsule actual_cycles(rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> int   Get the number of cycles used to close the loop. apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, pose : rosetta.core.pose.Pose) -> NoneType   Apply the corresponding move to <pose>. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, object_to_copy : rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover check_rama_scores(...) from builtins.PyCapsule check_rama_scores(*args, **kwargs) Overloaded function.   1. check_rama_scores(rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> bool   Are closure moves checked using the rama scores and the Metropolis criterion?   2. check_rama_scores(self : rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, setting : bool) -> NoneType   Set whether or not closure moves are checked using the rama scores and the Metropolis criterion. clone(...) from builtins.PyCapsule clone(rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> rosetta.protocols.moves.Mover deviation(...) from builtins.PyCapsule deviation(rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> float   Get the RMS deviation of the target atoms after completion of loop closure.      sqrt( dev / number_of_atoms ) fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> str   Return the name of the Mover. loop(...) from builtins.PyCapsule loop(*args, **kwargs) Overloaded function.   1. loop(rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> rosetta.protocols.loops.Loop   Get the Loop to be closed.   2. loop(self : rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, new_loop : rosetta.protocols.loops.Loop) -> NoneType   Set the Loop to be closed. max_cycles(...) from builtins.PyCapsule max_cycles(*args, **kwargs) Overloaded function.   1. max_cycles(rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> int   Get the maximum number of cycles to attempt if the tolerance is not satisfied.      Each cycle includes both forward and backward directions.   2. max_cycles(self : rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, input_ccd_cycles : int) -> NoneType   Set the maximum number of cycles to attempt if the tolerance is not satisfied.      Each cycle includes both forward and backward directions. max_per_move_torsion_delta_per_residue(...) from builtins.PyCapsule max_per_move_torsion_delta_per_residue(*args, **kwargs) Overloaded function.   1. max_per_move_torsion_delta_per_residue(self : rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, input_max_delta_helix : float, input_max_delta_strand : float, input_max_delta_coil : float) -> NoneType   Set the maximum change in torsion angle a residue is allowed per closure move for each of the three  secondary structure types.      of parameters is helix, strand, coil. Angles are in degrees.   2. max_per_move_torsion_delta_per_residue(self : rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, secstruct : rosetta.protocols.loops.loop_closure.ccd.SecondaryStructureType) -> float   Get the maximum change in torsion angle a residue is allowed for a single move for one of the  three secondary structure types.       angle in degrees   3. max_per_move_torsion_delta_per_residue(self : rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, secstruct : str) -> float   Get the maximum allowed torsion angle deviation for the entire closure run for one of the three  secondary structure types ( H, E, L). max_total_torsion_delta_per_residue(...) from builtins.PyCapsule max_total_torsion_delta_per_residue(*args, **kwargs) Overloaded function.   1. max_total_torsion_delta_per_residue(self : rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, secstruct : rosetta.protocols.loops.loop_closure.ccd.SecondaryStructureType) -> float   Get the maximum change in torsion angle a residue is allowed for the entire closure run for one of the  three secondary structure types.       angle in degrees   2. max_total_torsion_delta_per_residue(self : rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, secstruct : str) -> float   Get the maximum allowed torsion angle deviation for the entire closure run for one of the three  secondary structure types ( H, E, L).   3. max_total_torsion_delta_per_residue(self : rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, input_max_delta_helix : float, input_max_delta_strand : float, input_max_delta_coil : float) -> NoneType   Set the maximum change in torsion angle a residue is allowed for the entire closure run for each of  the three secondary structure types.      of parameters is helix, strand, coil.  Angles are in degrees. movemap(...) from builtins.PyCapsule movemap(*args, **kwargs) Overloaded function.   1. movemap(rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> rosetta.core.kinematics.MoveMap   Get the current MoveMap.   2. movemap(self : rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, new_movemap : rosetta.core.kinematics.MoveMap) -> NoneType   Set the MoveMap.   Positions outside of the defined loop will be ignored. rama(...) from builtins.PyCapsule rama(rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> protocols::loops::loop_closure::ccd::RamaCheckBase   Get a pointer to the RamaCheck instance being used. rama_delta(...) from builtins.PyCapsule rama_delta(rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> float   Get the average change in rama score for the residues in the loop after completion of loop closure.        This value will only be meaningful if the option for checking the rama score is turned on.        Change this name to match the datum. ~Labonte 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 set_verbose(...) from builtins.PyCapsule set_verbose(self : rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, setting : bool) -> NoneType   Set whether or not to output loop start/end points at beginning of Mover apply(). success(...) from builtins.PyCapsule success(rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> bool   Return true if the forward and backward RMS deviations are each lower than the tolerance value. tolerance(...) from builtins.PyCapsule tolerance(*args, **kwargs) Overloaded function.   1. tolerance(rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> float   Get the tolerance for loop closure in Angstroms.      A forward and backward splice of RMS over N, CA, and C (or target atoms) must be less than the tolerance for an early  return; otherwise, the algorithm will go through the loop the requested number of cycles.  RMS Deviation is calculation as sqrt( dev / number_of_atoms )   2. tolerance(self : rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, input_tolerance : float) -> NoneType   Set the tolerance for loop closure in Angstroms.      A forward and backward splice of RMS deviation over N, CA, and C (or target atoms)must be less than the tolerance for  an early return; otherwise, the algorithm will go through the loop the requested number of cycles.  RMS Deviation is calculation as sqrt( dev / number_of_atoms ) torsion_delta(...) from builtins.PyCapsule torsion_delta(rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> float   Get the average change in the main-chain torsion angles of the loop after completion of loop closure.        Change this name to match the datum. ~Labonte use_rama_2B(...) from builtins.PyCapsule use_rama_2B(*args, **kwargs) Overloaded function.   1. use_rama_2B(rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover) -> bool   Are two-body (neighbor-dependent) Ramachandran maps being used?   2. use_rama_2B(self : rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover, setting : bool) -> NoneType   Set whether or not two-body (neighbor-dependent) Ramachandran maps should be used. 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 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 CCDLoopClosureMoverCreator(rosetta.protocols.moves.MoverCreator)     %CCDLoopClosureMoverCreator allows the MoverFactory to create a CCDLoopClosureMover instance.     Method resolution order: CCDLoopClosureMoverCreator 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.loops.loop_closure.ccd.CCDLoopClosureMoverCreator,  : rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator) -> rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator) -> rosetta.protocols.moves.Mover   Return a up-casted owning pointer (MoverOP) to the mover. keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator) -> str   Return the string identifier for the associated Mover (CCDLoopClosureMover). mover_name(...) from builtins.PyCapsule mover_name() -> str   Static method that returns the keyname for performance reasons.   class ChainDirection(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.protocols.loops.loop_closure.ccd.ChainDirection, rosetta.protocols.loops.loop_closure.ccd.ChainDirection) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.protocols.loops.loop_closure.ccd.ChainDirection) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.loops.loop_closure.ccd.ChainDirection, int) -> NoneType   2. __init__(rosetta.protocols.loops.loop_closure.ccd.ChainDirection, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.protocols.loops.loop_closure.ccd.ChainDirection) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.protocols.loops.loop_closure.ccd.ChainDirection, rosetta.protocols.loops.loop_closure.ccd.ChainDirection) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.protocols.loops.loop_closure.ccd.ChainDirection) -> str Data and other attributes defined here: backward = ChainDirection.n_chain_directions forward = ChainDirection.forward n_chain_directions = ChainDirection.n_chain_directions   class FASelectSlidingWindowLoopClosure(WidthFirstSlidingWindowLoopClosure)       Method resolution order: FASelectSlidingWindowLoopClosure WidthFirstSlidingWindowLoopClosure SlidingWindowLoopClosure rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, fragset : rosetta.core.fragment.FragSet, scorefxn : rosetta.core.scoring.ScoreFunction, movemap : rosetta.core.kinematics.MoveMap) -> NoneType   2. __init__(handle) -> NoneType   3. __init__(handle, rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure) -> 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.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure,  : rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure) -> rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure fascore(...) from builtins.PyCapsule fascore(self : rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure, fa_pose : rosetta.core.pose.Pose) -> float get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure) -> 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 select_final_loop(...) from builtins.PyCapsule select_final_loop(self : rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure, more_cut : rosetta.core.pose.Pose, less_cut : rosetta.core.pose.Pose) -> NoneType set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure) -> NoneType set_fullatom_pose(...) from builtins.PyCapsule set_fullatom_pose(self : rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure, fa_pose : rosetta.core.pose.Pose) -> NoneType Methods inherited from WidthFirstSlidingWindowLoopClosure: sample_loops(...) from builtins.PyCapsule sample_loops(self : rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure, more_cut : rosetta.core.pose.Pose, less_cut : rosetta.core.pose.Pose) -> NoneType Methods inherited from SlidingWindowLoopClosure: apply(...) from builtins.PyCapsule apply(*args, **kwargs) Overloaded function.   1. apply(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut : rosetta.core.pose.Pose, less_cut : rosetta.core.pose.Pose) -> NoneType   2. apply(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut : rosetta.core.pose.Pose) -> NoneType bIdealLoopClosing(...) from builtins.PyCapsule bIdealLoopClosing(rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> bool closure_fragments(...) from builtins.PyCapsule closure_fragments(rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> rosetta.core.fragment.FragSet determine_loop(...) from builtins.PyCapsule determine_loop(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut : rosetta.core.pose.Pose, less_cut : rosetta.core.pose.Pose) -> rosetta.protocols.loops.Loop fragments(...) from builtins.PyCapsule fragments(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, frags : rosetta.core.fragment.FragSet) -> NoneType keep_fragments(...) from builtins.PyCapsule keep_fragments(*args, **kwargs) Overloaded function.   1. keep_fragments(rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> NoneType   2. keep_fragments(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting : bool) -> NoneType movemap(...) from builtins.PyCapsule movemap(*args, **kwargs) Overloaded function.   1. movemap(rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> rosetta.core.kinematics.MoveMap   2. movemap(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, movemap : rosetta.core.kinematics.MoveMap) -> NoneType output_debug_structure(...) from builtins.PyCapsule output_debug_structure(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, pose : rosetta.core.pose.Pose, prefix : str) -> NoneType scored_frag_cycle_ratio(...) from builtins.PyCapsule scored_frag_cycle_ratio(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting : float) -> NoneType scorefxn(...) from builtins.PyCapsule scorefxn(*args, **kwargs) Overloaded function.   1. scorefxn(rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> rosetta.core.scoring.ScoreFunction   2. scorefxn(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType setPoseExtraScore(...) from builtins.PyCapsule setPoseExtraScore(pose : rosetta.core.pose.Pose) -> NoneType set_bIdealLoopClosing(...) from builtins.PyCapsule set_bIdealLoopClosing(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting : bool) -> NoneType set_chainbreak_max(...) from builtins.PyCapsule set_chainbreak_max(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting : float) -> NoneType set_evaluation(...) from builtins.PyCapsule set_evaluation(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, ev : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType set_loop(...) from builtins.PyCapsule set_loop(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, loop_in : rosetta.protocols.loops.Loop) -> NoneType short_frag_cycle_ratio(...) from builtins.PyCapsule short_frag_cycle_ratio(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting : float) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply 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 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 LoopClosure(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, fragset : rosetta.core.fragment.FragSet, scorefxn : rosetta.core.scoring.ScoreFunction, loop_def : rosetta.protocols.loops.Loop, movemap : rosetta.core.kinematics.MoveMap) -> NoneType   2. __init__(handle, rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> 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.loops.loop_closure.ccd.LoopClosure, pose : rosetta.core.pose.Pose) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loops.loop_closure.ccd.LoopClosure,  : rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> rosetta.protocols.loops.loop_closure.ccd.LoopClosure closure_fragments(...) from builtins.PyCapsule closure_fragments(rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> rosetta.core.fragment.Frame mc(...) from builtins.PyCapsule mc(rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> rosetta.protocols.moves.MonteCarlo movemap(...) from builtins.PyCapsule movemap(rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> rosetta.core.kinematics.MoveMap nr_fragments(...) from builtins.PyCapsule nr_fragments(rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> int ramp_chainbreak(...) from builtins.PyCapsule ramp_chainbreak(*args, **kwargs) Overloaded function.   1. ramp_chainbreak(rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> NoneType   2. ramp_chainbreak(self : rosetta.protocols.loops.loop_closure.ccd.LoopClosure, setting : bool) -> NoneType scorefxn(...) from builtins.PyCapsule scorefxn(rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> rosetta.core.scoring.ScoreFunction set_cycles(...) from builtins.PyCapsule set_cycles(*args, **kwargs) Overloaded function.   1. set_cycles(rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> NoneType   2. set_cycles(self : rosetta.protocols.loops.loop_closure.ccd.LoopClosure, cycle_ratio : float) -> NoneType set_nr_fragments(...) from builtins.PyCapsule set_nr_fragments(*args, **kwargs) Overloaded function.   1. set_nr_fragments(rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> NoneType   2. set_nr_fragments(self : rosetta.protocols.loops.loop_closure.ccd.LoopClosure, nr_fragments : int) -> NoneType   class RamaCheck1B(RamaCheckBase)       Method resolution order: RamaCheck1B RamaCheckBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.loops.loop_closure.ccd.RamaCheck1B) -> 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.loops.loop_closure.ccd.RamaCheck1B, object_to_copy : rosetta.protocols.loops.loop_closure.ccd.RamaCheck1B) -> rosetta.protocols.loops.loop_closure.ccd.RamaCheck1B clone(...) from builtins.PyCapsule clone(rosetta.protocols.loops.loop_closure.ccd.RamaCheck1B) -> rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase   Return a pointer to a new, fully configured copy of RamaCheck1B compute_rama_score(...) from builtins.PyCapsule compute_rama_score(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheck1B, pose : rosetta.core.pose.Pose, seqpos : int, phi : float, psi : float) -> float   Compute the Ramachandran score of residue <seqpos> in <pose> with a hypothetical conformation <phi>, <psi>.  The score is independent of the identity of the neighboring residues. name(...) from builtins.PyCapsule name(rosetta.protocols.loops.loop_closure.ccd.RamaCheck1B) -> str   Return "RamaCheck1B" Methods inherited from RamaCheckBase: __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> str accept_new_conformation(...) from builtins.PyCapsule accept_new_conformation(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose : rosetta.core.pose.Pose, torsion_id : rosetta.core.id.TorsionID, alpha : float) -> bool   Determine whether or not a candidate conformation should be accepted based on the Ramachandran score.      true if the move should be accepted, false if it should be rejected. average_change_in_rama_score_over_range(...) from builtins.PyCapsule average_change_in_rama_score_over_range(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose : rosetta.core.pose.Pose, first_res : int, last_res : int) -> float   Compute the average change in Ramachandran score between the initial pose and the current pose from  <first_res> to <last_res>.      The average change in Ramachandran score. initialize_starting_rama_scores(...) from builtins.PyCapsule initialize_starting_rama_scores(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose : rosetta.core.pose.Pose) -> NoneType   Store the Ramachandran scores of each residue in the supplied pose. max_rama_score_increase(...) from builtins.PyCapsule max_rama_score_increase(*args, **kwargs) Overloaded function.   1. max_rama_score_increase(rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> float   Get the maximum rama score increase allowed during rama score-checking with the Metropolis criterion.        This value will only be used if the option for checking the rama score is turned on.   2. max_rama_score_increase(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, input_max_rama_score_increase : float) -> NoneType   Set the maximum rama score increase allowed during rama score-checking with the Metropolis criterion.        This value will only be used if the option for checking the rama score is turned on. parse_my_tag(...) from builtins.PyCapsule parse_my_tag(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, tag : rosetta.utility.tag.Tag) -> NoneType register_options(...) from builtins.PyCapsule register_options() -> NoneType   Register options with the option system. temperature(...) from builtins.PyCapsule temperature(*args, **kwargs) Overloaded function.   1. temperature(rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> float   Get the "temperature" used for rama score-checking with the Metropolis criterion.        This value will only be used if the option for checking the rama score is turned on.   2. temperature(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, input_temperature : float) -> NoneType   Set the "temperature" used for rama score-checking with the Metropolis criterion.        This value will only be used if the option for checking the rama score is turned on. total_net_change_in_rama_score_over_range(...) from builtins.PyCapsule total_net_change_in_rama_score_over_range(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose : rosetta.core.pose.Pose, first_res : int, last_res : int) -> float   Compute the total net change in Ramachandran score between the initial pose and the current pose from  <first_res> to <last_res>.      The total net change in Ramachandran score.   class RamaCheck2B(RamaCheckBase)       Method resolution order: RamaCheck2B RamaCheckBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B) -> 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.loops.loop_closure.ccd.RamaCheck2B, object_to_copy : rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B) -> rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B clone(...) from builtins.PyCapsule clone(rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B) -> rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase   Return a pointer to a new, fully configured copy of RamaCheck2B compute_rama_score(...) from builtins.PyCapsule compute_rama_score(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B, pose : rosetta.core.pose.Pose, seqpos : int, phi : float, psi : float) -> float   Compute the Ramachandran score of residue <seqpos> in <pose> with a hypothetical conformation <phi>, <psi>.  The score depends on the identity of the neighboring residues. name(...) from builtins.PyCapsule name(rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B) -> str   Return "RamaCheck2B" Methods inherited from RamaCheckBase: __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> str accept_new_conformation(...) from builtins.PyCapsule accept_new_conformation(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose : rosetta.core.pose.Pose, torsion_id : rosetta.core.id.TorsionID, alpha : float) -> bool   Determine whether or not a candidate conformation should be accepted based on the Ramachandran score.      true if the move should be accepted, false if it should be rejected. average_change_in_rama_score_over_range(...) from builtins.PyCapsule average_change_in_rama_score_over_range(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose : rosetta.core.pose.Pose, first_res : int, last_res : int) -> float   Compute the average change in Ramachandran score between the initial pose and the current pose from  <first_res> to <last_res>.      The average change in Ramachandran score. initialize_starting_rama_scores(...) from builtins.PyCapsule initialize_starting_rama_scores(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose : rosetta.core.pose.Pose) -> NoneType   Store the Ramachandran scores of each residue in the supplied pose. max_rama_score_increase(...) from builtins.PyCapsule max_rama_score_increase(*args, **kwargs) Overloaded function.   1. max_rama_score_increase(rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> float   Get the maximum rama score increase allowed during rama score-checking with the Metropolis criterion.        This value will only be used if the option for checking the rama score is turned on.   2. max_rama_score_increase(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, input_max_rama_score_increase : float) -> NoneType   Set the maximum rama score increase allowed during rama score-checking with the Metropolis criterion.        This value will only be used if the option for checking the rama score is turned on. parse_my_tag(...) from builtins.PyCapsule parse_my_tag(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, tag : rosetta.utility.tag.Tag) -> NoneType register_options(...) from builtins.PyCapsule register_options() -> NoneType   Register options with the option system. temperature(...) from builtins.PyCapsule temperature(*args, **kwargs) Overloaded function.   1. temperature(rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> float   Get the "temperature" used for rama score-checking with the Metropolis criterion.        This value will only be used if the option for checking the rama score is turned on.   2. temperature(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, input_temperature : float) -> NoneType   Set the "temperature" used for rama score-checking with the Metropolis criterion.        This value will only be used if the option for checking the rama score is turned on. total_net_change_in_rama_score_over_range(...) from builtins.PyCapsule total_net_change_in_rama_score_over_range(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose : rosetta.core.pose.Pose, first_res : int, last_res : int) -> float   Compute the total net change in Ramachandran score between the initial pose and the current pose from  <first_res> to <last_res>.      The total net change in Ramachandran score.   class RamaCheckBase(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> NoneType   2. __init__(rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> str accept_new_conformation(...) from builtins.PyCapsule accept_new_conformation(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose : rosetta.core.pose.Pose, torsion_id : rosetta.core.id.TorsionID, alpha : float) -> bool   Determine whether or not a candidate conformation should be accepted based on the Ramachandran score.      true if the move should be accepted, false if it should be rejected. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, object_to_copy : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase average_change_in_rama_score_over_range(...) from builtins.PyCapsule average_change_in_rama_score_over_range(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose : rosetta.core.pose.Pose, first_res : int, last_res : int) -> float   Compute the average change in Ramachandran score between the initial pose and the current pose from  <first_res> to <last_res>.      The average change in Ramachandran score. clone(...) from builtins.PyCapsule clone(rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase   Return a pointer to a new, fully configured copy of RamaCheckBase       The clone method should be used to copy an instance of RamaCheck if the derived class type is unknown. compute_rama_score(...) from builtins.PyCapsule compute_rama_score(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose : rosetta.core.pose.Pose, seqpos : int, phi : float, psi : float) -> float   Compute the Ramachandran score of residue <seqpos> in <pose> with a hypothetical conformation <phi>, <psi> initialize_starting_rama_scores(...) from builtins.PyCapsule initialize_starting_rama_scores(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose : rosetta.core.pose.Pose) -> NoneType   Store the Ramachandran scores of each residue in the supplied pose. max_rama_score_increase(...) from builtins.PyCapsule max_rama_score_increase(*args, **kwargs) Overloaded function.   1. max_rama_score_increase(rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> float   Get the maximum rama score increase allowed during rama score-checking with the Metropolis criterion.        This value will only be used if the option for checking the rama score is turned on.   2. max_rama_score_increase(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, input_max_rama_score_increase : float) -> NoneType   Set the maximum rama score increase allowed during rama score-checking with the Metropolis criterion.        This value will only be used if the option for checking the rama score is turned on. name(...) from builtins.PyCapsule name(rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> str   Return the name of the RamaCheck class being used parse_my_tag(...) from builtins.PyCapsule parse_my_tag(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, tag : rosetta.utility.tag.Tag) -> NoneType register_options(...) from builtins.PyCapsule register_options() -> NoneType   Register options with the option system. temperature(...) from builtins.PyCapsule temperature(*args, **kwargs) Overloaded function.   1. temperature(rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase) -> float   Get the "temperature" used for rama score-checking with the Metropolis criterion.        This value will only be used if the option for checking the rama score is turned on.   2. temperature(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, input_temperature : float) -> NoneType   Set the "temperature" used for rama score-checking with the Metropolis criterion.        This value will only be used if the option for checking the rama score is turned on. total_net_change_in_rama_score_over_range(...) from builtins.PyCapsule total_net_change_in_rama_score_over_range(self : rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase, pose : rosetta.core.pose.Pose, first_res : int, last_res : int) -> float   Compute the total net change in Ramachandran score between the initial pose and the current pose from  <first_res> to <last_res>.      The total net change in Ramachandran score.   class SecondaryStructureType(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.protocols.loops.loop_closure.ccd.SecondaryStructureType, rosetta.protocols.loops.loop_closure.ccd.SecondaryStructureType) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.protocols.loops.loop_closure.ccd.SecondaryStructureType) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.loops.loop_closure.ccd.SecondaryStructureType, int) -> NoneType   2. __init__(rosetta.protocols.loops.loop_closure.ccd.SecondaryStructureType, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.protocols.loops.loop_closure.ccd.SecondaryStructureType) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.protocols.loops.loop_closure.ccd.SecondaryStructureType, rosetta.protocols.loops.loop_closure.ccd.SecondaryStructureType) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.protocols.loops.loop_closure.ccd.SecondaryStructureType) -> str Data and other attributes defined here: coil = SecondaryStructureType.n_secondary_structure_types helix = SecondaryStructureType.helix n_secondary_structure_types = SecondaryStructureType.n_secondary_structure_types strand = SecondaryStructureType.strand   class ShortLoopClosure(LoopClosure)       Method resolution order: ShortLoopClosure LoopClosure builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, fragset : rosetta.core.fragment.FragSet, loop_def : rosetta.protocols.loops.Loop, movemap : rosetta.core.kinematics.MoveMap) -> 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.loops.loop_closure.ccd.ShortLoopClosure, pose : rosetta.core.pose.Pose) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loops.loop_closure.ccd.ShortLoopClosure,  : rosetta.protocols.loops.loop_closure.ccd.ShortLoopClosure) -> rosetta.protocols.loops.loop_closure.ccd.ShortLoopClosure catch_fragment(...) from builtins.PyCapsule catch_fragment(self : rosetta.protocols.loops.loop_closure.ccd.ShortLoopClosure, short_pose : rosetta.core.pose.Pose) -> NoneType   save the loop-fragment in closure_frames_ Methods inherited from LoopClosure: closure_fragments(...) from builtins.PyCapsule closure_fragments(rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> rosetta.core.fragment.Frame mc(...) from builtins.PyCapsule mc(rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> rosetta.protocols.moves.MonteCarlo movemap(...) from builtins.PyCapsule movemap(rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> rosetta.core.kinematics.MoveMap nr_fragments(...) from builtins.PyCapsule nr_fragments(rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> int ramp_chainbreak(...) from builtins.PyCapsule ramp_chainbreak(*args, **kwargs) Overloaded function.   1. ramp_chainbreak(rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> NoneType   2. ramp_chainbreak(self : rosetta.protocols.loops.loop_closure.ccd.LoopClosure, setting : bool) -> NoneType scorefxn(...) from builtins.PyCapsule scorefxn(rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> rosetta.core.scoring.ScoreFunction set_cycles(...) from builtins.PyCapsule set_cycles(*args, **kwargs) Overloaded function.   1. set_cycles(rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> NoneType   2. set_cycles(self : rosetta.protocols.loops.loop_closure.ccd.LoopClosure, cycle_ratio : float) -> NoneType set_nr_fragments(...) from builtins.PyCapsule set_nr_fragments(*args, **kwargs) Overloaded function.   1. set_nr_fragments(rosetta.protocols.loops.loop_closure.ccd.LoopClosure) -> NoneType   2. set_nr_fragments(self : rosetta.protocols.loops.loop_closure.ccd.LoopClosure, nr_fragments : int) -> NoneType   class SlidingWindowLoopClosure(rosetta.protocols.moves.Mover)       Method resolution order: SlidingWindowLoopClosure rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, fragset : rosetta.core.fragment.FragSet, scorefxn : rosetta.core.scoring.ScoreFunction, movemap : rosetta.core.kinematics.MoveMap) -> NoneType   2. __init__(handle) -> NoneType   3. __init__(handle, rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. apply(...) from builtins.PyCapsule apply(*args, **kwargs) Overloaded function.   1. apply(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut : rosetta.core.pose.Pose, less_cut : rosetta.core.pose.Pose) -> NoneType   2. apply(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure,  : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure bIdealLoopClosing(...) from builtins.PyCapsule bIdealLoopClosing(rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> bool closure_fragments(...) from builtins.PyCapsule closure_fragments(rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> rosetta.core.fragment.FragSet determine_loop(...) from builtins.PyCapsule determine_loop(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut : rosetta.core.pose.Pose, less_cut : rosetta.core.pose.Pose) -> rosetta.protocols.loops.Loop fragments(...) from builtins.PyCapsule fragments(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, frags : rosetta.core.fragment.FragSet) -> NoneType get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> str keep_fragments(...) from builtins.PyCapsule keep_fragments(*args, **kwargs) Overloaded function.   1. keep_fragments(rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> NoneType   2. keep_fragments(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting : bool) -> NoneType movemap(...) from builtins.PyCapsule movemap(*args, **kwargs) Overloaded function.   1. movemap(rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> rosetta.core.kinematics.MoveMap   2. movemap(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, movemap : rosetta.core.kinematics.MoveMap) -> NoneType output_debug_structure(...) from builtins.PyCapsule output_debug_structure(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, pose : rosetta.core.pose.Pose, prefix : str) -> NoneType sample_loops(...) from builtins.PyCapsule sample_loops(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut : rosetta.core.pose.Pose, less_cut : rosetta.core.pose.Pose) -> NoneType scored_frag_cycle_ratio(...) from builtins.PyCapsule scored_frag_cycle_ratio(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting : float) -> NoneType scorefxn(...) from builtins.PyCapsule scorefxn(*args, **kwargs) Overloaded function.   1. scorefxn(rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> rosetta.core.scoring.ScoreFunction   2. scorefxn(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType select_final_loop(...) from builtins.PyCapsule select_final_loop(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut : rosetta.core.pose.Pose, less_cut : rosetta.core.pose.Pose) -> NoneType setPoseExtraScore(...) from builtins.PyCapsule setPoseExtraScore(pose : rosetta.core.pose.Pose) -> NoneType set_bIdealLoopClosing(...) from builtins.PyCapsule set_bIdealLoopClosing(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting : bool) -> NoneType set_chainbreak_max(...) from builtins.PyCapsule set_chainbreak_max(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting : float) -> NoneType set_evaluation(...) from builtins.PyCapsule set_evaluation(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, ev : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType set_loop(...) from builtins.PyCapsule set_loop(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, loop_in : rosetta.protocols.loops.Loop) -> NoneType short_frag_cycle_ratio(...) from builtins.PyCapsule short_frag_cycle_ratio(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting : float) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply 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 WidthFirstSlidingWindowLoopClosure(SlidingWindowLoopClosure)     it will switch between different windows. If nothing good is found after one sweep of window sizes we bail out... (assuming that it is fruitless) if things look promising more sampling time is spend to find a good loop     Method resolution order: WidthFirstSlidingWindowLoopClosure SlidingWindowLoopClosure rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, fragset : rosetta.core.fragment.FragSet, scorefxn : rosetta.core.scoring.ScoreFunction, movemap : rosetta.core.kinematics.MoveMap) -> NoneType   2. __init__(handle) -> NoneType   3. __init__(handle, rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure) -> 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.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure,  : rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure) -> rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure) -> 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 sample_loops(...) from builtins.PyCapsule sample_loops(self : rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure, more_cut : rosetta.core.pose.Pose, less_cut : rosetta.core.pose.Pose) -> NoneType Methods inherited from SlidingWindowLoopClosure: apply(...) from builtins.PyCapsule apply(*args, **kwargs) Overloaded function.   1. apply(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut : rosetta.core.pose.Pose, less_cut : rosetta.core.pose.Pose) -> NoneType   2. apply(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut : rosetta.core.pose.Pose) -> NoneType bIdealLoopClosing(...) from builtins.PyCapsule bIdealLoopClosing(rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> bool closure_fragments(...) from builtins.PyCapsule closure_fragments(rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> rosetta.core.fragment.FragSet determine_loop(...) from builtins.PyCapsule determine_loop(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut : rosetta.core.pose.Pose, less_cut : rosetta.core.pose.Pose) -> rosetta.protocols.loops.Loop fragments(...) from builtins.PyCapsule fragments(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, frags : rosetta.core.fragment.FragSet) -> NoneType keep_fragments(...) from builtins.PyCapsule keep_fragments(*args, **kwargs) Overloaded function.   1. keep_fragments(rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> NoneType   2. keep_fragments(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting : bool) -> NoneType movemap(...) from builtins.PyCapsule movemap(*args, **kwargs) Overloaded function.   1. movemap(rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> rosetta.core.kinematics.MoveMap   2. movemap(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, movemap : rosetta.core.kinematics.MoveMap) -> NoneType output_debug_structure(...) from builtins.PyCapsule output_debug_structure(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, pose : rosetta.core.pose.Pose, prefix : str) -> NoneType scored_frag_cycle_ratio(...) from builtins.PyCapsule scored_frag_cycle_ratio(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting : float) -> NoneType scorefxn(...) from builtins.PyCapsule scorefxn(*args, **kwargs) Overloaded function.   1. scorefxn(rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> rosetta.core.scoring.ScoreFunction   2. scorefxn(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType select_final_loop(...) from builtins.PyCapsule select_final_loop(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, more_cut : rosetta.core.pose.Pose, less_cut : rosetta.core.pose.Pose) -> NoneType setPoseExtraScore(...) from builtins.PyCapsule setPoseExtraScore(pose : rosetta.core.pose.Pose) -> NoneType set_bIdealLoopClosing(...) from builtins.PyCapsule set_bIdealLoopClosing(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting : bool) -> NoneType set_chainbreak_max(...) from builtins.PyCapsule set_chainbreak_max(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting : float) -> NoneType set_evaluation(...) from builtins.PyCapsule set_evaluation(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, ev : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType set_loop(...) from builtins.PyCapsule set_loop(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, loop_in : rosetta.protocols.loops.Loop) -> NoneType short_frag_cycle_ratio(...) from builtins.PyCapsule short_frag_cycle_ratio(self : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure, setting : float) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply 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 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

Functions
		get_deviation(...) method of builtins.PyCapsule instance get_deviation(pose : rosetta.core.pose.Pose, cutpoint : int) -> (float, float)

Data
		backward = ChainDirection.n_chain_directions coil = SecondaryStructureType.n_secondary_structure_types forward = ChainDirection.forward helix = SecondaryStructureType.helix n_chain_directions = ChainDirection.n_chain_directions n_secondary_structure_types = SecondaryStructureType.n_secondary_structure_types strand = SecondaryStructureType.strand