Bindings for protocols::carbohydrates namespace

Classes
		rosetta.protocols.moves.Mover(builtins.object) GlycanRelaxMover LinkageConformerMover SimpleGlycosylateMover rosetta.protocols.moves.MoverCreator(builtins.object) GlycanRelaxMoverCreator LinkageConformerMoverCreator SimpleGlycosylateMoverCreator   class GlycanRelaxMover(rosetta.protocols.moves.Mover)     Main mover for Glycan Relax, which optimizes glycans in a pose. Each round optimizes either one residue for BB sampling, linkage, or multiple for minimization. Currently uses a random sampler with a set of weights to each mover for sampling.   Weights are currently as follows:  .40 Phi/Psi Sugar BB Sampling  .20 Linkage Conformer Sampling  .30 Small BB Sampling - equal weight to phi, psi, or omega    -> .17 +/- 15 degrees    -> .086 +/- 45 degrees    -> .044 +/- 90 degrees  .05 MinMover  .05 PackRotamersMover     Method resolution order: GlycanRelaxMover rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.kinematics.MoveMap, rosetta.core.scoring.ScoreFunction) -> NoneType   doc   3. __init__(self : handle, mm : rosetta.core.kinematics.MoveMap, scorefxn : rosetta.core.scoring.ScoreFunction, rounds : int) -> NoneType   4. __init__(handle, rosetta.protocols.carbohydrates.GlycanRelaxMover) -> 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.carbohydrates.GlycanRelaxMover) -> str apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.carbohydrates.GlycanRelaxMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.carbohydrates.GlycanRelaxMover,  : rosetta.protocols.carbohydrates.GlycanRelaxMover) -> rosetta.protocols.carbohydrates.GlycanRelaxMover clone(...) from builtins.PyCapsule clone(rosetta.protocols.carbohydrates.GlycanRelaxMover) -> rosetta.protocols.moves.Mover   required in the context of the parser/scripting scheme fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.carbohydrates.GlycanRelaxMover) -> rosetta.protocols.moves.Mover   required in the context of the parser/scripting scheme get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.carbohydrates.GlycanRelaxMover) -> str set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.carbohydrates.GlycanRelaxMover) -> NoneType set_kt(...) from builtins.PyCapsule set_kt(self : rosetta.protocols.carbohydrates.GlycanRelaxMover, kt : float) -> NoneType set_movemap(...) from builtins.PyCapsule set_movemap(self : rosetta.protocols.carbohydrates.GlycanRelaxMover, movemap : rosetta.core.kinematics.MoveMap) -> NoneType   Set the Movemap set_rounds(...) from builtins.PyCapsule set_rounds(self : rosetta.protocols.carbohydrates.GlycanRelaxMover, rounds : int) -> NoneType   Each round applys a random mover to pose.  This setting is multiplied by the number of glycan residues in the movemap for the total number of rounds set_scorefunction(...) from builtins.PyCapsule set_scorefunction(self : rosetta.protocols.carbohydrates.GlycanRelaxMover, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   Set the ScoreFunction set_taskfactory(...) from builtins.PyCapsule set_taskfactory(self : rosetta.protocols.carbohydrates.GlycanRelaxMover, tf : rosetta.core.pack.task.TaskFactory) -> NoneType   Set the TaskFactory to control side-chain packing of surrounding amino acids and the OH groups of the glycans. 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 GlycanRelaxMoverCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: GlycanRelaxMoverCreator 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.carbohydrates.GlycanRelaxMoverCreator,  : rosetta.protocols.carbohydrates.GlycanRelaxMoverCreator) -> rosetta.protocols.carbohydrates.GlycanRelaxMoverCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.carbohydrates.GlycanRelaxMoverCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.carbohydrates.GlycanRelaxMoverCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class LinkageConformerMover(rosetta.protocols.moves.Mover)     This code changes all of the dihedrals of a particular glycosidic linkage based on database info,   esentially sampling carbohydrate dihedral conformers of two residues.    The linkage conformers are carbohydrate residue type and (and linkage oxygen) dependant ie MAN-MAN  If data is not known here, by default we sample from restype-independant data.  If there are multiple conformers for a given linkage, will randomly select from them.    3 Main Conformer Sampling Strategies: /  1) Mean + uniform in X standard deviations (Default) /     ->Build conformers using the means of dihedrals + or - some amount within X standard deviations of the mean. / /     See Also: /      LinkageConformerMover.set_x_standard_deviations / /  2) Mean + probability in X standard deviations / /  3) Idealize /     -> Use only means when building linkage conformers. / /     See: /      LinkageConformerMover.set_idealize_torsions //     Method resolution order: LinkageConformerMover 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, movemap : rosetta.core.kinematics.MoveMap) -> NoneType   3. __init__(handle, rosetta.protocols.carbohydrates.LinkageConformerMover) -> 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.carbohydrates.LinkageConformerMover) -> str apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.carbohydrates.LinkageConformerMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.carbohydrates.LinkageConformerMover,  : rosetta.protocols.carbohydrates.LinkageConformerMover) -> rosetta.protocols.carbohydrates.LinkageConformerMover clone(...) from builtins.PyCapsule clone(rosetta.protocols.carbohydrates.LinkageConformerMover) -> rosetta.protocols.moves.Mover   required in the context of the parser/scripting scheme conformer_found(...) from builtins.PyCapsule conformer_found(rosetta.protocols.carbohydrates.LinkageConformerMover) -> bool   Boolean for if the restype-dependant conformer was found at apply. Resets at successive applies. fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.carbohydrates.LinkageConformerMover) -> rosetta.protocols.moves.Mover   required in the context of the parser/scripting scheme get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.carbohydrates.LinkageConformerMover) -> str set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.carbohydrates.LinkageConformerMover) -> NoneType   Set everything to default values, including linkage pairs. set_idealize_torsions(...) from builtins.PyCapsule set_idealize_torsions(self : rosetta.protocols.carbohydrates.LinkageConformerMover, idealize_torsions : bool) -> NoneType   Idealize the torsion angles instead of sampling from SD.  Default FALSE set_movemap(...) from builtins.PyCapsule set_movemap(self : rosetta.protocols.carbohydrates.LinkageConformerMover, movemap : rosetta.core.kinematics.MoveMap) -> NoneType   Set the Movemap.  Each apply will randomly sample on the movemap.  If the conformer is not found, will set move status to false.  Will optimize the linkage between the residue and the parent residue. set_prob_sd_sampling(...) from builtins.PyCapsule set_prob_sd_sampling(self : rosetta.protocols.carbohydrates.LinkageConformerMover, uniform_sd_sample : bool) -> NoneType   Set whether if we are sampling uniform within the set number of standard deviations or by uniform within the SD.  Default FALSE set_single_resnum(...) from builtins.PyCapsule set_single_resnum(self : rosetta.protocols.carbohydrates.LinkageConformerMover, resnum : int) -> NoneType   Set a single resnum to sample on instead of a movemap. set_use_conformer_population_stats(...) from builtins.PyCapsule set_use_conformer_population_stats(self : rosetta.protocols.carbohydrates.LinkageConformerMover, setting : bool) -> NoneType   Use conformer population data to weight sampling.  Default TRUE. set_use_sugar_bb_data_if_needed(...) from builtins.PyCapsule set_use_sugar_bb_data_if_needed(self : rosetta.protocols.carbohydrates.LinkageConformerMover, use_sugar_bb : bool) -> NoneType   Use phi/psi data if restype-dependant conformer data unavailable.  Will set phi/psi to lowest energy values if idealize is true.  Default FALSE set_x_standard_deviations(...) from builtins.PyCapsule set_x_standard_deviations(self : rosetta.protocols.carbohydrates.LinkageConformerMover, standard_deviations : float) -> NoneType   Sample within X standard_deviations of the means when building [non-idealized] conformers 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 LinkageConformerMoverCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: LinkageConformerMoverCreator 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.carbohydrates.LinkageConformerMoverCreator,  : rosetta.protocols.carbohydrates.LinkageConformerMoverCreator) -> rosetta.protocols.carbohydrates.LinkageConformerMoverCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.carbohydrates.LinkageConformerMoverCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.carbohydrates.LinkageConformerMoverCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class SimpleGlycosylateMover(rosetta.protocols.moves.Mover)     A mover for glycosylation of biological glycosylations. Currently glysolylation is done based on string, not from PDB. Use GlycanRelax to model the resulting glycosylation!.       Single Glycosylation:   If a single glycosylation is passed, it will glycosylate all positions set with this glycan.   Multiple Glycosylations:   If multiple glycosylations are passed, will randomly select from these on apply to sample glycan hetergenecity.   see glyco.set_weights to set weights for these glycans to sample non-random heterogenecity in the glycoform.   The site should be ASN for N-linked glycosylations OR SER/THR for O-linked glycosylations   If a glycan already exists, will strip off the current glycan by default.   set glyco.set_strip_existing_glycans( false ) to branch off existing glycans instead of deleting them.     see CreateGlycoSiteMover to create glyco sites (as N-linked glycosylations will need a specific motif to be biological)   Will randomly select from set positions and glycosylate all positions set.   Glycosylations:   1) If your name ends with .iupac or .gws (GlycoWorkBench), will try to load the file     2) Next, it will check the short names in the Rosetta database for your string.      If the string is in common_names.txt, will load the paired iupac sequence.      See database/chemical/carbohydrates/common_glycans/common_names.txt for accepted short names.    Names include man3, man5, and man9.     3)     If the name is not found, will attempt to build the glycan as an iupac sequence from the string.   TODO JAB: Add Glycosylate from pdb/cif files in addition to IUPAC and short names.  No current RosettaCarbohydrate functionality to load from PDB/CIF and attach to an existing pose..     Method resolution order: SimpleGlycosylateMover 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.carbohydrates.SimpleGlycosylateMover) -> 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.carbohydrates.SimpleGlycosylateMover) -> str apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.carbohydrates.SimpleGlycosylateMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.carbohydrates.SimpleGlycosylateMover,  : rosetta.protocols.carbohydrates.SimpleGlycosylateMover) -> rosetta.protocols.carbohydrates.SimpleGlycosylateMover clone(...) from builtins.PyCapsule clone(rosetta.protocols.carbohydrates.SimpleGlycosylateMover) -> rosetta.protocols.moves.Mover   required in the context of the parser/scripting scheme fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.carbohydrates.SimpleGlycosylateMover) -> rosetta.protocols.moves.Mover   required in the context of the parser/scripting scheme get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.carbohydrates.SimpleGlycosylateMover) -> str set_glycosylation(...) from builtins.PyCapsule set_glycosylation(self : rosetta.protocols.carbohydrates.SimpleGlycosylateMover, iupac_or_common_string : str) -> NoneType   Set the glycosylation that will happen.   See database/chemical/carbohydrates/common_glycans for common names.   Names include man3, man5, and man9.     Can also use full iupac names.     See also: glycosylate.set_glycosylation_weights set_glycosylation_weights(...) from builtins.PyCapsule set_glycosylation_weights(self : rosetta.protocols.carbohydrates.SimpleGlycosylateMover, weights : rosetta.utility.vector1_double) -> NoneType   Set weights for potential glycosylation if more than one is set. set_glycosylations(...) from builtins.PyCapsule set_glycosylations(self : rosetta.protocols.carbohydrates.SimpleGlycosylateMover, iupac_or_common_strings : rosetta.utility.vector1_std_string) -> NoneType   Set possible glycosylations - the mover will randomly pick these on apply   See database/chemical/carbohydrates/common_glycans for accepted names.   Names include man3, man5, and man9.     Can also use full iupac names.     See also: glycosylate.set_glycosylation_weights set_position(...) from builtins.PyCapsule set_position(self : rosetta.protocols.carbohydrates.SimpleGlycosylateMover, position : int) -> NoneType   Set a single resnum position set_positions(...) from builtins.PyCapsule set_positions(*args, **kwargs) Overloaded function.   1. set_positions(self : rosetta.protocols.carbohydrates.SimpleGlycosylateMover, positions : rosetta.utility.vector1_bool) -> NoneType   Set multiple positions to glycosylate   2. set_positions(self : rosetta.protocols.carbohydrates.SimpleGlycosylateMover, positions : rosetta.utility.vector1_unsigned_long) -> NoneType   Set mutliple positions to glycosylate set_positions_from_movemap(...) from builtins.PyCapsule set_positions_from_movemap(self : rosetta.protocols.carbohydrates.SimpleGlycosylateMover, mm : rosetta.core.kinematics.MoveMap) -> NoneType   Set positions to glycosylate using a movemap. set_strip_existing_glycans(...) from builtins.PyCapsule set_strip_existing_glycans(self : rosetta.protocols.carbohydrates.SimpleGlycosylateMover, strip_existing : bool) -> NoneType   This sets whether if we already have a glycan at a position, whether to extend it or delete the existing glycan.  Advanced functionality - use with caution.   Not yet work. 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 SimpleGlycosylateMoverCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: SimpleGlycosylateMoverCreator 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.carbohydrates.SimpleGlycosylateMoverCreator,  : rosetta.protocols.carbohydrates.SimpleGlycosylateMoverCreator) -> rosetta.protocols.carbohydrates.SimpleGlycosylateMoverCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.carbohydrates.SimpleGlycosylateMoverCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.carbohydrates.SimpleGlycosylateMoverCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str