Bindings for protocols::abinitio::abscript namespace

Classes
		builtins.object StageID rosetta.basic.datacache.WriteableCacheableData(rosetta.basic.datacache.CacheableData) JumpSampleData rosetta.basic.datacache.WriteableCacheableDataCreator(builtins.object) JumpSampleDataCreator rosetta.protocols.environment.ClientMover(rosetta.protocols.moves.Mover) AbscriptLoopCloserCM AbscriptMover FragmentCM FragmentJumpCM RigidChunkCM StagePreparer ConstraintPreparer StructPerturberCM rosetta.protocols.moves.Mover(builtins.object) AbscriptStageMover rosetta.protocols.moves.MoverCreator(builtins.object) AbscriptLoopCloserCMCreator AbscriptMoverCreator ConstraintPreparerCreator FragmentCMCreator FragmentJumpCMCreator RigidChunkCMCreator StructPerturberCMCreator   class AbscriptLoopCloserCM(rosetta.protocols.environment.ClientMover)       Method resolution order: AbscriptLoopCloserCM rosetta.protocols.environment.ClientMover 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, fragset : rosetta.core.fragment.FragSet, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   3. __init__(handle, rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM) -> 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.abinitio.abscript.AbscriptLoopCloserCM,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM,  : rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM) -> rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM broking_finished(...) from builtins.PyCapsule broking_finished(self : rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM,  : protocols::environment::EnvClaimBroker::BrokerResult) -> NoneType clone(...) from builtins.PyCapsule clone(rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM) -> str selector(...) from builtins.PyCapsule selector(rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM) -> rosetta.core.select.residue_selector.ResidueSelector set_selector(...) from builtins.PyCapsule set_selector(self : rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM, selector : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType yield_claims(...) from builtins.PyCapsule yield_claims(self : rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM,  : rosetta.core.pose.Pose,  : rosetta.basic.datacache.WriteableCacheableMap) -> rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_std_allocator_std_shared_ptr_protocols_environment_claims_EnvClaim_t Methods inherited from rosetta.protocols.environment.ClientMover: initialize(...) from builtins.PyCapsule initialize(self : rosetta.protocols.environment.ClientMover, conf : rosetta.core.pose.Pose) -> NoneType   this method is called by the broking system in response to a         successful initialization claim by this mover. The passport         will prevent any unauthorized changes. yield_submovers(...) from builtins.PyCapsule yield_submovers(self : rosetta.protocols.environment.ClientMover,  : rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_std_less_std_shared_ptr_protocols_environment_ClientMover_std_allocator_std_shared_ptr_protocols_environment_ClientMover_t) -> NoneType   this method is used to make sure any movers contained in this         mover (that want to make claims) also get registered with the         environment. 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 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 AbscriptLoopCloserCMCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: AbscriptLoopCloserCMCreator 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.abinitio.abscript.AbscriptLoopCloserCMCreator,  : rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCMCreator) -> rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCMCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCMCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCMCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class AbscriptMover(rosetta.protocols.environment.ClientMover)       Method resolution order: AbscriptMover rosetta.protocols.environment.ClientMover 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.abinitio.abscript.AbscriptMover) -> 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.abinitio.abscript.AbscriptMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.abscript.AbscriptMover,  : rosetta.protocols.abinitio.abscript.AbscriptMover) -> rosetta.protocols.abinitio.abscript.AbscriptMover clone(...) from builtins.PyCapsule clone(rosetta.protocols.abinitio.abscript.AbscriptMover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.abinitio.abscript.AbscriptMover) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.abscript.AbscriptMover) -> str initialize(...) from builtins.PyCapsule initialize(self : rosetta.protocols.abinitio.abscript.AbscriptMover,  : rosetta.core.pose.Pose) -> NoneType yield_claims(...) from builtins.PyCapsule yield_claims(self : rosetta.protocols.abinitio.abscript.AbscriptMover,  : rosetta.core.pose.Pose,  : rosetta.basic.datacache.WriteableCacheableMap) -> rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_std_allocator_std_shared_ptr_protocols_environment_claims_EnvClaim_t yield_submovers(...) from builtins.PyCapsule yield_submovers(self : rosetta.protocols.abinitio.abscript.AbscriptMover,  : rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_std_less_std_shared_ptr_protocols_environment_ClientMover_std_allocator_std_shared_ptr_protocols_environment_ClientMover_t) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class AbscriptMoverCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: AbscriptMoverCreator 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.abinitio.abscript.AbscriptMoverCreator,  : rosetta.protocols.abinitio.abscript.AbscriptMoverCreator) -> rosetta.protocols.abinitio.abscript.AbscriptMoverCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.abinitio.abscript.AbscriptMoverCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.abinitio.abscript.AbscriptMoverCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class AbscriptStageMover(rosetta.protocols.moves.Mover)       Method resolution order: AbscriptStageMover rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, stage : rosetta.protocols.abinitio.abscript.StageID, mc : rosetta.protocols.moves.MonteCarlo, score : rosetta.core.scoring.ScoreFunction, cycles : int) -> NoneType   2. __init__(handle, rosetta.protocols.abinitio.abscript.AbscriptStageMover) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_preparer(...) from builtins.PyCapsule add_preparer(self : rosetta.protocols.abinitio.abscript.AbscriptStageMover, mover : protocols::abinitio::abscript::StagePreparer) -> NoneType add_submover(...) from builtins.PyCapsule add_submover(self : rosetta.protocols.abinitio.abscript.AbscriptStageMover, mover : rosetta.protocols.environment.ClientMover, weight : float) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.abinitio.abscript.AbscriptStageMover,  : rosetta.core.pose.Pose) -> NoneType get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.abscript.AbscriptStageMover) -> str scorefxn(...) from builtins.PyCapsule scorefxn(rosetta.protocols.abinitio.abscript.AbscriptStageMover) -> rosetta.core.scoring.ScoreFunction seq_sep_intercept(...) from builtins.PyCapsule seq_sep_intercept(rosetta.protocols.abinitio.abscript.AbscriptStageMover) -> float set_chainbreak_ramping(...) from builtins.PyCapsule set_chainbreak_ramping(self : rosetta.protocols.abinitio.abscript.AbscriptStageMover, slope : float, intercept : float) -> NoneType set_cycles_adjust(...) from builtins.PyCapsule set_cycles_adjust(self : rosetta.protocols.abinitio.abscript.AbscriptStageMover, in : float) -> NoneType set_seq_sep_ramping(...) from builtins.PyCapsule set_seq_sep_ramping(self : rosetta.protocols.abinitio.abscript.AbscriptStageMover, slope : float, intercept : float) -> NoneType setup_stage(...) from builtins.PyCapsule setup_stage(self : rosetta.protocols.abinitio.abscript.AbscriptStageMover, pose : rosetta.core.pose.Pose, progress : float) -> bool yield_submovers(...) from builtins.PyCapsule yield_submovers(self : rosetta.protocols.abinitio.abscript.AbscriptStageMover, set : rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_std_less_std_shared_ptr_protocols_environment_ClientMover_std_allocator_std_shared_ptr_protocols_environment_ClientMover_t) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.moves.Mover, other : rosetta.protocols.moves.Mover) -> 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 ConstraintPreparer(StagePreparer)       Method resolution order: ConstraintPreparer StagePreparer rosetta.protocols.environment.ClientMover 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.abinitio.abscript.ConstraintPreparer) -> 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.abinitio.abscript.ConstraintPreparer,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.abscript.ConstraintPreparer,  : rosetta.protocols.abinitio.abscript.ConstraintPreparer) -> rosetta.protocols.abinitio.abscript.ConstraintPreparer clone(...) from builtins.PyCapsule clone(rosetta.protocols.abinitio.abscript.ConstraintPreparer) -> rosetta.protocols.moves.Mover combine_exclude_file(...) from builtins.PyCapsule combine_exclude_file(self : rosetta.protocols.abinitio.abscript.ConstraintPreparer, filename : str) -> NoneType combine_exclude_res(...) from builtins.PyCapsule combine_exclude_res(rosetta.protocols.abinitio.abscript.ConstraintPreparer) -> rosetta.utility.vector1_bool combine_ratio(...) from builtins.PyCapsule combine_ratio(*args, **kwargs) Overloaded function.   1. combine_ratio(self : rosetta.protocols.abinitio.abscript.ConstraintPreparer, s : int) -> NoneType   2. combine_ratio(rosetta.protocols.abinitio.abscript.ConstraintPreparer) -> int cst_file(...) from builtins.PyCapsule cst_file(*args, **kwargs) Overloaded function.   1. cst_file(self : rosetta.protocols.abinitio.abscript.ConstraintPreparer,  : str) -> NoneType   2. cst_file(rosetta.protocols.abinitio.abscript.ConstraintPreparer) -> str fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.abinitio.abscript.ConstraintPreparer) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.abscript.ConstraintPreparer) -> str prepare(...) from builtins.PyCapsule prepare(self : rosetta.protocols.abinitio.abscript.ConstraintPreparer, pose : rosetta.core.pose.Pose, progress : float) -> NoneType random_drop_rate(...) from builtins.PyCapsule random_drop_rate(*args, **kwargs) Overloaded function.   1. random_drop_rate(rosetta.protocols.abinitio.abscript.ConstraintPreparer) -> float   2. random_drop_rate(self : rosetta.protocols.abinitio.abscript.ConstraintPreparer, s : float) -> NoneType skip_redundant(...) from builtins.PyCapsule skip_redundant(*args, **kwargs) Overloaded function.   1. skip_redundant(rosetta.protocols.abinitio.abscript.ConstraintPreparer) -> bool   2. skip_redundant(self : rosetta.protocols.abinitio.abscript.ConstraintPreparer, s : bool) -> NoneType skip_redundant_width(...) from builtins.PyCapsule skip_redundant_width(*args, **kwargs) Overloaded function.   1. skip_redundant_width(rosetta.protocols.abinitio.abscript.ConstraintPreparer) -> int   2. skip_redundant_width(self : rosetta.protocols.abinitio.abscript.ConstraintPreparer, s : int) -> NoneType yield_claims(...) from builtins.PyCapsule yield_claims(self : rosetta.protocols.abinitio.abscript.ConstraintPreparer,  : rosetta.core.pose.Pose,  : rosetta.basic.datacache.WriteableCacheableMap) -> rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_std_allocator_std_shared_ptr_protocols_environment_claims_EnvClaim_t Methods inherited from rosetta.protocols.environment.ClientMover: initialize(...) from builtins.PyCapsule initialize(self : rosetta.protocols.environment.ClientMover, conf : rosetta.core.pose.Pose) -> NoneType   this method is called by the broking system in response to a         successful initialization claim by this mover. The passport         will prevent any unauthorized changes. yield_submovers(...) from builtins.PyCapsule yield_submovers(self : rosetta.protocols.environment.ClientMover,  : rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_std_less_std_shared_ptr_protocols_environment_ClientMover_std_allocator_std_shared_ptr_protocols_environment_ClientMover_t) -> NoneType   this method is used to make sure any movers contained in this         mover (that want to make claims) also get registered with the         environment. 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 ConstraintPreparerCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: ConstraintPreparerCreator 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.abinitio.abscript.ConstraintPreparerCreator,  : rosetta.protocols.abinitio.abscript.ConstraintPreparerCreator) -> rosetta.protocols.abinitio.abscript.ConstraintPreparerCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.abinitio.abscript.ConstraintPreparerCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.abinitio.abscript.ConstraintPreparerCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class FragmentCM(rosetta.protocols.environment.ClientMover)       Method resolution order: FragmentCM rosetta.protocols.environment.ClientMover 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.simple_moves.FragmentMover) -> NoneType   doc   3. __init__(self : handle,  : rosetta.protocols.simple_moves.FragmentMover,  : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType   4. __init__(handle, rosetta.protocols.abinitio.abscript.FragmentCM) -> 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.abinitio.abscript.FragmentCM, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.abscript.FragmentCM,  : rosetta.protocols.abinitio.abscript.FragmentCM) -> rosetta.protocols.abinitio.abscript.FragmentCM get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.abscript.FragmentCM) -> str initialize(...) from builtins.PyCapsule initialize(*args, **kwargs) Overloaded function.   1. initialize(self : rosetta.protocols.abinitio.abscript.FragmentCM, pose : rosetta.core.pose.Pose) -> NoneType   2. initialize(rosetta.protocols.abinitio.abscript.FragmentCM) -> bool   3. initialize(self : rosetta.protocols.abinitio.abscript.FragmentCM, setting : bool) -> NoneType selector(...) from builtins.PyCapsule selector(rosetta.protocols.abinitio.abscript.FragmentCM) -> rosetta.core.select.residue_selector.ResidueSelector set_mover(...) from builtins.PyCapsule set_mover(self : rosetta.protocols.abinitio.abscript.FragmentCM, mover : rosetta.protocols.simple_moves.FragmentMover) -> NoneType set_selector(...) from builtins.PyCapsule set_selector(self : rosetta.protocols.abinitio.abscript.FragmentCM,  : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType yield_claims(...) from builtins.PyCapsule yield_claims(self : rosetta.protocols.abinitio.abscript.FragmentCM,  : rosetta.core.pose.Pose,  : rosetta.basic.datacache.WriteableCacheableMap) -> rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_std_allocator_std_shared_ptr_protocols_environment_claims_EnvClaim_t yield_cut_bias(...) from builtins.PyCapsule yield_cut_bias(*args, **kwargs) Overloaded function.   1. yield_cut_bias(rosetta.protocols.abinitio.abscript.FragmentCM) -> bool   2. yield_cut_bias(self : rosetta.protocols.abinitio.abscript.FragmentCM, setting : bool) -> NoneType Methods inherited from rosetta.protocols.environment.ClientMover: yield_submovers(...) from builtins.PyCapsule yield_submovers(self : rosetta.protocols.environment.ClientMover,  : rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_std_less_std_shared_ptr_protocols_environment_ClientMover_std_allocator_std_shared_ptr_protocols_environment_ClientMover_t) -> NoneType   this method is used to make sure any movers contained in this         mover (that want to make claims) also get registered with the         environment. 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 FragmentCMCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: FragmentCMCreator 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.abinitio.abscript.FragmentCMCreator,  : rosetta.protocols.abinitio.abscript.FragmentCMCreator) -> rosetta.protocols.abinitio.abscript.FragmentCMCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.abinitio.abscript.FragmentCMCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.abinitio.abscript.FragmentCMCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class FragmentJumpCM(FragmentCM)       Method resolution order: FragmentJumpCM FragmentCM rosetta.protocols.environment.ClientMover 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, topol_filename : str, selector : rosetta.core.select.residue_selector.ResidueSelector, moverkey : str) -> NoneType   3. __init__(handle, rosetta.protocols.abinitio.abscript.FragmentJumpCM) -> 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.abinitio.abscript.FragmentJumpCM,  : rosetta.protocols.abinitio.abscript.FragmentJumpCM) -> rosetta.protocols.abinitio.abscript.FragmentJumpCM clone(...) from builtins.PyCapsule clone(rosetta.protocols.abinitio.abscript.FragmentJumpCM) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.abinitio.abscript.FragmentJumpCM) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.abscript.FragmentJumpCM) -> str moverkey(...) from builtins.PyCapsule moverkey(rosetta.protocols.abinitio.abscript.FragmentJumpCM) -> str set_moverkey(...) from builtins.PyCapsule set_moverkey(self : rosetta.protocols.abinitio.abscript.FragmentJumpCM, key : str) -> NoneType set_topology(...) from builtins.PyCapsule set_topology(*args, **kwargs) Overloaded function.   1. set_topology(self : rosetta.protocols.abinitio.abscript.FragmentJumpCM, topology_file : str) -> NoneType   Set the topology using a topology file.   2. set_topology(self : rosetta.protocols.abinitio.abscript.FragmentJumpCM, ss_info_file : str, pairing_file : str, n_sheets : int, bRandomSheets : bool) -> NoneType   Set the topology using a psipred_ss2 file, a pairing         list file, and a number of random sheets to pick. yield_claims(...) from builtins.PyCapsule yield_claims(self : rosetta.protocols.abinitio.abscript.FragmentJumpCM,  : rosetta.core.pose.Pose,  : rosetta.basic.datacache.WriteableCacheableMap) -> rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_std_allocator_std_shared_ptr_protocols_environment_claims_EnvClaim_t Methods inherited from FragmentCM: apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.abinitio.abscript.FragmentCM, pose : rosetta.core.pose.Pose) -> NoneType initialize(...) from builtins.PyCapsule initialize(*args, **kwargs) Overloaded function.   1. initialize(self : rosetta.protocols.abinitio.abscript.FragmentCM, pose : rosetta.core.pose.Pose) -> NoneType   2. initialize(rosetta.protocols.abinitio.abscript.FragmentCM) -> bool   3. initialize(self : rosetta.protocols.abinitio.abscript.FragmentCM, setting : bool) -> NoneType selector(...) from builtins.PyCapsule selector(rosetta.protocols.abinitio.abscript.FragmentCM) -> rosetta.core.select.residue_selector.ResidueSelector set_mover(...) from builtins.PyCapsule set_mover(self : rosetta.protocols.abinitio.abscript.FragmentCM, mover : rosetta.protocols.simple_moves.FragmentMover) -> NoneType set_selector(...) from builtins.PyCapsule set_selector(self : rosetta.protocols.abinitio.abscript.FragmentCM,  : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType yield_cut_bias(...) from builtins.PyCapsule yield_cut_bias(*args, **kwargs) Overloaded function.   1. yield_cut_bias(rosetta.protocols.abinitio.abscript.FragmentCM) -> bool   2. yield_cut_bias(self : rosetta.protocols.abinitio.abscript.FragmentCM, setting : bool) -> NoneType Methods inherited from rosetta.protocols.environment.ClientMover: yield_submovers(...) from builtins.PyCapsule yield_submovers(self : rosetta.protocols.environment.ClientMover,  : rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_std_less_std_shared_ptr_protocols_environment_ClientMover_std_allocator_std_shared_ptr_protocols_environment_ClientMover_t) -> NoneType   this method is used to make sure any movers contained in this         mover (that want to make claims) also get registered with the         environment. 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 FragmentJumpCMCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: FragmentJumpCMCreator 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.abinitio.abscript.FragmentJumpCMCreator,  : rosetta.protocols.abinitio.abscript.FragmentJumpCMCreator) -> rosetta.protocols.abinitio.abscript.FragmentJumpCMCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.abinitio.abscript.FragmentJumpCMCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.abinitio.abscript.FragmentJumpCMCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class JumpSampleData(rosetta.basic.datacache.WriteableCacheableData)       Method resolution order: JumpSampleData rosetta.basic.datacache.WriteableCacheableData rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, in : std::istream) -> NoneType   2. __init__(self : handle, moverkey : str,  : rosetta.protocols.jumping.JumpSample) -> NoneType   3. __init__(handle, rosetta.protocols.abinitio.abscript.JumpSampleData) -> 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.abinitio.abscript.JumpSampleData,  : rosetta.protocols.abinitio.abscript.JumpSampleData) -> rosetta.protocols.abinitio.abscript.JumpSampleData clone(...) from builtins.PyCapsule clone(rosetta.protocols.abinitio.abscript.JumpSampleData) -> rosetta.basic.datacache.CacheableData datatype(...) from builtins.PyCapsule datatype(rosetta.protocols.abinitio.abscript.JumpSampleData) -> str jump_sample(...) from builtins.PyCapsule jump_sample(rosetta.protocols.abinitio.abscript.JumpSampleData) -> rosetta.protocols.jumping.JumpSample moverkey(...) from builtins.PyCapsule moverkey(rosetta.protocols.abinitio.abscript.JumpSampleData) -> str Methods inherited from rosetta.basic.datacache.WriteableCacheableData: shared_from_this(...) from builtins.PyCapsule shared_from_this(rosetta.basic.datacache.WriteableCacheableData) -> rosetta.basic.datacache.WriteableCacheableData Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class JumpSampleDataCreator(rosetta.basic.datacache.WriteableCacheableDataCreator)       Method resolution order: JumpSampleDataCreator rosetta.basic.datacache.WriteableCacheableDataCreator 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.abinitio.abscript.JumpSampleDataCreator,  : rosetta.protocols.abinitio.abscript.JumpSampleDataCreator) -> rosetta.protocols.abinitio.abscript.JumpSampleDataCreator keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.abinitio.abscript.JumpSampleDataCreator) -> str   class RigidChunkCM(rosetta.protocols.environment.ClientMover)       Method resolution order: RigidChunkCM rosetta.protocols.environment.ClientMover 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, selector : rosetta.core.select.residue_selector.ResidueSelector, template_pose : rosetta.core.pose.Pose) -> NoneType   3. __init__(handle, rosetta.protocols.abinitio.abscript.RigidChunkCM) -> 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.abinitio.abscript.RigidChunkCM,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.abscript.RigidChunkCM,  : rosetta.protocols.abinitio.abscript.RigidChunkCM) -> rosetta.protocols.abinitio.abscript.RigidChunkCM clone(...) from builtins.PyCapsule clone(rosetta.protocols.abinitio.abscript.RigidChunkCM) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.abscript.RigidChunkCM) -> str initialize(...) from builtins.PyCapsule initialize(self : rosetta.protocols.abinitio.abscript.RigidChunkCM, pose : rosetta.core.pose.Pose) -> NoneType select_parts(...) from builtins.PyCapsule select_parts(self : rosetta.protocols.abinitio.abscript.RigidChunkCM, rigid_core : rosetta.protocols.loops.Loops, random_grow_loops_by : int) -> rosetta.protocols.loops.Loops sim_origin(...) from builtins.PyCapsule sim_origin(rosetta.protocols.abinitio.abscript.RigidChunkCM) -> rosetta.std.map_unsigned_long_unsigned_long sim_selector(...) from builtins.PyCapsule sim_selector(*args, **kwargs) Overloaded function.   1. sim_selector(self : rosetta.protocols.abinitio.abscript.RigidChunkCM, selector : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType   2. sim_selector(rosetta.protocols.abinitio.abscript.RigidChunkCM) -> rosetta.core.select.residue_selector.ResidueSelector templ(...) from builtins.PyCapsule templ(rosetta.protocols.abinitio.abscript.RigidChunkCM) -> rosetta.core.pose.Pose templ_selector(...) from builtins.PyCapsule templ_selector(*args, **kwargs) Overloaded function.   1. templ_selector(self : rosetta.protocols.abinitio.abscript.RigidChunkCM, selector : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType   2. templ_selector(rosetta.protocols.abinitio.abscript.RigidChunkCM) -> rosetta.core.select.residue_selector.ResidueSelector templ_target(...) from builtins.PyCapsule templ_target(rosetta.protocols.abinitio.abscript.RigidChunkCM) -> rosetta.std.map_unsigned_long_unsigned_long yield_claims(...) from builtins.PyCapsule yield_claims(self : rosetta.protocols.abinitio.abscript.RigidChunkCM,  : rosetta.core.pose.Pose,  : rosetta.basic.datacache.WriteableCacheableMap) -> rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_std_allocator_std_shared_ptr_protocols_environment_claims_EnvClaim_t Methods inherited from rosetta.protocols.environment.ClientMover: yield_submovers(...) from builtins.PyCapsule yield_submovers(self : rosetta.protocols.environment.ClientMover,  : rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_std_less_std_shared_ptr_protocols_environment_ClientMover_std_allocator_std_shared_ptr_protocols_environment_ClientMover_t) -> NoneType   this method is used to make sure any movers contained in this         mover (that want to make claims) also get registered with the         environment. 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 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 RigidChunkCMCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: RigidChunkCMCreator 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.abinitio.abscript.RigidChunkCMCreator,  : rosetta.protocols.abinitio.abscript.RigidChunkCMCreator) -> rosetta.protocols.abinitio.abscript.RigidChunkCMCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.abinitio.abscript.RigidChunkCMCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.abinitio.abscript.RigidChunkCMCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class StageID(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.protocols.abinitio.abscript.StageID, rosetta.protocols.abinitio.abscript.StageID) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.protocols.abinitio.abscript.StageID) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.abinitio.abscript.StageID, int) -> NoneType   2. __init__(rosetta.protocols.abinitio.abscript.StageID, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.protocols.abinitio.abscript.StageID) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.protocols.abinitio.abscript.StageID, rosetta.protocols.abinitio.abscript.StageID) -> 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.abinitio.abscript.StageID) -> str Data and other attributes defined here: END = StageID.END I = StageID.I II = StageID.II IIIa = StageID.IIIa IIIb = StageID.IIIb IVa = StageID.IVa IVb = StageID.IVb   class StagePreparer(rosetta.protocols.environment.ClientMover)       Method resolution order: StagePreparer rosetta.protocols.environment.ClientMover rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.abinitio.abscript.StagePreparer, rosetta.protocols.abinitio.abscript.StagePreparer) -> NoneType   2. __init__(rosetta.protocols.abinitio.abscript.StagePreparer) -> 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.abinitio.abscript.StagePreparer,  : rosetta.protocols.abinitio.abscript.StagePreparer) -> rosetta.protocols.abinitio.abscript.StagePreparer prepare(...) from builtins.PyCapsule prepare(self : rosetta.protocols.abinitio.abscript.StagePreparer, pose : rosetta.core.pose.Pose, progress : float) -> NoneType Methods inherited from rosetta.protocols.environment.ClientMover: initialize(...) from builtins.PyCapsule initialize(self : rosetta.protocols.environment.ClientMover, conf : rosetta.core.pose.Pose) -> NoneType   this method is called by the broking system in response to a         successful initialization claim by this mover. The passport         will prevent any unauthorized changes. yield_claims(...) from builtins.PyCapsule yield_claims(self : rosetta.protocols.environment.ClientMover,  : rosetta.core.pose.Pose,  : rosetta.basic.datacache.WriteableCacheableMap) -> rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_std_allocator_std_shared_ptr_protocols_environment_claims_EnvClaim_t   Returns a list of claims for this mover.      The pose passed as an argument is used for reference informational           purposes only (for example, you want to know the sequence) or access           the pose cache. Any changes to the conformation will get overwritten! yield_submovers(...) from builtins.PyCapsule yield_submovers(self : rosetta.protocols.environment.ClientMover,  : rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_std_less_std_shared_ptr_protocols_environment_ClientMover_std_allocator_std_shared_ptr_protocols_environment_ClientMover_t) -> NoneType   this method is used to make sure any movers contained in this         mover (that want to make claims) also get registered with the         environment. Methods inherited from rosetta.protocols.moves.Mover: apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.moves.Mover,  : rosetta.core.pose.Pose) -> NoneType 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_name(...) from builtins.PyCapsule get_name(rosetta.protocols.moves.Mover) -> str   Each derived class must specify its name.  The class name. 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 StructPerturberCM(rosetta.protocols.environment.ClientMover)       Method resolution order: StructPerturberCM rosetta.protocols.environment.ClientMover 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, label : str, magnitude : float) -> NoneType   3. __init__(handle, rosetta.protocols.abinitio.abscript.StructPerturberCM) -> 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.abinitio.abscript.StructPerturberCM,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.abscript.StructPerturberCM,  : rosetta.protocols.abinitio.abscript.StructPerturberCM) -> rosetta.protocols.abinitio.abscript.StructPerturberCM clone(...) from builtins.PyCapsule clone(rosetta.protocols.abinitio.abscript.StructPerturberCM) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.abscript.StructPerturberCM) -> str label(...) from builtins.PyCapsule label(*args, **kwargs) Overloaded function.   1. label(rosetta.protocols.abinitio.abscript.StructPerturberCM) -> str   2. label(self : rosetta.protocols.abinitio.abscript.StructPerturberCM, label : str) -> NoneType magnitude(...) from builtins.PyCapsule magnitude(*args, **kwargs) Overloaded function.   1. magnitude(rosetta.protocols.abinitio.abscript.StructPerturberCM) -> float   2. magnitude(self : rosetta.protocols.abinitio.abscript.StructPerturberCM, value : float) -> NoneType yield_claims(...) from builtins.PyCapsule yield_claims(self : rosetta.protocols.abinitio.abscript.StructPerturberCM,  : rosetta.core.pose.Pose,  : rosetta.basic.datacache.WriteableCacheableMap) -> rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_std_allocator_std_shared_ptr_protocols_environment_claims_EnvClaim_t Methods inherited from rosetta.protocols.environment.ClientMover: initialize(...) from builtins.PyCapsule initialize(self : rosetta.protocols.environment.ClientMover, conf : rosetta.core.pose.Pose) -> NoneType   this method is called by the broking system in response to a         successful initialization claim by this mover. The passport         will prevent any unauthorized changes. yield_submovers(...) from builtins.PyCapsule yield_submovers(self : rosetta.protocols.environment.ClientMover,  : rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_std_less_std_shared_ptr_protocols_environment_ClientMover_std_allocator_std_shared_ptr_protocols_environment_ClientMover_t) -> NoneType   this method is used to make sure any movers contained in this         mover (that want to make claims) also get registered with the         environment. 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 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 StructPerturberCMCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: StructPerturberCMCreator 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.abinitio.abscript.StructPerturberCMCreator,  : rosetta.protocols.abinitio.abscript.StructPerturberCMCreator) -> rosetta.protocols.abinitio.abscript.StructPerturberCMCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.abinitio.abscript.StructPerturberCMCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.abinitio.abscript.StructPerturberCMCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str

Data
		END = StageID.END I = StageID.I II = StageID.II IIIa = StageID.IIIa IIIb = StageID.IIIb IVa = StageID.IVa IVb = StageID.IVb