Bindings for protocols::abinitio namespace

Modules
		rosetta.protocols.abinitio.abscript

Classes
		builtins.object AbrelaxApplication AlternativePairings KinematicControl CoordinateConstraintKC PairingStatEntry PairingStatistics StageID StrandConstraints Template Templates rosetta.protocols.jd2.archive.EvaluatedArchive(rosetta.protocols.jd2.archive.ArchiveBase) HedgeArchive rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive(rosetta.protocols.jd2.archive.EvaluatedArchive) IterativeBase IterativeAbrelax IterativeCentroid IterativeFullatom rosetta.protocols.jumping.BaseJumpSetup(builtins.object) TemplateJumpSetup FixTemplateJumpSetup rosetta.protocols.moves.Mover(builtins.object) AbrelaxMover DomainAssembly FragmentSampler ConstraintFragmentSampler Protocol ClassicAbinitio FoldConstraints KinematicAbinitio JumpingFoldConstraintsWrapper KinematicTaskControl LoopJumpFoldCst DoubleLayerKinematicAbinitio MembraneAbinitio ResolutionSwitcher rosetta.protocols.moves.MoverCreator(builtins.object) DomainAssemblyCreator rosetta.protocols.moves.PoseCondition(builtins.object) AllResiduesChanged   class AbrelaxApplication(builtins.object)     application level code  for Abrelax, Foldconstraints and JumpingFoldconstraints WARNING WARNING WARNING. THREAD UNSAFE. INVOKES ConstraintFactory::replace_creator. CODE THAT ABUSES SINGLETONS LIKE THIS OUGHT TO BE SHOT.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.abinitio.AbrelaxApplication) -> NoneType   2. __init__(self : rosetta.protocols.abinitio.AbrelaxApplication,  : rosetta.protocols.abinitio.AbrelaxApplication) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.abinitio.AbrelaxApplication, pose : rosetta.core.pose.Pose) -> NoneType   read constraint set (self-initializing) and connect it to pose add_evaluation(...) from builtins.PyCapsule add_evaluation(self : rosetta.protocols.abinitio.AbrelaxApplication,  : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType   add a PoseEvaluator derived instance for decoy-processing assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.AbrelaxApplication,  : rosetta.protocols.abinitio.AbrelaxApplication) -> rosetta.protocols.abinitio.AbrelaxApplication check_filters(...) from builtins.PyCapsule check_filters(self : rosetta.protocols.abinitio.AbrelaxApplication, pose : rosetta.core.pose.Pose) -> bool   check if the given pose passes the set of abinitio filters. close_loops(...) from builtins.PyCapsule close_loops(self : rosetta.protocols.abinitio.AbrelaxApplication, pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, tag : str) -> bool   return pose with simple fold-tree that has small <0.1 RMSD to input pose do_distributed_rerun(...) from builtins.PyCapsule do_distributed_rerun(rosetta.protocols.abinitio.AbrelaxApplication) -> NoneType   run process_decoy on all poses in silent-in file -- use of JobDistributor do_rerun(...) from builtins.PyCapsule do_rerun(rosetta.protocols.abinitio.AbrelaxApplication) -> NoneType   run process_decoy on all poses in silent-in file fold(...) from builtins.PyCapsule fold(self : rosetta.protocols.abinitio.AbrelaxApplication, extended_pose : rosetta.core.pose.Pose, prot_ptr : protocols::abinitio::Protocol) -> NoneType   run abrelax-type protocols multi_fast_relax(...) from builtins.PyCapsule multi_fast_relax(self : rosetta.protocols.abinitio.AbrelaxApplication, abinitio_protocol : protocols::abinitio::Protocol,  : rosetta.core.scoring.ScoreFunction, jobdist : rosetta.protocols.jobdist.PlainSilentFileJobDistributor, curr_nstruct : int, curr_job : rosetta.protocols.jobdist.BasicJob) -> bool   relax multiple structures that are stored in abinitio_protocol.structure_store process_decoy(...) from builtins.PyCapsule process_decoy(self : rosetta.protocols.abinitio.AbrelaxApplication, pose : rosetta.core.pose.Pose,  : rosetta.core.scoring.ScoreFunction, tag : str,  : rosetta.core.io.silent.SilentStruct) -> NoneType   diagnostic stuff, i.e., computing numbers like an RMSD for each decoy and storing in silent-score-file  put everything in here. --- actually it mainly calls the evaluator_->apply method.  add diagnostic stuff either here as explicit code or  in form of a PoseEvaluator to evaluator_ ( see setup () )  the latter has the advantage that the specific evaluation can be carried out during the run of the protocol  e.g., for abinitio:debug ( output to stage1_outfile stage2_outfile... ) register_options(...) from builtins.PyCapsule register_options() -> NoneType relax(...) from builtins.PyCapsule relax(self : rosetta.protocols.abinitio.AbrelaxApplication, pose : rosetta.core.pose.Pose,  : rosetta.core.scoring.ScoreFunction, tag : str) -> NoneType   relax structure ( fast / classic as controlled by cmd-options ) run(...) from builtins.PyCapsule run(rosetta.protocols.abinitio.AbrelaxApplication) -> NoneType   run application code: calls do_rerun() or fold() depending on cmd-options setup(...) from builtins.PyCapsule setup(rosetta.protocols.abinitio.AbrelaxApplication) -> NoneType   initialization of application: read some pdb files,  set evaluator_ setup_fold(...) from builtins.PyCapsule setup_fold(self : rosetta.protocols.abinitio.AbrelaxApplication, extended_pose : rosetta.core.pose.Pose, prot_ptr : protocols::abinitio::Protocol) -> NoneType   setup everything needed for fold() --- calls helper functions below   class AbrelaxMover(rosetta.protocols.moves.Mover)       Method resolution order: AbrelaxMover 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.AbrelaxMover) -> 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.AbrelaxMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.AbrelaxMover,  : rosetta.protocols.abinitio.AbrelaxMover) -> rosetta.protocols.abinitio.AbrelaxMover clear(...) from builtins.PyCapsule clear(rosetta.protocols.abinitio.AbrelaxMover) -> NoneType closure_protocol(...) from builtins.PyCapsule closure_protocol(*args, **kwargs) Overloaded function.   1. closure_protocol(rosetta.protocols.abinitio.AbrelaxMover) -> protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure   2. closure_protocol(self : rosetta.protocols.abinitio.AbrelaxMover, set : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure) -> NoneType fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.abinitio.AbrelaxMover) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.AbrelaxMover) -> str post_loop_closure_protocol(...) from builtins.PyCapsule post_loop_closure_protocol(self : rosetta.protocols.abinitio.AbrelaxMover, move : rosetta.protocols.moves.Mover) -> NoneType pre_loop_closure_protocol(...) from builtins.PyCapsule pre_loop_closure_protocol(self : rosetta.protocols.abinitio.AbrelaxMover, move : rosetta.protocols.moves.Mover) -> NoneType relax_protocol(...) from builtins.PyCapsule relax_protocol(*args, **kwargs) Overloaded function.   1. relax_protocol(rosetta.protocols.abinitio.AbrelaxMover) -> protocols::relax::RelaxProtocolBase   2. relax_protocol(rosetta.protocols.abinitio.AbrelaxMover) -> protocols::relax::RelaxProtocolBase   3. relax_protocol(self : rosetta.protocols.abinitio.AbrelaxMover, set : protocols::relax::RelaxProtocolBase) -> NoneType sampling_protocol(...) from builtins.PyCapsule sampling_protocol(*args, **kwargs) Overloaded function.   1. sampling_protocol(rosetta.protocols.abinitio.AbrelaxMover) -> protocols::abinitio::FragmentSampler   2. sampling_protocol(self : rosetta.protocols.abinitio.AbrelaxMover, set : protocols::abinitio::FragmentSampler) -> NoneType set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.abinitio.AbrelaxMover) -> NoneType topology_broker(...) from builtins.PyCapsule topology_broker(rosetta.protocols.abinitio.AbrelaxMover) -> protocols::topology_broker::TopologyBroker 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 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 AllResiduesChanged(rosetta.protocols.moves.PoseCondition)     (helper) functor class which keeps track of initial phi/psi values.        calls of operator ( pose ) compare the initial phi/psi values /to the current values of the given pose. Returns false once all phi/psi values  have been modified.     Method resolution order: AllResiduesChanged rosetta.protocols.moves.PoseCondition builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.protocols.abinitio.AllResiduesChanged, pose : rosetta.core.pose.Pose) -> bool __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, pose : rosetta.core.pose.Pose, insert_map : rosetta.utility.vector1_unsigned_long, mm : rosetta.core.kinematics.MoveMap) -> NoneType   2. __init__(self : handle, pose : rosetta.core.pose.Pose) -> NoneType   3. __init__(handle, rosetta.protocols.abinitio.AllResiduesChanged) -> 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.AllResiduesChanged,  : rosetta.protocols.abinitio.AllResiduesChanged) -> rosetta.protocols.abinitio.AllResiduesChanged   class AlternativePairings(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.abinitio.AlternativePairings) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.abinitio.AlternativePairings) -> str add_pairing(...) from builtins.PyCapsule add_pairing(self : rosetta.protocols.abinitio.AlternativePairings,  : rosetta.protocols.abinitio.PairingStatEntry) -> bool antiparallel(...) from builtins.PyCapsule antiparallel(rosetta.protocols.abinitio.AlternativePairings) -> bool build_constraints(...) from builtins.PyCapsule build_constraints(self : rosetta.protocols.abinitio.AlternativePairings, pose : rosetta.core.pose.Pose, cst : rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t) -> NoneType compatible(...) from builtins.PyCapsule compatible(self : rosetta.protocols.abinitio.AlternativePairings, pairing : rosetta.core.scoring.dssp.StrandPairing) -> bool   class ClassicAbinitio(Protocol)     @ detail general usage: ClassicAbinitio  abinitio; abinitio.init( pose ); ... while(nstruct) { abinitio.apply( pose ); }   call ClassicAbinitio::register_options() before core::init::init to add relevant options to the applications help   , with the following stages, all of which uses a different ScoreFunction based on the cen_std.wts in minirosetta_database:   - Stage 1: large (usually 9mer) randomly selected fragment insertions, only VDW term turned on. Uses score0.wts_patch and runs for either a maximum of 2000 cycles or until all moveable phi/psi values have been changed.   - Stage 2: large randomly selected fragment insertions, more score terms turned on. Uses score1.wts_patch and runs for 2000 cycles.   - Stage 3: uses large randomly selected fragment insertions, although the size of the fragment insertions is tunable via the set_apply_large_frags( bool ) method. Alternates between score2.wts_patch and score5.wts_patch, running tunable numbers of 2000-cycle iterations between the two scoring functions.   - Stage 4: uses small (usually 3mer) fragment insertions with the fragment selection based on the Gunn cost for finding local fragment moves. Runs for 4000-cycles and uses score3.wts_patch.   The class implements the basic abinito approach as known from rosetta++. We tried to set this up, such that behaviour of the protocol can be changed in many different ways ( see, e.g., FoldConstraints ). To be able to change the behaviour of the protocol easily the class-apply function and methods called therein (e.g., prepare_XXX() / do_XXX_cycles() ) should not directly change moves or trials. A reference to the currently used score-function should be obtained by mc().score_function() ...   Behaviour can be changed in the following ways:   use non-classic FragmentMover  --> eg. not uniformly sampled fragments, but using some weighting --> large and small moves doesn't have to be 3mers and 9mers... use other movers... ---> or other fragets for the "convenience constructor" use custom trial classes --> overload update_moves()   change sampling behaviour: overload prepare_XXX() methods: these are called before the cycling for a certain stage begins overload do_stageX_cycles() : the actual loops over trial-moves ...   change scoring functions: overload set_default_scores() weight-changes effective for all stages: set_score_weight()     Method resolution order: ClassicAbinitio Protocol rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, brute_move_small : protocols::simple_moves::FragmentMover, brute_move_large : protocols::simple_moves::FragmentMover, smooth_move_small : protocols::simple_moves::FragmentMover,  : int) -> NoneType   2. __init__(self : handle, fragset_small : rosetta.core.fragment.FragSet, fragset_large : rosetta.core.fragment.FragSet, movemap : rosetta.core.kinematics.MoveMap) -> NoneType   3. __init__(handle, rosetta.protocols.abinitio.ClassicAbinitio) -> 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.ClassicAbinitio, pose : rosetta.core.pose.Pose) -> NoneType bQuickTest(...) from builtins.PyCapsule bQuickTest(rosetta.protocols.abinitio.ClassicAbinitio) -> bool brute_move_large(...) from builtins.PyCapsule brute_move_large(rosetta.protocols.abinitio.ClassicAbinitio) -> protocols::simple_moves::FragmentMover brute_move_small(...) from builtins.PyCapsule brute_move_small(rosetta.protocols.abinitio.ClassicAbinitio) -> protocols::simple_moves::FragmentMover clone(...) from builtins.PyCapsule clone(rosetta.protocols.abinitio.ClassicAbinitio) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.ClassicAbinitio) -> str init(...) from builtins.PyCapsule init(self : rosetta.protocols.abinitio.ClassicAbinitio, pose : rosetta.core.pose.Pose) -> NoneType just_smooth_cycles(...) from builtins.PyCapsule just_smooth_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> bool mc(...) from builtins.PyCapsule mc(*args, **kwargs) Overloaded function.   1. mc(rosetta.protocols.abinitio.ClassicAbinitio) -> protocols::moves::MonteCarlo   2. mc(rosetta.protocols.abinitio.ClassicAbinitio) -> protocols::moves::MonteCarlo movemap(...) from builtins.PyCapsule movemap(rosetta.protocols.abinitio.ClassicAbinitio) -> rosetta.core.kinematics.MoveMap register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType set_cycles(...) from builtins.PyCapsule set_cycles(*args, **kwargs) Overloaded function.   1. set_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> NoneType   2. set_cycles(self : rosetta.protocols.abinitio.ClassicAbinitio, increase_cycles : float) -> NoneType set_mc(...) from builtins.PyCapsule set_mc(self : rosetta.protocols.abinitio.ClassicAbinitio,  : protocols::moves::MonteCarlo) -> NoneType set_movemap(...) from builtins.PyCapsule set_movemap(self : rosetta.protocols.abinitio.ClassicAbinitio, mm : rosetta.core.kinematics.MoveMap) -> NoneType set_moves(...) from builtins.PyCapsule set_moves(self : rosetta.protocols.abinitio.ClassicAbinitio, brute_move_small : protocols::simple_moves::FragmentMover, brute_move_large : protocols::simple_moves::FragmentMover, smooth_move_small : protocols::simple_moves::FragmentMover) -> NoneType set_score_weight(...) from builtins.PyCapsule set_score_weight(*args, **kwargs) Overloaded function.   1. set_score_weight(self : rosetta.protocols.abinitio.ClassicAbinitio,  : rosetta.core.scoring.ScoreType, setting : float) -> NoneType   2. set_score_weight(self : rosetta.protocols.abinitio.ClassicAbinitio,  : rosetta.core.scoring.ScoreType, setting : float, stage : rosetta.protocols.abinitio.StageID) -> NoneType set_skip_stage1(...) from builtins.PyCapsule set_skip_stage1(self : rosetta.protocols.abinitio.ClassicAbinitio, setting : bool) -> NoneType set_skip_stage2(...) from builtins.PyCapsule set_skip_stage2(self : rosetta.protocols.abinitio.ClassicAbinitio, setting : bool) -> NoneType set_stage4_cycles(...) from builtins.PyCapsule set_stage4_cycles(self : rosetta.protocols.abinitio.ClassicAbinitio, stage4_cycles_new : int) -> NoneType smooth_move_small(...) from builtins.PyCapsule smooth_move_small(rosetta.protocols.abinitio.ClassicAbinitio) -> protocols::simple_moves::FragmentMover stage1_cycles(...) from builtins.PyCapsule stage1_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> int stage2_cycles(...) from builtins.PyCapsule stage2_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> int stage3_cycles(...) from builtins.PyCapsule stage3_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> int stage4_cycles(...) from builtins.PyCapsule stage4_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> int stage5_cycles(...) from builtins.PyCapsule stage5_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> int total_trials(...) from builtins.PyCapsule total_trials(rosetta.protocols.abinitio.ClassicAbinitio) -> int Data descriptors defined here: bSkipStage1_ bSkipStage2_ bSkipStage3_ bSkipStage4_ bSkipStage5_ recover_low_stages_ Data and other attributes defined here: ALL_STAGES = StageID.ALL_STAGES STAGE_1 = StageID.STAGE_1 STAGE_2 = StageID.STAGE_2 STAGE_3a = StageID.STAGE_3a STAGE_3b = StageID.STAGE_3b STAGE_4 = StageID.STAGE_4 STAGE_4rot = StageID.STAGE_4rot STAGE_5 = StageID.STAGE_5 StageID = <class 'rosetta.protocols.abinitio.ClassicAbinitio.StageID'> Methods inherited from Protocol: add_evaluation(...) from builtins.PyCapsule add_evaluation(self : rosetta.protocols.abinitio.Protocol, ev : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.Protocol,  : rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.abinitio.Protocol centroid_scorefxn(...) from builtins.PyCapsule centroid_scorefxn(rosetta.protocols.abinitio.Protocol) -> rosetta.core.scoring.ScoreFunction evaluate_pose(...) from builtins.PyCapsule evaluate_pose(self : rosetta.protocols.abinitio.Protocol, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType evaluator(...) from builtins.PyCapsule evaluator(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.evaluation.MetaPoseEvaluator fullatom_scorefxn(...) from builtins.PyCapsule fullatom_scorefxn(rosetta.protocols.abinitio.Protocol) -> rosetta.core.scoring.ScoreFunction get_checkpoints(...) from builtins.PyCapsule get_checkpoints(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.checkpoint.CheckPointer kinematics(...) from builtins.PyCapsule kinematics(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.abinitio.KinematicControl output_debug_structure(...) from builtins.PyCapsule output_debug_structure(self : rosetta.protocols.abinitio.Protocol, pose : rosetta.core.pose.Pose, prefix : str) -> NoneType return_centroid(...) from builtins.PyCapsule return_centroid(*args, **kwargs) Overloaded function.   1. return_centroid(rosetta.protocols.abinitio.Protocol) -> bool   2. return_centroid(self : rosetta.protocols.abinitio.Protocol, setting : bool) -> NoneType set_centroid_scorefxn(...) from builtins.PyCapsule set_centroid_scorefxn(self : rosetta.protocols.abinitio.Protocol, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_evaluation(...) from builtins.PyCapsule set_evaluation(self : rosetta.protocols.abinitio.Protocol, ev : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType set_fullatom_scorefxn(...) from builtins.PyCapsule set_fullatom_scorefxn(self : rosetta.protocols.abinitio.Protocol, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_kinematics(...) from builtins.PyCapsule set_kinematics(self : rosetta.protocols.abinitio.Protocol, kc : rosetta.protocols.abinitio.KinematicControl) -> NoneType set_silentout_file_name(...) from builtins.PyCapsule set_silentout_file_name(self : rosetta.protocols.abinitio.Protocol, str : str) -> NoneType start_from_centroid(...) from builtins.PyCapsule start_from_centroid(rosetta.protocols.abinitio.Protocol) -> bool 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 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 ConstraintFragmentSampler(FragmentSampler)     @ detail general usage: ConstraintFragmentSampler  abinitio; abinitio.init( pose ); ... while(nstruct) { abinitio.apply( pose ); }   call ConstraintFragmentSampler::register_options() before core::init::init to add relevant options to the applications help   , with the following stages, all of which uses a different ScoreFunction based on the cen_std.wts in minirosetta_database:   - Stage 1: large (usually 9mer) randomly selected fragment insertions, only VDW term turned on. Uses score0.wts_patch and runs for either a maximum of 2000 cycles or until all moveable phi/psi values have been changed.   - Stage 2: large randomly selected fragment insertions, more score terms turned on. Uses score1.wts_patch and runs for 2000 cycles.   - Stage 3: uses large randomly selected fragment insertions, although the size of the fragment insertions is tunable via the set_apply_large_frags( bool ) method. Alternates between score2.wts_patch and score5.wts_patch, running tunable numbers of 2000-cycle iterations between the two scoring functions.   - Stage 4: uses small (usually 3mer) fragment insertions with the fragment selection based on the Gunn cost for finding local fragment moves. Runs for 4000-cycles and uses score3.wts_patch.   The class implements the basic abinito approach as known from rosetta++. We tried to set this up, such that behaviour of the protocol can be changed in many different ways ( see, e.g., FoldConstraints ). To be able to change the behaviour of the protocol easily the class-apply function and methods called therein (e.g., prepare_XXX() / do_XXX_cycles() ) should not directly change moves or trials. A reference to the currently used score-function should be obtained by mc().score_function() ...   Behaviour can be changed in the following ways:   use non-classic FragmentMover  --> eg. not uniformly sampled fragments, but using some weighting --> large and small moves doesn't have to be 3mers and 9mers... use other movers... ---> or other fragets for the "convenience constructor" use custom trial classes --> overload update_moves()   change sampling behaviour: overload prepare_XXX() methods: these are called before the cycling for a certain stage begins overload do_stageX_cycles() : the actual loops over trial-moves ...   change scoring functions: overload set_default_scores() weight-changes effective for all stages: set_score_weight()     Method resolution order: ConstraintFragmentSampler FragmentSampler rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, broker : protocols::topology_broker::TopologyBroker) -> NoneType   2. __init__(handle, rosetta.protocols.abinitio.ConstraintFragmentSampler) -> 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.ConstraintFragmentSampler, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.ConstraintFragmentSampler,  : rosetta.protocols.abinitio.ConstraintFragmentSampler) -> rosetta.protocols.abinitio.ConstraintFragmentSampler clone(...) from builtins.PyCapsule clone(rosetta.protocols.abinitio.ConstraintFragmentSampler) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.ConstraintFragmentSampler) -> 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 Methods inherited from FragmentSampler: bQuickTest(...) from builtins.PyCapsule bQuickTest(rosetta.protocols.abinitio.FragmentSampler) -> bool check_loops(...) from builtins.PyCapsule check_loops(self : rosetta.protocols.abinitio.FragmentSampler, pose : rosetta.core.pose.Pose) -> bool current_scorefxn(...) from builtins.PyCapsule current_scorefxn(rosetta.protocols.abinitio.FragmentSampler) -> rosetta.core.scoring.ScoreFunction get_checkpoints(...) from builtins.PyCapsule get_checkpoints(rosetta.protocols.abinitio.FragmentSampler) -> rosetta.protocols.checkpoint.CheckPointer just_smooth_cycles(...) from builtins.PyCapsule just_smooth_cycles(rosetta.protocols.abinitio.FragmentSampler) -> bool set_cycles(...) from builtins.PyCapsule set_cycles(*args, **kwargs) Overloaded function.   1. set_cycles(rosetta.protocols.abinitio.FragmentSampler) -> NoneType   2. set_cycles(self : rosetta.protocols.abinitio.FragmentSampler, increase_cycles : float) -> NoneType set_score_weight(...) from builtins.PyCapsule set_score_weight(*args, **kwargs) Overloaded function.   1. set_score_weight(self : rosetta.protocols.abinitio.FragmentSampler,  : rosetta.core.scoring.ScoreType, setting : float) -> NoneType   2. set_score_weight(self : rosetta.protocols.abinitio.FragmentSampler,  : rosetta.core.scoring.ScoreType, setting : float, stage : rosetta.protocols.abinitio.StageID) -> NoneType set_stage4_cycles(...) from builtins.PyCapsule set_stage4_cycles(self : rosetta.protocols.abinitio.FragmentSampler, stage4_cycles_new : int) -> NoneType stage1_cycles(...) from builtins.PyCapsule stage1_cycles(rosetta.protocols.abinitio.FragmentSampler) -> int stage2_cycles(...) from builtins.PyCapsule stage2_cycles(rosetta.protocols.abinitio.FragmentSampler) -> int stage3_cycles(...) from builtins.PyCapsule stage3_cycles(rosetta.protocols.abinitio.FragmentSampler) -> int stage4_cycles(...) from builtins.PyCapsule stage4_cycles(rosetta.protocols.abinitio.FragmentSampler) -> int topology_broker(...) from builtins.PyCapsule topology_broker(self : rosetta.protocols.abinitio.FragmentSampler, set : protocols::topology_broker::TopologyBroker) -> 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 fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class CoordinateConstraintKC(KinematicControl)       Method resolution order: CoordinateConstraintKC KinematicControl builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, ramp : bool, final_weight : float) -> NoneType   2. __init__(handle, rosetta.protocols.abinitio.CoordinateConstraintKC) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_score_weights(...) from builtins.PyCapsule add_score_weights(self : rosetta.protocols.abinitio.CoordinateConstraintKC,  : rosetta.core.scoring.ScoreFunction, progress : float) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.CoordinateConstraintKC,  : rosetta.protocols.abinitio.CoordinateConstraintKC) -> rosetta.protocols.abinitio.CoordinateConstraintKC Methods inherited from KinematicControl: add_chainbreak_variants(...) from builtins.PyCapsule add_chainbreak_variants(*args, **kwargs) Overloaded function.   1. add_chainbreak_variants(self : rosetta.protocols.abinitio.KinematicControl, pose : rosetta.core.pose.Pose) -> NoneType   2. add_chainbreak_variants(self : rosetta.protocols.abinitio.KinematicControl, pose : rosetta.core.pose.Pose, max_dist : int,  : rosetta.core.kinematics.ShortestPathInFoldTree) -> NoneType final_fold_tree(...) from builtins.PyCapsule final_fold_tree(rosetta.protocols.abinitio.KinematicControl) -> rosetta.core.kinematics.FoldTree jump_mover(...) from builtins.PyCapsule jump_mover(rosetta.protocols.abinitio.KinematicControl) -> protocols::simple_moves::FragmentMover movemap(...) from builtins.PyCapsule movemap(rosetta.protocols.abinitio.KinematicControl) -> rosetta.core.kinematics.MoveMap movemap_ptr(...) from builtins.PyCapsule movemap_ptr(rosetta.protocols.abinitio.KinematicControl) -> rosetta.core.kinematics.MoveMap prepare_pose_for_sampling(...) from builtins.PyCapsule prepare_pose_for_sampling(self : rosetta.protocols.abinitio.KinematicControl, pose : rosetta.core.pose.Pose) -> bool sampling_fold_tree(...) from builtins.PyCapsule sampling_fold_tree(rosetta.protocols.abinitio.KinematicControl) -> rosetta.core.kinematics.FoldTree set_final_fold_tree(...) from builtins.PyCapsule set_final_fold_tree(self : rosetta.protocols.abinitio.KinematicControl, f : rosetta.core.kinematics.FoldTree) -> NoneType set_jump_mover(...) from builtins.PyCapsule set_jump_mover(self : rosetta.protocols.abinitio.KinematicControl, jm : protocols::simple_moves::FragmentMover) -> NoneType set_movemap(...) from builtins.PyCapsule set_movemap(self : rosetta.protocols.abinitio.KinematicControl, mm : rosetta.core.kinematics.MoveMap) -> NoneType set_sampling_fold_tree(...) from builtins.PyCapsule set_sampling_fold_tree(self : rosetta.protocols.abinitio.KinematicControl, f : rosetta.core.kinematics.FoldTree) -> NoneType set_strict_movemap(...) from builtins.PyCapsule set_strict_movemap(self : rosetta.protocols.abinitio.KinematicControl, mm : rosetta.core.kinematics.MoveMap) -> NoneType   class DomainAssembly(rosetta.protocols.moves.Mover)     insert fragments in a linker region. Very similar to what's in looprelax_main     Method resolution order: DomainAssembly 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, linker_start : int, linker_end : int, fragset_large : rosetta.core.fragment.FragSet, fragset_small : rosetta.core.fragment.FragSet) -> NoneType   3. __init__(handle, rosetta.protocols.abinitio.DomainAssembly) -> 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.DomainAssembly, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.DomainAssembly,  : rosetta.protocols.abinitio.DomainAssembly) -> rosetta.protocols.abinitio.DomainAssembly clone(...) from builtins.PyCapsule clone(rosetta.protocols.abinitio.DomainAssembly) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.abinitio.DomainAssembly) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.DomainAssembly) -> str Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class DomainAssemblyCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: DomainAssemblyCreator 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.DomainAssemblyCreator,  : rosetta.protocols.abinitio.DomainAssemblyCreator) -> rosetta.protocols.abinitio.DomainAssemblyCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.abinitio.DomainAssemblyCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.abinitio.DomainAssemblyCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class DoubleLayerKinematicAbinitio(LoopJumpFoldCst)       Method resolution order: DoubleLayerKinematicAbinitio LoopJumpFoldCst KinematicTaskControl Protocol rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle, rosetta.protocols.jumping.BaseJumpSetup, rosetta.protocols.loops.Loops, rosetta.protocols.loops.Loops, rosetta.protocols.abinitio.Protocol, rosetta.protocols.abinitio.Protocol, rosetta.core.fragment.SecondaryStructure, float) -> NoneType   doc   2. __init__(self : handle, jump_def : rosetta.protocols.jumping.BaseJumpSetup, extended_loops : rosetta.protocols.loops.Loops, rigid_core : rosetta.protocols.loops.Loops, sampler : rosetta.protocols.abinitio.Protocol, extended_chain_sampler : rosetta.protocols.abinitio.Protocol, ss_def : rosetta.core.fragment.SecondaryStructure, coord_cst_weight : float, bCstAllAtom : bool) -> NoneType   3. __init__(handle, rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio) -> 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.DoubleLayerKinematicAbinitio,  : rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio) -> rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio) -> str new_kinematics(...) from builtins.PyCapsule new_kinematics(self : rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio, pose : rosetta.core.pose.Pose) -> rosetta.protocols.abinitio.KinematicControl Methods inherited from LoopJumpFoldCst: set_coord_cst_weight_array(...) from builtins.PyCapsule set_coord_cst_weight_array(self : rosetta.protocols.abinitio.LoopJumpFoldCst, vec : rosetta.utility.vector1_double) -> NoneType set_dump_weights_file(...) from builtins.PyCapsule set_dump_weights_file(self : rosetta.protocols.abinitio.LoopJumpFoldCst, str : str) -> NoneType Methods inherited from KinematicTaskControl: apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.abinitio.KinematicTaskControl, pose : rosetta.core.pose.Pose) -> NoneType current_kinematics(...) from builtins.PyCapsule current_kinematics(rosetta.protocols.abinitio.KinematicTaskControl) -> rosetta.protocols.abinitio.KinematicControl get_checkpoints(...) from builtins.PyCapsule get_checkpoints(rosetta.protocols.abinitio.KinematicTaskControl) -> rosetta.protocols.checkpoint.CheckPointer init(...) from builtins.PyCapsule init(self : rosetta.protocols.abinitio.KinematicTaskControl, pose : rosetta.core.pose.Pose) -> NoneType sampling_protocol(...) from builtins.PyCapsule sampling_protocol(rosetta.protocols.abinitio.KinematicTaskControl) -> rosetta.protocols.abinitio.Protocol set_input_pose_is_fa(...) from builtins.PyCapsule set_input_pose_is_fa(*args, **kwargs) Overloaded function.   1. set_input_pose_is_fa(rosetta.protocols.abinitio.KinematicTaskControl) -> NoneType   2. set_input_pose_is_fa(self : rosetta.protocols.abinitio.KinematicTaskControl, setting : bool) -> NoneType Methods inherited from Protocol: add_evaluation(...) from builtins.PyCapsule add_evaluation(self : rosetta.protocols.abinitio.Protocol, ev : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType centroid_scorefxn(...) from builtins.PyCapsule centroid_scorefxn(rosetta.protocols.abinitio.Protocol) -> rosetta.core.scoring.ScoreFunction evaluate_pose(...) from builtins.PyCapsule evaluate_pose(self : rosetta.protocols.abinitio.Protocol, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType evaluator(...) from builtins.PyCapsule evaluator(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.evaluation.MetaPoseEvaluator fullatom_scorefxn(...) from builtins.PyCapsule fullatom_scorefxn(rosetta.protocols.abinitio.Protocol) -> rosetta.core.scoring.ScoreFunction kinematics(...) from builtins.PyCapsule kinematics(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.abinitio.KinematicControl output_debug_structure(...) from builtins.PyCapsule output_debug_structure(self : rosetta.protocols.abinitio.Protocol, pose : rosetta.core.pose.Pose, prefix : str) -> NoneType 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 return_centroid(...) from builtins.PyCapsule return_centroid(*args, **kwargs) Overloaded function.   1. return_centroid(rosetta.protocols.abinitio.Protocol) -> bool   2. return_centroid(self : rosetta.protocols.abinitio.Protocol, setting : bool) -> NoneType set_centroid_scorefxn(...) from builtins.PyCapsule set_centroid_scorefxn(self : rosetta.protocols.abinitio.Protocol, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_evaluation(...) from builtins.PyCapsule set_evaluation(self : rosetta.protocols.abinitio.Protocol, ev : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType set_fullatom_scorefxn(...) from builtins.PyCapsule set_fullatom_scorefxn(self : rosetta.protocols.abinitio.Protocol, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_kinematics(...) from builtins.PyCapsule set_kinematics(self : rosetta.protocols.abinitio.Protocol, kc : rosetta.protocols.abinitio.KinematicControl) -> NoneType set_silentout_file_name(...) from builtins.PyCapsule set_silentout_file_name(self : rosetta.protocols.abinitio.Protocol, str : str) -> NoneType start_from_centroid(...) from builtins.PyCapsule start_from_centroid(rosetta.protocols.abinitio.Protocol) -> bool Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply clone(...) from builtins.PyCapsule clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Return a clone of the Mover object. create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class FixTemplateJumpSetup(TemplateJumpSetup)       Method resolution order: FixTemplateJumpSetup TemplateJumpSetup rosetta.protocols.jumping.BaseJumpSetup builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, templates : protocols::abinitio::Templates, secstruct : rosetta.core.fragment.SecondaryStructure,  : rosetta.protocols.abinitio.PairingStatistics,  : rosetta.utility.vector1_core_scoring_dssp_Pairing, jump_def : rosetta.protocols.jumping.BaseJumpSetup) -> NoneType   2. __init__(self : handle, templ : rosetta.protocols.abinitio.TemplateJumpSetup, jump_def : rosetta.protocols.jumping.BaseJumpSetup) -> 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.FixTemplateJumpSetup,  : rosetta.protocols.abinitio.FixTemplateJumpSetup) -> rosetta.protocols.abinitio.FixTemplateJumpSetup create_jump_sample(...) from builtins.PyCapsule create_jump_sample(rosetta.protocols.abinitio.FixTemplateJumpSetup) -> rosetta.protocols.jumping.JumpSample Methods inherited from TemplateJumpSetup: clean_jumps(...) from builtins.PyCapsule clean_jumps(self : rosetta.protocols.abinitio.TemplateJumpSetup,  : rosetta.protocols.jumping.JumpSample) -> rosetta.protocols.jumping.JumpSample generate_jump_frags(...) from builtins.PyCapsule generate_jump_frags(self : rosetta.protocols.abinitio.TemplateJumpSetup,  : rosetta.protocols.jumping.JumpSample,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   returns an ordered FragSet that is compatible with the JumpSample  default: generate jumps from ss-library according to JumpSample is_helix_jump(...) from builtins.PyCapsule is_helix_jump(self : rosetta.protocols.abinitio.TemplateJumpSetup, p : rosetta.core.scoring.dssp.Pairing) -> bool type_name(...) from builtins.PyCapsule type_name(rosetta.protocols.abinitio.TemplateJumpSetup) -> str   class FoldConstraints(ClassicAbinitio)     extension of ClassicAbinitio Protocol to adapt the folding process for the presence of distance constraints     Main Function: switch distance constraints based on distance in the FoldTree ( i.e., in sequence for simple FoldTrees )     This is achieved by replacing the pose's ConstraintSet with the special purpose class MaxSeqSepConstraintSet     the latter class will only score constraints that are sufficiently close in FoldTree/Sequence     ( as controlled by the threshold with set_max_seq_sep()  )     the protocol ranks up the max_seq_sep parameter while folding proceeds through the stages.     to this extend it overloads methods prepare_stageX() do_stage1_cycles()       the other substantial difference to ClassicAbinitio is that minimizations are carried out.     method min_trial() is called each time the max_seq_sep is changed. ( inhibit: -no_minimize )     Method resolution order: FoldConstraints ClassicAbinitio Protocol rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, brute_move_small : protocols::simple_moves::FragmentMover, brute_move_large : protocols::simple_moves::FragmentMover, smooth_move_small : protocols::simple_moves::FragmentMover, dummy : int) -> NoneType   2. __init__(self : handle, fragset3mer : rosetta.core.fragment.FragSet, fragset9mer : rosetta.core.fragment.FragSet, movemap : rosetta.core.kinematics.MoveMap) -> NoneType   3. __init__(handle, rosetta.protocols.abinitio.FoldConstraints) -> 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.FoldConstraints, pose : rosetta.core.pose.Pose) -> NoneType   run the protocol clone(...) from builtins.PyCapsule clone(rosetta.protocols.abinitio.FoldConstraints) -> rosetta.protocols.moves.Mover   ... get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.FoldConstraints) -> 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 set_constraint_weight(...) from builtins.PyCapsule set_constraint_weight(self : rosetta.protocols.abinitio.FoldConstraints, setting : float) -> NoneType set_default_options(...) from builtins.PyCapsule set_default_options(rosetta.protocols.abinitio.FoldConstraints) -> NoneType set_default_scores(...) from builtins.PyCapsule set_default_scores(rosetta.protocols.abinitio.FoldConstraints) -> NoneType   sets the usual scores ( score0,score1, score2/5 etc. ) and additionally atom_pair_constraints to 1.0 set_show_viol_level(...) from builtins.PyCapsule set_show_viol_level(self : rosetta.protocols.abinitio.FoldConstraints, setting : int) -> NoneType Methods inherited from ClassicAbinitio: bQuickTest(...) from builtins.PyCapsule bQuickTest(rosetta.protocols.abinitio.ClassicAbinitio) -> bool brute_move_large(...) from builtins.PyCapsule brute_move_large(rosetta.protocols.abinitio.ClassicAbinitio) -> protocols::simple_moves::FragmentMover brute_move_small(...) from builtins.PyCapsule brute_move_small(rosetta.protocols.abinitio.ClassicAbinitio) -> protocols::simple_moves::FragmentMover init(...) from builtins.PyCapsule init(self : rosetta.protocols.abinitio.ClassicAbinitio, pose : rosetta.core.pose.Pose) -> NoneType just_smooth_cycles(...) from builtins.PyCapsule just_smooth_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> bool mc(...) from builtins.PyCapsule mc(*args, **kwargs) Overloaded function.   1. mc(rosetta.protocols.abinitio.ClassicAbinitio) -> protocols::moves::MonteCarlo   2. mc(rosetta.protocols.abinitio.ClassicAbinitio) -> protocols::moves::MonteCarlo movemap(...) from builtins.PyCapsule movemap(rosetta.protocols.abinitio.ClassicAbinitio) -> rosetta.core.kinematics.MoveMap set_cycles(...) from builtins.PyCapsule set_cycles(*args, **kwargs) Overloaded function.   1. set_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> NoneType   2. set_cycles(self : rosetta.protocols.abinitio.ClassicAbinitio, increase_cycles : float) -> NoneType set_mc(...) from builtins.PyCapsule set_mc(self : rosetta.protocols.abinitio.ClassicAbinitio,  : protocols::moves::MonteCarlo) -> NoneType set_movemap(...) from builtins.PyCapsule set_movemap(self : rosetta.protocols.abinitio.ClassicAbinitio, mm : rosetta.core.kinematics.MoveMap) -> NoneType set_moves(...) from builtins.PyCapsule set_moves(self : rosetta.protocols.abinitio.ClassicAbinitio, brute_move_small : protocols::simple_moves::FragmentMover, brute_move_large : protocols::simple_moves::FragmentMover, smooth_move_small : protocols::simple_moves::FragmentMover) -> NoneType set_score_weight(...) from builtins.PyCapsule set_score_weight(*args, **kwargs) Overloaded function.   1. set_score_weight(self : rosetta.protocols.abinitio.ClassicAbinitio,  : rosetta.core.scoring.ScoreType, setting : float) -> NoneType   2. set_score_weight(self : rosetta.protocols.abinitio.ClassicAbinitio,  : rosetta.core.scoring.ScoreType, setting : float, stage : rosetta.protocols.abinitio.StageID) -> NoneType set_skip_stage1(...) from builtins.PyCapsule set_skip_stage1(self : rosetta.protocols.abinitio.ClassicAbinitio, setting : bool) -> NoneType set_skip_stage2(...) from builtins.PyCapsule set_skip_stage2(self : rosetta.protocols.abinitio.ClassicAbinitio, setting : bool) -> NoneType set_stage4_cycles(...) from builtins.PyCapsule set_stage4_cycles(self : rosetta.protocols.abinitio.ClassicAbinitio, stage4_cycles_new : int) -> NoneType smooth_move_small(...) from builtins.PyCapsule smooth_move_small(rosetta.protocols.abinitio.ClassicAbinitio) -> protocols::simple_moves::FragmentMover stage1_cycles(...) from builtins.PyCapsule stage1_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> int stage2_cycles(...) from builtins.PyCapsule stage2_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> int stage3_cycles(...) from builtins.PyCapsule stage3_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> int stage4_cycles(...) from builtins.PyCapsule stage4_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> int stage5_cycles(...) from builtins.PyCapsule stage5_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> int total_trials(...) from builtins.PyCapsule total_trials(rosetta.protocols.abinitio.ClassicAbinitio) -> int Data descriptors inherited from ClassicAbinitio: bSkipStage1_ bSkipStage2_ bSkipStage3_ bSkipStage4_ bSkipStage5_ recover_low_stages_ Data and other attributes inherited from ClassicAbinitio: ALL_STAGES = StageID.ALL_STAGES STAGE_1 = StageID.STAGE_1 STAGE_2 = StageID.STAGE_2 STAGE_3a = StageID.STAGE_3a STAGE_3b = StageID.STAGE_3b STAGE_4 = StageID.STAGE_4 STAGE_4rot = StageID.STAGE_4rot STAGE_5 = StageID.STAGE_5 StageID = <class 'rosetta.protocols.abinitio.ClassicAbinitio.StageID'> Methods inherited from Protocol: add_evaluation(...) from builtins.PyCapsule add_evaluation(self : rosetta.protocols.abinitio.Protocol, ev : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.Protocol,  : rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.abinitio.Protocol centroid_scorefxn(...) from builtins.PyCapsule centroid_scorefxn(rosetta.protocols.abinitio.Protocol) -> rosetta.core.scoring.ScoreFunction evaluate_pose(...) from builtins.PyCapsule evaluate_pose(self : rosetta.protocols.abinitio.Protocol, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType evaluator(...) from builtins.PyCapsule evaluator(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.evaluation.MetaPoseEvaluator fullatom_scorefxn(...) from builtins.PyCapsule fullatom_scorefxn(rosetta.protocols.abinitio.Protocol) -> rosetta.core.scoring.ScoreFunction get_checkpoints(...) from builtins.PyCapsule get_checkpoints(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.checkpoint.CheckPointer kinematics(...) from builtins.PyCapsule kinematics(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.abinitio.KinematicControl output_debug_structure(...) from builtins.PyCapsule output_debug_structure(self : rosetta.protocols.abinitio.Protocol, pose : rosetta.core.pose.Pose, prefix : str) -> NoneType return_centroid(...) from builtins.PyCapsule return_centroid(*args, **kwargs) Overloaded function.   1. return_centroid(rosetta.protocols.abinitio.Protocol) -> bool   2. return_centroid(self : rosetta.protocols.abinitio.Protocol, setting : bool) -> NoneType set_centroid_scorefxn(...) from builtins.PyCapsule set_centroid_scorefxn(self : rosetta.protocols.abinitio.Protocol, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_evaluation(...) from builtins.PyCapsule set_evaluation(self : rosetta.protocols.abinitio.Protocol, ev : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType set_fullatom_scorefxn(...) from builtins.PyCapsule set_fullatom_scorefxn(self : rosetta.protocols.abinitio.Protocol, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_kinematics(...) from builtins.PyCapsule set_kinematics(self : rosetta.protocols.abinitio.Protocol, kc : rosetta.protocols.abinitio.KinematicControl) -> NoneType set_silentout_file_name(...) from builtins.PyCapsule set_silentout_file_name(self : rosetta.protocols.abinitio.Protocol, str : str) -> NoneType start_from_centroid(...) from builtins.PyCapsule start_from_centroid(rosetta.protocols.abinitio.Protocol) -> bool 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 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 FragmentSampler(rosetta.protocols.moves.Mover)     @ detail general usage: FragmentSampler  abinitio; abinitio.init( pose ); ... while(nstruct) { abinitio.apply( pose ); }   call FragmentSampler::register_options() before core::init::init to add relevant options to the applications help   , with the following stages, all of which uses a different ScoreFunction based on the cen_std.wts in minirosetta_database:   - Stage 1: large (usually 9mer) randomly selected fragment insertions, only VDW term turned on. Uses score0.wts_patch and runs for either a maximum of 2000 cycles or until all moveable phi/psi values have been changed.   - Stage 2: large randomly selected fragment insertions, more score terms turned on. Uses score1.wts_patch and runs for 2000 cycles.   - Stage 3: uses large randomly selected fragment insertions, although the size of the fragment insertions is tunable via the set_apply_large_frags( bool ) method. Alternates between score2.wts_patch and score5.wts_patch, running tunable numbers of 2000-cycle iterations between the two scoring functions.   - Stage 4: uses small (usually 3mer) fragment insertions with the fragment selection based on the Gunn cost for finding local fragment moves. Runs for 4000-cycles and uses score3.wts_patch.   The class implements the basic abinito approach as known from rosetta++. We tried to set this up, such that behaviour of the protocol can be changed in many different ways ( see, e.g., FoldConstraints ). To be able to change the behaviour of the protocol easily the class-apply function and methods called therein (e.g., prepare_XXX() / do_XXX_cycles() ) should not directly change moves or trials. A reference to the currently used score-function should be obtained by mc().score_function() ...   Behaviour can be changed in the following ways:   use non-classic FragmentMover  --> eg. not uniformly sampled fragments, but using some weighting --> large and small moves doesn't have to be 3mers and 9mers... use other movers... ---> or other fragets for the "convenience constructor" use custom trial classes --> overload update_moves()   change sampling behaviour: overload prepare_XXX() methods: these are called before the cycling for a certain stage begins overload do_stageX_cycles() : the actual loops over trial-moves ...   change scoring functions: overload set_default_scores() weight-changes effective for all stages: set_score_weight()     Method resolution order: FragmentSampler rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, broker : protocols::topology_broker::TopologyBroker) -> NoneType   2. __init__(handle, rosetta.protocols.abinitio.FragmentSampler) -> 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.FragmentSampler, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.FragmentSampler,  : rosetta.protocols.abinitio.FragmentSampler) -> rosetta.protocols.abinitio.FragmentSampler bQuickTest(...) from builtins.PyCapsule bQuickTest(rosetta.protocols.abinitio.FragmentSampler) -> bool check_loops(...) from builtins.PyCapsule check_loops(self : rosetta.protocols.abinitio.FragmentSampler, pose : rosetta.core.pose.Pose) -> bool clone(...) from builtins.PyCapsule clone(rosetta.protocols.abinitio.FragmentSampler) -> rosetta.protocols.moves.Mover current_scorefxn(...) from builtins.PyCapsule current_scorefxn(rosetta.protocols.abinitio.FragmentSampler) -> rosetta.core.scoring.ScoreFunction get_checkpoints(...) from builtins.PyCapsule get_checkpoints(rosetta.protocols.abinitio.FragmentSampler) -> rosetta.protocols.checkpoint.CheckPointer get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.FragmentSampler) -> str just_smooth_cycles(...) from builtins.PyCapsule just_smooth_cycles(rosetta.protocols.abinitio.FragmentSampler) -> bool register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType set_cycles(...) from builtins.PyCapsule set_cycles(*args, **kwargs) Overloaded function.   1. set_cycles(rosetta.protocols.abinitio.FragmentSampler) -> NoneType   2. set_cycles(self : rosetta.protocols.abinitio.FragmentSampler, increase_cycles : float) -> NoneType set_score_weight(...) from builtins.PyCapsule set_score_weight(*args, **kwargs) Overloaded function.   1. set_score_weight(self : rosetta.protocols.abinitio.FragmentSampler,  : rosetta.core.scoring.ScoreType, setting : float) -> NoneType   2. set_score_weight(self : rosetta.protocols.abinitio.FragmentSampler,  : rosetta.core.scoring.ScoreType, setting : float, stage : rosetta.protocols.abinitio.StageID) -> NoneType set_stage4_cycles(...) from builtins.PyCapsule set_stage4_cycles(self : rosetta.protocols.abinitio.FragmentSampler, stage4_cycles_new : int) -> NoneType stage1_cycles(...) from builtins.PyCapsule stage1_cycles(rosetta.protocols.abinitio.FragmentSampler) -> int stage2_cycles(...) from builtins.PyCapsule stage2_cycles(rosetta.protocols.abinitio.FragmentSampler) -> int stage3_cycles(...) from builtins.PyCapsule stage3_cycles(rosetta.protocols.abinitio.FragmentSampler) -> int stage4_cycles(...) from builtins.PyCapsule stage4_cycles(rosetta.protocols.abinitio.FragmentSampler) -> int topology_broker(...) from builtins.PyCapsule topology_broker(self : rosetta.protocols.abinitio.FragmentSampler, set : protocols::topology_broker::TopologyBroker) -> 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 fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class HedgeArchive(rosetta.protocols.jd2.archive.EvaluatedArchive)       Method resolution order: HedgeArchive rosetta.protocols.jd2.archive.EvaluatedArchive rosetta.protocols.jd2.archive.ArchiveBase rosetta.protocols.jd2.archive.AbstractArchiveBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, name : str) -> NoneType   2. __init__(handle, rosetta.protocols.abinitio.HedgeArchive) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_evaluated_structure(...) from builtins.PyCapsule add_evaluated_structure(self : rosetta.protocols.abinitio.HedgeArchive,  : rosetta.core.io.silent.SilentStruct, alternative_decoy : rosetta.core.io.silent.SilentStruct, batch : protocols::jd2::archive::Batch) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.HedgeArchive,  : rosetta.protocols.abinitio.HedgeArchive) -> rosetta.protocols.abinitio.HedgeArchive collect(...) from builtins.PyCapsule collect(self : rosetta.protocols.abinitio.HedgeArchive, batch : protocols::jd2::archive::Batch,  : rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType generate_batch(...) from builtins.PyCapsule generate_batch(rosetta.protocols.abinitio.HedgeArchive) -> NoneType init_from_decoy_set(...) from builtins.PyCapsule init_from_decoy_set(self : rosetta.protocols.abinitio.HedgeArchive,  : rosetta.core.io.silent.SilentFileData) -> NoneType   overloaded to make input decoys appear the same as decoys coming from batches rescore(...) from builtins.PyCapsule rescore(rosetta.protocols.abinitio.HedgeArchive) -> NoneType Methods inherited from rosetta.protocols.jd2.archive.EvaluatedArchive: add_evaluation(...) from builtins.PyCapsule add_evaluation(*args, **kwargs) Overloaded function.   1. add_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive,  : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType   add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()   2. add_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive,  : rosetta.protocols.evaluation.PoseEvaluator, weight : float) -> NoneType   add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score() add_structure(...) from builtins.PyCapsule add_structure(self : rosetta.protocols.jd2.archive.EvaluatedArchive, new_decoy : rosetta.core.io.silent.SilentStruct, alternative_decoy : rosetta.core.io.silent.SilentStruct, batch : protocols::jd2::archive::Batch) -> bool   add decoy to Archive      evaluate decoy and call add_evaluated_structure evaluate_local(...) from builtins.PyCapsule evaluate_local(rosetta.protocols.jd2.archive.EvaluatedArchive) -> bool   specify if decoys are evaluated on the master or (non-local i.e., on the individual slave nodes) evaluate_silent_struct(...) from builtins.PyCapsule evaluate_silent_struct(self : rosetta.protocols.jd2.archive.EvaluatedArchive, from_batch : rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct   yields an "evaluated" silent-struct which can be queried with select_score      will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct evaluators(...) from builtins.PyCapsule evaluators(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t get_weight(...) from builtins.PyCapsule get_weight(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> float has_evaluator(...) from builtins.PyCapsule has_evaluator(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> bool   is a certain elvaluator present ? read_structures(...) from builtins.PyCapsule read_structures(self : rosetta.protocols.jd2.archive.EvaluatedArchive, sfd : rosetta.core.io.silent.SilentFileData, alternative_decoys : rosetta.core.io.silent.SilentFileData, batch : protocols::jd2::archive::Batch) -> NoneType   only overloaded this to add some verbosity each time we read structures register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   2. register_options() -> NoneType   Archive specific options   3. register_options() -> NoneType   Archive specific options   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType remove_evaluation(...) from builtins.PyCapsule remove_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> NoneType   remove Evaluator restore_from_file(...) from builtins.PyCapsule restore_from_file(rosetta.protocols.jd2.archive.EvaluatedArchive) -> bool   overloaded that we can sort the pool after reading save_to_file(...) from builtins.PyCapsule save_to_file(*args, **kwargs) Overloaded function.   1. save_to_file(rosetta.protocols.jd2.archive.EvaluatedArchive) -> NoneType   overloaded to save / restore the variance_archive_   2. save_to_file(self : rosetta.protocols.jd2.archive.EvaluatedArchive, suffix : str) -> NoneType   overloaded to save / restore the variance_archive_ score_variation(...) from builtins.PyCapsule score_variation(self : rosetta.protocols.jd2.archive.EvaluatedArchive, col : str) -> float score_variations(...) from builtins.PyCapsule score_variations(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.std.map_std_string_double scorefxn(...) from builtins.PyCapsule scorefxn(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.core.scoring.ScoreFunction select_score(...) from builtins.PyCapsule select_score(self : rosetta.protocols.jd2.archive.EvaluatedArchive, evaluated_decoy : rosetta.core.io.silent.SilentStruct) -> float   compute score according to select_weights --- this can contain any evaluator columns set_evaluate_local(...) from builtins.PyCapsule set_evaluate_local(self : rosetta.protocols.jd2.archive.EvaluatedArchive, setting : bool) -> NoneType set_evaluators(...) from builtins.PyCapsule set_evaluators(self : rosetta.protocols.jd2.archive.EvaluatedArchive,  : rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t,  : rosetta.std.map_std_string_double) -> NoneType set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.jd2.archive.EvaluatedArchive, scorefxn_ : rosetta.core.scoring.ScoreFunction) -> NoneType   set scorefxn used for evaluation set_weight(...) from builtins.PyCapsule set_weight(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str, weight : float) -> NoneType   set weight of an evaluator or a column otherwise present in silent-structs  (i.e, score, chainbreak, external evaluation like score_final ) set_weights(...) from builtins.PyCapsule set_weights(self : rosetta.protocols.jd2.archive.EvaluatedArchive, setting : rosetta.std.map_std_string_double) -> NoneType setup_default_evaluators(...) from builtins.PyCapsule setup_default_evaluators(rosetta.protocols.jd2.archive.EvaluatedArchive) -> NoneType   set common evaluators: eg. ConstraintEvaluator if -cst_file is present start_evaluation_timer(...) from builtins.PyCapsule start_evaluation_timer(rosetta.protocols.jd2.archive.EvaluatedArchive) -> NoneType weights(...) from builtins.PyCapsule weights(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.std.map_std_string_double Methods inherited from rosetta.protocols.jd2.archive.ArchiveBase: accepts_since_last_batch(...) from builtins.PyCapsule accepts_since_last_batch(*args, **kwargs) Overloaded function.   1. accepts_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int   ---- methods to keep statistics of acceptance   2. accepts_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int current_acceptance_ratio(...) from builtins.PyCapsule current_acceptance_ratio(rosetta.protocols.jd2.archive.ArchiveBase) -> float decoys(...) from builtins.PyCapsule decoys(*args, **kwargs) Overloaded function.   1. decoys(rosetta.protocols.jd2.archive.ArchiveBase) -> rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t   2. decoys(rosetta.protocols.jd2.archive.ArchiveBase) -> rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t finished(...) from builtins.PyCapsule finished(rosetta.protocols.jd2.archive.ArchiveBase) -> bool idle(...) from builtins.PyCapsule idle(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType   called when nothing is happening initialize(...) from builtins.PyCapsule initialize(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType load_decoys(...) from builtins.PyCapsule load_decoys(self : rosetta.protocols.jd2.archive.ArchiveBase, filename : str, decoys : rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType nstruct(...) from builtins.PyCapsule nstruct(rosetta.protocols.jd2.archive.ArchiveBase) -> int   how many structures should be in archive .. varies from decoys().size() in startup phase. proposed_since_last_batch(...) from builtins.PyCapsule proposed_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int reset_accept_counter(...) from builtins.PyCapsule reset_accept_counter(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType save_decoys(...) from builtins.PyCapsule save_decoys(self : rosetta.protocols.jd2.archive.ArchiveBase, dirname : str, name : str, decoys : rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType   helper routine to save decoys properly set_nstruct(...) from builtins.PyCapsule set_nstruct(self : rosetta.protocols.jd2.archive.ArchiveBase, set : int) -> NoneType   set target size of pool statistics_valid(...) from builtins.PyCapsule statistics_valid(rosetta.protocols.jd2.archive.ArchiveBase) -> bool total_accepts(...) from builtins.PyCapsule total_accepts(rosetta.protocols.jd2.archive.ArchiveBase) -> int total_proposed(...) from builtins.PyCapsule total_proposed(rosetta.protocols.jd2.archive.ArchiveBase) -> int Methods inherited from rosetta.protocols.jd2.archive.AbstractArchiveBase: manager(...) from builtins.PyCapsule manager(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> protocols::jd2::archive::BaseArchiveManager   access to the ArchiveManager (control of batches) name(...) from builtins.PyCapsule name(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> str set_manager(...) from builtins.PyCapsule set_manager(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, manager : protocols::jd2::archive::BaseArchiveManager) -> NoneType set_name(...) from builtins.PyCapsule set_name(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, set : str) -> NoneType   set name of archive ( used also for save_to_file and restore_from_file ) still_interested(...) from builtins.PyCapsule still_interested(self : rosetta.protocols.jd2.archive.AbstractArchiveBase,  : protocols::jd2::archive::Batch) -> bool   old-batches might be outdated and should not be computed anymore  return true for this query if this is the case for old_batch   class IterativeAbrelax(IterativeBase)       Method resolution order: IterativeAbrelax IterativeBase rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive rosetta.protocols.jd2.archive.EvaluatedArchive rosetta.protocols.jd2.archive.ArchiveBase rosetta.protocols.jd2.archive.AbstractArchiveBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.abinitio.IterativeAbrelax) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. finished(...) from builtins.PyCapsule finished(rosetta.protocols.abinitio.IterativeAbrelax) -> bool generate_batch(...) from builtins.PyCapsule generate_batch(*args, **kwargs) Overloaded function.   1. generate_batch(rosetta.protocols.abinitio.IterativeAbrelax) -> NoneType   2. generate_batch(self : rosetta.protocols.abinitio.IterativeAbrelax,  : protocols::jd2::archive::Batch, repeat_id : int) -> int idle(...) from builtins.PyCapsule idle(rosetta.protocols.abinitio.IterativeAbrelax) -> NoneType init_from_decoy_set(...) from builtins.PyCapsule init_from_decoy_set(self : rosetta.protocols.abinitio.IterativeAbrelax,  : rosetta.core.io.silent.SilentFileData) -> NoneType initialize(...) from builtins.PyCapsule initialize(rosetta.protocols.abinitio.IterativeAbrelax) -> NoneType read_structures(...) from builtins.PyCapsule read_structures(self : rosetta.protocols.abinitio.IterativeAbrelax, sfd : rosetta.core.io.silent.SilentFileData, alternative_decoys : rosetta.core.io.silent.SilentFileData, batch : protocols::jd2::archive::Batch) -> NoneType register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   2. register_options() -> NoneType   Archive specific options   3. register_options() -> NoneType   Archive specific options   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType restore_from_file(...) from builtins.PyCapsule restore_from_file(rosetta.protocols.abinitio.IterativeAbrelax) -> bool save_to_file(...) from builtins.PyCapsule save_to_file(*args, **kwargs) Overloaded function.   1. save_to_file(rosetta.protocols.abinitio.IterativeAbrelax) -> NoneType   2. save_to_file(self : rosetta.protocols.abinitio.IterativeAbrelax, suffix : str) -> NoneType set_manager(...) from builtins.PyCapsule set_manager(self : rosetta.protocols.abinitio.IterativeAbrelax, manager : protocols::jd2::archive::BaseArchiveManager) -> NoneType still_interested(...) from builtins.PyCapsule still_interested(self : rosetta.protocols.abinitio.IterativeAbrelax, batch : protocols::jd2::archive::Batch) -> bool Methods inherited from IterativeBase: add_structure(...) from builtins.PyCapsule add_structure(self : rosetta.protocols.abinitio.IterativeBase, new_decoy : rosetta.core.io.silent.SilentStruct, alternative_decoy : rosetta.core.io.silent.SilentStruct,  : protocols::jd2::archive::Batch) -> bool   overloaded to handel special convergence check 'pool_converged_rmsd'      add structure to Archive.. return false if structure is rejected. gen_diversity_pool(...) from builtins.PyCapsule gen_diversity_pool(*args, **kwargs) Overloaded function.   1. gen_diversity_pool(self : rosetta.protocols.abinitio.IterativeBase,  : protocols::jd2::archive::Batch) -> NoneType   2. gen_diversity_pool(self : rosetta.protocols.abinitio.IterativeBase,  : protocols::jd2::archive::Batch, fullatom : bool) -> NoneType gen_dynamic_patches(...) from builtins.PyCapsule gen_dynamic_patches(self : rosetta.protocols.abinitio.IterativeBase, batch : protocols::jd2::archive::Batch) -> NoneType gen_evaluation_output(...) from builtins.PyCapsule gen_evaluation_output(*args, **kwargs) Overloaded function.   1. gen_evaluation_output(self : rosetta.protocols.abinitio.IterativeBase, batch : protocols::jd2::archive::Batch) -> NoneType   generate flags and stuff for the out-sourced evaluation ---> such that score_final column is returned for each decoy  note needs to be public, since IterativeCentroid calls this from IterativeFullatom to prepare evaluation for soon to be full-atom decoys   2. gen_evaluation_output(self : rosetta.protocols.abinitio.IterativeBase, batch : protocols::jd2::archive::Batch, fullatom : bool) -> NoneType   generate flags and stuff for the out-sourced evaluation ---> such that score_final column is returned for each decoy  note needs to be public, since IterativeCentroid calls this from IterativeFullatom to prepare evaluation for soon to be full-atom decoys ready_for_batch(...) from builtins.PyCapsule ready_for_batch(rosetta.protocols.abinitio.IterativeBase) -> bool   we are always ready to generate a new batch rescore(...) from builtins.PyCapsule rescore(rosetta.protocols.abinitio.IterativeBase) -> NoneType set_finish_stage(...) from builtins.PyCapsule set_finish_stage(self : rosetta.protocols.abinitio.IterativeBase, setting : rosetta.protocols.abinitio.IterationStage) -> NoneType   where to stop ? setup_default_evaluators(...) from builtins.PyCapsule setup_default_evaluators(rosetta.protocols.abinitio.IterativeBase) -> NoneType   setup JumpNrEvaluator test_for_stage_end(...) from builtins.PyCapsule test_for_stage_end(rosetta.protocols.abinitio.IterativeBase) -> NoneType   calls increment_stage() if appropriate update_noesy_filter_files(...) from builtins.PyCapsule update_noesy_filter_files(self : rosetta.protocols.abinitio.IterativeBase, current : str, fullatom : bool) -> NoneType Data and other attributes inherited from IterativeBase: CEN2FULLATOM = IterationStage.LAST_CENTROID_START ENUMERATION = IterationStage.ENUMERATION FINISHED = IterationStage.FINISHED IterationStage = <class 'rosetta.protocols.abinitio.IterativeBase.IterationStage'> LAST_CENTROID_START = IterationStage.LAST_CENTROID_START NOESY_PHASEII_S2_RESAMPLING = IterationStage.NOESY_PHASEII_S2_RESAMPLING NOESY_PHASEII_TOPO = IterationStage.NOESY_PHASEII_TOPO PURE_TOPO_RESAMPLING = IterationStage.PURE_TOPO_RESAMPLING RIGID_CORE_RESAMPLING = IterationStage.RIGID_CORE_RESAMPLING STAGE2_RESAMPLING = IterationStage.STAGE2_RESAMPLING TOPO_RESAMPLING = IterationStage.TOPO_RESAMPLING Methods inherited from rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive: add_evaluated_structure(...) from builtins.PyCapsule add_evaluated_structure(self : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, from_batch : rosetta.core.io.silent.SilentStruct, alternative_decoy : rosetta.core.io.silent.SilentStruct,  : protocols::jd2::archive::Batch) -> bool   add decoy to Archive      evaluate decoy and call add_evaluated_structure assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive,  : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive determine_score_variations(...) from builtins.PyCapsule determine_score_variations(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> bool   determine variation of scores (those that are non-zeros in select_weights_ ) init_from_options(...) from builtins.PyCapsule init_from_options(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> NoneType score_variation(...) from builtins.PyCapsule score_variation(self : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, col : str) -> float score_variations(...) from builtins.PyCapsule score_variations(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> rosetta.std.map_std_string_double Methods inherited from rosetta.protocols.jd2.archive.EvaluatedArchive: add_evaluation(...) from builtins.PyCapsule add_evaluation(*args, **kwargs) Overloaded function.   1. add_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive,  : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType   add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()   2. add_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive,  : rosetta.protocols.evaluation.PoseEvaluator, weight : float) -> NoneType   add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score() evaluate_local(...) from builtins.PyCapsule evaluate_local(rosetta.protocols.jd2.archive.EvaluatedArchive) -> bool   specify if decoys are evaluated on the master or (non-local i.e., on the individual slave nodes) evaluate_silent_struct(...) from builtins.PyCapsule evaluate_silent_struct(self : rosetta.protocols.jd2.archive.EvaluatedArchive, from_batch : rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct   yields an "evaluated" silent-struct which can be queried with select_score      will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct evaluators(...) from builtins.PyCapsule evaluators(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t get_weight(...) from builtins.PyCapsule get_weight(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> float has_evaluator(...) from builtins.PyCapsule has_evaluator(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> bool   is a certain elvaluator present ? remove_evaluation(...) from builtins.PyCapsule remove_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> NoneType   remove Evaluator scorefxn(...) from builtins.PyCapsule scorefxn(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.core.scoring.ScoreFunction select_score(...) from builtins.PyCapsule select_score(self : rosetta.protocols.jd2.archive.EvaluatedArchive, evaluated_decoy : rosetta.core.io.silent.SilentStruct) -> float   compute score according to select_weights --- this can contain any evaluator columns set_evaluate_local(...) from builtins.PyCapsule set_evaluate_local(self : rosetta.protocols.jd2.archive.EvaluatedArchive, setting : bool) -> NoneType set_evaluators(...) from builtins.PyCapsule set_evaluators(self : rosetta.protocols.jd2.archive.EvaluatedArchive,  : rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t,  : rosetta.std.map_std_string_double) -> NoneType set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.jd2.archive.EvaluatedArchive, scorefxn_ : rosetta.core.scoring.ScoreFunction) -> NoneType   set scorefxn used for evaluation set_weight(...) from builtins.PyCapsule set_weight(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str, weight : float) -> NoneType   set weight of an evaluator or a column otherwise present in silent-structs  (i.e, score, chainbreak, external evaluation like score_final ) set_weights(...) from builtins.PyCapsule set_weights(self : rosetta.protocols.jd2.archive.EvaluatedArchive, setting : rosetta.std.map_std_string_double) -> NoneType start_evaluation_timer(...) from builtins.PyCapsule start_evaluation_timer(rosetta.protocols.jd2.archive.EvaluatedArchive) -> NoneType weights(...) from builtins.PyCapsule weights(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.std.map_std_string_double Methods inherited from rosetta.protocols.jd2.archive.ArchiveBase: accepts_since_last_batch(...) from builtins.PyCapsule accepts_since_last_batch(*args, **kwargs) Overloaded function.   1. accepts_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int   ---- methods to keep statistics of acceptance   2. accepts_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int current_acceptance_ratio(...) from builtins.PyCapsule current_acceptance_ratio(rosetta.protocols.jd2.archive.ArchiveBase) -> float decoys(...) from builtins.PyCapsule decoys(*args, **kwargs) Overloaded function.   1. decoys(rosetta.protocols.jd2.archive.ArchiveBase) -> rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t   2. decoys(rosetta.protocols.jd2.archive.ArchiveBase) -> rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t load_decoys(...) from builtins.PyCapsule load_decoys(self : rosetta.protocols.jd2.archive.ArchiveBase, filename : str, decoys : rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType nstruct(...) from builtins.PyCapsule nstruct(rosetta.protocols.jd2.archive.ArchiveBase) -> int   how many structures should be in archive .. varies from decoys().size() in startup phase. proposed_since_last_batch(...) from builtins.PyCapsule proposed_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int reset_accept_counter(...) from builtins.PyCapsule reset_accept_counter(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType save_decoys(...) from builtins.PyCapsule save_decoys(self : rosetta.protocols.jd2.archive.ArchiveBase, dirname : str, name : str, decoys : rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType   helper routine to save decoys properly set_nstruct(...) from builtins.PyCapsule set_nstruct(self : rosetta.protocols.jd2.archive.ArchiveBase, set : int) -> NoneType   set target size of pool statistics_valid(...) from builtins.PyCapsule statistics_valid(rosetta.protocols.jd2.archive.ArchiveBase) -> bool total_accepts(...) from builtins.PyCapsule total_accepts(rosetta.protocols.jd2.archive.ArchiveBase) -> int total_proposed(...) from builtins.PyCapsule total_proposed(rosetta.protocols.jd2.archive.ArchiveBase) -> int Methods inherited from rosetta.protocols.jd2.archive.AbstractArchiveBase: manager(...) from builtins.PyCapsule manager(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> protocols::jd2::archive::BaseArchiveManager   access to the ArchiveManager (control of batches) name(...) from builtins.PyCapsule name(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> str set_name(...) from builtins.PyCapsule set_name(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, set : str) -> NoneType   set name of archive ( used also for save_to_file and restore_from_file )   class IterativeBase(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive)       Method resolution order: IterativeBase rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive rosetta.protocols.jd2.archive.EvaluatedArchive rosetta.protocols.jd2.archive.ArchiveBase rosetta.protocols.jd2.archive.AbstractArchiveBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, name : str) -> NoneType   2. __init__(handle, rosetta.protocols.abinitio.IterativeBase) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_structure(...) from builtins.PyCapsule add_structure(self : rosetta.protocols.abinitio.IterativeBase, new_decoy : rosetta.core.io.silent.SilentStruct, alternative_decoy : rosetta.core.io.silent.SilentStruct,  : protocols::jd2::archive::Batch) -> bool   overloaded to handel special convergence check 'pool_converged_rmsd'      add structure to Archive.. return false if structure is rejected. finished(...) from builtins.PyCapsule finished(rosetta.protocols.abinitio.IterativeBase) -> bool   archive is finished when at last stage gen_diversity_pool(...) from builtins.PyCapsule gen_diversity_pool(*args, **kwargs) Overloaded function.   1. gen_diversity_pool(self : rosetta.protocols.abinitio.IterativeBase,  : protocols::jd2::archive::Batch) -> NoneType   2. gen_diversity_pool(self : rosetta.protocols.abinitio.IterativeBase,  : protocols::jd2::archive::Batch, fullatom : bool) -> NoneType gen_dynamic_patches(...) from builtins.PyCapsule gen_dynamic_patches(self : rosetta.protocols.abinitio.IterativeBase, batch : protocols::jd2::archive::Batch) -> NoneType gen_evaluation_output(...) from builtins.PyCapsule gen_evaluation_output(*args, **kwargs) Overloaded function.   1. gen_evaluation_output(self : rosetta.protocols.abinitio.IterativeBase, batch : protocols::jd2::archive::Batch) -> NoneType   generate flags and stuff for the out-sourced evaluation ---> such that score_final column is returned for each decoy  note needs to be public, since IterativeCentroid calls this from IterativeFullatom to prepare evaluation for soon to be full-atom decoys   2. gen_evaluation_output(self : rosetta.protocols.abinitio.IterativeBase, batch : protocols::jd2::archive::Batch, fullatom : bool) -> NoneType   generate flags and stuff for the out-sourced evaluation ---> such that score_final column is returned for each decoy  note needs to be public, since IterativeCentroid calls this from IterativeFullatom to prepare evaluation for soon to be full-atom decoys generate_batch(...) from builtins.PyCapsule generate_batch(*args, **kwargs) Overloaded function.   1. generate_batch(rosetta.protocols.abinitio.IterativeBase) -> NoneType   generate a new batch, use different recipe according to current stage   2. generate_batch(self : rosetta.protocols.abinitio.IterativeBase,  : protocols::jd2::archive::Batch, repeat_id : int) -> int idle(...) from builtins.PyCapsule idle(rosetta.protocols.abinitio.IterativeBase) -> NoneType   while waiting for jobs to finish init_from_decoy_set(...) from builtins.PyCapsule init_from_decoy_set(self : rosetta.protocols.abinitio.IterativeBase, sfd : rosetta.core.io.silent.SilentFileData) -> NoneType   overloaded to make input decoys appear the same as decoys coming from batches initialize(...) from builtins.PyCapsule initialize(rosetta.protocols.abinitio.IterativeBase) -> NoneType   do initializing work that requires fully setup object here read_structures(...) from builtins.PyCapsule read_structures(self : rosetta.protocols.abinitio.IterativeBase, sfd : rosetta.core.io.silent.SilentFileData, alternative_decoys : rosetta.core.io.silent.SilentFileData, batch : protocols::jd2::archive::Batch) -> NoneType   overloaded so we can test for end of IterationStage after reading ready_for_batch(...) from builtins.PyCapsule ready_for_batch(rosetta.protocols.abinitio.IterativeBase) -> bool   we are always ready to generate a new batch register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   2. register_options() -> NoneType   Archive specific options   3. register_options() -> NoneType   Archive specific options   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType rescore(...) from builtins.PyCapsule rescore(rosetta.protocols.abinitio.IterativeBase) -> NoneType set_finish_stage(...) from builtins.PyCapsule set_finish_stage(self : rosetta.protocols.abinitio.IterativeBase, setting : rosetta.protocols.abinitio.IterationStage) -> NoneType   where to stop ? setup_default_evaluators(...) from builtins.PyCapsule setup_default_evaluators(rosetta.protocols.abinitio.IterativeBase) -> NoneType   setup JumpNrEvaluator still_interested(...) from builtins.PyCapsule still_interested(self : rosetta.protocols.abinitio.IterativeBase, batch : protocols::jd2::archive::Batch) -> bool   we are not interested in batches that were generated in old stages test_for_stage_end(...) from builtins.PyCapsule test_for_stage_end(rosetta.protocols.abinitio.IterativeBase) -> NoneType   calls increment_stage() if appropriate update_noesy_filter_files(...) from builtins.PyCapsule update_noesy_filter_files(self : rosetta.protocols.abinitio.IterativeBase, current : str, fullatom : bool) -> NoneType Data and other attributes defined here: CEN2FULLATOM = IterationStage.LAST_CENTROID_START ENUMERATION = IterationStage.ENUMERATION FINISHED = IterationStage.FINISHED IterationStage = <class 'rosetta.protocols.abinitio.IterativeBase.IterationStage'> LAST_CENTROID_START = IterationStage.LAST_CENTROID_START NOESY_PHASEII_S2_RESAMPLING = IterationStage.NOESY_PHASEII_S2_RESAMPLING NOESY_PHASEII_TOPO = IterationStage.NOESY_PHASEII_TOPO PURE_TOPO_RESAMPLING = IterationStage.PURE_TOPO_RESAMPLING RIGID_CORE_RESAMPLING = IterationStage.RIGID_CORE_RESAMPLING STAGE2_RESAMPLING = IterationStage.STAGE2_RESAMPLING TOPO_RESAMPLING = IterationStage.TOPO_RESAMPLING Methods inherited from rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive: add_evaluated_structure(...) from builtins.PyCapsule add_evaluated_structure(self : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, from_batch : rosetta.core.io.silent.SilentStruct, alternative_decoy : rosetta.core.io.silent.SilentStruct,  : protocols::jd2::archive::Batch) -> bool   add decoy to Archive      evaluate decoy and call add_evaluated_structure assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive,  : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive determine_score_variations(...) from builtins.PyCapsule determine_score_variations(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> bool   determine variation of scores (those that are non-zeros in select_weights_ ) init_from_options(...) from builtins.PyCapsule init_from_options(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> NoneType restore_from_file(...) from builtins.PyCapsule restore_from_file(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> bool   overloaded that we can sort the pool after reading save_to_file(...) from builtins.PyCapsule save_to_file(*args, **kwargs) Overloaded function.   1. save_to_file(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> NoneType   overloaded to save / restore the variance_archive_   2. save_to_file(self : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, suffix : str) -> NoneType   overloaded to save / restore the variance_archive_ score_variation(...) from builtins.PyCapsule score_variation(self : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, col : str) -> float score_variations(...) from builtins.PyCapsule score_variations(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> rosetta.std.map_std_string_double Methods inherited from rosetta.protocols.jd2.archive.EvaluatedArchive: add_evaluation(...) from builtins.PyCapsule add_evaluation(*args, **kwargs) Overloaded function.   1. add_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive,  : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType   add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()   2. add_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive,  : rosetta.protocols.evaluation.PoseEvaluator, weight : float) -> NoneType   add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score() evaluate_local(...) from builtins.PyCapsule evaluate_local(rosetta.protocols.jd2.archive.EvaluatedArchive) -> bool   specify if decoys are evaluated on the master or (non-local i.e., on the individual slave nodes) evaluate_silent_struct(...) from builtins.PyCapsule evaluate_silent_struct(self : rosetta.protocols.jd2.archive.EvaluatedArchive, from_batch : rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct   yields an "evaluated" silent-struct which can be queried with select_score      will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct evaluators(...) from builtins.PyCapsule evaluators(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t get_weight(...) from builtins.PyCapsule get_weight(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> float has_evaluator(...) from builtins.PyCapsule has_evaluator(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> bool   is a certain elvaluator present ? remove_evaluation(...) from builtins.PyCapsule remove_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> NoneType   remove Evaluator scorefxn(...) from builtins.PyCapsule scorefxn(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.core.scoring.ScoreFunction select_score(...) from builtins.PyCapsule select_score(self : rosetta.protocols.jd2.archive.EvaluatedArchive, evaluated_decoy : rosetta.core.io.silent.SilentStruct) -> float   compute score according to select_weights --- this can contain any evaluator columns set_evaluate_local(...) from builtins.PyCapsule set_evaluate_local(self : rosetta.protocols.jd2.archive.EvaluatedArchive, setting : bool) -> NoneType set_evaluators(...) from builtins.PyCapsule set_evaluators(self : rosetta.protocols.jd2.archive.EvaluatedArchive,  : rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t,  : rosetta.std.map_std_string_double) -> NoneType set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.jd2.archive.EvaluatedArchive, scorefxn_ : rosetta.core.scoring.ScoreFunction) -> NoneType   set scorefxn used for evaluation set_weight(...) from builtins.PyCapsule set_weight(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str, weight : float) -> NoneType   set weight of an evaluator or a column otherwise present in silent-structs  (i.e, score, chainbreak, external evaluation like score_final ) set_weights(...) from builtins.PyCapsule set_weights(self : rosetta.protocols.jd2.archive.EvaluatedArchive, setting : rosetta.std.map_std_string_double) -> NoneType start_evaluation_timer(...) from builtins.PyCapsule start_evaluation_timer(rosetta.protocols.jd2.archive.EvaluatedArchive) -> NoneType weights(...) from builtins.PyCapsule weights(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.std.map_std_string_double Methods inherited from rosetta.protocols.jd2.archive.ArchiveBase: accepts_since_last_batch(...) from builtins.PyCapsule accepts_since_last_batch(*args, **kwargs) Overloaded function.   1. accepts_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int   ---- methods to keep statistics of acceptance   2. accepts_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int current_acceptance_ratio(...) from builtins.PyCapsule current_acceptance_ratio(rosetta.protocols.jd2.archive.ArchiveBase) -> float decoys(...) from builtins.PyCapsule decoys(*args, **kwargs) Overloaded function.   1. decoys(rosetta.protocols.jd2.archive.ArchiveBase) -> rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t   2. decoys(rosetta.protocols.jd2.archive.ArchiveBase) -> rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t load_decoys(...) from builtins.PyCapsule load_decoys(self : rosetta.protocols.jd2.archive.ArchiveBase, filename : str, decoys : rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType nstruct(...) from builtins.PyCapsule nstruct(rosetta.protocols.jd2.archive.ArchiveBase) -> int   how many structures should be in archive .. varies from decoys().size() in startup phase. proposed_since_last_batch(...) from builtins.PyCapsule proposed_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int reset_accept_counter(...) from builtins.PyCapsule reset_accept_counter(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType save_decoys(...) from builtins.PyCapsule save_decoys(self : rosetta.protocols.jd2.archive.ArchiveBase, dirname : str, name : str, decoys : rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType   helper routine to save decoys properly set_nstruct(...) from builtins.PyCapsule set_nstruct(self : rosetta.protocols.jd2.archive.ArchiveBase, set : int) -> NoneType   set target size of pool statistics_valid(...) from builtins.PyCapsule statistics_valid(rosetta.protocols.jd2.archive.ArchiveBase) -> bool total_accepts(...) from builtins.PyCapsule total_accepts(rosetta.protocols.jd2.archive.ArchiveBase) -> int total_proposed(...) from builtins.PyCapsule total_proposed(rosetta.protocols.jd2.archive.ArchiveBase) -> int Methods inherited from rosetta.protocols.jd2.archive.AbstractArchiveBase: manager(...) from builtins.PyCapsule manager(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> protocols::jd2::archive::BaseArchiveManager   access to the ArchiveManager (control of batches) name(...) from builtins.PyCapsule name(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> str set_manager(...) from builtins.PyCapsule set_manager(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, manager : protocols::jd2::archive::BaseArchiveManager) -> NoneType set_name(...) from builtins.PyCapsule set_name(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, set : str) -> NoneType   set name of archive ( used also for save_to_file and restore_from_file )   class IterativeCentroid(IterativeBase)       Method resolution order: IterativeCentroid IterativeBase rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive rosetta.protocols.jd2.archive.EvaluatedArchive rosetta.protocols.jd2.archive.ArchiveBase rosetta.protocols.jd2.archive.AbstractArchiveBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, fullatom_pool_ptr : rosetta.protocols.abinitio.IterativeFullatom) -> NoneType   2. __init__(handle, rosetta.protocols.abinitio.IterativeCentroid) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. gen_diversity_pool(...) from builtins.PyCapsule gen_diversity_pool(*args, **kwargs) Overloaded function.   1. gen_diversity_pool(self : rosetta.protocols.abinitio.IterativeCentroid, batch : protocols::jd2::archive::Batch) -> NoneType   2. gen_diversity_pool(self : rosetta.protocols.abinitio.IterativeCentroid, batch : protocols::jd2::archive::Batch, fullatom : bool) -> NoneType restore_from_file(...) from builtins.PyCapsule restore_from_file(rosetta.protocols.abinitio.IterativeCentroid) -> bool save_to_file(...) from builtins.PyCapsule save_to_file(*args, **kwargs) Overloaded function.   1. save_to_file(rosetta.protocols.abinitio.IterativeCentroid) -> NoneType   save and restore archive to file-system   2. save_to_file(self : rosetta.protocols.abinitio.IterativeCentroid, suffix : str) -> NoneType   save and restore archive to file-system update_noesy_filter_files(...) from builtins.PyCapsule update_noesy_filter_files(self : rosetta.protocols.abinitio.IterativeCentroid, current : str, fullatom : bool) -> NoneType Methods inherited from IterativeBase: add_structure(...) from builtins.PyCapsule add_structure(self : rosetta.protocols.abinitio.IterativeBase, new_decoy : rosetta.core.io.silent.SilentStruct, alternative_decoy : rosetta.core.io.silent.SilentStruct,  : protocols::jd2::archive::Batch) -> bool   overloaded to handel special convergence check 'pool_converged_rmsd'      add structure to Archive.. return false if structure is rejected. finished(...) from builtins.PyCapsule finished(rosetta.protocols.abinitio.IterativeBase) -> bool   archive is finished when at last stage gen_dynamic_patches(...) from builtins.PyCapsule gen_dynamic_patches(self : rosetta.protocols.abinitio.IterativeBase, batch : protocols::jd2::archive::Batch) -> NoneType gen_evaluation_output(...) from builtins.PyCapsule gen_evaluation_output(*args, **kwargs) Overloaded function.   1. gen_evaluation_output(self : rosetta.protocols.abinitio.IterativeBase, batch : protocols::jd2::archive::Batch) -> NoneType   generate flags and stuff for the out-sourced evaluation ---> such that score_final column is returned for each decoy  note needs to be public, since IterativeCentroid calls this from IterativeFullatom to prepare evaluation for soon to be full-atom decoys   2. gen_evaluation_output(self : rosetta.protocols.abinitio.IterativeBase, batch : protocols::jd2::archive::Batch, fullatom : bool) -> NoneType   generate flags and stuff for the out-sourced evaluation ---> such that score_final column is returned for each decoy  note needs to be public, since IterativeCentroid calls this from IterativeFullatom to prepare evaluation for soon to be full-atom decoys generate_batch(...) from builtins.PyCapsule generate_batch(*args, **kwargs) Overloaded function.   1. generate_batch(rosetta.protocols.abinitio.IterativeBase) -> NoneType   generate a new batch, use different recipe according to current stage   2. generate_batch(self : rosetta.protocols.abinitio.IterativeBase,  : protocols::jd2::archive::Batch, repeat_id : int) -> int idle(...) from builtins.PyCapsule idle(rosetta.protocols.abinitio.IterativeBase) -> NoneType   while waiting for jobs to finish init_from_decoy_set(...) from builtins.PyCapsule init_from_decoy_set(self : rosetta.protocols.abinitio.IterativeBase, sfd : rosetta.core.io.silent.SilentFileData) -> NoneType   overloaded to make input decoys appear the same as decoys coming from batches initialize(...) from builtins.PyCapsule initialize(rosetta.protocols.abinitio.IterativeBase) -> NoneType   do initializing work that requires fully setup object here read_structures(...) from builtins.PyCapsule read_structures(self : rosetta.protocols.abinitio.IterativeBase, sfd : rosetta.core.io.silent.SilentFileData, alternative_decoys : rosetta.core.io.silent.SilentFileData, batch : protocols::jd2::archive::Batch) -> NoneType   overloaded so we can test for end of IterationStage after reading ready_for_batch(...) from builtins.PyCapsule ready_for_batch(rosetta.protocols.abinitio.IterativeBase) -> bool   we are always ready to generate a new batch register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   2. register_options() -> NoneType   Archive specific options   3. register_options() -> NoneType   Archive specific options   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType rescore(...) from builtins.PyCapsule rescore(rosetta.protocols.abinitio.IterativeBase) -> NoneType set_finish_stage(...) from builtins.PyCapsule set_finish_stage(self : rosetta.protocols.abinitio.IterativeBase, setting : rosetta.protocols.abinitio.IterationStage) -> NoneType   where to stop ? setup_default_evaluators(...) from builtins.PyCapsule setup_default_evaluators(rosetta.protocols.abinitio.IterativeBase) -> NoneType   setup JumpNrEvaluator still_interested(...) from builtins.PyCapsule still_interested(self : rosetta.protocols.abinitio.IterativeBase, batch : protocols::jd2::archive::Batch) -> bool   we are not interested in batches that were generated in old stages test_for_stage_end(...) from builtins.PyCapsule test_for_stage_end(rosetta.protocols.abinitio.IterativeBase) -> NoneType   calls increment_stage() if appropriate Data and other attributes inherited from IterativeBase: CEN2FULLATOM = IterationStage.LAST_CENTROID_START ENUMERATION = IterationStage.ENUMERATION FINISHED = IterationStage.FINISHED IterationStage = <class 'rosetta.protocols.abinitio.IterativeBase.IterationStage'> LAST_CENTROID_START = IterationStage.LAST_CENTROID_START NOESY_PHASEII_S2_RESAMPLING = IterationStage.NOESY_PHASEII_S2_RESAMPLING NOESY_PHASEII_TOPO = IterationStage.NOESY_PHASEII_TOPO PURE_TOPO_RESAMPLING = IterationStage.PURE_TOPO_RESAMPLING RIGID_CORE_RESAMPLING = IterationStage.RIGID_CORE_RESAMPLING STAGE2_RESAMPLING = IterationStage.STAGE2_RESAMPLING TOPO_RESAMPLING = IterationStage.TOPO_RESAMPLING Methods inherited from rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive: add_evaluated_structure(...) from builtins.PyCapsule add_evaluated_structure(self : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, from_batch : rosetta.core.io.silent.SilentStruct, alternative_decoy : rosetta.core.io.silent.SilentStruct,  : protocols::jd2::archive::Batch) -> bool   add decoy to Archive      evaluate decoy and call add_evaluated_structure assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive,  : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive determine_score_variations(...) from builtins.PyCapsule determine_score_variations(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> bool   determine variation of scores (those that are non-zeros in select_weights_ ) init_from_options(...) from builtins.PyCapsule init_from_options(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> NoneType score_variation(...) from builtins.PyCapsule score_variation(self : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, col : str) -> float score_variations(...) from builtins.PyCapsule score_variations(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> rosetta.std.map_std_string_double Methods inherited from rosetta.protocols.jd2.archive.EvaluatedArchive: add_evaluation(...) from builtins.PyCapsule add_evaluation(*args, **kwargs) Overloaded function.   1. add_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive,  : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType   add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()   2. add_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive,  : rosetta.protocols.evaluation.PoseEvaluator, weight : float) -> NoneType   add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score() evaluate_local(...) from builtins.PyCapsule evaluate_local(rosetta.protocols.jd2.archive.EvaluatedArchive) -> bool   specify if decoys are evaluated on the master or (non-local i.e., on the individual slave nodes) evaluate_silent_struct(...) from builtins.PyCapsule evaluate_silent_struct(self : rosetta.protocols.jd2.archive.EvaluatedArchive, from_batch : rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct   yields an "evaluated" silent-struct which can be queried with select_score      will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct evaluators(...) from builtins.PyCapsule evaluators(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t get_weight(...) from builtins.PyCapsule get_weight(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> float has_evaluator(...) from builtins.PyCapsule has_evaluator(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> bool   is a certain elvaluator present ? remove_evaluation(...) from builtins.PyCapsule remove_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> NoneType   remove Evaluator scorefxn(...) from builtins.PyCapsule scorefxn(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.core.scoring.ScoreFunction select_score(...) from builtins.PyCapsule select_score(self : rosetta.protocols.jd2.archive.EvaluatedArchive, evaluated_decoy : rosetta.core.io.silent.SilentStruct) -> float   compute score according to select_weights --- this can contain any evaluator columns set_evaluate_local(...) from builtins.PyCapsule set_evaluate_local(self : rosetta.protocols.jd2.archive.EvaluatedArchive, setting : bool) -> NoneType set_evaluators(...) from builtins.PyCapsule set_evaluators(self : rosetta.protocols.jd2.archive.EvaluatedArchive,  : rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t,  : rosetta.std.map_std_string_double) -> NoneType set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.jd2.archive.EvaluatedArchive, scorefxn_ : rosetta.core.scoring.ScoreFunction) -> NoneType   set scorefxn used for evaluation set_weight(...) from builtins.PyCapsule set_weight(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str, weight : float) -> NoneType   set weight of an evaluator or a column otherwise present in silent-structs  (i.e, score, chainbreak, external evaluation like score_final ) set_weights(...) from builtins.PyCapsule set_weights(self : rosetta.protocols.jd2.archive.EvaluatedArchive, setting : rosetta.std.map_std_string_double) -> NoneType start_evaluation_timer(...) from builtins.PyCapsule start_evaluation_timer(rosetta.protocols.jd2.archive.EvaluatedArchive) -> NoneType weights(...) from builtins.PyCapsule weights(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.std.map_std_string_double Methods inherited from rosetta.protocols.jd2.archive.ArchiveBase: accepts_since_last_batch(...) from builtins.PyCapsule accepts_since_last_batch(*args, **kwargs) Overloaded function.   1. accepts_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int   ---- methods to keep statistics of acceptance   2. accepts_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int current_acceptance_ratio(...) from builtins.PyCapsule current_acceptance_ratio(rosetta.protocols.jd2.archive.ArchiveBase) -> float decoys(...) from builtins.PyCapsule decoys(*args, **kwargs) Overloaded function.   1. decoys(rosetta.protocols.jd2.archive.ArchiveBase) -> rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t   2. decoys(rosetta.protocols.jd2.archive.ArchiveBase) -> rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t load_decoys(...) from builtins.PyCapsule load_decoys(self : rosetta.protocols.jd2.archive.ArchiveBase, filename : str, decoys : rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType nstruct(...) from builtins.PyCapsule nstruct(rosetta.protocols.jd2.archive.ArchiveBase) -> int   how many structures should be in archive .. varies from decoys().size() in startup phase. proposed_since_last_batch(...) from builtins.PyCapsule proposed_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int reset_accept_counter(...) from builtins.PyCapsule reset_accept_counter(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType save_decoys(...) from builtins.PyCapsule save_decoys(self : rosetta.protocols.jd2.archive.ArchiveBase, dirname : str, name : str, decoys : rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType   helper routine to save decoys properly set_nstruct(...) from builtins.PyCapsule set_nstruct(self : rosetta.protocols.jd2.archive.ArchiveBase, set : int) -> NoneType   set target size of pool statistics_valid(...) from builtins.PyCapsule statistics_valid(rosetta.protocols.jd2.archive.ArchiveBase) -> bool total_accepts(...) from builtins.PyCapsule total_accepts(rosetta.protocols.jd2.archive.ArchiveBase) -> int total_proposed(...) from builtins.PyCapsule total_proposed(rosetta.protocols.jd2.archive.ArchiveBase) -> int Methods inherited from rosetta.protocols.jd2.archive.AbstractArchiveBase: manager(...) from builtins.PyCapsule manager(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> protocols::jd2::archive::BaseArchiveManager   access to the ArchiveManager (control of batches) name(...) from builtins.PyCapsule name(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> str set_manager(...) from builtins.PyCapsule set_manager(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, manager : protocols::jd2::archive::BaseArchiveManager) -> NoneType set_name(...) from builtins.PyCapsule set_name(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, set : str) -> NoneType   set name of archive ( used also for save_to_file and restore_from_file )   class IterativeFullatom(IterativeBase)       Method resolution order: IterativeFullatom IterativeBase rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive rosetta.protocols.jd2.archive.EvaluatedArchive rosetta.protocols.jd2.archive.ArchiveBase rosetta.protocols.jd2.archive.AbstractArchiveBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.abinitio.IterativeFullatom) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. generate_batch(...) from builtins.PyCapsule generate_batch(*args, **kwargs) Overloaded function.   1. generate_batch(rosetta.protocols.abinitio.IterativeFullatom) -> NoneType   2. generate_batch(self : rosetta.protocols.abinitio.IterativeFullatom,  : protocols::jd2::archive::Batch, repeat_id : int) -> int initialize(...) from builtins.PyCapsule initialize(rosetta.protocols.abinitio.IterativeFullatom) -> NoneType   do initializing work that requires fully setup object here ready_for_batch(...) from builtins.PyCapsule ready_for_batch(rosetta.protocols.abinitio.IterativeFullatom) -> bool register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   2. register_options() -> NoneType   Archive specific options   3. register_options() -> NoneType   Archive specific options   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType Methods inherited from IterativeBase: add_structure(...) from builtins.PyCapsule add_structure(self : rosetta.protocols.abinitio.IterativeBase, new_decoy : rosetta.core.io.silent.SilentStruct, alternative_decoy : rosetta.core.io.silent.SilentStruct,  : protocols::jd2::archive::Batch) -> bool   overloaded to handel special convergence check 'pool_converged_rmsd'      add structure to Archive.. return false if structure is rejected. finished(...) from builtins.PyCapsule finished(rosetta.protocols.abinitio.IterativeBase) -> bool   archive is finished when at last stage gen_diversity_pool(...) from builtins.PyCapsule gen_diversity_pool(*args, **kwargs) Overloaded function.   1. gen_diversity_pool(self : rosetta.protocols.abinitio.IterativeBase,  : protocols::jd2::archive::Batch) -> NoneType   2. gen_diversity_pool(self : rosetta.protocols.abinitio.IterativeBase,  : protocols::jd2::archive::Batch, fullatom : bool) -> NoneType gen_dynamic_patches(...) from builtins.PyCapsule gen_dynamic_patches(self : rosetta.protocols.abinitio.IterativeBase, batch : protocols::jd2::archive::Batch) -> NoneType gen_evaluation_output(...) from builtins.PyCapsule gen_evaluation_output(*args, **kwargs) Overloaded function.   1. gen_evaluation_output(self : rosetta.protocols.abinitio.IterativeBase, batch : protocols::jd2::archive::Batch) -> NoneType   generate flags and stuff for the out-sourced evaluation ---> such that score_final column is returned for each decoy  note needs to be public, since IterativeCentroid calls this from IterativeFullatom to prepare evaluation for soon to be full-atom decoys   2. gen_evaluation_output(self : rosetta.protocols.abinitio.IterativeBase, batch : protocols::jd2::archive::Batch, fullatom : bool) -> NoneType   generate flags and stuff for the out-sourced evaluation ---> such that score_final column is returned for each decoy  note needs to be public, since IterativeCentroid calls this from IterativeFullatom to prepare evaluation for soon to be full-atom decoys idle(...) from builtins.PyCapsule idle(rosetta.protocols.abinitio.IterativeBase) -> NoneType   while waiting for jobs to finish init_from_decoy_set(...) from builtins.PyCapsule init_from_decoy_set(self : rosetta.protocols.abinitio.IterativeBase, sfd : rosetta.core.io.silent.SilentFileData) -> NoneType   overloaded to make input decoys appear the same as decoys coming from batches read_structures(...) from builtins.PyCapsule read_structures(self : rosetta.protocols.abinitio.IterativeBase, sfd : rosetta.core.io.silent.SilentFileData, alternative_decoys : rosetta.core.io.silent.SilentFileData, batch : protocols::jd2::archive::Batch) -> NoneType   overloaded so we can test for end of IterationStage after reading rescore(...) from builtins.PyCapsule rescore(rosetta.protocols.abinitio.IterativeBase) -> NoneType set_finish_stage(...) from builtins.PyCapsule set_finish_stage(self : rosetta.protocols.abinitio.IterativeBase, setting : rosetta.protocols.abinitio.IterationStage) -> NoneType   where to stop ? setup_default_evaluators(...) from builtins.PyCapsule setup_default_evaluators(rosetta.protocols.abinitio.IterativeBase) -> NoneType   setup JumpNrEvaluator still_interested(...) from builtins.PyCapsule still_interested(self : rosetta.protocols.abinitio.IterativeBase, batch : protocols::jd2::archive::Batch) -> bool   we are not interested in batches that were generated in old stages test_for_stage_end(...) from builtins.PyCapsule test_for_stage_end(rosetta.protocols.abinitio.IterativeBase) -> NoneType   calls increment_stage() if appropriate update_noesy_filter_files(...) from builtins.PyCapsule update_noesy_filter_files(self : rosetta.protocols.abinitio.IterativeBase, current : str, fullatom : bool) -> NoneType Data and other attributes inherited from IterativeBase: CEN2FULLATOM = IterationStage.LAST_CENTROID_START ENUMERATION = IterationStage.ENUMERATION FINISHED = IterationStage.FINISHED IterationStage = <class 'rosetta.protocols.abinitio.IterativeBase.IterationStage'> LAST_CENTROID_START = IterationStage.LAST_CENTROID_START NOESY_PHASEII_S2_RESAMPLING = IterationStage.NOESY_PHASEII_S2_RESAMPLING NOESY_PHASEII_TOPO = IterationStage.NOESY_PHASEII_TOPO PURE_TOPO_RESAMPLING = IterationStage.PURE_TOPO_RESAMPLING RIGID_CORE_RESAMPLING = IterationStage.RIGID_CORE_RESAMPLING STAGE2_RESAMPLING = IterationStage.STAGE2_RESAMPLING TOPO_RESAMPLING = IterationStage.TOPO_RESAMPLING Methods inherited from rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive: add_evaluated_structure(...) from builtins.PyCapsule add_evaluated_structure(self : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, from_batch : rosetta.core.io.silent.SilentStruct, alternative_decoy : rosetta.core.io.silent.SilentStruct,  : protocols::jd2::archive::Batch) -> bool   add decoy to Archive      evaluate decoy and call add_evaluated_structure assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive,  : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive determine_score_variations(...) from builtins.PyCapsule determine_score_variations(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> bool   determine variation of scores (those that are non-zeros in select_weights_ ) init_from_options(...) from builtins.PyCapsule init_from_options(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> NoneType restore_from_file(...) from builtins.PyCapsule restore_from_file(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> bool   overloaded that we can sort the pool after reading save_to_file(...) from builtins.PyCapsule save_to_file(*args, **kwargs) Overloaded function.   1. save_to_file(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> NoneType   overloaded to save / restore the variance_archive_   2. save_to_file(self : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, suffix : str) -> NoneType   overloaded to save / restore the variance_archive_ score_variation(...) from builtins.PyCapsule score_variation(self : rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, col : str) -> float score_variations(...) from builtins.PyCapsule score_variations(rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> rosetta.std.map_std_string_double Methods inherited from rosetta.protocols.jd2.archive.EvaluatedArchive: add_evaluation(...) from builtins.PyCapsule add_evaluation(*args, **kwargs) Overloaded function.   1. add_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive,  : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType   add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()   2. add_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive,  : rosetta.protocols.evaluation.PoseEvaluator, weight : float) -> NoneType   add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score() evaluate_local(...) from builtins.PyCapsule evaluate_local(rosetta.protocols.jd2.archive.EvaluatedArchive) -> bool   specify if decoys are evaluated on the master or (non-local i.e., on the individual slave nodes) evaluate_silent_struct(...) from builtins.PyCapsule evaluate_silent_struct(self : rosetta.protocols.jd2.archive.EvaluatedArchive, from_batch : rosetta.core.io.silent.SilentStruct) -> rosetta.core.io.silent.SilentStruct   yields an "evaluated" silent-struct which can be queried with select_score      will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct evaluators(...) from builtins.PyCapsule evaluators(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t get_weight(...) from builtins.PyCapsule get_weight(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> float has_evaluator(...) from builtins.PyCapsule has_evaluator(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> bool   is a certain elvaluator present ? remove_evaluation(...) from builtins.PyCapsule remove_evaluation(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str) -> NoneType   remove Evaluator scorefxn(...) from builtins.PyCapsule scorefxn(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.core.scoring.ScoreFunction select_score(...) from builtins.PyCapsule select_score(self : rosetta.protocols.jd2.archive.EvaluatedArchive, evaluated_decoy : rosetta.core.io.silent.SilentStruct) -> float   compute score according to select_weights --- this can contain any evaluator columns set_evaluate_local(...) from builtins.PyCapsule set_evaluate_local(self : rosetta.protocols.jd2.archive.EvaluatedArchive, setting : bool) -> NoneType set_evaluators(...) from builtins.PyCapsule set_evaluators(self : rosetta.protocols.jd2.archive.EvaluatedArchive,  : rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t,  : rosetta.std.map_std_string_double) -> NoneType set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.jd2.archive.EvaluatedArchive, scorefxn_ : rosetta.core.scoring.ScoreFunction) -> NoneType   set scorefxn used for evaluation set_weight(...) from builtins.PyCapsule set_weight(self : rosetta.protocols.jd2.archive.EvaluatedArchive, column : str, weight : float) -> NoneType   set weight of an evaluator or a column otherwise present in silent-structs  (i.e, score, chainbreak, external evaluation like score_final ) set_weights(...) from builtins.PyCapsule set_weights(self : rosetta.protocols.jd2.archive.EvaluatedArchive, setting : rosetta.std.map_std_string_double) -> NoneType start_evaluation_timer(...) from builtins.PyCapsule start_evaluation_timer(rosetta.protocols.jd2.archive.EvaluatedArchive) -> NoneType weights(...) from builtins.PyCapsule weights(rosetta.protocols.jd2.archive.EvaluatedArchive) -> rosetta.std.map_std_string_double Methods inherited from rosetta.protocols.jd2.archive.ArchiveBase: accepts_since_last_batch(...) from builtins.PyCapsule accepts_since_last_batch(*args, **kwargs) Overloaded function.   1. accepts_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int   ---- methods to keep statistics of acceptance   2. accepts_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int current_acceptance_ratio(...) from builtins.PyCapsule current_acceptance_ratio(rosetta.protocols.jd2.archive.ArchiveBase) -> float decoys(...) from builtins.PyCapsule decoys(*args, **kwargs) Overloaded function.   1. decoys(rosetta.protocols.jd2.archive.ArchiveBase) -> rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t   2. decoys(rosetta.protocols.jd2.archive.ArchiveBase) -> rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t load_decoys(...) from builtins.PyCapsule load_decoys(self : rosetta.protocols.jd2.archive.ArchiveBase, filename : str, decoys : rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType nstruct(...) from builtins.PyCapsule nstruct(rosetta.protocols.jd2.archive.ArchiveBase) -> int   how many structures should be in archive .. varies from decoys().size() in startup phase. proposed_since_last_batch(...) from builtins.PyCapsule proposed_since_last_batch(rosetta.protocols.jd2.archive.ArchiveBase) -> int reset_accept_counter(...) from builtins.PyCapsule reset_accept_counter(rosetta.protocols.jd2.archive.ArchiveBase) -> NoneType save_decoys(...) from builtins.PyCapsule save_decoys(self : rosetta.protocols.jd2.archive.ArchiveBase, dirname : str, name : str, decoys : rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) -> NoneType   helper routine to save decoys properly set_nstruct(...) from builtins.PyCapsule set_nstruct(self : rosetta.protocols.jd2.archive.ArchiveBase, set : int) -> NoneType   set target size of pool statistics_valid(...) from builtins.PyCapsule statistics_valid(rosetta.protocols.jd2.archive.ArchiveBase) -> bool total_accepts(...) from builtins.PyCapsule total_accepts(rosetta.protocols.jd2.archive.ArchiveBase) -> int total_proposed(...) from builtins.PyCapsule total_proposed(rosetta.protocols.jd2.archive.ArchiveBase) -> int Methods inherited from rosetta.protocols.jd2.archive.AbstractArchiveBase: manager(...) from builtins.PyCapsule manager(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> protocols::jd2::archive::BaseArchiveManager   access to the ArchiveManager (control of batches) name(...) from builtins.PyCapsule name(rosetta.protocols.jd2.archive.AbstractArchiveBase) -> str set_manager(...) from builtins.PyCapsule set_manager(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, manager : protocols::jd2::archive::BaseArchiveManager) -> NoneType set_name(...) from builtins.PyCapsule set_name(self : rosetta.protocols.jd2.archive.AbstractArchiveBase, set : str) -> NoneType   set name of archive ( used also for save_to_file and restore_from_file )   class JumpingFoldConstraintsWrapper(KinematicAbinitio)       Method resolution order: JumpingFoldConstraintsWrapper KinematicAbinitio FoldConstraints ClassicAbinitio Protocol rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, brute_move_small : protocols::simple_moves::FragmentMover, brute_move_large : protocols::simple_moves::FragmentMover, smooth_move_small : protocols::simple_moves::FragmentMover, jump_def : rosetta.protocols.jumping.BaseJumpSetup, dummy : int) -> NoneType   2. __init__(self : handle, fragset3mer : rosetta.core.fragment.FragSet, fragset9mer : rosetta.core.fragment.FragSet, movemap : rosetta.core.kinematics.MoveMap, jump_def : rosetta.protocols.jumping.BaseJumpSetup) -> NoneType   3. __init__(handle, rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper) -> 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.JumpingFoldConstraintsWrapper, pose : rosetta.core.pose.Pose) -> NoneType clone(...) from builtins.PyCapsule clone(rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper) -> str Methods inherited from KinematicAbinitio: closure_protocol(...) from builtins.PyCapsule closure_protocol(self : rosetta.protocols.abinitio.KinematicAbinitio, closure_protocol : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> NoneType   set the closure_protocol... if not set no closure... prepare_loop_in_stage3(...) from builtins.PyCapsule prepare_loop_in_stage3(self : rosetta.protocols.abinitio.KinematicAbinitio,  : rosetta.core.pose.Pose,  : int,  : int) -> bool prepare_loop_in_stage4(...) from builtins.PyCapsule prepare_loop_in_stage4(self : rosetta.protocols.abinitio.KinematicAbinitio,  : rosetta.core.pose.Pose,  : int,  : int) -> bool prepare_stage1(...) from builtins.PyCapsule prepare_stage1(self : rosetta.protocols.abinitio.KinematicAbinitio, pose : rosetta.core.pose.Pose) -> bool prepare_stage2(...) from builtins.PyCapsule prepare_stage2(self : rosetta.protocols.abinitio.KinematicAbinitio, pose : rosetta.core.pose.Pose) -> bool prepare_stage3(...) from builtins.PyCapsule prepare_stage3(self : rosetta.protocols.abinitio.KinematicAbinitio, pose : rosetta.core.pose.Pose) -> bool register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType set_max_seq_sep(...) from builtins.PyCapsule set_max_seq_sep(self : rosetta.protocols.abinitio.KinematicAbinitio, pose : rosetta.core.pose.Pose, setting : int) -> NoneType stage1_mover(...) from builtins.PyCapsule stage1_mover(self : rosetta.protocols.abinitio.KinematicAbinitio, pose : rosetta.core.pose.Pose, trials_in : protocols::moves::TrialMover) -> protocols::moves::TrialMover stage2_mover(...) from builtins.PyCapsule stage2_mover(self : rosetta.protocols.abinitio.KinematicAbinitio, pose : rosetta.core.pose.Pose, trials_in : protocols::moves::TrialMover) -> protocols::moves::TrialMover stage3_mover(...) from builtins.PyCapsule stage3_mover(self : rosetta.protocols.abinitio.KinematicAbinitio, pose : rosetta.core.pose.Pose, lct1 : int, lct2 : int, trials_in : protocols::moves::TrialMover) -> protocols::moves::TrialMover stage4_mover(...) from builtins.PyCapsule stage4_mover(self : rosetta.protocols.abinitio.KinematicAbinitio, pose : rosetta.core.pose.Pose, kk : int, trials_in : protocols::moves::TrialMover) -> protocols::moves::TrialMover Methods inherited from FoldConstraints: set_constraint_weight(...) from builtins.PyCapsule set_constraint_weight(self : rosetta.protocols.abinitio.FoldConstraints, setting : float) -> NoneType set_default_options(...) from builtins.PyCapsule set_default_options(rosetta.protocols.abinitio.FoldConstraints) -> NoneType set_default_scores(...) from builtins.PyCapsule set_default_scores(rosetta.protocols.abinitio.FoldConstraints) -> NoneType   sets the usual scores ( score0,score1, score2/5 etc. ) and additionally atom_pair_constraints to 1.0 set_show_viol_level(...) from builtins.PyCapsule set_show_viol_level(self : rosetta.protocols.abinitio.FoldConstraints, setting : int) -> NoneType Methods inherited from ClassicAbinitio: bQuickTest(...) from builtins.PyCapsule bQuickTest(rosetta.protocols.abinitio.ClassicAbinitio) -> bool brute_move_large(...) from builtins.PyCapsule brute_move_large(rosetta.protocols.abinitio.ClassicAbinitio) -> protocols::simple_moves::FragmentMover brute_move_small(...) from builtins.PyCapsule brute_move_small(rosetta.protocols.abinitio.ClassicAbinitio) -> protocols::simple_moves::FragmentMover init(...) from builtins.PyCapsule init(self : rosetta.protocols.abinitio.ClassicAbinitio, pose : rosetta.core.pose.Pose) -> NoneType just_smooth_cycles(...) from builtins.PyCapsule just_smooth_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> bool mc(...) from builtins.PyCapsule mc(*args, **kwargs) Overloaded function.   1. mc(rosetta.protocols.abinitio.ClassicAbinitio) -> protocols::moves::MonteCarlo   2. mc(rosetta.protocols.abinitio.ClassicAbinitio) -> protocols::moves::MonteCarlo movemap(...) from builtins.PyCapsule movemap(rosetta.protocols.abinitio.ClassicAbinitio) -> rosetta.core.kinematics.MoveMap set_cycles(...) from builtins.PyCapsule set_cycles(*args, **kwargs) Overloaded function.   1. set_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> NoneType   2. set_cycles(self : rosetta.protocols.abinitio.ClassicAbinitio, increase_cycles : float) -> NoneType set_mc(...) from builtins.PyCapsule set_mc(self : rosetta.protocols.abinitio.ClassicAbinitio,  : protocols::moves::MonteCarlo) -> NoneType set_movemap(...) from builtins.PyCapsule set_movemap(self : rosetta.protocols.abinitio.ClassicAbinitio, mm : rosetta.core.kinematics.MoveMap) -> NoneType set_moves(...) from builtins.PyCapsule set_moves(self : rosetta.protocols.abinitio.ClassicAbinitio, brute_move_small : protocols::simple_moves::FragmentMover, brute_move_large : protocols::simple_moves::FragmentMover, smooth_move_small : protocols::simple_moves::FragmentMover) -> NoneType set_score_weight(...) from builtins.PyCapsule set_score_weight(*args, **kwargs) Overloaded function.   1. set_score_weight(self : rosetta.protocols.abinitio.ClassicAbinitio,  : rosetta.core.scoring.ScoreType, setting : float) -> NoneType   2. set_score_weight(self : rosetta.protocols.abinitio.ClassicAbinitio,  : rosetta.core.scoring.ScoreType, setting : float, stage : rosetta.protocols.abinitio.StageID) -> NoneType set_skip_stage1(...) from builtins.PyCapsule set_skip_stage1(self : rosetta.protocols.abinitio.ClassicAbinitio, setting : bool) -> NoneType set_skip_stage2(...) from builtins.PyCapsule set_skip_stage2(self : rosetta.protocols.abinitio.ClassicAbinitio, setting : bool) -> NoneType set_stage4_cycles(...) from builtins.PyCapsule set_stage4_cycles(self : rosetta.protocols.abinitio.ClassicAbinitio, stage4_cycles_new : int) -> NoneType smooth_move_small(...) from builtins.PyCapsule smooth_move_small(rosetta.protocols.abinitio.ClassicAbinitio) -> protocols::simple_moves::FragmentMover stage1_cycles(...) from builtins.PyCapsule stage1_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> int stage2_cycles(...) from builtins.PyCapsule stage2_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> int stage3_cycles(...) from builtins.PyCapsule stage3_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> int stage4_cycles(...) from builtins.PyCapsule stage4_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> int stage5_cycles(...) from builtins.PyCapsule stage5_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> int total_trials(...) from builtins.PyCapsule total_trials(rosetta.protocols.abinitio.ClassicAbinitio) -> int Data descriptors inherited from ClassicAbinitio: bSkipStage1_ bSkipStage2_ bSkipStage3_ bSkipStage4_ bSkipStage5_ recover_low_stages_ Data and other attributes inherited from ClassicAbinitio: ALL_STAGES = StageID.ALL_STAGES STAGE_1 = StageID.STAGE_1 STAGE_2 = StageID.STAGE_2 STAGE_3a = StageID.STAGE_3a STAGE_3b = StageID.STAGE_3b STAGE_4 = StageID.STAGE_4 STAGE_4rot = StageID.STAGE_4rot STAGE_5 = StageID.STAGE_5 StageID = <class 'rosetta.protocols.abinitio.ClassicAbinitio.StageID'> Methods inherited from Protocol: add_evaluation(...) from builtins.PyCapsule add_evaluation(self : rosetta.protocols.abinitio.Protocol, ev : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.Protocol,  : rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.abinitio.Protocol centroid_scorefxn(...) from builtins.PyCapsule centroid_scorefxn(rosetta.protocols.abinitio.Protocol) -> rosetta.core.scoring.ScoreFunction evaluate_pose(...) from builtins.PyCapsule evaluate_pose(self : rosetta.protocols.abinitio.Protocol, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType evaluator(...) from builtins.PyCapsule evaluator(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.evaluation.MetaPoseEvaluator fullatom_scorefxn(...) from builtins.PyCapsule fullatom_scorefxn(rosetta.protocols.abinitio.Protocol) -> rosetta.core.scoring.ScoreFunction get_checkpoints(...) from builtins.PyCapsule get_checkpoints(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.checkpoint.CheckPointer kinematics(...) from builtins.PyCapsule kinematics(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.abinitio.KinematicControl output_debug_structure(...) from builtins.PyCapsule output_debug_structure(self : rosetta.protocols.abinitio.Protocol, pose : rosetta.core.pose.Pose, prefix : str) -> NoneType return_centroid(...) from builtins.PyCapsule return_centroid(*args, **kwargs) Overloaded function.   1. return_centroid(rosetta.protocols.abinitio.Protocol) -> bool   2. return_centroid(self : rosetta.protocols.abinitio.Protocol, setting : bool) -> NoneType set_centroid_scorefxn(...) from builtins.PyCapsule set_centroid_scorefxn(self : rosetta.protocols.abinitio.Protocol, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_evaluation(...) from builtins.PyCapsule set_evaluation(self : rosetta.protocols.abinitio.Protocol, ev : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType set_fullatom_scorefxn(...) from builtins.PyCapsule set_fullatom_scorefxn(self : rosetta.protocols.abinitio.Protocol, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_kinematics(...) from builtins.PyCapsule set_kinematics(self : rosetta.protocols.abinitio.Protocol, kc : rosetta.protocols.abinitio.KinematicControl) -> NoneType set_silentout_file_name(...) from builtins.PyCapsule set_silentout_file_name(self : rosetta.protocols.abinitio.Protocol, str : str) -> NoneType start_from_centroid(...) from builtins.PyCapsule start_from_centroid(rosetta.protocols.abinitio.Protocol) -> bool 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 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 KinematicAbinitio(FoldConstraints)       Method resolution order: KinematicAbinitio FoldConstraints ClassicAbinitio Protocol rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, brute_move_small : protocols::simple_moves::FragmentMover, brute_move_large : protocols::simple_moves::FragmentMover, smooth_move_small : protocols::simple_moves::FragmentMover, dummy : int) -> NoneType   2. __init__(self : handle, fragset3mer : rosetta.core.fragment.FragSet, fragset9mer : rosetta.core.fragment.FragSet, movemap : rosetta.core.kinematics.MoveMap) -> NoneType   3. __init__(handle, rosetta.protocols.abinitio.KinematicAbinitio) -> 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.KinematicAbinitio, pose : rosetta.core.pose.Pose) -> NoneType clone(...) from builtins.PyCapsule clone(rosetta.protocols.abinitio.KinematicAbinitio) -> rosetta.protocols.moves.Mover closure_protocol(...) from builtins.PyCapsule closure_protocol(self : rosetta.protocols.abinitio.KinematicAbinitio, closure_protocol : rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure) -> NoneType   set the closure_protocol... if not set no closure... get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.KinematicAbinitio) -> str prepare_loop_in_stage3(...) from builtins.PyCapsule prepare_loop_in_stage3(self : rosetta.protocols.abinitio.KinematicAbinitio,  : rosetta.core.pose.Pose,  : int,  : int) -> bool prepare_loop_in_stage4(...) from builtins.PyCapsule prepare_loop_in_stage4(self : rosetta.protocols.abinitio.KinematicAbinitio,  : rosetta.core.pose.Pose,  : int,  : int) -> bool prepare_stage1(...) from builtins.PyCapsule prepare_stage1(self : rosetta.protocols.abinitio.KinematicAbinitio, pose : rosetta.core.pose.Pose) -> bool prepare_stage2(...) from builtins.PyCapsule prepare_stage2(self : rosetta.protocols.abinitio.KinematicAbinitio, pose : rosetta.core.pose.Pose) -> bool prepare_stage3(...) from builtins.PyCapsule prepare_stage3(self : rosetta.protocols.abinitio.KinematicAbinitio, pose : rosetta.core.pose.Pose) -> bool register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType set_max_seq_sep(...) from builtins.PyCapsule set_max_seq_sep(self : rosetta.protocols.abinitio.KinematicAbinitio, pose : rosetta.core.pose.Pose, setting : int) -> NoneType stage1_mover(...) from builtins.PyCapsule stage1_mover(self : rosetta.protocols.abinitio.KinematicAbinitio, pose : rosetta.core.pose.Pose, trials_in : protocols::moves::TrialMover) -> protocols::moves::TrialMover stage2_mover(...) from builtins.PyCapsule stage2_mover(self : rosetta.protocols.abinitio.KinematicAbinitio, pose : rosetta.core.pose.Pose, trials_in : protocols::moves::TrialMover) -> protocols::moves::TrialMover stage3_mover(...) from builtins.PyCapsule stage3_mover(self : rosetta.protocols.abinitio.KinematicAbinitio, pose : rosetta.core.pose.Pose, lct1 : int, lct2 : int, trials_in : protocols::moves::TrialMover) -> protocols::moves::TrialMover stage4_mover(...) from builtins.PyCapsule stage4_mover(self : rosetta.protocols.abinitio.KinematicAbinitio, pose : rosetta.core.pose.Pose, kk : int, trials_in : protocols::moves::TrialMover) -> protocols::moves::TrialMover Methods inherited from FoldConstraints: set_constraint_weight(...) from builtins.PyCapsule set_constraint_weight(self : rosetta.protocols.abinitio.FoldConstraints, setting : float) -> NoneType set_default_options(...) from builtins.PyCapsule set_default_options(rosetta.protocols.abinitio.FoldConstraints) -> NoneType set_default_scores(...) from builtins.PyCapsule set_default_scores(rosetta.protocols.abinitio.FoldConstraints) -> NoneType   sets the usual scores ( score0,score1, score2/5 etc. ) and additionally atom_pair_constraints to 1.0 set_show_viol_level(...) from builtins.PyCapsule set_show_viol_level(self : rosetta.protocols.abinitio.FoldConstraints, setting : int) -> NoneType Methods inherited from ClassicAbinitio: bQuickTest(...) from builtins.PyCapsule bQuickTest(rosetta.protocols.abinitio.ClassicAbinitio) -> bool brute_move_large(...) from builtins.PyCapsule brute_move_large(rosetta.protocols.abinitio.ClassicAbinitio) -> protocols::simple_moves::FragmentMover brute_move_small(...) from builtins.PyCapsule brute_move_small(rosetta.protocols.abinitio.ClassicAbinitio) -> protocols::simple_moves::FragmentMover init(...) from builtins.PyCapsule init(self : rosetta.protocols.abinitio.ClassicAbinitio, pose : rosetta.core.pose.Pose) -> NoneType just_smooth_cycles(...) from builtins.PyCapsule just_smooth_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> bool mc(...) from builtins.PyCapsule mc(*args, **kwargs) Overloaded function.   1. mc(rosetta.protocols.abinitio.ClassicAbinitio) -> protocols::moves::MonteCarlo   2. mc(rosetta.protocols.abinitio.ClassicAbinitio) -> protocols::moves::MonteCarlo movemap(...) from builtins.PyCapsule movemap(rosetta.protocols.abinitio.ClassicAbinitio) -> rosetta.core.kinematics.MoveMap set_cycles(...) from builtins.PyCapsule set_cycles(*args, **kwargs) Overloaded function.   1. set_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> NoneType   2. set_cycles(self : rosetta.protocols.abinitio.ClassicAbinitio, increase_cycles : float) -> NoneType set_mc(...) from builtins.PyCapsule set_mc(self : rosetta.protocols.abinitio.ClassicAbinitio,  : protocols::moves::MonteCarlo) -> NoneType set_movemap(...) from builtins.PyCapsule set_movemap(self : rosetta.protocols.abinitio.ClassicAbinitio, mm : rosetta.core.kinematics.MoveMap) -> NoneType set_moves(...) from builtins.PyCapsule set_moves(self : rosetta.protocols.abinitio.ClassicAbinitio, brute_move_small : protocols::simple_moves::FragmentMover, brute_move_large : protocols::simple_moves::FragmentMover, smooth_move_small : protocols::simple_moves::FragmentMover) -> NoneType set_score_weight(...) from builtins.PyCapsule set_score_weight(*args, **kwargs) Overloaded function.   1. set_score_weight(self : rosetta.protocols.abinitio.ClassicAbinitio,  : rosetta.core.scoring.ScoreType, setting : float) -> NoneType   2. set_score_weight(self : rosetta.protocols.abinitio.ClassicAbinitio,  : rosetta.core.scoring.ScoreType, setting : float, stage : rosetta.protocols.abinitio.StageID) -> NoneType set_skip_stage1(...) from builtins.PyCapsule set_skip_stage1(self : rosetta.protocols.abinitio.ClassicAbinitio, setting : bool) -> NoneType set_skip_stage2(...) from builtins.PyCapsule set_skip_stage2(self : rosetta.protocols.abinitio.ClassicAbinitio, setting : bool) -> NoneType set_stage4_cycles(...) from builtins.PyCapsule set_stage4_cycles(self : rosetta.protocols.abinitio.ClassicAbinitio, stage4_cycles_new : int) -> NoneType smooth_move_small(...) from builtins.PyCapsule smooth_move_small(rosetta.protocols.abinitio.ClassicAbinitio) -> protocols::simple_moves::FragmentMover stage1_cycles(...) from builtins.PyCapsule stage1_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> int stage2_cycles(...) from builtins.PyCapsule stage2_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> int stage3_cycles(...) from builtins.PyCapsule stage3_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> int stage4_cycles(...) from builtins.PyCapsule stage4_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> int stage5_cycles(...) from builtins.PyCapsule stage5_cycles(rosetta.protocols.abinitio.ClassicAbinitio) -> int total_trials(...) from builtins.PyCapsule total_trials(rosetta.protocols.abinitio.ClassicAbinitio) -> int Data descriptors inherited from ClassicAbinitio: bSkipStage1_ bSkipStage2_ bSkipStage3_ bSkipStage4_ bSkipStage5_ recover_low_stages_ Data and other attributes inherited from ClassicAbinitio: ALL_STAGES = StageID.ALL_STAGES STAGE_1 = StageID.STAGE_1 STAGE_2 = StageID.STAGE_2 STAGE_3a = StageID.STAGE_3a STAGE_3b = StageID.STAGE_3b STAGE_4 = StageID.STAGE_4 STAGE_4rot = StageID.STAGE_4rot STAGE_5 = StageID.STAGE_5 StageID = <class 'rosetta.protocols.abinitio.ClassicAbinitio.StageID'> Methods inherited from Protocol: add_evaluation(...) from builtins.PyCapsule add_evaluation(self : rosetta.protocols.abinitio.Protocol, ev : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.Protocol,  : rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.abinitio.Protocol centroid_scorefxn(...) from builtins.PyCapsule centroid_scorefxn(rosetta.protocols.abinitio.Protocol) -> rosetta.core.scoring.ScoreFunction evaluate_pose(...) from builtins.PyCapsule evaluate_pose(self : rosetta.protocols.abinitio.Protocol, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType evaluator(...) from builtins.PyCapsule evaluator(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.evaluation.MetaPoseEvaluator fullatom_scorefxn(...) from builtins.PyCapsule fullatom_scorefxn(rosetta.protocols.abinitio.Protocol) -> rosetta.core.scoring.ScoreFunction get_checkpoints(...) from builtins.PyCapsule get_checkpoints(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.checkpoint.CheckPointer kinematics(...) from builtins.PyCapsule kinematics(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.abinitio.KinematicControl output_debug_structure(...) from builtins.PyCapsule output_debug_structure(self : rosetta.protocols.abinitio.Protocol, pose : rosetta.core.pose.Pose, prefix : str) -> NoneType return_centroid(...) from builtins.PyCapsule return_centroid(*args, **kwargs) Overloaded function.   1. return_centroid(rosetta.protocols.abinitio.Protocol) -> bool   2. return_centroid(self : rosetta.protocols.abinitio.Protocol, setting : bool) -> NoneType set_centroid_scorefxn(...) from builtins.PyCapsule set_centroid_scorefxn(self : rosetta.protocols.abinitio.Protocol, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_evaluation(...) from builtins.PyCapsule set_evaluation(self : rosetta.protocols.abinitio.Protocol, ev : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType set_fullatom_scorefxn(...) from builtins.PyCapsule set_fullatom_scorefxn(self : rosetta.protocols.abinitio.Protocol, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_kinematics(...) from builtins.PyCapsule set_kinematics(self : rosetta.protocols.abinitio.Protocol, kc : rosetta.protocols.abinitio.KinematicControl) -> NoneType set_silentout_file_name(...) from builtins.PyCapsule set_silentout_file_name(self : rosetta.protocols.abinitio.Protocol, str : str) -> NoneType start_from_centroid(...) from builtins.PyCapsule start_from_centroid(rosetta.protocols.abinitio.Protocol) -> bool 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 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 KinematicControl(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.abinitio.KinematicControl) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_chainbreak_variants(...) from builtins.PyCapsule add_chainbreak_variants(*args, **kwargs) Overloaded function.   1. add_chainbreak_variants(self : rosetta.protocols.abinitio.KinematicControl, pose : rosetta.core.pose.Pose) -> NoneType   2. add_chainbreak_variants(self : rosetta.protocols.abinitio.KinematicControl, pose : rosetta.core.pose.Pose, max_dist : int,  : rosetta.core.kinematics.ShortestPathInFoldTree) -> NoneType add_score_weights(...) from builtins.PyCapsule add_score_weights(self : rosetta.protocols.abinitio.KinematicControl,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.KinematicControl,  : rosetta.protocols.abinitio.KinematicControl) -> rosetta.protocols.abinitio.KinematicControl final_fold_tree(...) from builtins.PyCapsule final_fold_tree(rosetta.protocols.abinitio.KinematicControl) -> rosetta.core.kinematics.FoldTree jump_mover(...) from builtins.PyCapsule jump_mover(rosetta.protocols.abinitio.KinematicControl) -> protocols::simple_moves::FragmentMover movemap(...) from builtins.PyCapsule movemap(rosetta.protocols.abinitio.KinematicControl) -> rosetta.core.kinematics.MoveMap movemap_ptr(...) from builtins.PyCapsule movemap_ptr(rosetta.protocols.abinitio.KinematicControl) -> rosetta.core.kinematics.MoveMap prepare_pose_for_sampling(...) from builtins.PyCapsule prepare_pose_for_sampling(self : rosetta.protocols.abinitio.KinematicControl, pose : rosetta.core.pose.Pose) -> bool sampling_fold_tree(...) from builtins.PyCapsule sampling_fold_tree(rosetta.protocols.abinitio.KinematicControl) -> rosetta.core.kinematics.FoldTree set_final_fold_tree(...) from builtins.PyCapsule set_final_fold_tree(self : rosetta.protocols.abinitio.KinematicControl, f : rosetta.core.kinematics.FoldTree) -> NoneType set_jump_mover(...) from builtins.PyCapsule set_jump_mover(self : rosetta.protocols.abinitio.KinematicControl, jm : protocols::simple_moves::FragmentMover) -> NoneType set_movemap(...) from builtins.PyCapsule set_movemap(self : rosetta.protocols.abinitio.KinematicControl, mm : rosetta.core.kinematics.MoveMap) -> NoneType set_sampling_fold_tree(...) from builtins.PyCapsule set_sampling_fold_tree(self : rosetta.protocols.abinitio.KinematicControl, f : rosetta.core.kinematics.FoldTree) -> NoneType set_strict_movemap(...) from builtins.PyCapsule set_strict_movemap(self : rosetta.protocols.abinitio.KinematicControl, mm : rosetta.core.kinematics.MoveMap) -> NoneType   class KinematicTaskControl(Protocol)       Method resolution order: KinematicTaskControl Protocol rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.abinitio.KinematicTaskControl) -> NoneType   2. __init__(self : rosetta.protocols.abinitio.KinematicTaskControl, sampler : rosetta.protocols.abinitio.Protocol) -> NoneType   3. __init__(rosetta.protocols.abinitio.KinematicTaskControl, rosetta.protocols.abinitio.KinematicTaskControl) -> 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.KinematicTaskControl, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.KinematicTaskControl,  : rosetta.protocols.abinitio.KinematicTaskControl) -> rosetta.protocols.abinitio.KinematicTaskControl current_kinematics(...) from builtins.PyCapsule current_kinematics(rosetta.protocols.abinitio.KinematicTaskControl) -> rosetta.protocols.abinitio.KinematicControl get_checkpoints(...) from builtins.PyCapsule get_checkpoints(rosetta.protocols.abinitio.KinematicTaskControl) -> rosetta.protocols.checkpoint.CheckPointer get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.KinematicTaskControl) -> str init(...) from builtins.PyCapsule init(self : rosetta.protocols.abinitio.KinematicTaskControl, pose : rosetta.core.pose.Pose) -> NoneType new_kinematics(...) from builtins.PyCapsule new_kinematics(self : rosetta.protocols.abinitio.KinematicTaskControl, pose : rosetta.core.pose.Pose) -> rosetta.protocols.abinitio.KinematicControl sampling_protocol(...) from builtins.PyCapsule sampling_protocol(rosetta.protocols.abinitio.KinematicTaskControl) -> rosetta.protocols.abinitio.Protocol set_input_pose_is_fa(...) from builtins.PyCapsule set_input_pose_is_fa(*args, **kwargs) Overloaded function.   1. set_input_pose_is_fa(rosetta.protocols.abinitio.KinematicTaskControl) -> NoneType   2. set_input_pose_is_fa(self : rosetta.protocols.abinitio.KinematicTaskControl, setting : bool) -> NoneType Methods inherited from Protocol: add_evaluation(...) from builtins.PyCapsule add_evaluation(self : rosetta.protocols.abinitio.Protocol, ev : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType centroid_scorefxn(...) from builtins.PyCapsule centroid_scorefxn(rosetta.protocols.abinitio.Protocol) -> rosetta.core.scoring.ScoreFunction evaluate_pose(...) from builtins.PyCapsule evaluate_pose(self : rosetta.protocols.abinitio.Protocol, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType evaluator(...) from builtins.PyCapsule evaluator(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.evaluation.MetaPoseEvaluator fullatom_scorefxn(...) from builtins.PyCapsule fullatom_scorefxn(rosetta.protocols.abinitio.Protocol) -> rosetta.core.scoring.ScoreFunction kinematics(...) from builtins.PyCapsule kinematics(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.abinitio.KinematicControl output_debug_structure(...) from builtins.PyCapsule output_debug_structure(self : rosetta.protocols.abinitio.Protocol, pose : rosetta.core.pose.Pose, prefix : str) -> NoneType 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 return_centroid(...) from builtins.PyCapsule return_centroid(*args, **kwargs) Overloaded function.   1. return_centroid(rosetta.protocols.abinitio.Protocol) -> bool   2. return_centroid(self : rosetta.protocols.abinitio.Protocol, setting : bool) -> NoneType set_centroid_scorefxn(...) from builtins.PyCapsule set_centroid_scorefxn(self : rosetta.protocols.abinitio.Protocol, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_evaluation(...) from builtins.PyCapsule set_evaluation(self : rosetta.protocols.abinitio.Protocol, ev : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType set_fullatom_scorefxn(...) from builtins.PyCapsule set_fullatom_scorefxn(self : rosetta.protocols.abinitio.Protocol, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_kinematics(...) from builtins.PyCapsule set_kinematics(self : rosetta.protocols.abinitio.Protocol, kc : rosetta.protocols.abinitio.KinematicControl) -> NoneType set_silentout_file_name(...) from builtins.PyCapsule set_silentout_file_name(self : rosetta.protocols.abinitio.Protocol, str : str) -> NoneType start_from_centroid(...) from builtins.PyCapsule start_from_centroid(rosetta.protocols.abinitio.Protocol) -> bool Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply clone(...) from builtins.PyCapsule clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Return a clone of the Mover object. create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class LoopJumpFoldCst(KinematicTaskControl)       Method resolution order: LoopJumpFoldCst KinematicTaskControl Protocol rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle, rosetta.protocols.jumping.BaseJumpSetup, rosetta.protocols.loops.Loops, rosetta.protocols.abinitio.Protocol, rosetta.core.fragment.SecondaryStructure, float) -> NoneType   doc   2. __init__(self : handle, jump_def : rosetta.protocols.jumping.BaseJumpSetup, loops : rosetta.protocols.loops.Loops, sampler : rosetta.protocols.abinitio.Protocol, ss_def : rosetta.core.fragment.SecondaryStructure, coord_cst_weight : float, bCstAllAtom : bool) -> NoneType   3. __init__(handle, rosetta.protocols.abinitio.LoopJumpFoldCst) -> 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.LoopJumpFoldCst,  : rosetta.protocols.abinitio.LoopJumpFoldCst) -> rosetta.protocols.abinitio.LoopJumpFoldCst get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.LoopJumpFoldCst) -> str new_kinematics(...) from builtins.PyCapsule new_kinematics(self : rosetta.protocols.abinitio.LoopJumpFoldCst, pose : rosetta.core.pose.Pose) -> rosetta.protocols.abinitio.KinematicControl set_coord_cst_weight_array(...) from builtins.PyCapsule set_coord_cst_weight_array(self : rosetta.protocols.abinitio.LoopJumpFoldCst, vec : rosetta.utility.vector1_double) -> NoneType set_dump_weights_file(...) from builtins.PyCapsule set_dump_weights_file(self : rosetta.protocols.abinitio.LoopJumpFoldCst, str : str) -> NoneType Methods inherited from KinematicTaskControl: apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.abinitio.KinematicTaskControl, pose : rosetta.core.pose.Pose) -> NoneType current_kinematics(...) from builtins.PyCapsule current_kinematics(rosetta.protocols.abinitio.KinematicTaskControl) -> rosetta.protocols.abinitio.KinematicControl get_checkpoints(...) from builtins.PyCapsule get_checkpoints(rosetta.protocols.abinitio.KinematicTaskControl) -> rosetta.protocols.checkpoint.CheckPointer init(...) from builtins.PyCapsule init(self : rosetta.protocols.abinitio.KinematicTaskControl, pose : rosetta.core.pose.Pose) -> NoneType sampling_protocol(...) from builtins.PyCapsule sampling_protocol(rosetta.protocols.abinitio.KinematicTaskControl) -> rosetta.protocols.abinitio.Protocol set_input_pose_is_fa(...) from builtins.PyCapsule set_input_pose_is_fa(*args, **kwargs) Overloaded function.   1. set_input_pose_is_fa(rosetta.protocols.abinitio.KinematicTaskControl) -> NoneType   2. set_input_pose_is_fa(self : rosetta.protocols.abinitio.KinematicTaskControl, setting : bool) -> NoneType Methods inherited from Protocol: add_evaluation(...) from builtins.PyCapsule add_evaluation(self : rosetta.protocols.abinitio.Protocol, ev : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType centroid_scorefxn(...) from builtins.PyCapsule centroid_scorefxn(rosetta.protocols.abinitio.Protocol) -> rosetta.core.scoring.ScoreFunction evaluate_pose(...) from builtins.PyCapsule evaluate_pose(self : rosetta.protocols.abinitio.Protocol, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType evaluator(...) from builtins.PyCapsule evaluator(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.evaluation.MetaPoseEvaluator fullatom_scorefxn(...) from builtins.PyCapsule fullatom_scorefxn(rosetta.protocols.abinitio.Protocol) -> rosetta.core.scoring.ScoreFunction kinematics(...) from builtins.PyCapsule kinematics(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.abinitio.KinematicControl output_debug_structure(...) from builtins.PyCapsule output_debug_structure(self : rosetta.protocols.abinitio.Protocol, pose : rosetta.core.pose.Pose, prefix : str) -> NoneType 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 return_centroid(...) from builtins.PyCapsule return_centroid(*args, **kwargs) Overloaded function.   1. return_centroid(rosetta.protocols.abinitio.Protocol) -> bool   2. return_centroid(self : rosetta.protocols.abinitio.Protocol, setting : bool) -> NoneType set_centroid_scorefxn(...) from builtins.PyCapsule set_centroid_scorefxn(self : rosetta.protocols.abinitio.Protocol, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_evaluation(...) from builtins.PyCapsule set_evaluation(self : rosetta.protocols.abinitio.Protocol, ev : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType set_fullatom_scorefxn(...) from builtins.PyCapsule set_fullatom_scorefxn(self : rosetta.protocols.abinitio.Protocol, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_kinematics(...) from builtins.PyCapsule set_kinematics(self : rosetta.protocols.abinitio.Protocol, kc : rosetta.protocols.abinitio.KinematicControl) -> NoneType set_silentout_file_name(...) from builtins.PyCapsule set_silentout_file_name(self : rosetta.protocols.abinitio.Protocol, str : str) -> NoneType start_from_centroid(...) from builtins.PyCapsule start_from_centroid(rosetta.protocols.abinitio.Protocol) -> bool Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply clone(...) from builtins.PyCapsule clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Return a clone of the Mover object. create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class MembraneAbinitio(Protocol)     @ detail general usage: MembraneAbinitio  abinitio; abinitio.init( pose ); ... while(nstruct) { abinitio.apply( pose ); }   call MembraneAbinitio::register_options() before core::init::init to add relevant options to the applications help   , with the following stages, all of which uses a different ScoreFunction based on the cen_std.wts in minirosetta_database:   - Stage 1: large (usually 9mer) randomly selected fragment insertions, only VDW term turned on. Uses score0.wts_patch and runs for either a maximum of 2000 cycles or until all moveable phi/psi values have been changed.   - Stage 2: large randomly selected fragment insertions, more score terms turned on. Uses score1.wts_patch and runs for 2000 cycles.   - Stage 3: uses large randomly selected fragment insertions, although the size of the fragment insertions is tunable via the set_apply_large_frags( bool ) method. Alternates between score2.wts_patch and score5.wts_patch, running tunable numbers of 2000-cycle iterations between the two scoring functions.   - Stage 4: uses small (usually 3mer) fragment insertions with the fragment selection based on the Gunn cost for finding local fragment moves. Runs for 4000-cycles and uses score3.wts_patch.   The class implements the basic abinito approach as known from rosetta++. We tried to set this up, such that behaviour of the protocol can be changed in many different ways ( see, e.g., FoldConstraints ). To be able to change the behaviour of the protocol easily the class-apply function and methods called therein (e.g., prepare_XXX() / do_XXX_cycles() ) should not directly change moves or trials. A reference to the currently used score-function should be obtained by mc().score_function() ...   Behaviour can be changed in the following ways:   use non-classic FragmentMover  --> eg. not uniformly sampled fragments, but using some weighting --> large and small moves doesn't have to be 3mers and 9mers... use other movers... ---> or other fragets for the "convenience constructor" use custom trial classes --> overload update_moves()   change sampling behaviour: overload prepare_XXX() methods: these are called before the cycling for a certain stage begins overload do_stageX_cycles() : the actual loops over trial-moves ...   change scoring functions: overload set_default_scores() weight-changes effective for all stages: set_score_weight()     Method resolution order: MembraneAbinitio Protocol rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, brute_move_small : protocols::simple_moves::FragmentMover, brute_move_small_top25 : protocols::simple_moves::FragmentMover, brute_move_large : protocols::simple_moves::FragmentMover, smooth_move_small : protocols::simple_moves::FragmentMover,  : int) -> NoneType   2. __init__(self : handle, fragset_small : rosetta.core.fragment.FragSet, fragset_small_top25 : rosetta.core.fragment.FragSet, fragset_large : rosetta.core.fragment.FragSet, movemap : rosetta.core.kinematics.MoveMap) -> NoneType   3. __init__(handle, rosetta.protocols.abinitio.MembraneAbinitio) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_spanning_region(...) from builtins.PyCapsule add_spanning_region(self : rosetta.protocols.abinitio.MembraneAbinitio, pose : rosetta.core.pose.Pose) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.abinitio.MembraneAbinitio, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.MembraneAbinitio,  : rosetta.protocols.abinitio.MembraneAbinitio) -> rosetta.protocols.abinitio.MembraneAbinitio bQuickTest(...) from builtins.PyCapsule bQuickTest(rosetta.protocols.abinitio.MembraneAbinitio) -> bool brute_move_large(...) from builtins.PyCapsule brute_move_large(rosetta.protocols.abinitio.MembraneAbinitio) -> protocols::simple_moves::FragmentMover brute_move_small(...) from builtins.PyCapsule brute_move_small(rosetta.protocols.abinitio.MembraneAbinitio) -> protocols::simple_moves::FragmentMover brute_move_small_top25(...) from builtins.PyCapsule brute_move_small_top25(rosetta.protocols.abinitio.MembraneAbinitio) -> protocols::simple_moves::FragmentMover checkpoint(...) from builtins.PyCapsule checkpoint(self : rosetta.protocols.abinitio.MembraneAbinitio, pose : rosetta.core.pose.Pose, id : str) -> NoneType clear_checkpoints(...) from builtins.PyCapsule clear_checkpoints(rosetta.protocols.abinitio.MembraneAbinitio) -> NoneType clone(...) from builtins.PyCapsule clone(rosetta.protocols.abinitio.MembraneAbinitio) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.MembraneAbinitio) -> str init(...) from builtins.PyCapsule init(self : rosetta.protocols.abinitio.MembraneAbinitio, pose : rosetta.core.pose.Pose) -> NoneType just_smooth_cycles(...) from builtins.PyCapsule just_smooth_cycles(rosetta.protocols.abinitio.MembraneAbinitio) -> bool mc(...) from builtins.PyCapsule mc(*args, **kwargs) Overloaded function.   1. mc(rosetta.protocols.abinitio.MembraneAbinitio) -> rosetta.protocols.moves.MonteCarlo   2. mc(rosetta.protocols.abinitio.MembraneAbinitio) -> rosetta.protocols.moves.MonteCarlo move_all_inserted(...) from builtins.PyCapsule move_all_inserted(self : rosetta.protocols.abinitio.MembraneAbinitio, pose : rosetta.core.pose.Pose) -> NoneType movemap(...) from builtins.PyCapsule movemap(rosetta.protocols.abinitio.MembraneAbinitio) -> rosetta.core.kinematics.MoveMap print_debug(...) from builtins.PyCapsule print_debug(self : rosetta.protocols.abinitio.MembraneAbinitio, pose : rosetta.core.pose.Pose) -> NoneType recover_checkpoint(...) from builtins.PyCapsule recover_checkpoint(self : rosetta.protocols.abinitio.MembraneAbinitio, pose : rosetta.core.pose.Pose, id : str) -> bool register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType set_cycles(...) from builtins.PyCapsule set_cycles(*args, **kwargs) Overloaded function.   1. set_cycles(rosetta.protocols.abinitio.MembraneAbinitio) -> NoneType   2. set_cycles(self : rosetta.protocols.abinitio.MembraneAbinitio, increase_cycles : float) -> NoneType set_mc(...) from builtins.PyCapsule set_mc(self : rosetta.protocols.abinitio.MembraneAbinitio,  : rosetta.protocols.moves.MonteCarlo) -> NoneType set_movemap(...) from builtins.PyCapsule set_movemap(self : rosetta.protocols.abinitio.MembraneAbinitio, mm : rosetta.core.kinematics.MoveMap) -> NoneType set_moves(...) from builtins.PyCapsule set_moves(self : rosetta.protocols.abinitio.MembraneAbinitio, brute_move_small : protocols::simple_moves::FragmentMover, brute_move_large : protocols::simple_moves::FragmentMover, smooth_move_small : protocols::simple_moves::FragmentMover) -> NoneType set_only_stage4(...) from builtins.PyCapsule set_only_stage4(self : rosetta.protocols.abinitio.MembraneAbinitio, value : bool) -> NoneType set_score_weight(...) from builtins.PyCapsule set_score_weight(*args, **kwargs) Overloaded function.   1. set_score_weight(self : rosetta.protocols.abinitio.MembraneAbinitio,  : rosetta.core.scoring.ScoreType, setting : float) -> NoneType   2. set_score_weight(self : rosetta.protocols.abinitio.MembraneAbinitio,  : rosetta.core.scoring.ScoreType, setting : float, stage : rosetta.protocols.abinitio.StageID) -> NoneType set_stage4_cycles(...) from builtins.PyCapsule set_stage4_cycles(self : rosetta.protocols.abinitio.MembraneAbinitio, stage4_cycles_new : int) -> NoneType smooth_move_small(...) from builtins.PyCapsule smooth_move_small(rosetta.protocols.abinitio.MembraneAbinitio) -> protocols::simple_moves::FragmentMover stage1_cycles(...) from builtins.PyCapsule stage1_cycles(rosetta.protocols.abinitio.MembraneAbinitio) -> int stage2_cycles(...) from builtins.PyCapsule stage2_cycles(rosetta.protocols.abinitio.MembraneAbinitio) -> int stage3_cycles(...) from builtins.PyCapsule stage3_cycles(rosetta.protocols.abinitio.MembraneAbinitio) -> int stage4_cycles(...) from builtins.PyCapsule stage4_cycles(rosetta.protocols.abinitio.MembraneAbinitio) -> int total_trials(...) from builtins.PyCapsule total_trials(rosetta.protocols.abinitio.MembraneAbinitio) -> int Data and other attributes defined here: ALL_STAGES = StageID.ALL_STAGES STAGE_1 = StageID.STAGE_1 STAGE_2 = StageID.STAGE_2 STAGE_3a = StageID.STAGE_3a STAGE_3b = StageID.STAGE_3b STAGE_4 = StageID.STAGE_4 StageID = <class 'rosetta.protocols.abinitio.MembraneAbinitio.StageID'> Methods inherited from Protocol: add_evaluation(...) from builtins.PyCapsule add_evaluation(self : rosetta.protocols.abinitio.Protocol, ev : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType centroid_scorefxn(...) from builtins.PyCapsule centroid_scorefxn(rosetta.protocols.abinitio.Protocol) -> rosetta.core.scoring.ScoreFunction evaluate_pose(...) from builtins.PyCapsule evaluate_pose(self : rosetta.protocols.abinitio.Protocol, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType evaluator(...) from builtins.PyCapsule evaluator(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.evaluation.MetaPoseEvaluator fullatom_scorefxn(...) from builtins.PyCapsule fullatom_scorefxn(rosetta.protocols.abinitio.Protocol) -> rosetta.core.scoring.ScoreFunction get_checkpoints(...) from builtins.PyCapsule get_checkpoints(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.checkpoint.CheckPointer kinematics(...) from builtins.PyCapsule kinematics(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.abinitio.KinematicControl output_debug_structure(...) from builtins.PyCapsule output_debug_structure(self : rosetta.protocols.abinitio.Protocol, pose : rosetta.core.pose.Pose, prefix : str) -> NoneType return_centroid(...) from builtins.PyCapsule return_centroid(*args, **kwargs) Overloaded function.   1. return_centroid(rosetta.protocols.abinitio.Protocol) -> bool   2. return_centroid(self : rosetta.protocols.abinitio.Protocol, setting : bool) -> NoneType set_centroid_scorefxn(...) from builtins.PyCapsule set_centroid_scorefxn(self : rosetta.protocols.abinitio.Protocol, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_evaluation(...) from builtins.PyCapsule set_evaluation(self : rosetta.protocols.abinitio.Protocol, ev : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType set_fullatom_scorefxn(...) from builtins.PyCapsule set_fullatom_scorefxn(self : rosetta.protocols.abinitio.Protocol, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_kinematics(...) from builtins.PyCapsule set_kinematics(self : rosetta.protocols.abinitio.Protocol, kc : rosetta.protocols.abinitio.KinematicControl) -> NoneType set_silentout_file_name(...) from builtins.PyCapsule set_silentout_file_name(self : rosetta.protocols.abinitio.Protocol, str : str) -> NoneType start_from_centroid(...) from builtins.PyCapsule start_from_centroid(rosetta.protocols.abinitio.Protocol) -> bool 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 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 PairingStatEntry(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.protocols.abinitio.PairingStatEntry, other : rosetta.protocols.abinitio.PairingStatEntry) -> bool __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.abinitio.PairingStatEntry) -> NoneType   2. __init__(self : rosetta.protocols.abinitio.PairingStatEntry, strand : rosetta.core.scoring.dssp.StrandPairing, id : str) -> NoneType   3. __init__(self : rosetta.protocols.abinitio.PairingStatEntry,  : rosetta.protocols.abinitio.PairingStatEntry) -> NoneType __ne__(...) from builtins.PyCapsule __ne__(self : rosetta.protocols.abinitio.PairingStatEntry, other : rosetta.protocols.abinitio.PairingStatEntry) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.abinitio.PairingStatEntry) -> str add_pairing(...) from builtins.PyCapsule add_pairing(self : rosetta.protocols.abinitio.PairingStatEntry,  : rosetta.core.scoring.dssp.StrandPairing,  : str) -> bool compatible(...) from builtins.PyCapsule compatible(self : rosetta.protocols.abinitio.PairingStatEntry,  : rosetta.core.scoring.dssp.StrandPairing) -> bool contact_order(...) from builtins.PyCapsule contact_order(rosetta.protocols.abinitio.PairingStatEntry) -> int frequency(...) from builtins.PyCapsule frequency(rosetta.protocols.abinitio.PairingStatEntry) -> int has_model(...) from builtins.PyCapsule has_model(self : rosetta.protocols.abinitio.PairingStatEntry,  : str) -> bool models(...) from builtins.PyCapsule models(*args, **kwargs) Overloaded function.   1. models(rosetta.protocols.abinitio.PairingStatEntry) -> rosetta.utility.vector1_std_string   2. models(rosetta.protocols.abinitio.PairingStatEntry) -> rosetta.utility.vector1_std_string pairing(...) from builtins.PyCapsule pairing(rosetta.protocols.abinitio.PairingStatEntry) -> rosetta.core.scoring.dssp.StrandPairing set_weight(...) from builtins.PyCapsule set_weight(self : rosetta.protocols.abinitio.PairingStatEntry, setting : float) -> NoneType size(...) from builtins.PyCapsule size(rosetta.protocols.abinitio.PairingStatEntry) -> int weight(...) from builtins.PyCapsule weight(rosetta.protocols.abinitio.PairingStatEntry) -> float   class PairingStatistics(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.abinitio.PairingStatistics) -> NoneType   2. __init__(self : rosetta.protocols.abinitio.PairingStatistics, templates : protocols::abinitio::Templates) -> NoneType   3. __init__(self : rosetta.protocols.abinitio.PairingStatistics, topology : rosetta.core.scoring.dssp.StrandPairingSet) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.abinitio.PairingStatistics) -> str add_entry(...) from builtins.PyCapsule add_entry(self : rosetta.protocols.abinitio.PairingStatistics, ps : rosetta.core.scoring.dssp.StrandPairing, id : str) -> NoneType add_topology(...) from builtins.PyCapsule add_topology(self : rosetta.protocols.abinitio.PairingStatistics, topology : rosetta.core.scoring.dssp.StrandPairingSet, id : str) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.PairingStatistics,  : rosetta.protocols.abinitio.PairingStatistics) -> rosetta.protocols.abinitio.PairingStatistics compute_model_weights(...) from builtins.PyCapsule compute_model_weights(self : rosetta.protocols.abinitio.PairingStatistics,  : rosetta.std.map_std_string_unsigned_long) -> NoneType get_native_topology(...) from builtins.PyCapsule get_native_topology(rosetta.protocols.abinitio.PairingStatistics) -> rosetta.core.scoring.dssp.StrandPairingSet is_native_pairing(...) from builtins.PyCapsule is_native_pairing(self : rosetta.protocols.abinitio.PairingStatistics, pairing : rosetta.core.scoring.dssp.StrandPairing) -> bool nr_models(...) from builtins.PyCapsule nr_models(rosetta.protocols.abinitio.PairingStatistics) -> int ranked_model(...) from builtins.PyCapsule ranked_model(self : rosetta.protocols.abinitio.PairingStatistics, nr : int) -> str register_options(...) from builtins.PyCapsule register_options() -> NoneType set_native_topology(...) from builtins.PyCapsule set_native_topology(self : rosetta.protocols.abinitio.PairingStatistics, topology : rosetta.core.scoring.dssp.StrandPairingSet) -> NoneType strand_weight(...) from builtins.PyCapsule strand_weight(self : rosetta.protocols.abinitio.PairingStatistics, pairing : rosetta.core.scoring.dssp.StrandPairing) -> float suggest_topology(...) from builtins.PyCapsule suggest_topology(self : rosetta.protocols.abinitio.PairingStatistics, topol_id : str) -> rosetta.core.scoring.dssp.StrandPairingSet topology(...) from builtins.PyCapsule topology(self : rosetta.protocols.abinitio.PairingStatistics, id : str) -> rosetta.core.scoring.dssp.StrandPairingSet weight(...) from builtins.PyCapsule weight(*args, **kwargs) Overloaded function.   1. weight(self : rosetta.protocols.abinitio.PairingStatistics, nr : int) -> float   2. weight(self : rosetta.protocols.abinitio.PairingStatistics, id : str) -> float   class Protocol(rosetta.protocols.moves.Mover)       Method resolution order: Protocol 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.Protocol) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_evaluation(...) from builtins.PyCapsule add_evaluation(self : rosetta.protocols.abinitio.Protocol, ev : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.abinitio.Protocol,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.Protocol,  : rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.abinitio.Protocol centroid_scorefxn(...) from builtins.PyCapsule centroid_scorefxn(rosetta.protocols.abinitio.Protocol) -> rosetta.core.scoring.ScoreFunction evaluate_pose(...) from builtins.PyCapsule evaluate_pose(self : rosetta.protocols.abinitio.Protocol, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType evaluator(...) from builtins.PyCapsule evaluator(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.evaluation.MetaPoseEvaluator fullatom_scorefxn(...) from builtins.PyCapsule fullatom_scorefxn(rosetta.protocols.abinitio.Protocol) -> rosetta.core.scoring.ScoreFunction get_checkpoints(...) from builtins.PyCapsule get_checkpoints(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.checkpoint.CheckPointer get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.Protocol) -> str init(...) from builtins.PyCapsule init(self : rosetta.protocols.abinitio.Protocol,  : rosetta.core.pose.Pose) -> NoneType kinematics(...) from builtins.PyCapsule kinematics(rosetta.protocols.abinitio.Protocol) -> rosetta.protocols.abinitio.KinematicControl output_debug_structure(...) from builtins.PyCapsule output_debug_structure(self : rosetta.protocols.abinitio.Protocol, pose : rosetta.core.pose.Pose, prefix : str) -> NoneType 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 return_centroid(...) from builtins.PyCapsule return_centroid(*args, **kwargs) Overloaded function.   1. return_centroid(rosetta.protocols.abinitio.Protocol) -> bool   2. return_centroid(self : rosetta.protocols.abinitio.Protocol, setting : bool) -> NoneType set_centroid_scorefxn(...) from builtins.PyCapsule set_centroid_scorefxn(self : rosetta.protocols.abinitio.Protocol, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_evaluation(...) from builtins.PyCapsule set_evaluation(self : rosetta.protocols.abinitio.Protocol, ev : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType set_fullatom_scorefxn(...) from builtins.PyCapsule set_fullatom_scorefxn(self : rosetta.protocols.abinitio.Protocol, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_kinematics(...) from builtins.PyCapsule set_kinematics(self : rosetta.protocols.abinitio.Protocol, kc : rosetta.protocols.abinitio.KinematicControl) -> NoneType set_silentout_file_name(...) from builtins.PyCapsule set_silentout_file_name(self : rosetta.protocols.abinitio.Protocol, str : str) -> NoneType start_from_centroid(...) from builtins.PyCapsule start_from_centroid(rosetta.protocols.abinitio.Protocol) -> bool Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply clone(...) from builtins.PyCapsule clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Return a clone of the Mover object. create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class ResolutionSwitcher(rosetta.protocols.moves.Mover)       Method resolution order: ResolutionSwitcher rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle,  : rosetta.core.pose.Pose, fullatom : bool, start_centroid : bool, apply_to_centroid : bool) -> NoneType   2. __init__(handle, rosetta.protocols.abinitio.ResolutionSwitcher) -> 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.ResolutionSwitcher,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.ResolutionSwitcher,  : rosetta.protocols.abinitio.ResolutionSwitcher) -> rosetta.protocols.abinitio.ResolutionSwitcher get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.abinitio.ResolutionSwitcher) -> str init_pose(...) from builtins.PyCapsule init_pose(*args, **kwargs) Overloaded function.   1. init_pose(rosetta.protocols.abinitio.ResolutionSwitcher) -> rosetta.core.pose.Pose   2. init_pose(rosetta.protocols.abinitio.ResolutionSwitcher) -> rosetta.core.pose.Pose set_map_cst_from_centroid_to_fa(...) from builtins.PyCapsule set_map_cst_from_centroid_to_fa(self : rosetta.protocols.abinitio.ResolutionSwitcher, setting : bool) -> NoneType set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.abinitio.ResolutionSwitcher, scorefxn_fa : rosetta.core.scoring.ScoreFunction) -> NoneType start_pose(...) from builtins.PyCapsule start_pose(rosetta.protocols.abinitio.ResolutionSwitcher) -> rosetta.core.pose.Pose 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 StageID(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.protocols.abinitio.StageID, rosetta.protocols.abinitio.StageID) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.protocols.abinitio.StageID) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.abinitio.StageID, int) -> NoneType   2. __init__(rosetta.protocols.abinitio.StageID, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.protocols.abinitio.StageID) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.protocols.abinitio.StageID, rosetta.protocols.abinitio.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.StageID) -> str Data and other attributes defined here: ALL_STAGES = StageID.ALL_STAGES END_ABINITIO = StageID.END_ABINITIO LAST_STAGE = StageID.LAST_STAGE LOOP_CLOSURE = StageID.LOOP_CLOSURE RELAX = StageID.RELAX STAGE_1 = StageID.STAGE_1 STAGE_2 = StageID.STAGE_2 STAGE_3 = StageID.STAGE_3 STAGE_3a = StageID.STAGE_3a STAGE_3b = StageID.STAGE_3b STAGE_4 = StageID.STAGE_4 SWITCH_TO_FULLATOM = StageID.SWITCH_TO_FULLATOM   class StrandConstraints(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.protocols.abinitio.StrandConstraints, strand_stats_ : rosetta.protocols.abinitio.PairingStatistics) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.abinitio.StrandConstraints) -> str add_pairing(...) from builtins.PyCapsule add_pairing(*args, **kwargs) Overloaded function.   1. add_pairing(self : rosetta.protocols.abinitio.StrandConstraints,  : rosetta.core.scoring.dssp.StrandPairing) -> NoneType   2. add_pairing(self : rosetta.protocols.abinitio.StrandConstraints,  : rosetta.core.scoring.dssp.StrandPairing, model : str) -> NoneType   3. add_pairing(self : rosetta.protocols.abinitio.StrandConstraints,  : rosetta.protocols.abinitio.PairingStatEntry) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.StrandConstraints,  : rosetta.protocols.abinitio.StrandConstraints) -> rosetta.protocols.abinitio.StrandConstraints build_constraints(...) from builtins.PyCapsule build_constraints(self : rosetta.protocols.abinitio.StrandConstraints, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t   class Template(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.abinitio.Template, name : str,  : rosetta.core.pose.Pose, mapping : rosetta.core.sequence.DerivedSequenceMapping) -> NoneType   2. __init__(self : rosetta.protocols.abinitio.Template, name : str,  : rosetta.core.pose.Pose, map_file : str, offset : int, score : float) -> NoneType   3. __init__(self : rosetta.protocols.abinitio.Template,  : rosetta.protocols.abinitio.Template) -> 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.Template,  : rosetta.protocols.abinitio.Template) -> rosetta.protocols.abinitio.Template constraints(...) from builtins.PyCapsule constraints(rosetta.protocols.abinitio.Template) -> rosetta.utility.vector1_std_shared_ptr_core_scoring_constraints_Obsolet_NamedAtomPairConstraint_t cull_violators(...) from builtins.PyCapsule cull_violators(self : rosetta.protocols.abinitio.Template, target_list : rosetta.utility.vector1_std_shared_ptr_core_scoring_constraints_Obsolet_NamedAtomPairConstraint_t, culled_list : rosetta.utility.vector1_std_shared_ptr_core_scoring_constraints_Obsolet_NamedAtomPairConstraint_t) -> NoneType external_score(...) from builtins.PyCapsule external_score(rosetta.protocols.abinitio.Template) -> float has_constraints(...) from builtins.PyCapsule has_constraints(rosetta.protocols.abinitio.Template) -> bool is_good(...) from builtins.PyCapsule is_good(rosetta.protocols.abinitio.Template) -> bool map2target(...) from builtins.PyCapsule map2target(*args, **kwargs) Overloaded function.   1. map2target(self : rosetta.protocols.abinitio.Template, template_frames : rosetta.core.fragment.FrameList, target_frames : rosetta.core.fragment.FrameList) -> NoneType   2. map2target(self : rosetta.protocols.abinitio.Template,  : rosetta.core.fragment.FrameList) -> NoneType   3. map2target(self : rosetta.protocols.abinitio.Template,  : rosetta.utility.vector1_std_shared_ptr_core_scoring_constraints_Obsolet_NamedAtomPairConstraint_t,  : rosetta.utility.vector1_std_shared_ptr_core_scoring_constraints_Obsolet_NamedAtomPairConstraint_t) -> NoneType map2template(...) from builtins.PyCapsule map2template(*args, **kwargs) Overloaded function.   1. map2template(self : rosetta.protocols.abinitio.Template, target_frames : rosetta.core.fragment.FrameList, template_frames : rosetta.core.fragment.FrameList) -> NoneType   2. map2template(self : rosetta.protocols.abinitio.Template,  : rosetta.core.fragment.FrameList) -> NoneType   3. map2template(self : rosetta.protocols.abinitio.Template,  : rosetta.utility.vector1_std_shared_ptr_core_scoring_constraints_Obsolet_NamedAtomPairConstraint_t,  : rosetta.utility.vector1_std_shared_ptr_core_scoring_constraints_Obsolet_NamedAtomPairConstraint_t) -> NoneType map_pairings2target(...) from builtins.PyCapsule map_pairings2target(self : rosetta.protocols.abinitio.Template, in : rosetta.utility.vector1_core_scoring_dssp_Pairing, out : rosetta.utility.vector1_core_scoring_dssp_Pairing) -> NoneType map_pairings2template(...) from builtins.PyCapsule map_pairings2template(self : rosetta.protocols.abinitio.Template, in : rosetta.utility.vector1_core_scoring_dssp_Pairing, out : rosetta.utility.vector1_core_scoring_dssp_Pairing) -> NoneType name(...) from builtins.PyCapsule name(rosetta.protocols.abinitio.Template) -> str pick_large_frags(...) from builtins.PyCapsule pick_large_frags(*args, **kwargs) Overloaded function.   1. pick_large_frags(self : rosetta.protocols.abinitio.Template, frag_set : rosetta.core.fragment.FragSet, frag_type : rosetta.core.fragment.SingleResidueFragData) -> int   2. pick_large_frags(self : rosetta.protocols.abinitio.Template, frag_set : rosetta.core.fragment.FragSet, frag_type : rosetta.core.fragment.SingleResidueFragData, ncopies : int) -> int query_sequence(...) from builtins.PyCapsule query_sequence(rosetta.protocols.abinitio.Template) -> str read_constraints(...) from builtins.PyCapsule read_constraints(self : rosetta.protocols.abinitio.Template, cst_file : str) -> NoneType register_options(...) from builtins.PyCapsule register_options() -> NoneType steal_frags(...) from builtins.PyCapsule steal_frags(*args, **kwargs) Overloaded function.   1. steal_frags(self : rosetta.protocols.abinitio.Template, target_frames : rosetta.core.fragment.FrameList, accumulator : rosetta.core.fragment.FragSet) -> int   2. steal_frags(self : rosetta.protocols.abinitio.Template, target_frames : rosetta.core.fragment.FrameList, accumulator : rosetta.core.fragment.FragSet, ncopies : int) -> int strand_pairings(...) from builtins.PyCapsule strand_pairings(rosetta.protocols.abinitio.Template) -> rosetta.core.scoring.dssp.StrandPairingSet topology_score(...) from builtins.PyCapsule topology_score(*args, **kwargs) Overloaded function.   1. topology_score(rosetta.protocols.abinitio.Template) -> float   2. topology_score(self : rosetta.protocols.abinitio.Template, setting : float) -> NoneType   class TemplateJumpSetup(rosetta.protocols.jumping.BaseJumpSetup)       Method resolution order: TemplateJumpSetup rosetta.protocols.jumping.BaseJumpSetup builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, templates : protocols::abinitio::Templates, secstruct : rosetta.core.fragment.SecondaryStructure,  : rosetta.protocols.abinitio.PairingStatistics, helix_pairings : rosetta.utility.vector1_core_scoring_dssp_Pairing) -> 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.TemplateJumpSetup,  : rosetta.protocols.abinitio.TemplateJumpSetup) -> rosetta.protocols.abinitio.TemplateJumpSetup clean_jumps(...) from builtins.PyCapsule clean_jumps(self : rosetta.protocols.abinitio.TemplateJumpSetup,  : rosetta.protocols.jumping.JumpSample) -> rosetta.protocols.jumping.JumpSample create_jump_sample(...) from builtins.PyCapsule create_jump_sample(rosetta.protocols.abinitio.TemplateJumpSetup) -> rosetta.protocols.jumping.JumpSample generate_jump_frags(...) from builtins.PyCapsule generate_jump_frags(self : rosetta.protocols.abinitio.TemplateJumpSetup,  : rosetta.protocols.jumping.JumpSample,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   returns an ordered FragSet that is compatible with the JumpSample  default: generate jumps from ss-library according to JumpSample is_helix_jump(...) from builtins.PyCapsule is_helix_jump(self : rosetta.protocols.abinitio.TemplateJumpSetup, p : rosetta.core.scoring.dssp.Pairing) -> bool type_name(...) from builtins.PyCapsule type_name(rosetta.protocols.abinitio.TemplateJumpSetup) -> str   class Templates(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.abinitio.Templates, str) -> NoneType   doc   2. __init__(self : rosetta.protocols.abinitio.Templates, config_file : str, native : rosetta.core.pose.Pose) -> NoneType   3. __init__(self : rosetta.protocols.abinitio.Templates,  : rosetta.protocols.abinitio.Templates) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_target_constraints(...) from builtins.PyCapsule add_target_constraints(self : rosetta.protocols.abinitio.Templates,  : rosetta.core.scoring.constraints.ConstraintSet,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.abinitio.Templates,  : rosetta.protocols.abinitio.Templates) -> rosetta.protocols.abinitio.Templates begin(...) from builtins.PyCapsule begin(rosetta.protocols.abinitio.Templates) -> std::_Rb_tree_const_iterator<std::pair<std::string const, std::shared_ptr<protocols::abinitio::Template> > > create_jump_def(...) from builtins.PyCapsule create_jump_def(*args, **kwargs) Overloaded function.   1. create_jump_def(rosetta.protocols.abinitio.Templates) -> rosetta.protocols.abinitio.TemplateJumpSetup   2. create_jump_def(self : rosetta.protocols.abinitio.Templates,  : rosetta.core.fragment.SecondaryStructure) -> rosetta.protocols.abinitio.TemplateJumpSetup end(...) from builtins.PyCapsule end(rosetta.protocols.abinitio.Templates) -> std::_Rb_tree_const_iterator<std::pair<std::string const, std::shared_ptr<protocols::abinitio::Template> > > get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.abinitio.Templates) -> rosetta.protocols.abinitio.Templates   2. get_self_ptr(rosetta.protocols.abinitio.Templates) -> rosetta.protocols.abinitio.Templates get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.abinitio.Templates) -> rosetta.std.weak_ptr_const_protocols_abinitio_Templates_t   2. get_self_weak_ptr(rosetta.protocols.abinitio.Templates) -> rosetta.std.weak_ptr_protocols_abinitio_Templates_t get_template(...) from builtins.PyCapsule get_template(self : rosetta.protocols.abinitio.Templates, ModelID : str) -> rosetta.protocols.abinitio.Template has_pairings(...) from builtins.PyCapsule has_pairings(rosetta.protocols.abinitio.Templates) -> bool has_template(...) from builtins.PyCapsule has_template(self : rosetta.protocols.abinitio.Templates, ModelID : str) -> bool helixjump_picks(...) from builtins.PyCapsule helixjump_picks(rosetta.protocols.abinitio.Templates) -> rosetta.utility.vector1_std_shared_ptr_const_protocols_abinitio_Template_t is_good(...) from builtins.PyCapsule is_good(rosetta.protocols.abinitio.Templates) -> bool pairings(...) from builtins.PyCapsule pairings(rosetta.protocols.abinitio.Templates) -> rosetta.utility.vector1_core_scoring_dssp_Pairing pick_frags(...) from builtins.PyCapsule pick_frags(*args, **kwargs) Overloaded function.   1. pick_frags(self : rosetta.protocols.abinitio.Templates,  : rosetta.core.fragment.FragSet, frag_type : rosetta.core.fragment.FragData, min_nr_frags : int) -> rosetta.core.fragment.FragSet   2. pick_frags(self : rosetta.protocols.abinitio.Templates,  : rosetta.core.fragment.FragSet, frag_type : rosetta.core.fragment.FragData, min_nr_frags : int, ncopies : int) -> rosetta.core.fragment.FragSet   3. pick_frags(self : rosetta.protocols.abinitio.Templates,  : rosetta.core.fragment.FragSet, frag_type : rosetta.core.fragment.FragData) -> int   4. pick_frags(self : rosetta.protocols.abinitio.Templates,  : rosetta.core.fragment.FragSet, frag_type : rosetta.core.fragment.FragData, ncopies : int) -> int pick_large_frags(...) from builtins.PyCapsule pick_large_frags(*args, **kwargs) Overloaded function.   1. pick_large_frags(self : rosetta.protocols.abinitio.Templates, frag_set : rosetta.core.fragment.FragSet, frag_type : rosetta.core.fragment.SingleResidueFragData) -> int   2. pick_large_frags(self : rosetta.protocols.abinitio.Templates, frag_set : rosetta.core.fragment.FragSet, frag_type : rosetta.core.fragment.SingleResidueFragData, ncopies : int) -> int read_pairings(...) from builtins.PyCapsule read_pairings(self : rosetta.protocols.abinitio.Templates, filename : str,  : rosetta.utility.vector1_core_scoring_dssp_Pairing) -> NoneType register_options(...) from builtins.PyCapsule register_options() -> NoneType set_native(...) from builtins.PyCapsule set_native(self : rosetta.protocols.abinitio.Templates, native : rosetta.core.pose.Pose) -> NoneType strand_pairing_stats(...) from builtins.PyCapsule strand_pairing_stats(rosetta.protocols.abinitio.Templates) -> rosetta.protocols.abinitio.PairingStatistics target_sequence(...) from builtins.PyCapsule target_sequence(*args, **kwargs) Overloaded function.   1. target_sequence(rosetta.protocols.abinitio.Templates) -> str   2. target_sequence(rosetta.protocols.abinitio.Templates) -> str target_total_residue(...) from builtins.PyCapsule target_total_residue(rosetta.protocols.abinitio.Templates) -> int