Bindings for protocols::dna namespace

Classes
		builtins.object DNABase DNABasepair DNABasestep DNAParameters DnaChains DnaDesignDef DnaInterfaceFinder DnaNeighbor DnaPosition PositionType ResTypeSequence_lt rosetta.core.pack.rotamer_set.RotamerOperation(builtins.object) RotamerDNAHBondFilter rosetta.core.pack.task.operation.TaskOperation(builtins.object) RestrictDesignToProteinDNAInterface WatsonCrickRotamerCouplings rosetta.core.pack.task.operation.TaskOperationCreator(builtins.object) RestrictDesignToProteinDNAInterfaceCreator WatsonCrickRotamerCouplingsCreator rosetta.protocols.jd2.PDBJobOutputter(rosetta.protocols.jd2.FileJobOutputter) PDBOutput rosetta.protocols.moves.Mover(builtins.object) SeparateDnaFromNonDna rosetta.protocols.moves.MoverCreator(builtins.object) DesignProteinBackboneAroundDNACreator DnaInterfaceMinMoverCreator DnaInterfaceMultiStateDesignCreator DnaInterfacePackerCreator SeparateDnaFromNonDnaCreator rosetta.protocols.simple_moves.MinMover(rosetta.protocols.moves.MoveMapMover) DnaInterfaceMinMover rosetta.protocols.simple_moves.PackRotamersMover(rosetta.protocols.moves.Mover) DesignProteinBackboneAroundDNA DnaInterfaceMultiStateDesign DnaInterfacePacker   class DNABase(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.dna.DNABase) -> NoneType   2. __init__(self : rosetta.protocols.dna.DNABase, rsd : rosetta.core.conformation.Residue) -> NoneType   3. __init__(self : rosetta.protocols.dna.DNABase,  : rosetta.protocols.dna.DNABase) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. alpha(...) from builtins.PyCapsule alpha(*args, **kwargs) Overloaded function.   1. alpha(rosetta.protocols.dna.DNABase) -> float   2. alpha(self : rosetta.protocols.dna.DNABase, in_value : float) -> NoneType amplitude(...) from builtins.PyCapsule amplitude(*args, **kwargs) Overloaded function.   1. amplitude(rosetta.protocols.dna.DNABase) -> float   2. amplitude(self : rosetta.protocols.dna.DNABase, in_value : float) -> NoneType beta(...) from builtins.PyCapsule beta(*args, **kwargs) Overloaded function.   1. beta(rosetta.protocols.dna.DNABase) -> float   2. beta(self : rosetta.protocols.dna.DNABase, in_value : float) -> NoneType chi(...) from builtins.PyCapsule chi(*args, **kwargs) Overloaded function.   1. chi(rosetta.protocols.dna.DNABase) -> float   2. chi(self : rosetta.protocols.dna.DNABase, in_value : float) -> NoneType delta(...) from builtins.PyCapsule delta(*args, **kwargs) Overloaded function.   1. delta(rosetta.protocols.dna.DNABase) -> float   2. delta(self : rosetta.protocols.dna.DNABase, in_value : float) -> NoneType epsilon(...) from builtins.PyCapsule epsilon(*args, **kwargs) Overloaded function.   1. epsilon(rosetta.protocols.dna.DNABase) -> float   2. epsilon(self : rosetta.protocols.dna.DNABase, in_value : float) -> NoneType gamma(...) from builtins.PyCapsule gamma(*args, **kwargs) Overloaded function.   1. gamma(rosetta.protocols.dna.DNABase) -> float   2. gamma(self : rosetta.protocols.dna.DNABase, in_value : float) -> NoneType pseudorotation(...) from builtins.PyCapsule pseudorotation(*args, **kwargs) Overloaded function.   1. pseudorotation(rosetta.protocols.dna.DNABase) -> float   2. pseudorotation(self : rosetta.protocols.dna.DNABase, in_value : float) -> NoneType zeta(...) from builtins.PyCapsule zeta(*args, **kwargs) Overloaded function.   1. zeta(rosetta.protocols.dna.DNABase) -> float   2. zeta(self : rosetta.protocols.dna.DNABase, in_value : float) -> NoneType   class DNABasepair(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.dna.DNABasepair) -> NoneType   2. __init__(self : rosetta.protocols.dna.DNABasepair, init_values : rosetta.utility.vector1_double) -> NoneType   3. __init__(self : rosetta.protocols.dna.DNABasepair, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue) -> NoneType   4. __init__(self : rosetta.protocols.dna.DNABasepair,  : rosetta.protocols.dna.DNABasepair) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. buckle(...) from builtins.PyCapsule buckle(*args, **kwargs) Overloaded function.   1. buckle(rosetta.protocols.dna.DNABasepair) -> float   2. buckle(self : rosetta.protocols.dna.DNABasepair, in_value : float) -> NoneType opening(...) from builtins.PyCapsule opening(*args, **kwargs) Overloaded function.   1. opening(rosetta.protocols.dna.DNABasepair) -> float   2. opening(self : rosetta.protocols.dna.DNABasepair, in_value : float) -> NoneType propeller(...) from builtins.PyCapsule propeller(*args, **kwargs) Overloaded function.   1. propeller(rosetta.protocols.dna.DNABasepair) -> float   2. propeller(self : rosetta.protocols.dna.DNABasepair, in_value : float) -> NoneType shear(...) from builtins.PyCapsule shear(*args, **kwargs) Overloaded function.   1. shear(rosetta.protocols.dna.DNABasepair) -> float   2. shear(self : rosetta.protocols.dna.DNABasepair, in_value : float) -> NoneType stagger(...) from builtins.PyCapsule stagger(*args, **kwargs) Overloaded function.   1. stagger(rosetta.protocols.dna.DNABasepair) -> float   2. stagger(self : rosetta.protocols.dna.DNABasepair, in_value : float) -> NoneType stretch(...) from builtins.PyCapsule stretch(*args, **kwargs) Overloaded function.   1. stretch(rosetta.protocols.dna.DNABasepair) -> float   2. stretch(self : rosetta.protocols.dna.DNABasepair, in_value : float) -> NoneType   class DNABasestep(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.dna.DNABasestep) -> NoneType   2. __init__(self : rosetta.protocols.dna.DNABasestep, init_values : rosetta.utility.vector1_double) -> NoneType   3. __init__(self : rosetta.protocols.dna.DNABasestep, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, rsd1_next : rosetta.core.conformation.Residue, rsd2_prev : rosetta.core.conformation.Residue) -> NoneType   4. __init__(self : rosetta.protocols.dna.DNABasestep,  : rosetta.protocols.dna.DNABasestep) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. rise(...) from builtins.PyCapsule rise(*args, **kwargs) Overloaded function.   1. rise(rosetta.protocols.dna.DNABasestep) -> float   2. rise(self : rosetta.protocols.dna.DNABasestep, in_value : float) -> NoneType roll(...) from builtins.PyCapsule roll(*args, **kwargs) Overloaded function.   1. roll(rosetta.protocols.dna.DNABasestep) -> float   2. roll(self : rosetta.protocols.dna.DNABasestep, in_value : float) -> NoneType shift(...) from builtins.PyCapsule shift(*args, **kwargs) Overloaded function.   1. shift(rosetta.protocols.dna.DNABasestep) -> float   2. shift(self : rosetta.protocols.dna.DNABasestep, in_value : float) -> NoneType slide(...) from builtins.PyCapsule slide(*args, **kwargs) Overloaded function.   1. slide(rosetta.protocols.dna.DNABasestep) -> float   2. slide(self : rosetta.protocols.dna.DNABasestep, in_value : float) -> NoneType tilt(...) from builtins.PyCapsule tilt(*args, **kwargs) Overloaded function.   1. tilt(rosetta.protocols.dna.DNABasestep) -> float   2. tilt(self : rosetta.protocols.dna.DNABasestep, in_value : float) -> NoneType twist(...) from builtins.PyCapsule twist(*args, **kwargs) Overloaded function.   1. twist(rosetta.protocols.dna.DNABasestep) -> float   2. twist(self : rosetta.protocols.dna.DNABasestep, in_value : float) -> NoneType   class DNAParameters(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.dna.DNAParameters) -> NoneType   2. __init__(self : rosetta.protocols.dna.DNAParameters, pose : rosetta.core.pose.Pose) -> 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.dna.DNAParameters,  : rosetta.protocols.dna.DNAParameters) -> rosetta.protocols.dna.DNAParameters base(...) from builtins.PyCapsule base(self : rosetta.protocols.dna.DNAParameters, resid : int) -> rosetta.protocols.dna.DNABase basepair(...) from builtins.PyCapsule basepair(self : rosetta.protocols.dna.DNAParameters, resid : int) -> rosetta.protocols.dna.DNABasepair basepairs_begin(...) from builtins.PyCapsule basepairs_begin(rosetta.protocols.dna.DNAParameters) -> std::_Rb_tree_const_iterator<std::pair<unsigned long const, protocols::dna::DNABasepair> > basepairs_end(...) from builtins.PyCapsule basepairs_end(rosetta.protocols.dna.DNAParameters) -> std::_Rb_tree_const_iterator<std::pair<unsigned long const, protocols::dna::DNABasepair> > bases_begin(...) from builtins.PyCapsule bases_begin(rosetta.protocols.dna.DNAParameters) -> std::_Rb_tree_const_iterator<std::pair<unsigned long const, protocols::dna::DNABase> > bases_end(...) from builtins.PyCapsule bases_end(rosetta.protocols.dna.DNAParameters) -> std::_Rb_tree_const_iterator<std::pair<unsigned long const, protocols::dna::DNABase> > basestep(...) from builtins.PyCapsule basestep(self : rosetta.protocols.dna.DNAParameters, resid : int) -> rosetta.protocols.dna.DNABasestep basesteps_begin(...) from builtins.PyCapsule basesteps_begin(rosetta.protocols.dna.DNAParameters) -> std::_Rb_tree_const_iterator<std::pair<unsigned long const, protocols::dna::DNABasestep> > basesteps_end(...) from builtins.PyCapsule basesteps_end(rosetta.protocols.dna.DNAParameters) -> std::_Rb_tree_const_iterator<std::pair<unsigned long const, protocols::dna::DNABasestep> > calculate(...) from builtins.PyCapsule calculate(self : rosetta.protocols.dna.DNAParameters, pose : rosetta.core.pose.Pose) -> NoneType find_partner(...) from builtins.PyCapsule find_partner(self : rosetta.protocols.dna.DNAParameters, resid : int) -> int is_base_paired(...) from builtins.PyCapsule is_base_paired(self : rosetta.protocols.dna.DNAParameters, resid : int) -> bool nth_dna_base(...) from builtins.PyCapsule nth_dna_base(self : rosetta.protocols.dna.DNAParameters, index : int) -> int number_of_basepairs(...) from builtins.PyCapsule number_of_basepairs(rosetta.protocols.dna.DNAParameters) -> int number_of_bases(...) from builtins.PyCapsule number_of_bases(rosetta.protocols.dna.DNAParameters) -> int number_of_basesteps(...) from builtins.PyCapsule number_of_basesteps(rosetta.protocols.dna.DNAParameters) -> int random_basepair(...) from builtins.PyCapsule random_basepair(rosetta.protocols.dna.DNAParameters) -> int random_basestep(...) from builtins.PyCapsule random_basestep(rosetta.protocols.dna.DNAParameters) -> int valid_basestep_start(...) from builtins.PyCapsule valid_basestep_start(self : rosetta.protocols.dna.DNAParameters, resid : int) -> bool   class DesignProteinBackboneAroundDNA(rosetta.protocols.simple_moves.PackRotamersMover)       Method resolution order: DesignProteinBackboneAroundDNA rosetta.protocols.simple_moves.PackRotamersMover 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,  : str,  : rosetta.core.scoring.ScoreFunction) -> NoneType   3. __init__(handle, rosetta.protocols.dna.DesignProteinBackboneAroundDNA) -> 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.dna.DesignProteinBackboneAroundDNA,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.dna.DesignProteinBackboneAroundDNA,  : rosetta.protocols.dna.DesignProteinBackboneAroundDNA) -> rosetta.protocols.dna.DesignProteinBackboneAroundDNA clone(...) from builtins.PyCapsule clone(rosetta.protocols.dna.DesignProteinBackboneAroundDNA) -> rosetta.protocols.moves.Mover   required in the context of the parser/scripting scheme fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.dna.DesignProteinBackboneAroundDNA) -> rosetta.protocols.moves.Mover   required in the context of the parser/scripting scheme get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.dna.DesignProteinBackboneAroundDNA) -> str targeted_dna(...) from builtins.PyCapsule targeted_dna(*args, **kwargs) Overloaded function.   1. targeted_dna(self : rosetta.protocols.dna.DesignProteinBackboneAroundDNA,  : rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t) -> NoneType   2. targeted_dna(rosetta.protocols.dna.DesignProteinBackboneAroundDNA) -> rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t Methods inherited from rosetta.protocols.simple_moves.PackRotamersMover: __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.simple_moves.PackRotamersMover) -> str ig(...) from builtins.PyCapsule ig(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase nloop(...) from builtins.PyCapsule nloop(*args, **kwargs) Overloaded function.   1. nloop(self : rosetta.protocols.simple_moves.PackRotamersMover, nloop_in : int) -> NoneType   2. nloop(rosetta.protocols.simple_moves.PackRotamersMover) -> int provide_xml_schema(...) from builtins.PyCapsule provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType rotamer_sets(...) from builtins.PyCapsule rotamer_sets(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.core.pack.rotamer_set.RotamerSets score_function(...) from builtins.PyCapsule score_function(*args, **kwargs) Overloaded function.   1. score_function(self : rosetta.protocols.simple_moves.PackRotamersMover, sf : rosetta.core.scoring.ScoreFunction) -> NoneType   Sets the ScoreFunction to  <sf>    example(s):      packmover.score_function(scorefxn)  See Also:      PackRotamersMover      PackRotamersMover.task   2. score_function(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.core.scoring.ScoreFunction   Returns the ScoreFunction    example(s):      packmover.score_function()  See Also:      PackRotamersMover      PackRotamersMover.task task(...) from builtins.PyCapsule task(*args, **kwargs) Overloaded function.   1. task(self : rosetta.protocols.simple_moves.PackRotamersMover, t : rosetta.core.pack.task.PackerTask) -> NoneType   Sets the PackerTask to  <t>    example(s):      packmover.task(task_pack)  See Also:      PackRotamersMover      PackRotamersMover.task_factory   2. task(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.core.pack.task.PackerTask   Returns the PackerTask    example(s):      packmover.task()  See Also:      PackRotamersMover      PackRotamersMover.task_factory task_factory(...) from builtins.PyCapsule task_factory(*args, **kwargs) Overloaded function.   1. task_factory(self : rosetta.protocols.simple_moves.PackRotamersMover, tf : rosetta.core.pack.task.TaskFactory) -> NoneType   Sets the TaskFactory to  <tf>    example(s):      packmover.task_factory(task_design)  See Also:      PackRotamersMover      PackRotamersMover.task   2. task_factory(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.core.pack.task.TaskFactory   Returns the TaskFactory    example(s):      packmover.task_factory()  See Also:      PackRotamersMover      PackRotamersMover.task task_is_valid(...) from builtins.PyCapsule task_is_valid(self : rosetta.protocols.simple_moves.PackRotamersMover, pose : rosetta.core.pose.Pose) -> 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 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 DesignProteinBackboneAroundDNACreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: DesignProteinBackboneAroundDNACreator 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.dna.DesignProteinBackboneAroundDNACreator,  : rosetta.protocols.dna.DesignProteinBackboneAroundDNACreator) -> rosetta.protocols.dna.DesignProteinBackboneAroundDNACreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.dna.DesignProteinBackboneAroundDNACreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.dna.DesignProteinBackboneAroundDNACreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class DnaChains(builtins.object)       Methods defined here: __getitem__(...) from builtins.PyCapsule __getitem__(*args, **kwargs) Overloaded function.   1. __getitem__(self : rosetta.protocols.dna.DnaChains, resindex : int) -> rosetta.protocols.dna.DnaPosition   2. __getitem__(self : rosetta.protocols.dna.DnaChains, resindex : int) -> rosetta.protocols.dna.DnaPosition __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.dna.DnaChains) -> NoneType   2. __init__(self : rosetta.protocols.dna.DnaChains, other : rosetta.protocols.dna.DnaChains) -> 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.dna.DnaChains,  : rosetta.protocols.dna.DnaChains) -> rosetta.protocols.dna.DnaChains begin(...) from builtins.PyCapsule begin(rosetta.protocols.dna.DnaChains) -> std::_Rb_tree_const_iterator<std::pair<unsigned long const, protocols::dna::DnaPosition> > clear(...) from builtins.PyCapsule clear(rosetta.protocols.dna.DnaChains) -> NoneType clone(...) from builtins.PyCapsule clone(rosetta.protocols.dna.DnaChains) -> rosetta.protocols.dna.DnaChains contains(...) from builtins.PyCapsule contains(self : rosetta.protocols.dna.DnaChains, index : int) -> bool empty(...) from builtins.PyCapsule empty(rosetta.protocols.dna.DnaChains) -> bool end(...) from builtins.PyCapsule end(rosetta.protocols.dna.DnaChains) -> std::_Rb_tree_const_iterator<std::pair<unsigned long const, protocols::dna::DnaPosition> > is_top(...) from builtins.PyCapsule is_top(self : rosetta.protocols.dna.DnaChains, index : int) -> bool positions(...) from builtins.PyCapsule positions(*args, **kwargs) Overloaded function.   1. positions(rosetta.protocols.dna.DnaChains) -> rosetta.std.map_unsigned_long_protocols_dna_DnaPosition   2. positions(rosetta.protocols.dna.DnaChains) -> rosetta.std.map_unsigned_long_protocols_dna_DnaPosition size(...) from builtins.PyCapsule size(rosetta.protocols.dna.DnaChains) -> int   class DnaDesignDef(builtins.object)     command-line dna_defs are of the format "C.501.ADE" they are parsed here into this little class for convenience     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.dna.DnaDesignDef,  : str) -> NoneType   2. __init__(self : rosetta.protocols.dna.DnaDesignDef,  : rosetta.protocols.dna.DnaDesignDef) -> 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.dna.DnaDesignDef) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.dna.DnaDesignDef,  : rosetta.protocols.dna.DnaDesignDef) -> rosetta.protocols.dna.DnaDesignDef Data descriptors defined here: chain name3 pdbpos   class DnaInterfaceFinder(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.dna.DnaInterfaceFinder) -> NoneType   doc   2. __init__(rosetta.protocols.dna.DnaInterfaceFinder, float) -> NoneType   doc   3. __init__(rosetta.protocols.dna.DnaInterfaceFinder, float, float) -> NoneType   doc   4. __init__(rosetta.protocols.dna.DnaInterfaceFinder, float, float, float) -> NoneType   doc   5. __init__(self : rosetta.protocols.dna.DnaInterfaceFinder, close_threshold : float, contact_threshold : float, z_cutoff : float, base_only : bool) -> NoneType   6. __init__(self : rosetta.protocols.dna.DnaInterfaceFinder,  : rosetta.protocols.dna.DnaInterfaceFinder) -> 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.dna.DnaInterfaceFinder,  : rosetta.protocols.dna.DnaInterfaceFinder) -> rosetta.protocols.dna.DnaInterfaceFinder clone(...) from builtins.PyCapsule clone(rosetta.protocols.dna.DnaInterfaceFinder) -> rosetta.protocols.dna.DnaInterfaceFinder determine_dna_interface(...) from builtins.PyCapsule determine_dna_interface(self : rosetta.protocols.dna.DnaInterfaceFinder, pose : rosetta.core.pose.Pose, protein_positions : rosetta.utility.vector1_unsigned_long, dna_positions : rosetta.utility.vector1_unsigned_long) -> NoneType determine_interface(...) from builtins.PyCapsule determine_interface(*args, **kwargs) Overloaded function.   1. determine_interface(self : rosetta.protocols.dna.DnaInterfaceFinder, pose : rosetta.core.pose.Pose, protein_positions : rosetta.utility.vector1_unsigned_long, dna_positions : rosetta.utility.vector1_unsigned_long) -> NoneType   2. determine_interface(self : rosetta.protocols.dna.DnaInterfaceFinder, pose : rosetta.core.pose.Pose) -> NoneType determine_protein_interface(...) from builtins.PyCapsule determine_protein_interface(*args, **kwargs) Overloaded function.   1. determine_protein_interface(self : rosetta.protocols.dna.DnaInterfaceFinder, pose : rosetta.core.pose.Pose) -> NoneType   2. determine_protein_interface(self : rosetta.protocols.dna.DnaInterfaceFinder, pose : rosetta.core.pose.Pose, protein_positions : rosetta.utility.vector1_unsigned_long, dna_positions : rosetta.utility.vector1_unsigned_long) -> NoneType dna_neighbors(...) from builtins.PyCapsule dna_neighbors(rosetta.protocols.dna.DnaInterfaceFinder) -> rosetta.std.map_unsigned_long_protocols_dna_DnaNeighbor initialized(...) from builtins.PyCapsule initialized(rosetta.protocols.dna.DnaInterfaceFinder) -> bool protein_neighbors(...) from builtins.PyCapsule protein_neighbors(rosetta.protocols.dna.DnaInterfaceFinder) -> rosetta.std.map_unsigned_long_protocols_dna_DnaNeighbor   class DnaInterfaceMinMover(rosetta.protocols.simple_moves.MinMover)       Method resolution order: DnaInterfaceMinMover rosetta.protocols.simple_moves.MinMover rosetta.protocols.moves.MoveMapMover 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.dna.DnaInterfaceMinMover) -> NoneType   3. __init__(self : handle,  : rosetta.protocols.dna.DnaInterfaceFinder) -> 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.dna.DnaInterfaceMinMover,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.dna.DnaInterfaceMinMover,  : rosetta.protocols.dna.DnaInterfaceMinMover) -> rosetta.protocols.dna.DnaInterfaceMinMover bb(...) from builtins.PyCapsule bb(self : rosetta.protocols.dna.DnaInterfaceMinMover, value : bool) -> NoneType chi(...) from builtins.PyCapsule chi(self : rosetta.protocols.dna.DnaInterfaceMinMover, value : bool) -> NoneType clone(...) from builtins.PyCapsule clone(rosetta.protocols.dna.DnaInterfaceMinMover) -> rosetta.protocols.moves.Mover   required in the context of the parser/scripting scheme fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.dna.DnaInterfaceMinMover) -> rosetta.protocols.moves.Mover   required in the context of the parser/scripting scheme get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.dna.DnaInterfaceMinMover) -> str reset_from_interface(...) from builtins.PyCapsule reset_from_interface(rosetta.protocols.dna.DnaInterfaceMinMover) -> NoneType use_interface(...) from builtins.PyCapsule use_interface(self : rosetta.protocols.dna.DnaInterfaceMinMover,  : rosetta.protocols.dna.DnaInterfaceFinder) -> NoneType Methods inherited from rosetta.protocols.simple_moves.MinMover: __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.simple_moves.MinMover) -> str cartesian(...) from builtins.PyCapsule cartesian(*args, **kwargs) Overloaded function.   1. cartesian(self : rosetta.protocols.simple_moves.MinMover, newval : bool) -> NoneType   2. cartesian(rosetta.protocols.simple_moves.MinMover) -> bool deriv_check(...) from builtins.PyCapsule deriv_check(*args, **kwargs) Overloaded function.   1. deriv_check(self : rosetta.protocols.simple_moves.MinMover, deriv_check_in : bool) -> NoneType   2. deriv_check(rosetta.protocols.simple_moves.MinMover) -> bool max_iter(...) from builtins.PyCapsule max_iter(self : rosetta.protocols.simple_moves.MinMover, max_iter_in : int) -> NoneType min_options(...) from builtins.PyCapsule min_options(*args, **kwargs) Overloaded function.   1. min_options(rosetta.protocols.simple_moves.MinMover) -> rosetta.core.optimization.MinimizerOptions   allow non-const access to the internal minimizer options object   2. min_options(rosetta.protocols.simple_moves.MinMover) -> rosetta.core.optimization.MinimizerOptions   allow const access to the internal minimizer options object   3. min_options(self : rosetta.protocols.simple_moves.MinMover, min_options : rosetta.core.optimization.MinimizerOptions) -> NoneType   directly set the internal minimizer options object min_type(...) from builtins.PyCapsule min_type(*args, **kwargs) Overloaded function.   1. min_type(self : rosetta.protocols.simple_moves.MinMover, min_type_in : str) -> NoneType   2. min_type(rosetta.protocols.simple_moves.MinMover) -> str movemap(...) from builtins.PyCapsule movemap(*args, **kwargs) Overloaded function.   1. movemap(self : rosetta.protocols.simple_moves.MinMover, movemap_in : rosetta.core.kinematics.MoveMap) -> NoneType   Sets the MoveMap to  <movemap_in>  determines which DOF to minimize    example(s):      minmover.movemap(movemap1)  See also:      MinMover      MinMover.apply      MinMover.score_function      MoveMap   2. movemap(rosetta.protocols.simple_moves.MinMover) -> rosetta.core.kinematics.MoveMap nb_list(...) from builtins.PyCapsule nb_list(*args, **kwargs) Overloaded function.   1. nb_list(self : rosetta.protocols.simple_moves.MinMover, nb_list_in : bool) -> NoneType   core::optimization::MinimizerOptions::use_nblist(bool)   2. nb_list(rosetta.protocols.simple_moves.MinMover) -> bool   core::optimization::MinimizerOptions::use_nblist() omega(...) from builtins.PyCapsule omega(*args, **kwargs) Overloaded function.   1. omega(rosetta.protocols.simple_moves.MinMover) -> bool   2. omega(self : rosetta.protocols.simple_moves.MinMover, b : bool) -> NoneType parse_chi_and_bb(...) from builtins.PyCapsule parse_chi_and_bb(self : rosetta.protocols.simple_moves.MinMover,  : rosetta.utility.tag.Tag) -> NoneType parse_dof_task_type(...) from builtins.PyCapsule parse_dof_task_type(self : rosetta.protocols.simple_moves.MinMover, tag_name : str, dof_type : rosetta.core.id.DOF_Type, torsion_type : rosetta.core.id.TorsionType, tag : rosetta.utility.tag.Tag, data : rosetta.basic.datacache.DataMap) -> NoneType parse_dof_tasks(...) from builtins.PyCapsule parse_dof_tasks(self : rosetta.protocols.simple_moves.MinMover, tag : rosetta.utility.tag.Tag, data : rosetta.basic.datacache.DataMap) -> NoneType provide_xml_schema(...) from builtins.PyCapsule provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType score_function(...) from builtins.PyCapsule score_function(*args, **kwargs) Overloaded function.   1. score_function(self : rosetta.protocols.simple_moves.MinMover, scorefxn_in : rosetta.core.scoring.ScoreFunction) -> NoneType   Sets the ScoreFunction to  <scorefxn_in>  determines which function to minimize    example(s):      minmover.score_function(scorefxn)  See also:      MinMover      MinMover.apply      MinMover.movemap      ScoreFunction   2. score_function(rosetta.protocols.simple_moves.MinMover) -> rosetta.core.scoring.ScoreFunction set_movemap(...) from builtins.PyCapsule set_movemap(self : rosetta.protocols.simple_moves.MinMover, movemap_in : rosetta.core.kinematics.MoveMap) -> NoneType tolerance(...) from builtins.PyCapsule tolerance(*args, **kwargs) Overloaded function.   1. tolerance(self : rosetta.protocols.simple_moves.MinMover, tolerance_in : float) -> NoneType   2. tolerance(rosetta.protocols.simple_moves.MinMover) -> float Methods inherited from rosetta.protocols.moves.MoveMapMover: initialize(...) from builtins.PyCapsule initialize(self : rosetta.protocols.moves.MoveMapMover,  : rosetta.core.pose.Pose) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class DnaInterfaceMinMoverCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: DnaInterfaceMinMoverCreator 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.dna.DnaInterfaceMinMoverCreator,  : rosetta.protocols.dna.DnaInterfaceMinMoverCreator) -> rosetta.protocols.dna.DnaInterfaceMinMoverCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.dna.DnaInterfaceMinMoverCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.dna.DnaInterfaceMinMoverCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class DnaInterfaceMultiStateDesign(rosetta.protocols.simple_moves.PackRotamersMover)     wraps DNA-interface specific considerations around the general multistate design / genetic algorithm framework     Method resolution order: DnaInterfaceMultiStateDesign rosetta.protocols.simple_moves.PackRotamersMover 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.dna.DnaInterfaceMultiStateDesign) -> 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.dna.DnaInterfaceMultiStateDesign,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.dna.DnaInterfaceMultiStateDesign,  : rosetta.protocols.dna.DnaInterfaceMultiStateDesign) -> rosetta.protocols.dna.DnaInterfaceMultiStateDesign clone(...) from builtins.PyCapsule clone(rosetta.protocols.dna.DnaInterfaceMultiStateDesign) -> rosetta.protocols.moves.Mover   required in the context of the parser/scripting scheme copy_dna_chains(...) from builtins.PyCapsule copy_dna_chains(self : rosetta.protocols.dna.DnaInterfaceMultiStateDesign,  : rosetta.protocols.dna.DnaChains) -> NoneType copy_targeted_dna(...) from builtins.PyCapsule copy_targeted_dna(self : rosetta.protocols.dna.DnaInterfaceMultiStateDesign,  : rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t) -> NoneType fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.dna.DnaInterfaceMultiStateDesign) -> rosetta.protocols.moves.Mover   required in the context of the parser/scripting scheme get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.dna.DnaInterfaceMultiStateDesign) -> str output_results(...) from builtins.PyCapsule output_results(self : rosetta.protocols.dna.DnaInterfaceMultiStateDesign,  : rosetta.core.pose.Pose) -> NoneType Methods inherited from rosetta.protocols.simple_moves.PackRotamersMover: __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.simple_moves.PackRotamersMover) -> str ig(...) from builtins.PyCapsule ig(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase nloop(...) from builtins.PyCapsule nloop(*args, **kwargs) Overloaded function.   1. nloop(self : rosetta.protocols.simple_moves.PackRotamersMover, nloop_in : int) -> NoneType   2. nloop(rosetta.protocols.simple_moves.PackRotamersMover) -> int provide_xml_schema(...) from builtins.PyCapsule provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType rotamer_sets(...) from builtins.PyCapsule rotamer_sets(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.core.pack.rotamer_set.RotamerSets score_function(...) from builtins.PyCapsule score_function(*args, **kwargs) Overloaded function.   1. score_function(self : rosetta.protocols.simple_moves.PackRotamersMover, sf : rosetta.core.scoring.ScoreFunction) -> NoneType   Sets the ScoreFunction to  <sf>    example(s):      packmover.score_function(scorefxn)  See Also:      PackRotamersMover      PackRotamersMover.task   2. score_function(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.core.scoring.ScoreFunction   Returns the ScoreFunction    example(s):      packmover.score_function()  See Also:      PackRotamersMover      PackRotamersMover.task task(...) from builtins.PyCapsule task(*args, **kwargs) Overloaded function.   1. task(self : rosetta.protocols.simple_moves.PackRotamersMover, t : rosetta.core.pack.task.PackerTask) -> NoneType   Sets the PackerTask to  <t>    example(s):      packmover.task(task_pack)  See Also:      PackRotamersMover      PackRotamersMover.task_factory   2. task(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.core.pack.task.PackerTask   Returns the PackerTask    example(s):      packmover.task()  See Also:      PackRotamersMover      PackRotamersMover.task_factory task_factory(...) from builtins.PyCapsule task_factory(*args, **kwargs) Overloaded function.   1. task_factory(self : rosetta.protocols.simple_moves.PackRotamersMover, tf : rosetta.core.pack.task.TaskFactory) -> NoneType   Sets the TaskFactory to  <tf>    example(s):      packmover.task_factory(task_design)  See Also:      PackRotamersMover      PackRotamersMover.task   2. task_factory(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.core.pack.task.TaskFactory   Returns the TaskFactory    example(s):      packmover.task_factory()  See Also:      PackRotamersMover      PackRotamersMover.task task_is_valid(...) from builtins.PyCapsule task_is_valid(self : rosetta.protocols.simple_moves.PackRotamersMover, pose : rosetta.core.pose.Pose) -> 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 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 DnaInterfaceMultiStateDesignCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: DnaInterfaceMultiStateDesignCreator 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.dna.DnaInterfaceMultiStateDesignCreator,  : rosetta.protocols.dna.DnaInterfaceMultiStateDesignCreator) -> rosetta.protocols.dna.DnaInterfaceMultiStateDesignCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.dna.DnaInterfaceMultiStateDesignCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.dna.DnaInterfaceMultiStateDesignCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class DnaInterfacePacker(rosetta.protocols.simple_moves.PackRotamersMover)       Method resolution order: DnaInterfacePacker rosetta.protocols.simple_moves.PackRotamersMover rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.scoring.ScoreFunction) -> NoneType   doc   3. __init__(handle, rosetta.core.scoring.ScoreFunction, bool) -> NoneType   doc   4. __init__(self : handle,  : rosetta.core.scoring.ScoreFunction, minimize : bool, filename_root : str) -> NoneType   5. __init__(handle, rosetta.protocols.dna.DnaInterfacePacker) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. allowed_types(...) from builtins.PyCapsule allowed_types(rosetta.protocols.dna.DnaInterfacePacker) -> str apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.dna.DnaInterfacePacker,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.dna.DnaInterfacePacker,  : rosetta.protocols.dna.DnaInterfacePacker) -> rosetta.protocols.dna.DnaInterfacePacker clear_initialization(...) from builtins.PyCapsule clear_initialization(rosetta.protocols.dna.DnaInterfacePacker) -> NoneType clone(...) from builtins.PyCapsule clone(rosetta.protocols.dna.DnaInterfacePacker) -> rosetta.protocols.moves.Mover current_dna_design_string(...) from builtins.PyCapsule current_dna_design_string(self : rosetta.protocols.dna.DnaInterfacePacker,  : rosetta.core.pose.Pose) -> str fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.dna.DnaInterfacePacker) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.dna.DnaInterfacePacker) -> str initialized(...) from builtins.PyCapsule initialized(rosetta.protocols.dna.DnaInterfacePacker) -> bool measure_specificity(...) from builtins.PyCapsule measure_specificity(self : rosetta.protocols.dna.DnaInterfacePacker,  : rosetta.core.pose.Pose) -> (float, float) pdbname(...) from builtins.PyCapsule pdbname(rosetta.protocols.dna.DnaInterfacePacker) -> str pdboutput(...) from builtins.PyCapsule pdboutput(self : rosetta.protocols.dna.DnaInterfacePacker,  : protocols::dna::PDBOutput) -> NoneType reference_pose(...) from builtins.PyCapsule reference_pose(*args, **kwargs) Overloaded function.   1. reference_pose(self : rosetta.protocols.dna.DnaInterfacePacker,  : rosetta.core.pose.Pose) -> NoneType   2. reference_pose(rosetta.protocols.dna.DnaInterfacePacker) -> rosetta.core.pose.Pose reversion_scan(...) from builtins.PyCapsule reversion_scan(*args, **kwargs) Overloaded function.   1. reversion_scan(self : rosetta.protocols.dna.DnaInterfacePacker,  : rosetta.core.pose.Pose) -> NoneType   2. reversion_scan(self : rosetta.protocols.dna.DnaInterfacePacker,  : rosetta.core.pose.Pose, bound_score : float) -> NoneType   3. reversion_scan(self : rosetta.protocols.dna.DnaInterfacePacker,  : rosetta.core.pose.Pose, bound_score : float, binding_score : float) -> NoneType   4. reversion_scan(self : rosetta.protocols.dna.DnaInterfacePacker,  : rosetta.core.pose.Pose, bound_score : float, binding_score : float, specificities : (float, float)) -> NoneType set_filename_root(...) from builtins.PyCapsule set_filename_root(self : rosetta.protocols.dna.DnaInterfacePacker, name : str) -> NoneType targeted_dna(...) from builtins.PyCapsule targeted_dna(*args, **kwargs) Overloaded function.   1. targeted_dna(self : rosetta.protocols.dna.DnaInterfacePacker,  : rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t) -> NoneType   2. targeted_dna(rosetta.protocols.dna.DnaInterfacePacker) -> rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t unbound_score(...) from builtins.PyCapsule unbound_score(*args, **kwargs) Overloaded function.   1. unbound_score(self : rosetta.protocols.dna.DnaInterfacePacker,  : rosetta.core.pose.Pose) -> float   2. unbound_score(self : rosetta.protocols.dna.DnaInterfacePacker,  : rosetta.core.pose.Pose, output_pdb : bool) -> float   3. unbound_score(self : rosetta.protocols.dna.DnaInterfacePacker,  : rosetta.core.pose.Pose, output_pdb : bool, pdbname : str) -> float Methods inherited from rosetta.protocols.simple_moves.PackRotamersMover: __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.simple_moves.PackRotamersMover) -> str ig(...) from builtins.PyCapsule ig(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase nloop(...) from builtins.PyCapsule nloop(*args, **kwargs) Overloaded function.   1. nloop(self : rosetta.protocols.simple_moves.PackRotamersMover, nloop_in : int) -> NoneType   2. nloop(rosetta.protocols.simple_moves.PackRotamersMover) -> int provide_xml_schema(...) from builtins.PyCapsule provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType rotamer_sets(...) from builtins.PyCapsule rotamer_sets(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.core.pack.rotamer_set.RotamerSets score_function(...) from builtins.PyCapsule score_function(*args, **kwargs) Overloaded function.   1. score_function(self : rosetta.protocols.simple_moves.PackRotamersMover, sf : rosetta.core.scoring.ScoreFunction) -> NoneType   Sets the ScoreFunction to  <sf>    example(s):      packmover.score_function(scorefxn)  See Also:      PackRotamersMover      PackRotamersMover.task   2. score_function(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.core.scoring.ScoreFunction   Returns the ScoreFunction    example(s):      packmover.score_function()  See Also:      PackRotamersMover      PackRotamersMover.task task(...) from builtins.PyCapsule task(*args, **kwargs) Overloaded function.   1. task(self : rosetta.protocols.simple_moves.PackRotamersMover, t : rosetta.core.pack.task.PackerTask) -> NoneType   Sets the PackerTask to  <t>    example(s):      packmover.task(task_pack)  See Also:      PackRotamersMover      PackRotamersMover.task_factory   2. task(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.core.pack.task.PackerTask   Returns the PackerTask    example(s):      packmover.task()  See Also:      PackRotamersMover      PackRotamersMover.task_factory task_factory(...) from builtins.PyCapsule task_factory(*args, **kwargs) Overloaded function.   1. task_factory(self : rosetta.protocols.simple_moves.PackRotamersMover, tf : rosetta.core.pack.task.TaskFactory) -> NoneType   Sets the TaskFactory to  <tf>    example(s):      packmover.task_factory(task_design)  See Also:      PackRotamersMover      PackRotamersMover.task   2. task_factory(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.core.pack.task.TaskFactory   Returns the TaskFactory    example(s):      packmover.task_factory()  See Also:      PackRotamersMover      PackRotamersMover.task task_is_valid(...) from builtins.PyCapsule task_is_valid(self : rosetta.protocols.simple_moves.PackRotamersMover, pose : rosetta.core.pose.Pose) -> 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 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 DnaInterfacePackerCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: DnaInterfacePackerCreator 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.dna.DnaInterfacePackerCreator,  : rosetta.protocols.dna.DnaInterfacePackerCreator) -> rosetta.protocols.dna.DnaInterfacePackerCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.dna.DnaInterfacePackerCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.dna.DnaInterfacePackerCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class DnaNeighbor(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.dna.DnaNeighbor) -> NoneType   2. __init__(self : rosetta.protocols.dna.DnaNeighbor,  : rosetta.protocols.dna.DnaNeighbor) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. close(...) from builtins.PyCapsule close(*args, **kwargs) Overloaded function.   1. close(self : rosetta.protocols.dna.DnaNeighbor, val : bool) -> NoneType   2. close(rosetta.protocols.dna.DnaNeighbor) -> bool contact(...) from builtins.PyCapsule contact(*args, **kwargs) Overloaded function.   1. contact(self : rosetta.protocols.dna.DnaNeighbor, val : bool) -> NoneType   2. contact(rosetta.protocols.dna.DnaNeighbor) -> bool   class DnaPosition(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.dna.DnaPosition) -> NoneType   2. __init__(self : rosetta.protocols.dna.DnaPosition, i : int) -> NoneType   3. __init__(self : rosetta.protocols.dna.DnaPosition, i : int, j : int) -> NoneType   4. __init__(self : rosetta.protocols.dna.DnaPosition,  : rosetta.protocols.dna.DnaPosition) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. bottom(...) from builtins.PyCapsule bottom(rosetta.protocols.dna.DnaPosition) -> int paired(...) from builtins.PyCapsule paired(rosetta.protocols.dna.DnaPosition) -> bool top(...) from builtins.PyCapsule top(rosetta.protocols.dna.DnaPosition) -> int   class PDBOutput(rosetta.protocols.jd2.PDBJobOutputter)       Method resolution order: PDBOutput rosetta.protocols.jd2.PDBJobOutputter rosetta.protocols.jd2.FileJobOutputter rosetta.protocols.jd2.JobOutputter builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.protocols.dna.PDBOutput,  : rosetta.core.pose.Pose,  : str) -> NoneType   functor for non-JobDistributor usage __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. add_info(...) from builtins.PyCapsule add_info(*args, **kwargs) Overloaded function.   1. add_info(self : rosetta.protocols.dna.PDBOutput,  : str,  : rosetta.std.list_std_string_std_allocator_std_string_t) -> NoneType   2. add_info(self : rosetta.protocols.dna.PDBOutput,  : str,  : rosetta.std.list_std_string_std_allocator_std_string_t, append : bool) -> NoneType designed_residue(...) from builtins.PyCapsule designed_residue(*args, **kwargs) Overloaded function.   1. designed_residue(self : rosetta.protocols.dna.PDBOutput,  : int) -> NoneType   2. designed_residue(self : rosetta.protocols.dna.PDBOutput,  : int, value : bool) -> NoneType enabled(...) from builtins.PyCapsule enabled(*args, **kwargs) Overloaded function.   1. enabled(self : rosetta.protocols.dna.PDBOutput, value : bool) -> NoneType   2. enabled(rosetta.protocols.dna.PDBOutput) -> bool final_pose(...) from builtins.PyCapsule final_pose(self : rosetta.protocols.dna.PDBOutput,  : rosetta.protocols.jd2.Job,  : rosetta.core.pose.Pose,  : str) -> NoneType   JobDistributor calls this method note_designed_residues(...) from builtins.PyCapsule note_designed_residues(self : rosetta.protocols.dna.PDBOutput,  : rosetta.core.pack.task.PackerTask) -> NoneType reference_pose(...) from builtins.PyCapsule reference_pose(*args, **kwargs) Overloaded function.   1. reference_pose(self : rosetta.protocols.dna.PDBOutput,  : rosetta.core.pose.Pose) -> NoneType   2. reference_pose(rosetta.protocols.dna.PDBOutput) -> rosetta.core.pose.Pose remove_info(...) from builtins.PyCapsule remove_info(self : rosetta.protocols.dna.PDBOutput,  : str) -> bool residues_are_different(...) from builtins.PyCapsule residues_are_different(self : rosetta.protocols.dna.PDBOutput,  : rosetta.core.conformation.Residue,  : rosetta.core.conformation.Residue) -> bool score_function(...) from builtins.PyCapsule score_function(*args, **kwargs) Overloaded function.   1. score_function(self : rosetta.protocols.dna.PDBOutput, sf : rosetta.core.scoring.ScoreFunction) -> NoneType   2. score_function(rosetta.protocols.dna.PDBOutput) -> rosetta.core.scoring.ScoreFunction starting_pose(...) from builtins.PyCapsule starting_pose(self : rosetta.protocols.dna.PDBOutput,  : rosetta.core.pose.Pose) -> NoneType Methods inherited from rosetta.protocols.jd2.PDBJobOutputter: job_has_completed(...) from builtins.PyCapsule job_has_completed(self : rosetta.protocols.jd2.PDBJobOutputter, job : rosetta.protocols.jd2.Job) -> bool   this function is not used for output, but it belongs here since it needs to check the same output locations as the class normally writes to.  This class checks wherever output goes to see if the job's expected output already exists (on disk or whatever).  This is the most basic form of checkpointing.  The base implementation looks for a pdb with the job's name already in existence. other_pose(...) from builtins.PyCapsule other_pose(*args, **kwargs) Overloaded function.   1. other_pose(self : rosetta.protocols.jd2.PDBJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str) -> NoneType   this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol.  This implementation will write a PDB file (plus scores).   2. other_pose(self : rosetta.protocols.jd2.PDBJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str, copy_count : int) -> NoneType   this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol.  This implementation will write a PDB file (plus scores).   3. other_pose(self : rosetta.protocols.jd2.PDBJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str, copy_count : int, score_only : bool) -> NoneType   this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol.  This implementation will write a PDB file (plus scores). output_name(...) from builtins.PyCapsule output_name(self : rosetta.protocols.jd2.PDBJobOutputter, job : rosetta.protocols.jd2.Job) -> str   this is the master function for determining the unique output identifier for a job Methods inherited from rosetta.protocols.jd2.FileJobOutputter: file(...) from builtins.PyCapsule file(self : rosetta.protocols.jd2.FileJobOutputter, job : rosetta.protocols.jd2.Job, data : str) -> NoneType   this function takes a string and writes it to disk (separately from Tracer output). scorefile_name(...) from builtins.PyCapsule scorefile_name(rosetta.protocols.jd2.FileJobOutputter) -> rosetta.utility.file.FileName set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.jd2.FileJobOutputter) -> NoneType write_scorefile(...) from builtins.PyCapsule write_scorefile(rosetta.protocols.jd2.FileJobOutputter) -> bool Methods inherited from rosetta.protocols.jd2.JobOutputter: add_evaluation(...) from builtins.PyCapsule add_evaluation(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType   ////////////////////////////// evaluator interface //////////////////////////////////////////// call_output_observers(...) from builtins.PyCapsule call_output_observers(self : rosetta.protocols.jd2.JobOutputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType   call all output_observers clear_evaluators(...) from builtins.PyCapsule clear_evaluators(rosetta.protocols.jd2.JobOutputter) -> NoneType evaluate(...) from builtins.PyCapsule evaluate(self : rosetta.protocols.jd2.JobOutputter, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType evaluators(...) from builtins.PyCapsule evaluators(rosetta.protocols.jd2.JobOutputter) -> rosetta.protocols.evaluation.MetaPoseEvaluator filename(...) from builtins.PyCapsule filename(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.jd2.Job) -> str flush(...) from builtins.PyCapsule flush(rosetta.protocols.jd2.JobOutputter) -> NoneType   this function is meant to be redefined in child classes to allow for flushing of memory buffers.  Here's the long version: The SilentFileJobOutputter wanted to buffer output, but needed to guaruntee that  the output would be flushed at end of runtime.  The original implementation was to A) bend over backward to ensure  that the destructor was run (JobOutputter lives inside static JobDistributor, which was previously not destructed  because it's static) and B) flush the buffers in the destructor.  This caused a problem because the buffer-flushing  tried to use the Tracers, which had already been destructed...boom crash.    New solution: re-forbid use of destructors within the static JobDistributor system, and create a flush  function to force this stuff out.  So here it is: set_evaluators(...) from builtins.PyCapsule set_evaluators(self : rosetta.protocols.jd2.JobOutputter,  : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType   class PositionType(builtins.object)     basic struct for remembering position/type information before/during/after design     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.dna.PositionType) -> NoneType   doc   2. __init__(rosetta.protocols.dna.PositionType, int) -> NoneType   doc   3. __init__(rosetta.protocols.dna.PositionType, int, rosetta.core.chemical.ResidueType) -> NoneType   doc   4. __init__(self : rosetta.protocols.dna.PositionType, pos : int, rt : rosetta.core.chemical.ResidueType, design : bool) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Data descriptors defined here: designable position type   class ResTypeSequence_lt(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.dna.ResTypeSequence_lt) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature.   class RestrictDesignToProteinDNAInterface(rosetta.core.pack.task.operation.TaskOperation)       Method resolution order: RestrictDesignToProteinDNAInterface rosetta.core.pack.task.operation.TaskOperation builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.dna.RestrictDesignToProteinDNAInterface) -> 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.dna.RestrictDesignToProteinDNAInterface, pose : rosetta.core.pose.Pose, ptask : rosetta.core.pack.task.PackerTask) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.dna.RestrictDesignToProteinDNAInterface,  : rosetta.protocols.dna.RestrictDesignToProteinDNAInterface) -> rosetta.protocols.dna.RestrictDesignToProteinDNAInterface base_only(...) from builtins.PyCapsule base_only(rosetta.protocols.dna.RestrictDesignToProteinDNAInterface) -> bool clone(...) from builtins.PyCapsule clone(rosetta.protocols.dna.RestrictDesignToProteinDNAInterface) -> rosetta.core.pack.task.operation.TaskOperation copy_dna_chains(...) from builtins.PyCapsule copy_dna_chains(self : rosetta.protocols.dna.RestrictDesignToProteinDNAInterface, chains : rosetta.protocols.dna.DnaChains) -> NoneType copy_interface(...) from builtins.PyCapsule copy_interface(self : rosetta.protocols.dna.RestrictDesignToProteinDNAInterface, interface : rosetta.protocols.dna.DnaInterfaceFinder) -> NoneType copy_targeted_dna(...) from builtins.PyCapsule copy_targeted_dna(self : rosetta.protocols.dna.RestrictDesignToProteinDNAInterface, targeted_dna : rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t) -> NoneType dna_chains(...) from builtins.PyCapsule dna_chains(rosetta.protocols.dna.RestrictDesignToProteinDNAInterface) -> rosetta.protocols.dna.DnaChains forget_chains_and_interface(...) from builtins.PyCapsule forget_chains_and_interface(rosetta.protocols.dna.RestrictDesignToProteinDNAInterface) -> bool interface(...) from builtins.PyCapsule interface(rosetta.protocols.dna.RestrictDesignToProteinDNAInterface) -> rosetta.protocols.dna.DnaInterfaceFinder keyname(...) from builtins.PyCapsule keyname() -> str parse_tag(...) from builtins.PyCapsule parse_tag(self : rosetta.protocols.dna.RestrictDesignToProteinDNAInterface,  : rosetta.utility.tag.Tag,  : rosetta.basic.datacache.DataMap) -> NoneType provide_xml_schema(...) from builtins.PyCapsule provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType reference_pose(...) from builtins.PyCapsule reference_pose(rosetta.protocols.dna.RestrictDesignToProteinDNAInterface) -> rosetta.core.pose.Pose set_base_only(...) from builtins.PyCapsule set_base_only(self : rosetta.protocols.dna.RestrictDesignToProteinDNAInterface, value : bool) -> NoneType set_forget_chains_and_interface(...) from builtins.PyCapsule set_forget_chains_and_interface(self : rosetta.protocols.dna.RestrictDesignToProteinDNAInterface, value : bool) -> NoneType set_reference_pose(...) from builtins.PyCapsule set_reference_pose(self : rosetta.protocols.dna.RestrictDesignToProteinDNAInterface, pose : rosetta.core.pose.Pose) -> NoneType targeted_dna(...) from builtins.PyCapsule targeted_dna(rosetta.protocols.dna.RestrictDesignToProteinDNAInterface) -> rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t   class RestrictDesignToProteinDNAInterfaceCreator(rosetta.core.pack.task.operation.TaskOperationCreator)       Method resolution order: RestrictDesignToProteinDNAInterfaceCreator rosetta.core.pack.task.operation.TaskOperationCreator 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.dna.RestrictDesignToProteinDNAInterfaceCreator,  : rosetta.protocols.dna.RestrictDesignToProteinDNAInterfaceCreator) -> rosetta.protocols.dna.RestrictDesignToProteinDNAInterfaceCreator create_task_operation(...) from builtins.PyCapsule create_task_operation(rosetta.protocols.dna.RestrictDesignToProteinDNAInterfaceCreator) -> rosetta.core.pack.task.operation.TaskOperation keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.dna.RestrictDesignToProteinDNAInterfaceCreator) -> str provide_xml_schema(...) from builtins.PyCapsule provide_xml_schema(self : rosetta.protocols.dna.RestrictDesignToProteinDNAInterfaceCreator, xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType   class RotamerDNAHBondFilter(rosetta.core.pack.rotamer_set.RotamerOperation)       Method resolution order: RotamerDNAHBondFilter rosetta.core.pack.rotamer_set.RotamerOperation builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.protocols.dna.RotamerDNAHBondFilter, rotamer : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, rtask : rosetta.core.pack.task.ResidueLevelTask, packer_neighbor_graph : rosetta.core.graph.Graph, chi_set : rosetta.core.pack.dunbrack.ChiSet) -> bool __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   doc   2. __init__(handle, float) -> NoneType   doc   3. __init__(self : handle, threshold : float, base_only : bool) -> 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.dna.RotamerDNAHBondFilter,  : rosetta.protocols.dna.RotamerDNAHBondFilter) -> rosetta.protocols.dna.RotamerDNAHBondFilter report(...) from builtins.PyCapsule report(rosetta.protocols.dna.RotamerDNAHBondFilter) -> NoneType   class SeparateDnaFromNonDna(rosetta.protocols.moves.Mover)       Method resolution order: SeparateDnaFromNonDna 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, x : float, y : float, z : float) -> NoneType   3. __init__(self : handle, xyz : rosetta.numeric.xyzVector_double_t) -> NoneType   4. __init__(handle, rosetta.protocols.dna.SeparateDnaFromNonDna) -> 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.dna.SeparateDnaFromNonDna, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.dna.SeparateDnaFromNonDna,  : rosetta.protocols.dna.SeparateDnaFromNonDna) -> rosetta.protocols.dna.SeparateDnaFromNonDna clone(...) from builtins.PyCapsule clone(rosetta.protocols.dna.SeparateDnaFromNonDna) -> rosetta.protocols.moves.Mover   required in the context of the parser/scripting scheme fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.dna.SeparateDnaFromNonDna) -> rosetta.protocols.moves.Mover   required in the context of the parser/scripting scheme get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.dna.SeparateDnaFromNonDna) -> str translation(...) from builtins.PyCapsule translation(rosetta.protocols.dna.SeparateDnaFromNonDna) -> rosetta.numeric.xyzVector_double_t 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 SeparateDnaFromNonDnaCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: SeparateDnaFromNonDnaCreator 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.dna.SeparateDnaFromNonDnaCreator,  : rosetta.protocols.dna.SeparateDnaFromNonDnaCreator) -> rosetta.protocols.dna.SeparateDnaFromNonDnaCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.dna.SeparateDnaFromNonDnaCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.dna.SeparateDnaFromNonDnaCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class WatsonCrickRotamerCouplings(rosetta.core.pack.task.operation.TaskOperation)       Method resolution order: WatsonCrickRotamerCouplings rosetta.core.pack.task.operation.TaskOperation 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. apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.dna.WatsonCrickRotamerCouplings, pose : rosetta.core.pose.Pose, ptask : rosetta.core.pack.task.PackerTask) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.dna.WatsonCrickRotamerCouplings,  : rosetta.protocols.dna.WatsonCrickRotamerCouplings) -> rosetta.protocols.dna.WatsonCrickRotamerCouplings clone(...) from builtins.PyCapsule clone(rosetta.protocols.dna.WatsonCrickRotamerCouplings) -> rosetta.core.pack.task.operation.TaskOperation keyname(...) from builtins.PyCapsule keyname() -> str parse_tag(...) from builtins.PyCapsule parse_tag(self : rosetta.protocols.dna.WatsonCrickRotamerCouplings,  : rosetta.utility.tag.Tag,  : rosetta.basic.datacache.DataMap) -> NoneType provide_xml_schema(...) from builtins.PyCapsule provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType   class WatsonCrickRotamerCouplingsCreator(rosetta.core.pack.task.operation.TaskOperationCreator)       Method resolution order: WatsonCrickRotamerCouplingsCreator rosetta.core.pack.task.operation.TaskOperationCreator 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.dna.WatsonCrickRotamerCouplingsCreator,  : rosetta.protocols.dna.WatsonCrickRotamerCouplingsCreator) -> rosetta.protocols.dna.WatsonCrickRotamerCouplingsCreator create_task_operation(...) from builtins.PyCapsule create_task_operation(rosetta.protocols.dna.WatsonCrickRotamerCouplingsCreator) -> rosetta.core.pack.task.operation.TaskOperation keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.dna.WatsonCrickRotamerCouplingsCreator) -> str provide_xml_schema(...) from builtins.PyCapsule provide_xml_schema(self : rosetta.protocols.dna.WatsonCrickRotamerCouplingsCreator, xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType

Functions
		add_constraints_from_file(...) method of builtins.PyCapsule instance add_constraints_from_file(pose : rosetta.core.pose.Pose) -> NoneType argrot_dna_dis2(...) method of builtins.PyCapsule instance argrot_dna_dis2(*args, **kwargs) Overloaded function.   1. argrot_dna_dis2(pose : rosetta.core.pose.Pose, presid : int, pres : rosetta.core.conformation.Residue, dres : rosetta.core.conformation.Residue, threshold : float) -> float   arginine rotamer sweep at a protein residue to see if it should be considered a (potentially) 'dna-contacting' residue      ashworth   2. argrot_dna_dis2(pose : rosetta.core.pose.Pose, presid : int, pres : rosetta.core.conformation.Residue, dres : rosetta.core.conformation.Residue, threshold : float, base_only : bool) -> float   arginine rotamer sweep at a protein residue to see if it should be considered a (potentially) 'dna-contacting' residue      ashworth checkpoint_cleanup(...) method of builtins.PyCapsule instance checkpoint_cleanup() -> NoneType close_to_dna(...) method of builtins.PyCapsule instance close_to_dna(*args, **kwargs) Overloaded function.   1. close_to_dna(pres : rosetta.core.conformation.Residue, dres : rosetta.core.conformation.Residue, cut2 : float) -> bool   checks c-beta (except glycine) to base atom-atom distances, not including ribose or phosphate backbone.      ashworth   2. close_to_dna(pres : rosetta.core.conformation.Residue, dres : rosetta.core.conformation.Residue, cut2 : float, base_only : bool) -> bool   checks c-beta (except glycine) to base atom-atom distances, not including ribose or phosphate backbone.      ashworth contact_distance2(...) method of builtins.PyCapsule instance contact_distance2(*args, **kwargs) Overloaded function.   1. contact_distance2(a_begin : __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >, a_end : __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >, b_begin : __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >, b_end : __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >) -> float   distance check for contact between two sets of atoms      ashworth   2. contact_distance2(a_begin : __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >, a_end : __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >, b_begin : __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >, b_end : __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >, threshold : float) -> float   distance check for contact between two sets of atoms      ashworth dna_base_partner(...) method of builtins.PyCapsule instance dna_base_partner(na : rosetta.core.chemical.AA) -> rosetta.core.chemical.AA dna_comp_name_str(...) method of builtins.PyCapsule instance dna_comp_name_str(dna : str) -> str   also consider using the dna_base_partner function below      ashworth dna_full_name3(...) method of builtins.PyCapsule instance dna_full_name3(name3 : str) -> str   intended to convert any DNA "threeletter code" into the full three-letter code. Note that this does not (necessarily) return the same thing as residue_type::name3 (which returns "  N" format as of Dec 2008) find_basepairs(...) method of builtins.PyCapsule instance find_basepairs(*args, **kwargs) Overloaded function.   1. find_basepairs(pose : rosetta.core.pose.Pose, dna_chains : rosetta.protocols.dna.DnaChains) -> NoneType   DnaChains version, adapted from pbradley's code.  More paranoid geometry checks, in order to allow highly distorted basepairs without making mistakes      ashworth   2. find_basepairs(pose : rosetta.core.pose.Pose, dna_chains : rosetta.protocols.dna.DnaChains, include_unpaired : bool) -> NoneType   DnaChains version, adapted from pbradley's code.  More paranoid geometry checks, in order to allow highly distorted basepairs without making mistakes      ashworth load_checkpoint(...) method of builtins.PyCapsule instance load_checkpoint(pose : rosetta.core.pose.Pose, iter : int) -> NoneType load_dna_design_defs_from_file(...) method of builtins.PyCapsule instance load_dna_design_defs_from_file(defs : rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t, filename : str, pdb_prefix : str) -> NoneType load_dna_design_defs_from_options(...) method of builtins.PyCapsule instance load_dna_design_defs_from_options(*args, **kwargs) Overloaded function.   1. load_dna_design_defs_from_options(defs : rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t) -> NoneType   2. load_dna_design_defs_from_options(defs : rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t, pdb_prefix : str) -> NoneType load_dna_design_defs_from_strings(...) method of builtins.PyCapsule instance load_dna_design_defs_from_strings(defs : rosetta.utility.vector1_std_shared_ptr_protocols_dna_DnaDesignDef_t, str_defs : rosetta.utility.vector1_std_string) -> NoneType   loads command-line dna design definitions (shorthand alternative to using resfile)  option value is string vector    i.e. -dna_defs C.-6 C.-5    or   -dna_defs C.-6.GUA C.-5.CYT      ashworth make_base_pair_aware_fold_tree(...) method of builtins.PyCapsule instance make_base_pair_aware_fold_tree(pose : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree make_subdirs(...) method of builtins.PyCapsule instance make_subdirs( : str) -> NoneType not_already_connected(...) method of builtins.PyCapsule instance not_already_connected(pose : rosetta.core.pose.Pose, num_jumps : int, this_chain : str, other_chain : str, jump_pairs : ObjexxFCL::FArray2D<int>) -> bool restrict_to_single_sequence(...) method of builtins.PyCapsule instance restrict_to_single_sequence(rotamer_sets : rosetta.core.pack.rotamer_set.RotamerSets, single_sequence : rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t, rot_to_pack : rosetta.utility.vector0_int) -> NoneType   for packing a single sequence out of a RotamerSets that (potentially) represents sequence variability      ashworth set_base_segment_chainbreak_constraints(...) method of builtins.PyCapsule instance set_base_segment_chainbreak_constraints(pose : rosetta.core.pose.Pose, this_base : int, end_base : int) -> NoneType substitute_residue(...) method of builtins.PyCapsule instance substitute_residue(pose : rosetta.core.pose.Pose, index : int, new_type : rosetta.core.chemical.ResidueType) -> NoneType write_checkpoint(...) method of builtins.PyCapsule instance write_checkpoint(pose : rosetta.core.pose.Pose, iter : int) -> NoneType z_axis_dist(...) method of builtins.PyCapsule instance z_axis_dist(pres : rosetta.core.conformation.Residue, dres : rosetta.core.conformation.Residue) -> float   A sanity check for the arginine rotamer screen. Can prevent the design of positions that are best left alone because they are too far away along the helical axis ('laterally').      ashworth