Bindings for protocols::antibody namespace

Modules
		rosetta.protocols.antibody.clusters rosetta.protocols.antibody.constraints rosetta.protocols.antibody.design rosetta.protocols.antibody.grafting rosetta.protocols.antibody.residue_selector rosetta.protocols.antibody.snugdock rosetta.protocols.antibody.task_operations

Classes
		builtins.object Ab_TemplateInfo AntibodyDatabaseManager AntibodyEnumManager AntibodyInfo AntibodyNumbering AntibodyNumberingParser AntibodyNumberingSchemeEnum AntibodyRegionEnum CDRDBPose CDRDBSequence CDRDefinitionEnum CDRLandmarkEnum CDRNameEnum CDRSetOptions CDRSetOptionsParser FrameWork H3BaseTypeEnum LightChainTypeEnum PDBLandmark PackingAngleEnum ParatopeMetric_long_t rosetta.protocols.features.FeaturesReporterCreator(builtins.object) AntibodyFeaturesCreator rosetta.protocols.features.InterfaceFeatures(rosetta.protocols.features.FeaturesReporter) AntibodyFeatures rosetta.protocols.moves.Mover(builtins.object) AntibodyCDRGrafter AntibodyModelerProtocol CDRsMinPackMin CloseOneCDRLoop GraftCDRLoopsProtocol GraftOneCDRLoop GraftedStemOptimizer H3CterInsert H3PerturbCCD H3RefineCCD LHRepulsiveRamp LHRepulsiveRampLegacy LHSnugFitLegacy ModelCDRH3 RefineBetaBarrel RefineOneCDRLoop RefineOneCDRLoopCentroid rosetta.protocols.moves.MoverCreator(builtins.object) AntibodyCDRGrafterCreator   class Ab_TemplateInfo(builtins.object)     Specifically for AntibodyModeling protocol templates. Not for general use.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.Ab_TemplateInfo) -> NoneType   2. __init__(self : rosetta.protocols.antibody.Ab_TemplateInfo, load_L1 : bool, load_L2 : bool, load_L3 : bool, load_H1 : bool, load_H2 : bool, load_H3 : bool) -> NoneType   3. __init__(self : rosetta.protocols.antibody.Ab_TemplateInfo, load_L1 : bool, load_L2 : bool, load_L3 : bool, load_H1 : bool, load_H2 : bool, load_H3 : bool, camelid : bool) -> NoneType   4. __init__(self : rosetta.protocols.antibody.Ab_TemplateInfo,  : rosetta.protocols.antibody.Ab_TemplateInfo) -> 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.antibody.Ab_TemplateInfo) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.Ab_TemplateInfo,  : rosetta.protocols.antibody.Ab_TemplateInfo) -> rosetta.protocols.antibody.Ab_TemplateInfo get_one_template_pose(...) from builtins.PyCapsule get_one_template_pose(self : rosetta.protocols.antibody.Ab_TemplateInfo, cdr_name : str) -> rosetta.core.pose.Pose is_camelid(...) from builtins.PyCapsule is_camelid(rosetta.protocols.antibody.Ab_TemplateInfo) -> bool load_templates_from_pdbs(...) from builtins.PyCapsule load_templates_from_pdbs(self : rosetta.protocols.antibody.Ab_TemplateInfo, load_L1 : bool, load_L2 : bool, load_L3 : bool, load_H1 : bool, load_H2 : bool, load_H3 : bool, camelid : bool) -> NoneType   class AntibodyCDRGrafter(rosetta.protocols.moves.Mover)     Class to graft CDR loops from an antibody to a new antibody or from a CDR pose into a different antibody.  Independant of antibody and CDR modeling.  Results in 100 percent loop closure if using both graft algorithms.     Recommended to use cluster-based or general dihedral constraints on the CDR with a min or relax to optimize graft. Use optimiize_cdrs option to optimize the CDRs that were grafted and any neighbor CDRs using these dihedral constraints during relax.   By default, uses two residues on N and C terminal of insert CDR and scaffold to close loop. Use getters of primary and secondary graft mover to change this if needed. By default, stops after the graft is closed!     Method resolution order: AntibodyCDRGrafter 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, ab_info : protocols::antibody::AntibodyInfo) -> NoneType   3. __init__(handle, protocols::antibody::AntibodyInfo, rosetta.core.pose.Pose, rosetta.utility.vector1_bool) -> NoneType   doc   4. __init__(handle, protocols::antibody::AntibodyInfo, rosetta.core.pose.Pose, rosetta.utility.vector1_bool, int) -> NoneType   doc   5. __init__(self : handle, ab_info : protocols::antibody::AntibodyInfo, donor_structure : rosetta.core.pose.Pose, cdrs_to_graft : rosetta.utility.vector1_bool, nter_overhang : int, cter_overhang : int) -> NoneType   6. __init__(handle, rosetta.protocols.antibody.AntibodyCDRGrafter) -> 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.antibody.AntibodyCDRGrafter, pose : rosetta.core.pose.Pose) -> NoneType apply_to_cdr(...) from builtins.PyCapsule apply_to_cdr(self : rosetta.protocols.antibody.AntibodyCDRGrafter, pose : rosetta.core.pose.Pose, cdr_region_with_overhang : rosetta.core.pose.Pose, cdr : rosetta.protocols.antibody.CDRNameEnum, grafter : rosetta.protocols.grafting.AnchoredGraftMover) -> (bool, int)   Apply graft mover to pose, inserting the cdr_region.      Return success or failure of the graft and the position of the failure.  Public in case one wants to use it by itself... assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.AntibodyCDRGrafter,  : rosetta.protocols.antibody.AntibodyCDRGrafter) -> rosetta.protocols.antibody.AntibodyCDRGrafter clone(...) from builtins.PyCapsule clone(rosetta.protocols.antibody.AntibodyCDRGrafter) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.antibody.AntibodyCDRGrafter) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.antibody.AntibodyCDRGrafter) -> str get_primary_graft_mover(...) from builtins.PyCapsule get_primary_graft_mover(rosetta.protocols.antibody.AntibodyCDRGrafter) -> rosetta.protocols.grafting.CCDEndsGraftMover   Get a reference of the main graft mover to tweak settings. get_secondary_graft_mover(...) from builtins.PyCapsule get_secondary_graft_mover(rosetta.protocols.antibody.AntibodyCDRGrafter) -> rosetta.protocols.grafting.AnchoredGraftMover   Get a reference of the secondary graft mover to tweak settings. set_cdr_only(...) from builtins.PyCapsule set_cdr_only(self : rosetta.protocols.antibody.AntibodyCDRGrafter, cdr : rosetta.protocols.antibody.CDRNameEnum) -> NoneType   Set a single CDR we are going to graft in. set_cdrs(...) from builtins.PyCapsule set_cdrs(self : rosetta.protocols.antibody.AntibodyCDRGrafter, cdrs : rosetta.utility.vector1_bool) -> NoneType   Set the CDRs to graft.  Boolean vector of CDRNameEnums (1-8) (includes CDR4/DE loop) set_dihedral_constraint_weight(...) from builtins.PyCapsule set_dihedral_constraint_weight(self : rosetta.protocols.antibody.AntibodyCDRGrafter, dih_cst_wt : float) -> NoneType   Set the dihedral constraint weight used if optimization is done and the scorefxn dihedral_constraint  weight is zero.  Default = 2.0 set_donor_structure(...) from builtins.PyCapsule set_donor_structure(self : rosetta.protocols.antibody.AntibodyCDRGrafter, pose : rosetta.core.pose.Pose) -> NoneType   Set a donor structure.  Culd be a single CDR, multiple CDRs or a whole other antibody. set_idealize_insert(...) from builtins.PyCapsule set_idealize_insert(self : rosetta.protocols.antibody.AntibodyCDRGrafter, idealize_insert : bool) -> NoneType   Idealize the insert.  Default TRUE. set_include_cdr4_in_optimization(...) from builtins.PyCapsule set_include_cdr4_in_optimization(self : rosetta.protocols.antibody.AntibodyCDRGrafter, include_cdr4 : bool) -> NoneType   Set to include the DE loop, or CDR4 if it is a neighbor to a grafted CDR and optimization is set to on.  Recommended if optimizing.  Default TRUE. set_optimize_cdrs(...) from builtins.PyCapsule set_optimize_cdrs(self : rosetta.protocols.antibody.AntibodyCDRGrafter, optimize_cdrs : bool) -> NoneType   Set to optimize any grafted and neighbor CDRs using dihdedral constrained relax on them. Default FALSE.   Recommended if using secondary graft mover. set_overhang(...) from builtins.PyCapsule set_overhang(self : rosetta.protocols.antibody.AntibodyCDRGrafter, nter_overhang : int, cter_overhang : int) -> NoneType   Set the N and Cterminal overhang used for superposition before the graft. set_scorefxn_low(...) from builtins.PyCapsule set_scorefxn_low(self : rosetta.protocols.antibody.AntibodyCDRGrafter, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   Set the (low-res) scorefunction used by the graft movers to close loop.   Default is to use Frank Dimaio's smoothed low-res terms. set_scorefxn_pack(...) from builtins.PyCapsule set_scorefxn_pack(self : rosetta.protocols.antibody.AntibodyCDRGrafter, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   Set the (all-atom) scorefunction used by the graft movers for packing  Otherwise use cmd-line default set_stop_after_closure(...) from builtins.PyCapsule set_stop_after_closure(self : rosetta.protocols.antibody.AntibodyCDRGrafter, stop_after_closure : bool) -> NoneType   Set a boolean for whether to stop after closure or not.  Default TRUE. set_use_secondary_graft_mover_if_needed(...) from builtins.PyCapsule set_use_secondary_graft_mover_if_needed(self : rosetta.protocols.antibody.AntibodyCDRGrafter, use_secondary_graft_mover : bool) -> NoneType   Set a boolean for whether to use the secondary graft mover is the graft is not closed using the first.   Default FALSE.         Using this results in 100% graft closure, however, in order to fix the structure, a dihedral constrained relax is   done on the CDR while repacking neighbor residues.   85% Graft closure without (slight chainbreaks  - not as bad as what used to be used for antibody modeling.) 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 AntibodyCDRGrafterCreator(rosetta.protocols.moves.MoverCreator)       Method resolution order: AntibodyCDRGrafterCreator 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.antibody.AntibodyCDRGrafterCreator,  : rosetta.protocols.antibody.AntibodyCDRGrafterCreator) -> rosetta.protocols.antibody.AntibodyCDRGrafterCreator create_mover(...) from builtins.PyCapsule create_mover(rosetta.protocols.antibody.AntibodyCDRGrafterCreator) -> rosetta.protocols.moves.Mover keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.antibody.AntibodyCDRGrafterCreator) -> str mover_name(...) from builtins.PyCapsule mover_name() -> str   class AntibodyDatabaseManager(builtins.object)     Class responsible for loading information from the AntibodyDatabase.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.AntibodyDatabaseManager, rosetta.protocols.antibody.AntibodyInfo) -> NoneType   doc   2. __init__(self : rosetta.protocols.antibody.AntibodyDatabaseManager, ab_info : rosetta.protocols.antibody.AntibodyInfo, force_north_paper_db : bool) -> NoneType   3. __init__(self : rosetta.protocols.antibody.AntibodyDatabaseManager, ab_info : rosetta.protocols.antibody.AntibodyInfo, database_path : str) -> NoneType   4. __init__(self : rosetta.protocols.antibody.AntibodyDatabaseManager,  : rosetta.protocols.antibody.AntibodyDatabaseManager) -> 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.antibody.AntibodyDatabaseManager,  : rosetta.protocols.antibody.AntibodyDatabaseManager) -> rosetta.protocols.antibody.AntibodyDatabaseManager load_cdr_design_data(...) from builtins.PyCapsule load_cdr_design_data(self : rosetta.protocols.antibody.AntibodyDatabaseManager, options : rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRSeqDesignOptions_t, pose : rosetta.core.pose.Pose, prob_set : rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t, cutoff : int) -> rosetta.utility.vector1_bool   Load probability data for CDR Design.  Returns CDRs where data could not be loaded. Cutoff indicates number of total sequences needed to use the data.      Will attempt to use Pose Datacache for identification of CDR clusters first. load_cdr_design_data_for_cdrs(...) from builtins.PyCapsule load_cdr_design_data_for_cdrs(self : rosetta.protocols.antibody.AntibodyDatabaseManager, cdrs : rosetta.utility.vector1_bool, pose : rosetta.core.pose.Pose, prob_set : rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t, cutoff : int) -> rosetta.utility.vector1_bool set_outlier_use(...) from builtins.PyCapsule set_outlier_use(self : rosetta.protocols.antibody.AntibodyDatabaseManager, use_outliers : bool) -> NoneType   Set to parse outliers for both sequence and structural data.  Default False. use_light_chain_type(...) from builtins.PyCapsule use_light_chain_type(*args, **kwargs) Overloaded function.   1. use_light_chain_type(self : rosetta.protocols.antibody.AntibodyDatabaseManager, use_light_chain_type : bool) -> NoneType   Use the light chain type for CDRPoses and CDRSequences if set in AntibodyInfo.   2. use_light_chain_type(rosetta.protocols.antibody.AntibodyDatabaseManager) -> bool   class AntibodyEnumManager(builtins.object)     Interface to this class is in AntibodyInfo.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.antibody.AntibodyEnumManager) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. antibody_region_enum_to_string(...) from builtins.PyCapsule antibody_region_enum_to_string(self : rosetta.protocols.antibody.AntibodyEnumManager, antibody_region : rosetta.protocols.antibody.AntibodyRegionEnum) -> str antibody_region_string_to_enum(...) from builtins.PyCapsule antibody_region_string_to_enum(self : rosetta.protocols.antibody.AntibodyEnumManager, antibody_region : str) -> rosetta.protocols.antibody.AntibodyRegionEnum   ////////////// Antibody Region  //////////////////////////////////////////// assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.AntibodyEnumManager,  : rosetta.protocols.antibody.AntibodyEnumManager) -> rosetta.protocols.antibody.AntibodyEnumManager cdr_definition_enum_to_string(...) from builtins.PyCapsule cdr_definition_enum_to_string(self : rosetta.protocols.antibody.AntibodyEnumManager, cdr_definition : rosetta.protocols.antibody.CDRDefinitionEnum) -> str cdr_definition_is_present(...) from builtins.PyCapsule cdr_definition_is_present(self : rosetta.protocols.antibody.AntibodyEnumManager, cdr_definition : str) -> bool cdr_definition_string_to_enum(...) from builtins.PyCapsule cdr_definition_string_to_enum(self : rosetta.protocols.antibody.AntibodyEnumManager, cdr_definition : str) -> rosetta.protocols.antibody.CDRDefinitionEnum   /////////////// CDR Definitions  /////////////////////////////////////// cdr_landmark_enum_to_string(...) from builtins.PyCapsule cdr_landmark_enum_to_string(self : rosetta.protocols.antibody.AntibodyEnumManager, landmark : rosetta.protocols.antibody.CDRLandmarkEnum) -> str cdr_landmark_is_present(...) from builtins.PyCapsule cdr_landmark_is_present(self : rosetta.protocols.antibody.AntibodyEnumManager, landmark : str) -> bool cdr_landmark_string_to_enum(...) from builtins.PyCapsule cdr_landmark_string_to_enum(self : rosetta.protocols.antibody.AntibodyEnumManager, landmark : str) -> rosetta.protocols.antibody.CDRLandmarkEnum   ////////////// Antibody Landmarks //////////////////////////////////////////// cdr_name_enum_to_string(...) from builtins.PyCapsule cdr_name_enum_to_string(self : rosetta.protocols.antibody.AntibodyEnumManager, cdr_name : rosetta.protocols.antibody.CDRNameEnum) -> str cdr_name_is_present(...) from builtins.PyCapsule cdr_name_is_present(self : rosetta.protocols.antibody.AntibodyEnumManager, cdr_name : str) -> bool cdr_name_string_to_enum(...) from builtins.PyCapsule cdr_name_string_to_enum(self : rosetta.protocols.antibody.AntibodyEnumManager, cdr_name : str) -> rosetta.protocols.antibody.CDRNameEnum   /////////////// CDR names /////////////////////////////////////////////// h3_base_type_enum_to_string(...) from builtins.PyCapsule h3_base_type_enum_to_string(self : rosetta.protocols.antibody.AntibodyEnumManager, base_type : rosetta.protocols.antibody.H3BaseTypeEnum) -> str h3_base_type_string_to_enum(...) from builtins.PyCapsule h3_base_type_string_to_enum(self : rosetta.protocols.antibody.AntibodyEnumManager, base_type : str) -> rosetta.protocols.antibody.H3BaseTypeEnum   /////////////// H3 Base Type //////////////////////////////////////////// light_chain_type_enum_to_string(...) from builtins.PyCapsule light_chain_type_enum_to_string(self : rosetta.protocols.antibody.AntibodyEnumManager, light_chain : rosetta.protocols.antibody.LightChainTypeEnum) -> str light_chain_type_is_present(...) from builtins.PyCapsule light_chain_type_is_present(self : rosetta.protocols.antibody.AntibodyEnumManager, light_chain : str) -> bool light_chain_type_string_to_enum(...) from builtins.PyCapsule light_chain_type_string_to_enum(self : rosetta.protocols.antibody.AntibodyEnumManager, light_chain : str) -> rosetta.protocols.antibody.LightChainTypeEnum   ////////////// LightChain Types //////////////////////////////////////////// numbering_scheme_enum_to_string(...) from builtins.PyCapsule numbering_scheme_enum_to_string(self : rosetta.protocols.antibody.AntibodyEnumManager, numbering_scheme : rosetta.protocols.antibody.AntibodyNumberingSchemeEnum) -> str numbering_scheme_is_present(...) from builtins.PyCapsule numbering_scheme_is_present(self : rosetta.protocols.antibody.AntibodyEnumManager, numbering_scheme : str) -> bool numbering_scheme_string_to_enum(...) from builtins.PyCapsule numbering_scheme_string_to_enum(self : rosetta.protocols.antibody.AntibodyEnumManager, numbering_scheme : str) -> rosetta.protocols.antibody.AntibodyNumberingSchemeEnum   /////////////// Numbering Schemes /////////////////////////////////////// packing_angle_enum_to_string(...) from builtins.PyCapsule packing_angle_enum_to_string(self : rosetta.protocols.antibody.AntibodyEnumManager, angle_type : rosetta.protocols.antibody.PackingAngleEnum) -> str packing_angle_string_to_enum(...) from builtins.PyCapsule packing_angle_string_to_enum(self : rosetta.protocols.antibody.AntibodyEnumManager, angle_type : str) -> rosetta.protocols.antibody.PackingAngleEnum   ////////////// Packing Angle ////////////////////////////////////////////   class AntibodyFeatures(rosetta.protocols.features.InterfaceFeatures)     Collects data on an antibody including CDRs, interfaces of L_H, L_A, H_A, and LH_A (this can be set), and other metrics.     Adds .... tables to the database.  See also protocols/antibody/clusters/CDRClusterFeatures     Method resolution order: AntibodyFeatures rosetta.protocols.features.InterfaceFeatures rosetta.protocols.features.FeaturesReporter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo) -> NoneType   3. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   4. __init__(handle, rosetta.protocols.antibody.AntibodyFeatures) -> 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.antibody.AntibodyFeatures,  : rosetta.protocols.antibody.AntibodyFeatures) -> rosetta.protocols.antibody.AntibodyFeatures report_ab_H3_kink_metrics_features(...) from builtins.PyCapsule report_ab_H3_kink_metrics_features(self : rosetta.protocols.antibody.AntibodyFeatures, pose : rosetta.core.pose.Pose, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType report_ab_metrics_features(...) from builtins.PyCapsule report_ab_metrics_features(self : rosetta.protocols.antibody.AntibodyFeatures, pose : rosetta.core.pose.Pose, struct_id : int, db_session : rosetta.utility.sql_database.session) -> NoneType report_cdr_metrics_features(...) from builtins.PyCapsule report_cdr_metrics_features(self : rosetta.protocols.antibody.AntibodyFeatures, pose : rosetta.core.pose.Pose, struct_id : int, db_session : rosetta.utility.sql_database.session, cdr : rosetta.protocols.antibody.CDRNameEnum) -> NoneType report_cdr_residue_features(...) from builtins.PyCapsule report_cdr_residue_features(self : rosetta.protocols.antibody.AntibodyFeatures, pose : rosetta.core.pose.Pose, struct_id : int, db_session : rosetta.utility.sql_database.session, cdr : rosetta.protocols.antibody.CDRNameEnum, relevant_residues : rosetta.utility.vector1_bool) -> NoneType report_cdr_residue_features_row(...) from builtins.PyCapsule report_cdr_residue_features_row(self : rosetta.protocols.antibody.AntibodyFeatures, pose : rosetta.core.pose.Pose, struct_id : int, db_session : rosetta.utility.sql_database.session, cdr : rosetta.protocols.antibody.CDRNameEnum, resnum : int, position : int) -> NoneType report_features(...) from builtins.PyCapsule report_features(self : rosetta.protocols.antibody.AntibodyFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session) -> int   collect all the feature data for the pose set_ab_info(...) from builtins.PyCapsule set_ab_info(self : rosetta.protocols.antibody.AntibodyFeatures, ab_info : rosetta.protocols.antibody.AntibodyInfo) -> NoneType set_interface_chains(...) from builtins.PyCapsule set_interface_chains(self : rosetta.protocols.antibody.AntibodyFeatures, intermediate_interfaces : rosetta.utility.vector1_std_string) -> NoneType   Set intermediate interface chains: Example: L_A, H_A, L_H, LH_A (A stands for antigen)      Any other chains, use InterfaceFeatures. type_name(...) from builtins.PyCapsule type_name(rosetta.protocols.antibody.AntibodyFeatures) -> str   return string with class name write_ab_H3_kink_metrics_schema_to_db(...) from builtins.PyCapsule write_ab_H3_kink_metrics_schema_to_db(self : rosetta.protocols.antibody.AntibodyFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType   Write kink metrics schema.  Please add or modify as needed. write_ab_metrics_schema_to_db(...) from builtins.PyCapsule write_ab_metrics_schema_to_db(self : rosetta.protocols.antibody.AntibodyFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType write_cdr_metrics_schema_to_db(...) from builtins.PyCapsule write_cdr_metrics_schema_to_db(self : rosetta.protocols.antibody.AntibodyFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType write_cdr_residue_schema_to_db(...) from builtins.PyCapsule write_cdr_residue_schema_to_db(self : rosetta.protocols.antibody.AntibodyFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType write_schema_to_db(...) from builtins.PyCapsule write_schema_to_db(self : rosetta.protocols.antibody.AntibodyFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType Methods inherited from rosetta.protocols.features.InterfaceFeatures: features_reporter_dependencies(...) from builtins.PyCapsule features_reporter_dependencies(rosetta.protocols.features.InterfaceFeatures) -> rosetta.utility.vector1_std_string   return the set of features reporters that are required to also already be extracted by the time this one is used. make_interface_combos(...) from builtins.PyCapsule make_interface_combos(self : rosetta.protocols.features.InterfaceFeatures, pose : rosetta.core.pose.Pose, interfaces : rosetta.utility.vector1_std_string) -> NoneType   Gets all possible interface combinations of a given pose. report_all_interface_features(...) from builtins.PyCapsule report_all_interface_features(self : rosetta.protocols.features.InterfaceFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session, interface : str, db_interface : str) -> NoneType   Report all features.  Called by report_features.  Easy interface for subclassing specific interfaces.      interface is the interface analyzed, db_interface is the name that is actually inserted into the database  Usually this is the same, but useful when dealing with different chain ids but same interface type. db_interface should have sides as well (L_H)) report_interface_features(...) from builtins.PyCapsule report_interface_features(self : rosetta.protocols.features.InterfaceFeatures, pose : rosetta.core.pose.Pose, struct_id : int, db_session : rosetta.utility.sql_database.session, chains_side1 : str, chains_side2 : str) -> NoneType   Add interfaces table data to table report_interface_residue_features(...) from builtins.PyCapsule report_interface_residue_features(self : rosetta.protocols.features.InterfaceFeatures, pose : rosetta.core.pose.Pose, relevant_residues : rosetta.utility.vector1_bool, struct_id : int, db_session : rosetta.utility.sql_database.session, chains_side1 : str, chains_side2 : str) -> NoneType   Add interface_residues data to table report_interface_side_features(...) from builtins.PyCapsule report_interface_side_features(self : rosetta.protocols.features.InterfaceFeatures, pose : rosetta.core.pose.Pose, struct_id : int, db_session : rosetta.utility.sql_database.session, chains_side1 : str, chains_side2 : str, region : rosetta.protocols.analysis.InterfaceRegion, region_string : str) -> NoneType   Add interface_sides table data to table set_compute_packstat(...) from builtins.PyCapsule set_compute_packstat(self : rosetta.protocols.features.InterfaceFeatures, compute_packstat : bool) -> NoneType   Compute the packstat score?  Default true set_dSASA_cutoff(...) from builtins.PyCapsule set_dSASA_cutoff(self : rosetta.protocols.features.InterfaceFeatures, dSASA_cutoff : float) -> NoneType   Set the reporter to only include interfaces >dSASA_cutoff. set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.features.InterfaceFeatures) -> NoneType set_pack_separated(...) from builtins.PyCapsule set_pack_separated(self : rosetta.protocols.features.InterfaceFeatures, pack_separated : bool) -> NoneType   Pack the interface before separation? Default is false. set_pack_together(...) from builtins.PyCapsule set_pack_together(self : rosetta.protocols.features.InterfaceFeatures, pack_together : bool) -> NoneType   Pack the interface after separation?  Default is true. set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.features.InterfaceFeatures, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType write_interface_residues_schema_to_db(...) from builtins.PyCapsule write_interface_residues_schema_to_db(self : rosetta.protocols.features.InterfaceFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType write_interface_schema_to_db(...) from builtins.PyCapsule write_interface_schema_to_db(self : rosetta.protocols.features.InterfaceFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType   ///////////////////////////////////////////////////////////////////////// write_interface_side_schema_to_db(...) from builtins.PyCapsule write_interface_side_schema_to_db(self : rosetta.protocols.features.InterfaceFeatures, db_session : rosetta.utility.sql_database.session) -> NoneType Methods inherited from rosetta.protocols.features.FeaturesReporter: check_relevant_residues(...) from builtins.PyCapsule check_relevant_residues(*args, **kwargs) Overloaded function.   1. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int) -> bool   2. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool   3. check_relevant_residues(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, residues : rosetta.utility.vector1_unsigned_long) -> bool check_relevant_residues_range(...) from builtins.PyCapsule check_relevant_residues_range(self : rosetta.protocols.features.FeaturesReporter, relevant_residues : rosetta.utility.vector1_bool, res1 : int, res2 : int) -> bool delete_record(...) from builtins.PyCapsule delete_record(self : rosetta.protocols.features.FeaturesReporter,  : int,  : rosetta.utility.sql_database.session) -> NoneType get_relevant_residues_mode(...) from builtins.PyCapsule get_relevant_residues_mode(rosetta.protocols.features.FeaturesReporter) -> rosetta.protocols.features.RelevantResiduesMode.T load_into_pose(...) from builtins.PyCapsule load_into_pose(self : rosetta.protocols.features.FeaturesReporter,  : rosetta.utility.sql_database.session,  : int,  : rosetta.core.pose.Pose) -> NoneType schema(...) from builtins.PyCapsule schema(rosetta.protocols.features.FeaturesReporter) -> str   return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator set_relevant_residues_mode(...) from builtins.PyCapsule set_relevant_residues_mode(self : rosetta.protocols.features.FeaturesReporter, setting : rosetta.protocols.features.RelevantResiduesMode.T) -> NoneType   class AntibodyFeaturesCreator(rosetta.protocols.features.FeaturesReporterCreator)     creator for the HBondParameterFeatures class     Method resolution order: AntibodyFeaturesCreator rosetta.protocols.features.FeaturesReporterCreator 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.antibody.AntibodyFeaturesCreator,  : rosetta.protocols.antibody.AntibodyFeaturesCreator) -> rosetta.protocols.antibody.AntibodyFeaturesCreator create_features_reporter(...) from builtins.PyCapsule create_features_reporter(rosetta.protocols.antibody.AntibodyFeaturesCreator) -> rosetta.protocols.features.FeaturesReporter type_name(...) from builtins.PyCapsule type_name(rosetta.protocols.antibody.AntibodyFeaturesCreator) -> str   class AntibodyInfo(builtins.object)     This class is used to get all relevant information you would need when dealing with an antibody.     It mainly holds numbering information, but passes out a variety of Rosetta specific objects like movemaps, Loops, taskfactories, etc.  as well as other information such as CDR cluster type, camelid, H3 types, etc.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.AntibodyInfo, rosetta.core.pose.Pose) -> NoneType   doc   2. __init__(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, cdr_pdb_numbered : bool) -> NoneType   3. __init__(rosetta.protocols.antibody.AntibodyInfo, rosetta.core.pose.Pose, rosetta.protocols.antibody.AntibodyNumberingSchemeEnum, rosetta.protocols.antibody.CDRDefinitionEnum) -> NoneType   doc   4. __init__(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, numbering_scheme : rosetta.protocols.antibody.AntibodyNumberingSchemeEnum, cdr_definition : rosetta.protocols.antibody.CDRDefinitionEnum, cdr_pdb_numbered : bool) -> NoneType   5. __init__(rosetta.protocols.antibody.AntibodyInfo, rosetta.core.pose.Pose, rosetta.protocols.antibody.CDRDefinitionEnum) -> NoneType   doc   6. __init__(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, cdr_definition : rosetta.protocols.antibody.CDRDefinitionEnum, cdr_pdb_numbered : bool) -> NoneType   7. __init__(self : rosetta.protocols.antibody.AntibodyInfo, src : rosetta.protocols.antibody.AntibodyInfo) -> 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.antibody.AntibodyInfo) -> str add_CDR_to_MoveMap(...) from builtins.PyCapsule add_CDR_to_MoveMap(*args, **kwargs) Overloaded function.   1. add_CDR_to_MoveMap(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, movemap : rosetta.core.kinematics.MoveMap, cdr_name : rosetta.protocols.antibody.CDRNameEnum) -> NoneType   Add CDR flexibility to a movemap. Uses pose for numbering.   2. add_CDR_to_MoveMap(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, movemap : rosetta.core.kinematics.MoveMap, cdr_name : rosetta.protocols.antibody.CDRNameEnum, bb_only : bool) -> NoneType   Add CDR flexibility to a movemap. Uses pose for numbering.   3. add_CDR_to_MoveMap(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, movemap : rosetta.core.kinematics.MoveMap, cdr_name : rosetta.protocols.antibody.CDRNameEnum, bb_only : bool, include_nb_sc : bool) -> NoneType   Add CDR flexibility to a movemap. Uses pose for numbering.   4. add_CDR_to_MoveMap(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, movemap : rosetta.core.kinematics.MoveMap, cdr_name : rosetta.protocols.antibody.CDRNameEnum, bb_only : bool, include_nb_sc : bool, nb_dist : float) -> NoneType   Add CDR flexibility to a movemap. Uses pose for numbering. antigen_present(...) from builtins.PyCapsule antigen_present(rosetta.protocols.antibody.AntibodyInfo) -> bool   return whether this pose has antigen or not assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.AntibodyInfo,  : rosetta.protocols.antibody.AntibodyInfo) -> rosetta.protocols.antibody.AntibodyInfo clone(...) from builtins.PyCapsule clone(rosetta.protocols.antibody.AntibodyInfo) -> rosetta.protocols.antibody.AntibodyInfo   Clone the pointer. get_AllCDRs_in_loopsop(...) from builtins.PyCapsule get_AllCDRs_in_loopsop(rosetta.protocols.antibody.AntibodyInfo) -> rosetta.protocols.loops.Loops   return a LoopsOP object, initialized upon class construction. get_CDR_chain(...) from builtins.PyCapsule get_CDR_chain(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum) -> str get_CDR_cluster(...) from builtins.PyCapsule get_CDR_cluster(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum) -> rosetta.protocols.antibody.clusters.CDRCluster   get the cdr's cluster identity and distance to cluster using it's structure as a CDRCluster object.      See North, B., A. Lehmann, et al. (2011). JMB 406(2): 228-256.   Must use setup_CDR_clusters first.      If this AbInfo does not have all 6 chains, CDRClusterOP may be NULL if the CDR is not present to begin with. get_CDR_cluster_set(...) from builtins.PyCapsule get_CDR_cluster_set(rosetta.protocols.antibody.AntibodyInfo) -> rosetta.protocols.antibody.clusters.CDRClusterSet get_CDR_end(...) from builtins.PyCapsule get_CDR_end(*args, **kwargs) Overloaded function.   1. get_CDR_end(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum, pose : rosetta.core.pose.Pose) -> int   Return pose number of CDR end residue in the definition of the numbering scheme of transform.   2. get_CDR_end(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum, pose : rosetta.core.pose.Pose, transform : rosetta.protocols.antibody.CDRDefinitionEnum) -> int get_CDR_end_PDB_num(...) from builtins.PyCapsule get_CDR_end_PDB_num(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum) -> int   Return PDB residue number of CDR end residue get_CDR_in_loopsop(...) from builtins.PyCapsule get_CDR_in_loopsop(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum) -> rosetta.protocols.loops.Loops   return the loop of a certain loop type get_CDR_length(...) from builtins.PyCapsule get_CDR_length(*args, **kwargs) Overloaded function.   1. get_CDR_length(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum) -> int   get the length of the cdr upon construction of AntibodyInfo      Does not work for proto CDR4 (DE loop)   2. get_CDR_length(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum, pose : rosetta.core.pose.Pose) -> int   On-the-fly CDR length.   3. get_CDR_length(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum, pose : rosetta.core.pose.Pose, transform : rosetta.protocols.antibody.CDRDefinitionEnum) -> int get_CDR_loop(...) from builtins.PyCapsule get_CDR_loop(*args, **kwargs) Overloaded function.   1. get_CDR_loop(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum) -> rosetta.protocols.loops.Loop   return the loop of a certain loop type   2. get_CDR_loop(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum, pose : rosetta.core.pose.Pose) -> rosetta.protocols.loops.Loop   return the loop of a certain loop type on the fly   3. get_CDR_loop(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum, pose : rosetta.core.pose.Pose, overhang : int) -> rosetta.protocols.loops.Loop   return the loop of a certain loop type on the fly   4. get_CDR_loop(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum, pose : rosetta.core.pose.Pose, transform : rosetta.protocols.antibody.CDRDefinitionEnum) -> rosetta.protocols.loops.Loop   return the loop of a certain loop type in definitions of the numbering scheme transform.   5. get_CDR_loop(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum, pose : rosetta.core.pose.Pose, transform : rosetta.protocols.antibody.CDRDefinitionEnum, overhang : int) -> rosetta.protocols.loops.Loop   return the loop of a certain loop type in definitions of the numbering scheme transform. get_CDR_loops(...) from builtins.PyCapsule get_CDR_loops(*args, **kwargs) Overloaded function.   1. get_CDR_loops(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> rosetta.protocols.loops.Loops   On-the-fly CDR LoopsOP   2. get_CDR_loops(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, overhang : int) -> rosetta.protocols.loops.Loops   On-the-fly CDR LoopsOP   3. get_CDR_loops(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, cdrs : rosetta.utility.vector1_bool) -> rosetta.protocols.loops.Loops   4. get_CDR_loops(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, cdrs : rosetta.utility.vector1_bool, overhang : int) -> rosetta.protocols.loops.Loops get_CDR_name(...) from builtins.PyCapsule get_CDR_name(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum) -> str get_CDR_name_enum(...) from builtins.PyCapsule get_CDR_name_enum(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : str) -> rosetta.protocols.antibody.CDRNameEnum get_CDR_sequence_with_stem(...) from builtins.PyCapsule get_CDR_sequence_with_stem(*args, **kwargs) Overloaded function.   1. get_CDR_sequence_with_stem(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum) -> str   return the sequence of a particular CDR loop   2. get_CDR_sequence_with_stem(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum, left_stem : int) -> str   return the sequence of a particular CDR loop   3. get_CDR_sequence_with_stem(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum, left_stem : int, right_stem : int) -> str   return the sequence of a particular CDR loop   4. get_CDR_sequence_with_stem(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum, pose : rosetta.core.pose.Pose, transform : rosetta.protocols.antibody.CDRDefinitionEnum) -> str   On-The-Fly CDR sequence   5. get_CDR_sequence_with_stem(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum, pose : rosetta.core.pose.Pose, transform : rosetta.protocols.antibody.CDRDefinitionEnum, left_stem : int) -> str   On-The-Fly CDR sequence   6. get_CDR_sequence_with_stem(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum, pose : rosetta.core.pose.Pose, transform : rosetta.protocols.antibody.CDRDefinitionEnum, left_stem : int, right_stem : int) -> str   On-The-Fly CDR sequence get_CDR_start(...) from builtins.PyCapsule get_CDR_start(*args, **kwargs) Overloaded function.   1. get_CDR_start(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum, pose : rosetta.core.pose.Pose) -> int   Return pose number of CDR start residue   2. get_CDR_start(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum, pose : rosetta.core.pose.Pose, transform : rosetta.protocols.antibody.CDRDefinitionEnum) -> int get_CDR_start_PDB_num(...) from builtins.PyCapsule get_CDR_start_PDB_num(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum) -> int   Return PDB residue number of CDR start residue get_FoldTree_AllCDRs(...) from builtins.PyCapsule get_FoldTree_AllCDRs(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree get_FoldTree_AllCDRs_LHDock(...) from builtins.PyCapsule get_FoldTree_AllCDRs_LHDock(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree get_FoldTree_LA_H(...) from builtins.PyCapsule get_FoldTree_LA_H(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree get_FoldTree_LH_A(...) from builtins.PyCapsule get_FoldTree_LH_A(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   SnugDock foldtrees get_FoldTree_L_HA(...) from builtins.PyCapsule get_FoldTree_L_HA(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree get_H3_kink_type(...) from builtins.PyCapsule get_H3_kink_type(rosetta.protocols.antibody.AntibodyInfo) -> rosetta.protocols.antibody.H3BaseTypeEnum   get H3 cterminal kink/extended conformation (predicted by constructor) get_H3_kink_type_name(...) from builtins.PyCapsule get_H3_kink_type_name(rosetta.protocols.antibody.AntibodyInfo) -> str get_MoveMap_for_AllCDRsSideChains_and_H3backbone(...) from builtins.PyCapsule get_MoveMap_for_AllCDRsSideChains_and_H3backbone(*args, **kwargs) Overloaded function.   1. get_MoveMap_for_AllCDRsSideChains_and_H3backbone(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> rosetta.core.kinematics.MoveMap   2. get_MoveMap_for_AllCDRsSideChains_and_H3backbone(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, include_nb_sc : bool) -> rosetta.core.kinematics.MoveMap   3. get_MoveMap_for_AllCDRsSideChains_and_H3backbone(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, include_nb_sc : bool, nb_dist : float) -> rosetta.core.kinematics.MoveMap get_MoveMap_for_Loops(...) from builtins.PyCapsule get_MoveMap_for_Loops(*args, **kwargs) Overloaded function.   1. get_MoveMap_for_Loops(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, the_loops : rosetta.protocols.loops.Loops) -> rosetta.core.kinematics.MoveMap   TODO: this should be a standard utility for loops?      get a movemap for loops.   2. get_MoveMap_for_Loops(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, the_loops : rosetta.protocols.loops.Loops, bb_only : bool) -> rosetta.core.kinematics.MoveMap   TODO: this should be a standard utility for loops?      get a movemap for loops.   3. get_MoveMap_for_Loops(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, the_loops : rosetta.protocols.loops.Loops, bb_only : bool, include_nb_sc : bool) -> rosetta.core.kinematics.MoveMap   TODO: this should be a standard utility for loops?      get a movemap for loops.   4. get_MoveMap_for_Loops(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, the_loops : rosetta.protocols.loops.Loops, bb_only : bool, include_nb_sc : bool, nb_dist : float) -> rosetta.core.kinematics.MoveMap   TODO: this should be a standard utility for loops?      get a movemap for loops. get_MoveMap_for_LoopsandDock(...) from builtins.PyCapsule get_MoveMap_for_LoopsandDock(*args, **kwargs) Overloaded function.   1. get_MoveMap_for_LoopsandDock(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, the_loops : rosetta.protocols.loops.Loops) -> rosetta.core.kinematics.MoveMap   get a movemap for loops and set the first jump be true   2. get_MoveMap_for_LoopsandDock(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, the_loops : rosetta.protocols.loops.Loops, bb_only : bool) -> rosetta.core.kinematics.MoveMap   get a movemap for loops and set the first jump be true   3. get_MoveMap_for_LoopsandDock(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, the_loops : rosetta.protocols.loops.Loops, bb_only : bool, include_nb_sc : bool) -> rosetta.core.kinematics.MoveMap   get a movemap for loops and set the first jump be true   4. get_MoveMap_for_LoopsandDock(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, the_loops : rosetta.protocols.loops.Loops, bb_only : bool, include_nb_sc : bool, nb_dist : float) -> rosetta.core.kinematics.MoveMap   get a movemap for loops and set the first jump be true get_PackingAngleResidues(...) from builtins.PyCapsule get_PackingAngleResidues(rosetta.protocols.antibody.AntibodyInfo) -> rosetta.utility.vector1_unsigned_long   get residues used to calculate VL/VH packing angle get_TaskFactory_AllCDRs(...) from builtins.PyCapsule get_TaskFactory_AllCDRs(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> rosetta.core.pack.task.TaskFactory   TaskFactory get_TaskFactory_OneCDR(...) from builtins.PyCapsule get_TaskFactory_OneCDR(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, cdr_name : rosetta.protocols.antibody.CDRNameEnum) -> rosetta.core.pack.task.TaskFactory get_antibody_chain_ids(...) from builtins.PyCapsule get_antibody_chain_ids(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long get_antibody_chain_string(...) from builtins.PyCapsule get_antibody_chain_string(rosetta.protocols.antibody.AntibodyInfo) -> str   Returns H or LH depeding on camelid. get_antibody_chains(...) from builtins.PyCapsule get_antibody_chains(rosetta.protocols.antibody.AntibodyInfo) -> rosetta.utility.vector1_char get_antibody_enum_manager(...) from builtins.PyCapsule get_antibody_enum_manager(rosetta.protocols.antibody.AntibodyInfo) -> rosetta.protocols.antibody.AntibodyEnumManager get_antibody_sequence(...) from builtins.PyCapsule get_antibody_sequence(rosetta.protocols.antibody.AntibodyInfo) -> str   return the antibody sequence of LH or just H for camelid get_antigen_chain_ids(...) from builtins.PyCapsule get_antigen_chain_ids(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long get_antigen_chain_string(...) from builtins.PyCapsule get_antigen_chain_string(rosetta.protocols.antibody.AntibodyInfo) -> str   Return the antigen chains as a string get_antigen_chains(...) from builtins.PyCapsule get_antigen_chains(rosetta.protocols.antibody.AntibodyInfo) -> rosetta.utility.vector1_char   gets all non-LH chains.  Empty vector if no antigen present. get_cdr_cluster_enum_manager(...) from builtins.PyCapsule get_cdr_cluster_enum_manager(rosetta.protocols.antibody.AntibodyInfo) -> rosetta.protocols.antibody.clusters.CDRClusterEnumManager get_cdr_enum_for_cluster(...) from builtins.PyCapsule get_cdr_enum_for_cluster(self : rosetta.protocols.antibody.AntibodyInfo, cluster : rosetta.protocols.antibody.clusters.CDRClusterEnum) -> rosetta.protocols.antibody.CDRNameEnum get_cluster_enum(...) from builtins.PyCapsule get_cluster_enum(self : rosetta.protocols.antibody.AntibodyInfo, cluster : str) -> rosetta.protocols.antibody.clusters.CDRClusterEnum get_cluster_length(...) from builtins.PyCapsule get_cluster_length(self : rosetta.protocols.antibody.AntibodyInfo, cluster : rosetta.protocols.antibody.clusters.CDRClusterEnum) -> int get_cluster_name(...) from builtins.PyCapsule get_cluster_name(self : rosetta.protocols.antibody.AntibodyInfo, cluster : rosetta.protocols.antibody.clusters.CDRClusterEnum) -> str get_current_AntibodyNumberingScheme(...) from builtins.PyCapsule get_current_AntibodyNumberingScheme(rosetta.protocols.antibody.AntibodyInfo) -> str   : get the current numbering scheme being used get_current_CDRDefinition(...) from builtins.PyCapsule get_current_CDRDefinition(rosetta.protocols.antibody.AntibodyInfo) -> str get_landmark_resnum(...) from builtins.PyCapsule get_landmark_resnum(*args, **kwargs) Overloaded function.   1. get_landmark_resnum(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, scheme : rosetta.protocols.antibody.AntibodyNumberingSchemeEnum, chain : str, pdb_resnum : int) -> int   Used to get a residue number of a particular place in the framework or conserved residue in the CDR.  Use this instead of PDBInfo!!      If the current numbering scheme is not 'scheme', will return the equivalent position of the current numbering scheme using the transform scheme file in the database.  Should not be used for residues within CDRs since numbering schemes vary greatly in their within cdr alignments and numbering.  Use get_CDR_start/end/loop functions with relative positions for this purpose.  Returns 0 if residue is not found in pose   2. get_landmark_resnum(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, scheme : rosetta.protocols.antibody.AntibodyNumberingSchemeEnum, chain : str, pdb_resnum : int, insertion_code : str) -> int   Used to get a residue number of a particular place in the framework or conserved residue in the CDR.  Use this instead of PDBInfo!!      If the current numbering scheme is not 'scheme', will return the equivalent position of the current numbering scheme using the transform scheme file in the database.  Should not be used for residues within CDRs since numbering schemes vary greatly in their within cdr alignments and numbering.  Use get_CDR_start/end/loop functions with relative positions for this purpose.  Returns 0 if residue is not found in pose   3. get_landmark_resnum(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, scheme : rosetta.protocols.antibody.AntibodyNumberingSchemeEnum, chain : str, pdb_resnum : int, insertion_code : str, fail_on_missing_resnum : bool) -> int   Used to get a residue number of a particular place in the framework or conserved residue in the CDR.  Use this instead of PDBInfo!!      If the current numbering scheme is not 'scheme', will return the equivalent position of the current numbering scheme using the transform scheme file in the database.  Should not be used for residues within CDRs since numbering schemes vary greatly in their within cdr alignments and numbering.  Use get_CDR_start/end/loop functions with relative positions for this purpose.  Returns 0 if residue is not found in pose get_light_chain_type(...) from builtins.PyCapsule get_light_chain_type(rosetta.protocols.antibody.AntibodyInfo) -> str   Return if antibody is lambda, kappa or unknown.  Type set via cmd-line option for now get_light_chain_type_enum(...) from builtins.PyCapsule get_light_chain_type_enum(rosetta.protocols.antibody.AntibodyInfo) -> rosetta.protocols.antibody.LightChainTypeEnum   Return if antibody is lambda, kappa or unknown.  Type set via cmd-line option for now get_region_of_residue(...) from builtins.PyCapsule get_region_of_residue(*args, **kwargs) Overloaded function.   1. get_region_of_residue(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, resnum : int) -> rosetta.protocols.antibody.AntibodyRegionEnum   Get the region of the resnum - aka - antigen_region, cdr_region, or framework_region   By default, count the DE region (CDR4) as framework.   2. get_region_of_residue(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, resnum : int, de_as_framework : bool) -> rosetta.protocols.antibody.AntibodyRegionEnum   Get the region of the resnum - aka - antigen_region, cdr_region, or framework_region   By default, count the DE region (CDR4) as framework. get_total_num_CDRs(...) from builtins.PyCapsule get_total_num_CDRs(*args, **kwargs) Overloaded function.   1. get_total_num_CDRs(rosetta.protocols.antibody.AntibodyInfo) -> rosetta.protocols.antibody.CDRNameEnum   return num of cdr loops, 3 (nanobody) or 6 (regular antibody)   2. get_total_num_CDRs(self : rosetta.protocols.antibody.AntibodyInfo, include_proto_cdr4 : bool) -> rosetta.protocols.antibody.CDRNameEnum   return num of cdr loops, 3 (nanobody) or 6 (regular antibody) has_CDR(...) from builtins.PyCapsule has_CDR(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum) -> bool   Does the antibody have this CDR?  See also:                    is_camelid())                    get_total_num_CDRs()) has_cluster_for_cdr(...) from builtins.PyCapsule has_cluster_for_cdr(self : rosetta.protocols.antibody.AntibodyInfo, cdr_name : rosetta.protocols.antibody.CDRNameEnum) -> bool   Check to make sure AbInfo has a cluster object for this CDR.  In that all 6 CDRs not nessessarily present for each antibody. is_camelid(...) from builtins.PyCapsule is_camelid(rosetta.protocols.antibody.AntibodyInfo) -> bool   return this antibody is camelid or not kink_anion_atoms(...) from builtins.PyCapsule kink_anion_atoms(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> rosetta.std.vector_numeric_xyzVector_double_t   return side chain anion atoms (typically Asp/Glu oxygens) in the kink bulge HBond kink_anion_residue(...) from builtins.PyCapsule kink_anion_residue(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> int   return pose residue number of the kink 'anion' (typically Asp/Glu) residue in the kink bulge HBond kink_begin(...) from builtins.PyCapsule kink_begin(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> int   return pose residue number of the first residue of the H3 kink kink_cation_atoms(...) from builtins.PyCapsule kink_cation_atoms(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> rosetta.std.vector_numeric_xyzVector_double_t   return side chain cation atoms (typically Lys/His nitrogens) in the kink bulge HBond kink_cation_residue(...) from builtins.PyCapsule kink_cation_residue(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> int   return pose residue number of the kink 'cation' (typically Arg/Lys) residue in the kink bulge HBond kink_end(...) from builtins.PyCapsule kink_end(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> int   return pose residue number of the last residue of the H3 kink kink_trp(...) from builtins.PyCapsule kink_trp(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> int   return pose residue number of the last residue of the H3 kink set_CDR_cluster(...) from builtins.PyCapsule set_CDR_cluster(self : rosetta.protocols.antibody.AntibodyInfo, cdr : rosetta.protocols.antibody.CDRNameEnum, cluster : rosetta.protocols.antibody.clusters.CDRCluster) -> NoneType   Manually set the CDR cluster for a particular CDR setup_CDR_cluster(...) from builtins.PyCapsule setup_CDR_cluster(*args, **kwargs) Overloaded function.   1. setup_CDR_cluster(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, cdr : rosetta.protocols.antibody.CDRNameEnum) -> NoneType   setup the clustering information for a particular CDR.   Optionally, attempt to set the CDR cluster from the Pose data cache if any data is there.   2. setup_CDR_cluster(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, cdr : rosetta.protocols.antibody.CDRNameEnum, attempt_set_from_pose : bool) -> NoneType   setup the clustering information for a particular CDR.   Optionally, attempt to set the CDR cluster from the Pose data cache if any data is there. setup_CDR_clusters(...) from builtins.PyCapsule setup_CDR_clusters(*args, **kwargs) Overloaded function.   1. setup_CDR_clusters(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose) -> NoneType   setup the clustering information for each CDR to totalCDRLoops   Optionally, attempt to set the CDR cluster from the Pose data cache if any data is there.   2. setup_CDR_clusters(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, attempt_set_from_pose : bool) -> NoneType   setup the clustering information for each CDR to totalCDRLoops   Optionally, attempt to set the CDR cluster from the Pose data cache if any data is there.   3. setup_CDR_clusters(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, cdrs : rosetta.utility.vector1_bool) -> NoneType   setup the clustering information for each CDR according to boolean vector.   Optionally, attempt to set the CDR cluster from the Pose data cache if any data is there.   4. setup_CDR_clusters(self : rosetta.protocols.antibody.AntibodyInfo, pose : rosetta.core.pose.Pose, cdrs : rosetta.utility.vector1_bool, attempt_set_from_pose : bool) -> NoneType   setup the clustering information for each CDR according to boolean vector.   Optionally, attempt to set the CDR cluster from the Pose data cache if any data is there. setup_simple_fold_tree(...) from builtins.PyCapsule setup_simple_fold_tree(self : rosetta.protocols.antibody.AntibodyInfo, jumppoint1 : int, cutpoint : int, jumppoint2 : int, pose : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   ////////////////////////////////////////////////   class AntibodyModelerProtocol(rosetta.protocols.moves.Mover)       Method resolution order: AntibodyModelerProtocol 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.antibody.AntibodyModelerProtocol) -> 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.antibody.AntibodyModelerProtocol) -> str apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.antibody.AntibodyModelerProtocol, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.AntibodyModelerProtocol,  : rosetta.protocols.antibody.AntibodyModelerProtocol) -> rosetta.protocols.antibody.AntibodyModelerProtocol clone(...) from builtins.PyCapsule clone(rosetta.protocols.antibody.AntibodyModelerProtocol) -> rosetta.protocols.moves.Mover display_constraint_residues(...) from builtins.PyCapsule display_constraint_residues(self : rosetta.protocols.antibody.AntibodyModelerProtocol, pose : rosetta.core.pose.Pose) -> NoneType get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.antibody.AntibodyModelerProtocol) -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType set_BenchMark(...) from builtins.PyCapsule set_BenchMark(self : rosetta.protocols.antibody.AntibodyModelerProtocol, setting : bool) -> NoneType set_CterInsert(...) from builtins.PyCapsule set_CterInsert(self : rosetta.protocols.antibody.AntibodyModelerProtocol, setting : bool) -> NoneType set_H3Filter(...) from builtins.PyCapsule set_H3Filter(self : rosetta.protocols.antibody.AntibodyModelerProtocol, setting : bool) -> NoneType set_H3Filter_Tolerance(...) from builtins.PyCapsule set_H3Filter_Tolerance(self : rosetta.protocols.antibody.AntibodyModelerProtocol, number : int) -> NoneType set_ModelH3(...) from builtins.PyCapsule set_ModelH3(self : rosetta.protocols.antibody.AntibodyModelerProtocol, setting : bool) -> NoneType set_SnugFit(...) from builtins.PyCapsule set_SnugFit(self : rosetta.protocols.antibody.AntibodyModelerProtocol, setting : bool) -> NoneType set_all_atom_mode_kink_constraint(...) from builtins.PyCapsule set_all_atom_mode_kink_constraint(self : rosetta.protocols.antibody.AntibodyModelerProtocol, setting : bool) -> NoneType set_auto_constraint(...) from builtins.PyCapsule set_auto_constraint(self : rosetta.protocols.antibody.AntibodyModelerProtocol, setting : bool) -> NoneType set_bad_nter(...) from builtins.PyCapsule set_bad_nter(self : rosetta.protocols.antibody.AntibodyModelerProtocol, setting : bool) -> NoneType set_constrain_cter(...) from builtins.PyCapsule set_constrain_cter(self : rosetta.protocols.antibody.AntibodyModelerProtocol, setting : bool) -> NoneType set_constrain_vlvh_qq(...) from builtins.PyCapsule set_constrain_vlvh_qq(self : rosetta.protocols.antibody.AntibodyModelerProtocol, setting : bool) -> NoneType set_cst_weight(...) from builtins.PyCapsule set_cst_weight(self : rosetta.protocols.antibody.AntibodyModelerProtocol, cst_weight : float) -> NoneType set_default(...) from builtins.PyCapsule set_default(rosetta.protocols.antibody.AntibodyModelerProtocol) -> NoneType   Assigns default values to primitive members set_extend_h3_before_modeling(...) from builtins.PyCapsule set_extend_h3_before_modeling(self : rosetta.protocols.antibody.AntibodyModelerProtocol, setting : bool) -> NoneType set_flank_residue_min(...) from builtins.PyCapsule set_flank_residue_min(self : rosetta.protocols.antibody.AntibodyModelerProtocol, setting : bool) -> NoneType set_flank_residue_size(...) from builtins.PyCapsule set_flank_residue_size(self : rosetta.protocols.antibody.AntibodyModelerProtocol, flank_residue_size : float) -> NoneType set_idealize_h3_stems_before_modeling(...) from builtins.PyCapsule set_idealize_h3_stems_before_modeling(self : rosetta.protocols.antibody.AntibodyModelerProtocol, setting : bool) -> NoneType set_middle_pack_min(...) from builtins.PyCapsule set_middle_pack_min(self : rosetta.protocols.antibody.AntibodyModelerProtocol, middle_pack_min : bool) -> NoneType set_packonly_after_graft(...) from builtins.PyCapsule set_packonly_after_graft(self : rosetta.protocols.antibody.AntibodyModelerProtocol, setting : bool) -> NoneType set_perturb_type(...) from builtins.PyCapsule set_perturb_type(self : rosetta.protocols.antibody.AntibodyModelerProtocol, remodel : str) -> NoneType set_refine_h3(...) from builtins.PyCapsule set_refine_h3(self : rosetta.protocols.antibody.AntibodyModelerProtocol, setting : bool) -> NoneType set_refine_type(...) from builtins.PyCapsule set_refine_type(self : rosetta.protocols.antibody.AntibodyModelerProtocol, refine : str) -> NoneType set_rt_min(...) from builtins.PyCapsule set_rt_min(self : rosetta.protocols.antibody.AntibodyModelerProtocol, setting : bool) -> NoneType set_sc_min(...) from builtins.PyCapsule set_sc_min(self : rosetta.protocols.antibody.AntibodyModelerProtocol, setting : bool) -> NoneType set_use_constraints(...) from builtins.PyCapsule set_use_constraints(self : rosetta.protocols.antibody.AntibodyModelerProtocol, use_csts : bool) -> NoneType sync_objects_with_flags(...) from builtins.PyCapsule sync_objects_with_flags(rosetta.protocols.antibody.AntibodyModelerProtocol) -> NoneType   Instantiates non-primitive members based on the value of the primitive members Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class AntibodyNumbering(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.antibody.AntibodyNumbering) -> 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.antibody.AntibodyNumbering,  : rosetta.protocols.antibody.AntibodyNumbering) -> rosetta.protocols.antibody.AntibodyNumbering Data descriptors defined here: cdr_definition cdr_definition_transform cdr_numbering numbering_scheme numbering_scheme_transform   class AntibodyNumberingParser(builtins.object)     Class responsible for reading database Numbering Scheme definitions and their transforms from the database.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.antibody.AntibodyNumberingParser, enum_manager : rosetta.protocols.antibody.AntibodyEnumManager) -> NoneType   2. __init__(self : rosetta.protocols.antibody.AntibodyNumberingParser,  : rosetta.protocols.antibody.AntibodyNumberingParser) -> 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.antibody.AntibodyNumberingParser,  : rosetta.protocols.antibody.AntibodyNumberingParser) -> rosetta.protocols.antibody.AntibodyNumberingParser get_antibody_numbering(...) from builtins.PyCapsule get_antibody_numbering(self : rosetta.protocols.antibody.AntibodyNumberingParser, numbering_scheme : rosetta.protocols.antibody.AntibodyNumberingSchemeEnum, cdr_definition : rosetta.protocols.antibody.CDRDefinitionEnum) -> rosetta.protocols.antibody.AntibodyNumbering   Read numbering file and return AntibodyNumbering structure   class AntibodyNumberingSchemeEnum(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.protocols.antibody.AntibodyNumberingSchemeEnum, rosetta.protocols.antibody.AntibodyNumberingSchemeEnum) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.protocols.antibody.AntibodyNumberingSchemeEnum) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.AntibodyNumberingSchemeEnum, int) -> NoneType   2. __init__(rosetta.protocols.antibody.AntibodyNumberingSchemeEnum, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.protocols.antibody.AntibodyNumberingSchemeEnum) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.protocols.antibody.AntibodyNumberingSchemeEnum, rosetta.protocols.antibody.AntibodyNumberingSchemeEnum) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.protocols.antibody.AntibodyNumberingSchemeEnum) -> str Data and other attributes defined here: AHO_Scheme = AntibodyNumberingSchemeEnum.AntibodyNumberingSchemeEnum_total AntibodyNumberingSchemeEnum_start = AntibodyNumberingSchemeEnum.AntibodyNumberingSchemeEnum_start AntibodyNumberingSchemeEnum_total = AntibodyNumberingSchemeEnum.AntibodyNumberingSchemeEnum_total Chothia_Scheme = AntibodyNumberingSchemeEnum.AntibodyNumberingSchemeEnum_start Enhanced_Chothia_Scheme = AntibodyNumberingSchemeEnum.Enhanced_Chothia_Scheme IMGT_Scheme = AntibodyNumberingSchemeEnum.IMGT_Scheme Kabat_Scheme = AntibodyNumberingSchemeEnum.Kabat_Scheme NONE = AntibodyNumberingSchemeEnum.NONE   class AntibodyRegionEnum(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.protocols.antibody.AntibodyRegionEnum, rosetta.protocols.antibody.AntibodyRegionEnum) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.protocols.antibody.AntibodyRegionEnum) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.AntibodyRegionEnum, int) -> NoneType   2. __init__(rosetta.protocols.antibody.AntibodyRegionEnum, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.protocols.antibody.AntibodyRegionEnum) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.protocols.antibody.AntibodyRegionEnum, rosetta.protocols.antibody.AntibodyRegionEnum) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.protocols.antibody.AntibodyRegionEnum) -> str Data and other attributes defined here: AntibodyRegionEnum_start = AntibodyRegionEnum.AntibodyRegionEnum_start AntibodyRegionEnum_total = AntibodyRegionEnum.AntibodyRegionEnum_total antigen_region = AntibodyRegionEnum.AntibodyRegionEnum_start cdr_region = AntibodyRegionEnum.cdr_region framework_region = AntibodyRegionEnum.AntibodyRegionEnum_total unknown_ab_region = AntibodyRegionEnum.unknown_ab_region   class CDRDBPose(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.antibody.CDRDBPose, pose : rosetta.core.pose.Pose, cluster : rosetta.protocols.antibody.clusters.CDRClusterEnum, pdb : str, distance : float, normalized_distance : float, resolution : float) -> NoneType   2. __init__(self : rosetta.protocols.antibody.CDRDBPose,  : rosetta.protocols.antibody.CDRDBPose) -> 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.antibody.CDRDBPose,  : rosetta.protocols.antibody.CDRDBPose) -> rosetta.protocols.antibody.CDRDBPose Data descriptors defined here: cluster distance normalized_distance pdb pose resolution   class CDRDBSequence(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.antibody.CDRDBSequence, sequence : str, cluster : rosetta.protocols.antibody.clusters.CDRClusterEnum, pdb : str, distance : float, normalized_distance : float, resolution : float) -> NoneType   2. __init__(self : rosetta.protocols.antibody.CDRDBSequence,  : rosetta.protocols.antibody.CDRDBSequence) -> 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.antibody.CDRDBSequence,  : rosetta.protocols.antibody.CDRDBSequence) -> rosetta.protocols.antibody.CDRDBSequence Data descriptors defined here: cluster distance normalized_distance pdb resolution sequence   class CDRDefinitionEnum(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.protocols.antibody.CDRDefinitionEnum, rosetta.protocols.antibody.CDRDefinitionEnum) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.protocols.antibody.CDRDefinitionEnum) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.CDRDefinitionEnum, int) -> NoneType   2. __init__(rosetta.protocols.antibody.CDRDefinitionEnum, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.protocols.antibody.CDRDefinitionEnum) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.protocols.antibody.CDRDefinitionEnum, rosetta.protocols.antibody.CDRDefinitionEnum) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.protocols.antibody.CDRDefinitionEnum) -> str Data and other attributes defined here: Aroop = CDRDefinitionEnum.Aroop CDRDefinitionEnum_start = CDRDefinitionEnum.CDRDefinitionEnum_start CDRDefinitionEnum_total = CDRDefinitionEnum.CDRDefinitionEnum_total Chothia = CDRDefinitionEnum.CDRDefinitionEnum_start Kabat = CDRDefinitionEnum.Kabat Martin = CDRDefinitionEnum.Martin North = CDRDefinitionEnum.CDRDefinitionEnum_total   class CDRLandmarkEnum(builtins.object)     Main enumerator for AntibodyNumbering.     Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.protocols.antibody.CDRLandmarkEnum, rosetta.protocols.antibody.CDRLandmarkEnum) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.protocols.antibody.CDRLandmarkEnum) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.CDRLandmarkEnum, int) -> NoneType   2. __init__(rosetta.protocols.antibody.CDRLandmarkEnum, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.protocols.antibody.CDRLandmarkEnum) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.protocols.antibody.CDRLandmarkEnum, rosetta.protocols.antibody.CDRLandmarkEnum) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.protocols.antibody.CDRLandmarkEnum) -> str Data and other attributes defined here: CDRLandmarkEnum_total = CDRLandmarkEnum.CDRLandmarkEnum_total cdr_end = CDRLandmarkEnum.CDRLandmarkEnum_total cdr_start = CDRLandmarkEnum.cdr_start   class CDRNameEnum(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.protocols.antibody.CDRNameEnum, rosetta.protocols.antibody.CDRNameEnum) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.protocols.antibody.CDRNameEnum) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.CDRNameEnum, int) -> NoneType   2. __init__(rosetta.protocols.antibody.CDRNameEnum, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.protocols.antibody.CDRNameEnum) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.protocols.antibody.CDRNameEnum, rosetta.protocols.antibody.CDRNameEnum) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.protocols.antibody.CDRNameEnum) -> str Data and other attributes defined here: CDRNameEnum_proto_start = CDRNameEnum.h4 CDRNameEnum_proto_total = CDRNameEnum.l4 CDRNameEnum_start = CDRNameEnum.CDRNameEnum_start CDRNameEnum_total = CDRNameEnum.CDRNameEnum_total H_chain_last_loop = CDRNameEnum.camelid_last_loop L_chain_last_loop = CDRNameEnum.CDRNameEnum_total camelid_last_loop = CDRNameEnum.camelid_last_loop h1 = CDRNameEnum.CDRNameEnum_start h2 = CDRNameEnum.h2 h3 = CDRNameEnum.camelid_last_loop h4 = CDRNameEnum.h4 l1 = CDRNameEnum.l1 l2 = CDRNameEnum.l2 l3 = CDRNameEnum.CDRNameEnum_total l4 = CDRNameEnum.l4 num_cdr_loops = CDRNameEnum.CDRNameEnum_total proto_h4 = CDRNameEnum.h4 proto_l4 = CDRNameEnum.l4 start_cdr_loop = CDRNameEnum.CDRNameEnum_start   class CDRSetOptions(builtins.object)     Class that holds instructions for a single CDR for loading from the antibody database. Default is instructions to load all CDRs from the database     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.CDRSetOptions) -> NoneType   doc   2. __init__(self : rosetta.protocols.antibody.CDRSetOptions, load : bool) -> NoneType   3. __init__(rosetta.protocols.antibody.CDRSetOptions, rosetta.protocols.antibody.CDRNameEnum) -> NoneType   doc   4. __init__(self : rosetta.protocols.antibody.CDRSetOptions, cdr : rosetta.protocols.antibody.CDRNameEnum, load : bool) -> NoneType   5. __init__(self : rosetta.protocols.antibody.CDRSetOptions, src : rosetta.protocols.antibody.CDRSetOptions) -> 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.antibody.CDRSetOptions,  : rosetta.protocols.antibody.CDRSetOptions) -> rosetta.protocols.antibody.CDRSetOptions cdr(...) from builtins.PyCapsule cdr(rosetta.protocols.antibody.CDRSetOptions) -> rosetta.protocols.antibody.CDRNameEnum clone(...) from builtins.PyCapsule clone(rosetta.protocols.antibody.CDRSetOptions) -> rosetta.protocols.antibody.CDRSetOptions cluster_sampling_cutoff(...) from builtins.PyCapsule cluster_sampling_cutoff(*args, **kwargs) Overloaded function.   1. cluster_sampling_cutoff(self : rosetta.protocols.antibody.CDRSetOptions, cutoff : int) -> NoneType   Set a sampling cutoff.  Use zero for no cutoff as default.   2. cluster_sampling_cutoff(rosetta.protocols.antibody.CDRSetOptions) -> int exclude_clusters(...) from builtins.PyCapsule exclude_clusters(*args, **kwargs) Overloaded function.   1. exclude_clusters(self : rosetta.protocols.antibody.CDRSetOptions, exclude : rosetta.utility.vector1_protocols_antibody_clusters_CDRClusterEnum) -> NoneType   /////////// Clusters /////////////////   2. exclude_clusters(rosetta.protocols.antibody.CDRSetOptions) -> rosetta.utility.vector1_protocols_antibody_clusters_CDRClusterEnum exclude_clusters_add(...) from builtins.PyCapsule exclude_clusters_add(self : rosetta.protocols.antibody.CDRSetOptions, exclude : rosetta.protocols.antibody.clusters.CDRClusterEnum) -> NoneType exclude_clusters_clear(...) from builtins.PyCapsule exclude_clusters_clear(rosetta.protocols.antibody.CDRSetOptions) -> NoneType exclude_germlines(...) from builtins.PyCapsule exclude_germlines(*args, **kwargs) Overloaded function.   1. exclude_germlines(self : rosetta.protocols.antibody.CDRSetOptions, exclude : rosetta.utility.vector1_std_string) -> NoneType   //////// Germlines ////////////////////   2. exclude_germlines(rosetta.protocols.antibody.CDRSetOptions) -> rosetta.utility.vector1_std_string exclude_germlines_add(...) from builtins.PyCapsule exclude_germlines_add(self : rosetta.protocols.antibody.CDRSetOptions, exclude : str) -> NoneType exclude_germlines_clear(...) from builtins.PyCapsule exclude_germlines_clear(rosetta.protocols.antibody.CDRSetOptions) -> NoneType exclude_pdbs(...) from builtins.PyCapsule exclude_pdbs(*args, **kwargs) Overloaded function.   1. exclude_pdbs(self : rosetta.protocols.antibody.CDRSetOptions, exclude_pdbids : rosetta.utility.vector1_std_string) -> NoneType   /////////// PDBIds ///////////////////   2. exclude_pdbs(rosetta.protocols.antibody.CDRSetOptions) -> rosetta.utility.vector1_std_string exclude_pdbs_add(...) from builtins.PyCapsule exclude_pdbs_add(self : rosetta.protocols.antibody.CDRSetOptions, pdbid : str) -> NoneType exclude_pdbs_clear(...) from builtins.PyCapsule exclude_pdbs_clear(rosetta.protocols.antibody.CDRSetOptions) -> NoneType exclude_species(...) from builtins.PyCapsule exclude_species(*args, **kwargs) Overloaded function.   1. exclude_species(self : rosetta.protocols.antibody.CDRSetOptions, exclude : rosetta.utility.vector1_std_string) -> NoneType   ////////// Species ////////////////////   2. exclude_species(rosetta.protocols.antibody.CDRSetOptions) -> rosetta.utility.vector1_std_string exclude_species_add(...) from builtins.PyCapsule exclude_species_add(self : rosetta.protocols.antibody.CDRSetOptions, exclude : str) -> NoneType exclude_species_clear(...) from builtins.PyCapsule exclude_species_clear(rosetta.protocols.antibody.CDRSetOptions) -> NoneType include_only_center_clusters(...) from builtins.PyCapsule include_only_center_clusters(*args, **kwargs) Overloaded function.   1. include_only_center_clusters(self : rosetta.protocols.antibody.CDRSetOptions, centers_only : bool) -> NoneType   Do we only include the center members of the clusters in the CDRSet?   2. include_only_center_clusters(rosetta.protocols.antibody.CDRSetOptions) -> bool include_only_clusters(...) from builtins.PyCapsule include_only_clusters(*args, **kwargs) Overloaded function.   1. include_only_clusters(self : rosetta.protocols.antibody.CDRSetOptions, include_only : rosetta.utility.vector1_protocols_antibody_clusters_CDRClusterEnum) -> NoneType   2. include_only_clusters(rosetta.protocols.antibody.CDRSetOptions) -> rosetta.utility.vector1_protocols_antibody_clusters_CDRClusterEnum include_only_clusters_add(...) from builtins.PyCapsule include_only_clusters_add(self : rosetta.protocols.antibody.CDRSetOptions, include_only : rosetta.protocols.antibody.clusters.CDRClusterEnum) -> NoneType include_only_clusters_clear(...) from builtins.PyCapsule include_only_clusters_clear(rosetta.protocols.antibody.CDRSetOptions) -> NoneType include_only_current_cluster(...) from builtins.PyCapsule include_only_current_cluster(*args, **kwargs) Overloaded function.   1. include_only_current_cluster(self : rosetta.protocols.antibody.CDRSetOptions, only_current_cluster : bool) -> NoneType   If antibody CDRs are loaded in relation to the current PDB in whatever algorithm or app is using this,   Should we only pull clusters of the same type as this PDB?        May or may not be used.  In AntibodyGraftDesign, this is used.   2. include_only_current_cluster(rosetta.protocols.antibody.CDRSetOptions) -> bool include_only_germlines(...) from builtins.PyCapsule include_only_germlines(*args, **kwargs) Overloaded function.   1. include_only_germlines(self : rosetta.protocols.antibody.CDRSetOptions, include_only : rosetta.utility.vector1_std_string) -> NoneType   2. include_only_germlines(rosetta.protocols.antibody.CDRSetOptions) -> rosetta.utility.vector1_std_string include_only_germlines_add(...) from builtins.PyCapsule include_only_germlines_add(self : rosetta.protocols.antibody.CDRSetOptions, include_only : str) -> NoneType include_only_germlines_clear(...) from builtins.PyCapsule include_only_germlines_clear(rosetta.protocols.antibody.CDRSetOptions) -> NoneType include_only_pdbs(...) from builtins.PyCapsule include_only_pdbs(*args, **kwargs) Overloaded function.   1. include_only_pdbs(self : rosetta.protocols.antibody.CDRSetOptions, include_pdbids : rosetta.utility.vector1_std_string) -> NoneType   2. include_only_pdbs(rosetta.protocols.antibody.CDRSetOptions) -> rosetta.utility.vector1_std_string include_only_pdbs_add(...) from builtins.PyCapsule include_only_pdbs_add(self : rosetta.protocols.antibody.CDRSetOptions, pdbid : str) -> NoneType include_only_pdbs_clear(...) from builtins.PyCapsule include_only_pdbs_clear(rosetta.protocols.antibody.CDRSetOptions) -> NoneType include_only_species(...) from builtins.PyCapsule include_only_species(*args, **kwargs) Overloaded function.   1. include_only_species(self : rosetta.protocols.antibody.CDRSetOptions, include_only : rosetta.utility.vector1_std_string) -> NoneType   2. include_only_species(rosetta.protocols.antibody.CDRSetOptions) -> rosetta.utility.vector1_std_string include_only_species_add(...) from builtins.PyCapsule include_only_species_add(self : rosetta.protocols.antibody.CDRSetOptions, include_only : str) -> NoneType include_only_species_clear(...) from builtins.PyCapsule include_only_species_clear(rosetta.protocols.antibody.CDRSetOptions) -> NoneType length_type(...) from builtins.PyCapsule length_type(*args, **kwargs) Overloaded function.   1. length_type(self : rosetta.protocols.antibody.CDRSetOptions, type : int, setting : bool) -> NoneType   Set to only sample with clusters of the given type for this CDR.   2. length_type(rosetta.protocols.antibody.CDRSetOptions) -> rosetta.utility.vector1_bool load(...) from builtins.PyCapsule load(*args, **kwargs) Overloaded function.   1. load(self : rosetta.protocols.antibody.CDRSetOptions, load : bool) -> NoneType   2. load(rosetta.protocols.antibody.CDRSetOptions) -> bool max_length(...) from builtins.PyCapsule max_length(*args, **kwargs) Overloaded function.   1. max_length(self : rosetta.protocols.antibody.CDRSetOptions, length : int) -> NoneType   set the maximum cdr length to sample.  Nothing longer then this will be used.  Useful for H3.   2. max_length(rosetta.protocols.antibody.CDRSetOptions) -> int min_length(...) from builtins.PyCapsule min_length(*args, **kwargs) Overloaded function.   1. min_length(self : rosetta.protocols.antibody.CDRSetOptions, length : int) -> NoneType   set the minimum cdr length to sample.  Nothing shorter then this will be used during graft.   2. min_length(rosetta.protocols.antibody.CDRSetOptions) -> int set_cdr(...) from builtins.PyCapsule set_cdr(self : rosetta.protocols.antibody.CDRSetOptions, cdr : rosetta.protocols.antibody.CDRNameEnum) -> NoneType   /// General settings ////////////// set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.antibody.CDRSetOptions) -> NoneType   class CDRSetOptionsParser(builtins.object)     Parses CDRSetOptions for a single CDR at a time from a simple instruction file     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.CDRSetOptionsParser) -> NoneType   2. __init__(self : rosetta.protocols.antibody.CDRSetOptionsParser,  : rosetta.protocols.antibody.CDRSetOptionsParser) -> 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.antibody.CDRSetOptionsParser,  : rosetta.protocols.antibody.CDRSetOptionsParser) -> rosetta.protocols.antibody.CDRSetOptionsParser parse_default_and_user_options(...) from builtins.PyCapsule parse_default_and_user_options(*args, **kwargs) Overloaded function.   1. parse_default_and_user_options(self : rosetta.protocols.antibody.CDRSetOptionsParser, cdr : rosetta.protocols.antibody.CDRNameEnum, filename : str) -> rosetta.protocols.antibody.CDRSetOptions   Parse default instructions (mainly used for AbDesign) then parse user file   2. parse_default_and_user_options(self : rosetta.protocols.antibody.CDRSetOptionsParser, filename : str) -> rosetta.utility.vector1_std_shared_ptr_protocols_antibody_CDRSetOptions_t parse_options(...) from builtins.PyCapsule parse_options(*args, **kwargs) Overloaded function.   1. parse_options(self : rosetta.protocols.antibody.CDRSetOptionsParser, cdr : rosetta.protocols.antibody.CDRNameEnum, filename : str) -> rosetta.protocols.antibody.CDRSetOptions   2. parse_options(self : rosetta.protocols.antibody.CDRSetOptionsParser, filename : str) -> rosetta.utility.vector1_std_shared_ptr_protocols_antibody_CDRSetOptions_t   //////////Parse Options for all CDRs////////////////   class CDRsMinPackMin(rosetta.protocols.moves.Mover)       Method resolution order: CDRsMinPackMin rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, antibody_info : rosetta.protocols.antibody.AntibodyInfo) -> NoneType   2. __init__(self : handle, antibody_info : rosetta.protocols.antibody.AntibodyInfo, scorefxn : rosetta.core.scoring.ScoreFunction, tf : rosetta.core.pack.task.TaskFactory, movemap : rosetta.core.kinematics.MoveMap) -> NoneType   3. __init__(handle, rosetta.protocols.antibody.CDRsMinPackMin) -> 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.antibody.CDRsMinPackMin) -> str apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.antibody.CDRsMinPackMin, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.CDRsMinPackMin,  : rosetta.protocols.antibody.CDRsMinPackMin) -> rosetta.protocols.antibody.CDRsMinPackMin get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.antibody.CDRsMinPackMin) -> str set_move_map(...) from builtins.PyCapsule set_move_map(self : rosetta.protocols.antibody.CDRsMinPackMin, movemap : rosetta.core.kinematics.MoveMap) -> NoneType set_rt_min(...) from builtins.PyCapsule set_rt_min(self : rosetta.protocols.antibody.CDRsMinPackMin, rtmin : bool) -> NoneType set_sc_min(...) from builtins.PyCapsule set_sc_min(self : rosetta.protocols.antibody.CDRsMinPackMin, scmin : bool) -> NoneType set_task_factory(...) from builtins.PyCapsule set_task_factory(self : rosetta.protocols.antibody.CDRsMinPackMin, tf : rosetta.core.pack.task.TaskFactory) -> NoneType set_turnoff_minimization(...) from builtins.PyCapsule set_turnoff_minimization(self : rosetta.protocols.antibody.CDRsMinPackMin, setting : bool) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply clone(...) from builtins.PyCapsule clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Return a clone of the Mover object. create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class CloseOneCDRLoop(rosetta.protocols.moves.Mover)     Closes only one CDR onto a framework     Method resolution order: CloseOneCDRLoop 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, query_start : int, query_end : int) -> NoneType   3. __init__(handle, rosetta.protocols.antibody.CloseOneCDRLoop) -> 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.antibody.CloseOneCDRLoop, pose_in : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.CloseOneCDRLoop,  : rosetta.protocols.antibody.CloseOneCDRLoop) -> rosetta.protocols.antibody.CloseOneCDRLoop enable_benchmark_mode(...) from builtins.PyCapsule enable_benchmark_mode(self : rosetta.protocols.antibody.CloseOneCDRLoop, setting : bool) -> NoneType   enable benchmark mode get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.antibody.CloseOneCDRLoop) -> str set_default(...) from builtins.PyCapsule set_default(rosetta.protocols.antibody.CloseOneCDRLoop) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply clone(...) from builtins.PyCapsule clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Return a clone of the Mover object. create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class FrameWork(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.FrameWork) -> NoneType   2. __init__(self : rosetta.protocols.antibody.FrameWork,  : rosetta.protocols.antibody.FrameWork) -> 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.antibody.FrameWork,  : rosetta.protocols.antibody.FrameWork) -> rosetta.protocols.antibody.FrameWork Data descriptors defined here: chain_name start stop   class GraftCDRLoopsProtocol(rosetta.protocols.moves.Mover)       Method resolution order: GraftCDRLoopsProtocol 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.antibody.GraftCDRLoopsProtocol) -> 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.antibody.GraftCDRLoopsProtocol) -> str apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.antibody.GraftCDRLoopsProtocol, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.GraftCDRLoopsProtocol,  : rosetta.protocols.antibody.GraftCDRLoopsProtocol) -> rosetta.protocols.antibody.GraftCDRLoopsProtocol clone(...) from builtins.PyCapsule clone(rosetta.protocols.antibody.GraftCDRLoopsProtocol) -> rosetta.protocols.moves.Mover display_constraint_residues(...) from builtins.PyCapsule display_constraint_residues(self : rosetta.protocols.antibody.GraftCDRLoopsProtocol, pose : rosetta.core.pose.Pose) -> NoneType get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.antibody.GraftCDRLoopsProtocol) -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType set_benchmark(...) from builtins.PyCapsule set_benchmark(self : rosetta.protocols.antibody.GraftCDRLoopsProtocol, benchmark : bool) -> NoneType set_camelid(...) from builtins.PyCapsule set_camelid(self : rosetta.protocols.antibody.GraftCDRLoopsProtocol, camelid : bool) -> NoneType set_camelid_constraints(...) from builtins.PyCapsule set_camelid_constraints(self : rosetta.protocols.antibody.GraftCDRLoopsProtocol, camelid_constraints : bool) -> NoneType set_cst_weight(...) from builtins.PyCapsule set_cst_weight(self : rosetta.protocols.antibody.GraftCDRLoopsProtocol, cst_weight : float) -> NoneType set_default(...) from builtins.PyCapsule set_default(rosetta.protocols.antibody.GraftCDRLoopsProtocol) -> NoneType   Assigns default values to primitive members set_graft_h1(...) from builtins.PyCapsule set_graft_h1(self : rosetta.protocols.antibody.GraftCDRLoopsProtocol, graft_h1 : bool) -> NoneType set_graft_h2(...) from builtins.PyCapsule set_graft_h2(self : rosetta.protocols.antibody.GraftCDRLoopsProtocol, graft_h2 : bool) -> NoneType set_graft_h3(...) from builtins.PyCapsule set_graft_h3(self : rosetta.protocols.antibody.GraftCDRLoopsProtocol, graft_h3 : bool) -> NoneType set_graft_l1(...) from builtins.PyCapsule set_graft_l1(self : rosetta.protocols.antibody.GraftCDRLoopsProtocol, graft_l1 : bool) -> NoneType set_graft_l2(...) from builtins.PyCapsule set_graft_l2(self : rosetta.protocols.antibody.GraftCDRLoopsProtocol, graft_l2 : bool) -> NoneType set_graft_l3(...) from builtins.PyCapsule set_graft_l3(self : rosetta.protocols.antibody.GraftCDRLoopsProtocol, graft_l3 : bool) -> NoneType set_h3_stem_graft(...) from builtins.PyCapsule set_h3_stem_graft(self : rosetta.protocols.antibody.GraftCDRLoopsProtocol, h3_stem_graft : bool) -> NoneType set_packonly_after_graft(...) from builtins.PyCapsule set_packonly_after_graft(self : rosetta.protocols.antibody.GraftCDRLoopsProtocol, setting : bool) -> NoneType set_rt_min(...) from builtins.PyCapsule set_rt_min(self : rosetta.protocols.antibody.GraftCDRLoopsProtocol, rtmin : bool) -> NoneType set_sc_min(...) from builtins.PyCapsule set_sc_min(self : rosetta.protocols.antibody.GraftCDRLoopsProtocol, scmin : bool) -> NoneType set_stem_optimize(...) from builtins.PyCapsule set_stem_optimize(self : rosetta.protocols.antibody.GraftCDRLoopsProtocol, setting : bool) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class GraftOneCDRLoop(rosetta.protocols.moves.Mover)     Grafts only one CDR onto a framework     Method resolution order: GraftOneCDRLoop 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, cdr_name : rosetta.protocols.antibody.CDRNameEnum, antibody_info : rosetta.protocols.antibody.AntibodyInfo, ab_t_info : rosetta.protocols.antibody.Ab_TemplateInfo) -> NoneType   3. __init__(handle, rosetta.protocols.antibody.GraftOneCDRLoop) -> 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.antibody.GraftOneCDRLoop, pose_in : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.GraftOneCDRLoop, rhs : rosetta.protocols.antibody.GraftOneCDRLoop) -> rosetta.protocols.antibody.GraftOneCDRLoop   assignment operator enable_benchmark_mode(...) from builtins.PyCapsule enable_benchmark_mode(self : rosetta.protocols.antibody.GraftOneCDRLoop, setting : bool) -> NoneType   enable benchmark mode get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.antibody.GraftOneCDRLoop) -> str set_flank_size(...) from builtins.PyCapsule set_flank_size(self : rosetta.protocols.antibody.GraftOneCDRLoop, setting : int) -> NoneType set_no_stem_copy(...) from builtins.PyCapsule set_no_stem_copy(self : rosetta.protocols.antibody.GraftOneCDRLoop, setting : bool) -> NoneType   R2 just graft R2 by copying some stem residues, and remove H3 to do        H3 loop modeling later. But the terminal has been changed by this        grafting. Therefore, in R3, an option for not copying h3 stem is        provided. set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.antibody.GraftOneCDRLoop, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   users can pass their own scorefunction for packing after grafting Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply clone(...) from builtins.PyCapsule clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Return a clone of the Mover object. create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class GraftedStemOptimizer(rosetta.protocols.moves.Mover)     Grafts only one CDR onto a framework     Method resolution order: GraftedStemOptimizer rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, cdr_name : rosetta.protocols.antibody.CDRNameEnum, antibody_info : rosetta.protocols.antibody.AntibodyInfo) -> NoneType   2. __init__(handle, rosetta.protocols.antibody.GraftedStemOptimizer) -> 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.antibody.GraftedStemOptimizer, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.GraftedStemOptimizer, rhs : rosetta.protocols.antibody.GraftedStemOptimizer) -> rosetta.protocols.antibody.GraftedStemOptimizer   assignment operator enable_benchmark_mode(...) from builtins.PyCapsule enable_benchmark_mode(self : rosetta.protocols.antibody.GraftedStemOptimizer, setting : bool) -> NoneType   enable benchmark mode get_Cstem_foldtree(...) from builtins.PyCapsule get_Cstem_foldtree(self : rosetta.protocols.antibody.GraftedStemOptimizer, pose : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree get_N_C_stems_foldtree(...) from builtins.PyCapsule get_N_C_stems_foldtree(self : rosetta.protocols.antibody.GraftedStemOptimizer, pose : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree get_Nstem_foldtree(...) from builtins.PyCapsule get_Nstem_foldtree(self : rosetta.protocols.antibody.GraftedStemOptimizer, pose : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.antibody.GraftedStemOptimizer) -> str get_stem_movemap(...) from builtins.PyCapsule get_stem_movemap(*args, **kwargs) Overloaded function.   1. get_stem_movemap(self : rosetta.protocols.antibody.GraftedStemOptimizer, pose : rosetta.core.pose.Pose, type : str) -> rosetta.core.kinematics.MoveMap   2. get_stem_movemap(self : rosetta.protocols.antibody.GraftedStemOptimizer, pose : rosetta.core.pose.Pose, type : str, include_nb_sc : bool) -> rosetta.core.kinematics.MoveMap get_stem_taskfactory(...) from builtins.PyCapsule get_stem_taskfactory(*args, **kwargs) Overloaded function.   1. get_stem_taskfactory(self : rosetta.protocols.antibody.GraftedStemOptimizer, pose : rosetta.core.pose.Pose, type : str) -> rosetta.core.pack.task.TaskFactory   2. get_stem_taskfactory(self : rosetta.protocols.antibody.GraftedStemOptimizer, pose : rosetta.core.pose.Pose, type : str, include_nb_sc : bool) -> rosetta.core.pack.task.TaskFactory set_deep_optimization(...) from builtins.PyCapsule set_deep_optimization(self : rosetta.protocols.antibody.GraftedStemOptimizer, setting : bool) -> NoneType   deep optimization will do small_share_ccd set_scorefxn(...) from builtins.PyCapsule set_scorefxn(self : rosetta.protocols.antibody.GraftedStemOptimizer, setting : rosetta.core.scoring.ScoreFunction) -> NoneType   users can pass their own scorefunction, foldtree, movemap, and taskfactory set_stem_size(...) from builtins.PyCapsule set_stem_size(self : rosetta.protocols.antibody.GraftedStemOptimizer, setting : int) -> NoneType   stem that was replaced by the extra reesidues at the end of the        loop terminus. Default is "2" Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply clone(...) from builtins.PyCapsule clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Return a clone of the Mover object. create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class H3BaseTypeEnum(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.protocols.antibody.H3BaseTypeEnum, rosetta.protocols.antibody.H3BaseTypeEnum) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.protocols.antibody.H3BaseTypeEnum) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.H3BaseTypeEnum, int) -> NoneType   2. __init__(rosetta.protocols.antibody.H3BaseTypeEnum, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.protocols.antibody.H3BaseTypeEnum) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.protocols.antibody.H3BaseTypeEnum, rosetta.protocols.antibody.H3BaseTypeEnum) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.protocols.antibody.H3BaseTypeEnum) -> str Data and other attributes defined here: Extended = H3BaseTypeEnum.Extended H3BaseTypeEnum_start = H3BaseTypeEnum.H3BaseTypeEnum_start H3BaseTypeEnum_total = H3BaseTypeEnum.H3BaseTypeEnum_total Kinked = H3BaseTypeEnum.H3BaseTypeEnum_start Neutral = H3BaseTypeEnum.Neutral Unknown = H3BaseTypeEnum.H3BaseTypeEnum_total   class H3CterInsert(rosetta.protocols.moves.Mover)     ///////////////////////////////////////////////////////////////////////     H3 CDR, Fragment Insertion and CCD     Method resolution order: H3CterInsert 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, antibody_info : rosetta.protocols.antibody.AntibodyInfo, camelid : bool) -> NoneType   3. __init__(handle, rosetta.protocols.antibody.H3CterInsert) -> 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.antibody.H3CterInsert, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.H3CterInsert,  : rosetta.protocols.antibody.H3CterInsert) -> rosetta.protocols.antibody.H3CterInsert get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.antibody.H3CterInsert) -> str read_H3_cter_fragment(...) from builtins.PyCapsule read_H3_cter_fragment(rosetta.protocols.antibody.H3CterInsert) -> NoneType set_default(...) from builtins.PyCapsule set_default(rosetta.protocols.antibody.H3CterInsert) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply clone(...) from builtins.PyCapsule clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Return a clone of the Mover object. create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class H3PerturbCCD(rosetta.protocols.moves.Mover)       Method resolution order: H3PerturbCCD 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, antibody_in : rosetta.protocols.antibody.AntibodyInfo) -> NoneType   3. __init__(self : handle, antibody_in : rosetta.protocols.antibody.AntibodyInfo, highres_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   4. __init__(handle, rosetta.protocols.antibody.H3PerturbCCD) -> 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.antibody.H3PerturbCCD, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.H3PerturbCCD,  : rosetta.protocols.antibody.H3PerturbCCD) -> rosetta.protocols.antibody.H3PerturbCCD clone(...) from builtins.PyCapsule clone(rosetta.protocols.antibody.H3PerturbCCD) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.antibody.H3PerturbCCD) -> str pass_the_loop(...) from builtins.PyCapsule pass_the_loop(self : rosetta.protocols.antibody.H3PerturbCCD, input_loop : rosetta.protocols.loops.Loop) -> NoneType read_and_store_fragments(...) from builtins.PyCapsule read_and_store_fragments(rosetta.protocols.antibody.H3PerturbCCD) -> NoneType set_lowres_score_func(...) from builtins.PyCapsule set_lowres_score_func(self : rosetta.protocols.antibody.H3PerturbCCD, lowres_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   set scorefunction for low resolution of CDR H3 modeling turn_off_H3_filter(...) from builtins.PyCapsule turn_off_H3_filter(rosetta.protocols.antibody.H3PerturbCCD) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str 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 H3RefineCCD(rosetta.protocols.moves.Mover)       Method resolution order: H3RefineCCD 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, antibody_info : rosetta.protocols.antibody.AntibodyInfo, loop_name : rosetta.protocols.antibody.CDRNameEnum) -> NoneType   3. __init__(self : handle, antibody_info : rosetta.protocols.antibody.AntibodyInfo, loop_name : rosetta.protocols.antibody.CDRNameEnum, highres_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   4. __init__(self : handle, antibody_info : rosetta.protocols.antibody.AntibodyInfo) -> NoneType   5. __init__(handle, rosetta.protocols.antibody.H3RefineCCD) -> 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.antibody.H3RefineCCD, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.H3RefineCCD,  : rosetta.protocols.antibody.H3RefineCCD) -> rosetta.protocols.antibody.H3RefineCCD clone(...) from builtins.PyCapsule clone(rosetta.protocols.antibody.H3RefineCCD) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.antibody.H3RefineCCD) -> str pass_start_pose(...) from builtins.PyCapsule pass_start_pose(self : rosetta.protocols.antibody.H3RefineCCD, start_pose : rosetta.core.pose.Pose) -> NoneType set_highres_score_func(...) from builtins.PyCapsule set_highres_score_func(self : rosetta.protocols.antibody.H3RefineCCD, highres_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_task_factory(...) from builtins.PyCapsule set_task_factory(self : rosetta.protocols.antibody.H3RefineCCD, tf : rosetta.core.pack.task.TaskFactory) -> NoneType turn_off_flank_relax(...) from builtins.PyCapsule turn_off_flank_relax(rosetta.protocols.antibody.H3RefineCCD) -> NoneType turn_off_h3_filter(...) from builtins.PyCapsule turn_off_h3_filter(rosetta.protocols.antibody.H3RefineCCD) -> NoneType turn_on_benchmark(...) from builtins.PyCapsule turn_on_benchmark(rosetta.protocols.antibody.H3RefineCCD) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str 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 LHRepulsiveRamp(rosetta.protocols.moves.Mover)       Method resolution order: LHRepulsiveRamp 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, movable_jumps : rosetta.utility.vector1_int, dock_scorefxn : rosetta.core.scoring.ScoreFunction, pack_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   3. __init__(handle, rosetta.protocols.antibody.LHRepulsiveRamp) -> 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.antibody.LHRepulsiveRamp, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.LHRepulsiveRamp,  : rosetta.protocols.antibody.LHRepulsiveRamp) -> rosetta.protocols.antibody.LHRepulsiveRamp clone(...) from builtins.PyCapsule clone(rosetta.protocols.antibody.LHRepulsiveRamp) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.antibody.LHRepulsiveRamp) -> str set_default(...) from builtins.PyCapsule set_default(rosetta.protocols.antibody.LHRepulsiveRamp) -> NoneType set_dock_jump(...) from builtins.PyCapsule set_dock_jump(self : rosetta.protocols.antibody.LHRepulsiveRamp, jump : rosetta.utility.vector1_int) -> NoneType set_dock_score_func(...) from builtins.PyCapsule set_dock_score_func(self : rosetta.protocols.antibody.LHRepulsiveRamp, dock_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_move_map(...) from builtins.PyCapsule set_move_map(self : rosetta.protocols.antibody.LHRepulsiveRamp, movemap : rosetta.core.kinematics.MoveMap) -> NoneType set_pack_score_func(...) from builtins.PyCapsule set_pack_score_func(self : rosetta.protocols.antibody.LHRepulsiveRamp, pack_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_rot_mag(...) from builtins.PyCapsule set_rot_mag(self : rosetta.protocols.antibody.LHRepulsiveRamp, rot_mag : float) -> float set_rt_min(...) from builtins.PyCapsule set_rt_min(self : rosetta.protocols.antibody.LHRepulsiveRamp, rt_min : bool) -> NoneType set_sc_min(...) from builtins.PyCapsule set_sc_min(self : rosetta.protocols.antibody.LHRepulsiveRamp, sc_min : bool) -> NoneType set_task_factory(...) from builtins.PyCapsule set_task_factory(self : rosetta.protocols.antibody.LHRepulsiveRamp, tf : rosetta.core.pack.task.TaskFactory) -> NoneType set_trans_mag(...) from builtins.PyCapsule set_trans_mag(self : rosetta.protocols.antibody.LHRepulsiveRamp, trans_mag : float) -> float Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class LHRepulsiveRampLegacy(rosetta.protocols.moves.Mover)       Method resolution order: LHRepulsiveRampLegacy 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, loops_in : rosetta.protocols.loops.Loops) -> NoneType   3. __init__(self : handle, antibody_in : rosetta.protocols.antibody.AntibodyInfo) -> NoneType   4. __init__(self : handle, antibody_in : rosetta.protocols.antibody.AntibodyInfo, camelid : bool) -> NoneType   5. __init__(self : handle, loops_in : rosetta.protocols.loops.Loops, dock_scorefxn : rosetta.core.scoring.ScoreFunction, pack_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   6. __init__(self : handle, antibody_in : rosetta.protocols.antibody.AntibodyInfo, dock_scorefxn : rosetta.core.scoring.ScoreFunction, pack_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   7. __init__(handle, rosetta.protocols.antibody.LHRepulsiveRampLegacy) -> 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.antibody.LHRepulsiveRampLegacy, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.LHRepulsiveRampLegacy,  : rosetta.protocols.antibody.LHRepulsiveRampLegacy) -> rosetta.protocols.antibody.LHRepulsiveRampLegacy clone(...) from builtins.PyCapsule clone(rosetta.protocols.antibody.LHRepulsiveRampLegacy) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.antibody.LHRepulsiveRampLegacy) -> str set_default(...) from builtins.PyCapsule set_default(rosetta.protocols.antibody.LHRepulsiveRampLegacy) -> NoneType set_dock_score_func(...) from builtins.PyCapsule set_dock_score_func(self : rosetta.protocols.antibody.LHRepulsiveRampLegacy, dock_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_pack_score_func(...) from builtins.PyCapsule set_pack_score_func(self : rosetta.protocols.antibody.LHRepulsiveRampLegacy, pack_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_rot_mag(...) from builtins.PyCapsule set_rot_mag(self : rosetta.protocols.antibody.LHRepulsiveRampLegacy, rot_mag : float) -> float set_task_factory(...) from builtins.PyCapsule set_task_factory(self : rosetta.protocols.antibody.LHRepulsiveRampLegacy, tf : rosetta.core.pack.task.TaskFactory) -> NoneType set_trans_mag(...) from builtins.PyCapsule set_trans_mag(self : rosetta.protocols.antibody.LHRepulsiveRampLegacy, trans_mag : float) -> float Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class LHSnugFitLegacy(rosetta.protocols.moves.Mover)       Method resolution order: LHSnugFitLegacy 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, loops_in : rosetta.protocols.loops.Loops) -> NoneType   3. __init__(self : handle, antibody_in : rosetta.protocols.antibody.AntibodyInfo) -> NoneType   4. __init__(self : handle, antibody_in : rosetta.protocols.antibody.AntibodyInfo, camelid : bool) -> NoneType   5. __init__(handle, rosetta.protocols.antibody.LHSnugFitLegacy) -> 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.antibody.LHSnugFitLegacy, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.LHSnugFitLegacy,  : rosetta.protocols.antibody.LHSnugFitLegacy) -> rosetta.protocols.antibody.LHSnugFitLegacy clone(...) from builtins.PyCapsule clone(rosetta.protocols.antibody.LHSnugFitLegacy) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.antibody.LHSnugFitLegacy) -> str set_default(...) from builtins.PyCapsule set_default(rosetta.protocols.antibody.LHSnugFitLegacy) -> NoneType set_task_factory(...) from builtins.PyCapsule set_task_factory(self : rosetta.protocols.antibody.LHSnugFitLegacy, tf : rosetta.core.pack.task.TaskFactory) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str 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 LightChainTypeEnum(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.protocols.antibody.LightChainTypeEnum, rosetta.protocols.antibody.LightChainTypeEnum) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.protocols.antibody.LightChainTypeEnum) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.LightChainTypeEnum, int) -> NoneType   2. __init__(rosetta.protocols.antibody.LightChainTypeEnum, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.protocols.antibody.LightChainTypeEnum) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.protocols.antibody.LightChainTypeEnum, rosetta.protocols.antibody.LightChainTypeEnum) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.protocols.antibody.LightChainTypeEnum) -> str Data and other attributes defined here: LightChainTypeEnum_start = LightChainTypeEnum.LightChainTypeEnum_start LightChainTypeEnum_total = LightChainTypeEnum.LightChainTypeEnum_total kappa = LightChainTypeEnum.kappa lambda = LightChainTypeEnum.LightChainTypeEnum_start lambda6 = LightChainTypeEnum.lambda6 unknown = LightChainTypeEnum.LightChainTypeEnum_total   class ModelCDRH3(rosetta.protocols.moves.Mover)     ///////////////////////////////////////////////////////////////////////     Ab initio modeling of CDR H3 loop     Method resolution order: ModelCDRH3 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, antibody_info : rosetta.protocols.antibody.AntibodyInfo) -> NoneType   3. __init__(self : handle, antibody_info : rosetta.protocols.antibody.AntibodyInfo, lowres_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   4. __init__(handle, rosetta.protocols.antibody.ModelCDRH3) -> 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.antibody.ModelCDRH3, pose_in : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.ModelCDRH3,  : rosetta.protocols.antibody.ModelCDRH3) -> rosetta.protocols.antibody.ModelCDRH3 enable_benchmark_mode(...) from builtins.PyCapsule enable_benchmark_mode(self : rosetta.protocols.antibody.ModelCDRH3, setting : bool) -> NoneType   enable benchmark mode get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.antibody.ModelCDRH3) -> str set_bad_nter(...) from builtins.PyCapsule set_bad_nter(self : rosetta.protocols.antibody.ModelCDRH3, setting : bool) -> NoneType set_camelid(...) from builtins.PyCapsule set_camelid(self : rosetta.protocols.antibody.ModelCDRH3, setting : bool) -> NoneType   enable camelid modeling mode set_default(...) from builtins.PyCapsule set_default(rosetta.protocols.antibody.ModelCDRH3) -> NoneType set_extend_h3(...) from builtins.PyCapsule set_extend_h3(self : rosetta.protocols.antibody.ModelCDRH3, setting : bool) -> NoneType set_idealize_h3_stems(...) from builtins.PyCapsule set_idealize_h3_stems(self : rosetta.protocols.antibody.ModelCDRH3, setting : bool) -> NoneType set_lowres_score_func(...) from builtins.PyCapsule set_lowres_score_func(self : rosetta.protocols.antibody.ModelCDRH3, lowres_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   set scorefunction for low resolution of CDR H3 modeling set_perturb_type(...) from builtins.PyCapsule set_perturb_type(self : rosetta.protocols.antibody.ModelCDRH3, setting : str) -> NoneType set_task_factory(...) from builtins.PyCapsule set_task_factory(self : rosetta.protocols.antibody.ModelCDRH3, tf : rosetta.core.pack.task.TaskFactory) -> NoneType   set task factory turn_off_H3_filter(...) from builtins.PyCapsule turn_off_H3_filter(rosetta.protocols.antibody.ModelCDRH3) -> NoneType turn_off_cter_insert(...) from builtins.PyCapsule turn_off_cter_insert(rosetta.protocols.antibody.ModelCDRH3) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply clone(...) from builtins.PyCapsule clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Return a clone of the Mover object. create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class PDBLandmark(builtins.object)     Class that was once a struct; Used for matching pdb information between numbering schemes and cdr definitions.     Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.protocols.antibody.PDBLandmark, compare : rosetta.protocols.antibody.PDBLandmark) -> bool __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.antibody.PDBLandmark, chain : str, resnum : int, insertion_code : str) -> NoneType   2. __init__(self : rosetta.protocols.antibody.PDBLandmark, chain : str, resnum : int, insertion_code : str, scheme : rosetta.protocols.antibody.AntibodyNumberingSchemeEnum) -> NoneType __ne__(...) from builtins.PyCapsule __ne__(self : rosetta.protocols.antibody.PDBLandmark, compare : rosetta.protocols.antibody.PDBLandmark) -> bool __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.antibody.PDBLandmark, src : rosetta.protocols.antibody.PDBLandmark) -> rosetta.protocols.antibody.PDBLandmark chain(...) from builtins.PyCapsule chain(rosetta.protocols.antibody.PDBLandmark) -> str get_string(...) from builtins.PyCapsule get_string(rosetta.protocols.antibody.PDBLandmark) -> str insertion_code(...) from builtins.PyCapsule insertion_code(rosetta.protocols.antibody.PDBLandmark) -> str numbering_scheme(...) from builtins.PyCapsule numbering_scheme(rosetta.protocols.antibody.PDBLandmark) -> rosetta.protocols.antibody.AntibodyNumberingSchemeEnum resnum(...) from builtins.PyCapsule resnum(rosetta.protocols.antibody.PDBLandmark) -> int   class PackingAngleEnum(builtins.object)     These are used to determine the VL_VH packing angle.     Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.protocols.antibody.PackingAngleEnum, rosetta.protocols.antibody.PackingAngleEnum) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.protocols.antibody.PackingAngleEnum) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.PackingAngleEnum, int) -> NoneType   2. __init__(rosetta.protocols.antibody.PackingAngleEnum, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.protocols.antibody.PackingAngleEnum) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.protocols.antibody.PackingAngleEnum, rosetta.protocols.antibody.PackingAngleEnum) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.protocols.antibody.PackingAngleEnum) -> str Data and other attributes defined here: PackingAngleEnum_start = PackingAngleEnum.PackingAngleEnum_start PackingAngleEnum_total = PackingAngleEnum.PackingAngleEnum_total VH_sheet_1 = PackingAngleEnum.VH_sheet_1 VH_sheet_2 = PackingAngleEnum.PackingAngleEnum_total VL_sheet_1 = PackingAngleEnum.PackingAngleEnum_start VL_sheet_2 = PackingAngleEnum.VL_sheet_2   class ParatopeMetric_long_t(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.antibody.ParatopeMetric_long_t) -> NoneType   2. __init__(self : rosetta.protocols.antibody.ParatopeMetric_long_t,  : rosetta.protocols.antibody.ParatopeMetric_long_t) -> 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.antibody.ParatopeMetric_long_t,  : rosetta.protocols.antibody.ParatopeMetric_long_t) -> rosetta.protocols.antibody.ParatopeMetric_long_t Data descriptors defined here: cdr paratope paratope_heavy paratope_light   class RefineBetaBarrel(rosetta.protocols.moves.Mover)       Method resolution order: RefineBetaBarrel 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, antibody_info : rosetta.protocols.antibody.AntibodyInfo) -> NoneType   3. __init__(self : handle, antibody_info : rosetta.protocols.antibody.AntibodyInfo, dock_scorefxn : rosetta.core.scoring.ScoreFunction, pack_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   4. __init__(handle, rosetta.protocols.antibody.RefineBetaBarrel) -> 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.antibody.RefineBetaBarrel, pose_in : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.RefineBetaBarrel,  : rosetta.protocols.antibody.RefineBetaBarrel) -> rosetta.protocols.antibody.RefineBetaBarrel get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.antibody.RefineBetaBarrel) -> str set_dock_score_func(...) from builtins.PyCapsule set_dock_score_func(self : rosetta.protocols.antibody.RefineBetaBarrel, dock_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_pack_score_func(...) from builtins.PyCapsule set_pack_score_func(self : rosetta.protocols.antibody.RefineBetaBarrel, pack_scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_rt_min(...) from builtins.PyCapsule set_rt_min(self : rosetta.protocols.antibody.RefineBetaBarrel, rt_min : bool) -> NoneType set_sc_min(...) from builtins.PyCapsule set_sc_min(self : rosetta.protocols.antibody.RefineBetaBarrel, sc_min : bool) -> NoneType set_task_factory(...) from builtins.PyCapsule set_task_factory(self : rosetta.protocols.antibody.RefineBetaBarrel, tf : rosetta.core.pack.task.TaskFactory) -> NoneType turn_off_repulsive_ramp(...) from builtins.PyCapsule turn_off_repulsive_ramp(rosetta.protocols.antibody.RefineBetaBarrel) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply clone(...) from builtins.PyCapsule clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Return a clone of the Mover object. create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class RefineOneCDRLoop(rosetta.protocols.moves.Mover)       Method resolution order: RefineOneCDRLoop 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, antibody_info : rosetta.protocols.antibody.AntibodyInfo) -> NoneType   3. __init__(self : handle, antibody_info : rosetta.protocols.antibody.AntibodyInfo, refine_mode : str) -> NoneType   4. __init__(self : handle, antibody_info : rosetta.protocols.antibody.AntibodyInfo, refine_mode : str, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   5. __init__(self : handle, antibody_info : rosetta.protocols.antibody.AntibodyInfo, cdr_loop_name : rosetta.protocols.antibody.CDRNameEnum, refine_mode : str, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   6. __init__(handle, rosetta.protocols.antibody.RefineOneCDRLoop) -> 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.antibody.RefineOneCDRLoop, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.RefineOneCDRLoop,  : rosetta.protocols.antibody.RefineOneCDRLoop) -> rosetta.protocols.antibody.RefineOneCDRLoop clone(...) from builtins.PyCapsule clone(rosetta.protocols.antibody.RefineOneCDRLoop) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.antibody.RefineOneCDRLoop) -> str pass_start_pose(...) from builtins.PyCapsule pass_start_pose(self : rosetta.protocols.antibody.RefineOneCDRLoop, start_pose : rosetta.core.pose.Pose) -> NoneType set_flank_relax(...) from builtins.PyCapsule set_flank_relax(self : rosetta.protocols.antibody.RefineOneCDRLoop, setting : bool) -> NoneType set_flank_size(...) from builtins.PyCapsule set_flank_size(self : rosetta.protocols.antibody.RefineOneCDRLoop, setting : int) -> NoneType set_h3_filter(...) from builtins.PyCapsule set_h3_filter(self : rosetta.protocols.antibody.RefineOneCDRLoop, setting : bool) -> NoneType set_num_filter_tries(...) from builtins.PyCapsule set_num_filter_tries(self : rosetta.protocols.antibody.RefineOneCDRLoop, setting : int) -> NoneType set_refine_mode(...) from builtins.PyCapsule set_refine_mode(self : rosetta.protocols.antibody.RefineOneCDRLoop, refine_mode : str) -> NoneType set_score_function(...) from builtins.PyCapsule set_score_function(self : rosetta.protocols.antibody.RefineOneCDRLoop, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType turn_on_benchmark(...) from builtins.PyCapsule turn_on_benchmark(rosetta.protocols.antibody.RefineOneCDRLoop) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str 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 RefineOneCDRLoopCentroid(rosetta.protocols.moves.Mover)       Method resolution order: RefineOneCDRLoopCentroid rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, antibody_info : rosetta.protocols.antibody.AntibodyInfo, loop_name : rosetta.protocols.antibody.CDRNameEnum) -> NoneType   2. __init__(self : handle, antibody_info : rosetta.protocols.antibody.AntibodyInfo, loop_name : rosetta.protocols.antibody.CDRNameEnum, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   3. __init__(self : handle, a_cdr_loop : rosetta.protocols.loops.Loop) -> NoneType   4. __init__(self : handle, a_cdr_loop : rosetta.protocols.loops.Loop, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   5. __init__(handle, rosetta.protocols.antibody.RefineOneCDRLoopCentroid) -> 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.antibody.RefineOneCDRLoopCentroid, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.antibody.RefineOneCDRLoopCentroid,  : rosetta.protocols.antibody.RefineOneCDRLoopCentroid) -> rosetta.protocols.antibody.RefineOneCDRLoopCentroid get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.antibody.RefineOneCDRLoopCentroid) -> str set_benchmark(...) from builtins.PyCapsule set_benchmark(self : rosetta.protocols.antibody.RefineOneCDRLoopCentroid, setting : bool) -> NoneType set_refine_input_loop(...) from builtins.PyCapsule set_refine_input_loop(self : rosetta.protocols.antibody.RefineOneCDRLoopCentroid, setting : bool) -> NoneType set_score_function(...) from builtins.PyCapsule set_score_function(self : rosetta.protocols.antibody.RefineOneCDRLoopCentroid, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType set_snugfit(...) from builtins.PyCapsule set_snugfit(self : rosetta.protocols.antibody.RefineOneCDRLoopCentroid, setting : bool) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply clone(...) from builtins.PyCapsule clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Return a clone of the Mover object. create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType