Bindings for protocols::topology_broker namespace

Modules
		rosetta.protocols.topology_broker.claims rosetta.protocols.topology_broker.weights

Classes
		builtins.object ClaimerMessage SuggestValueMessage SequenceNumberResolver TopologyBroker TopologyClaimer AsymFoldandDockClaimer BasicJumpClaimer ConstraintClaimer CoordConstraintClaimer CutBiasClaimer DensityScoringClaimer FibrilModelingClaimer FoldandDockClaimer FragmentClaimer DisulfJumpClaimer FragmentJumpClaimer TemplateJumpClaimer LoopFragmentClaimer StartStructClaimer TemplateFragmentClaimer MembraneTopologyClaimer PcsEnergyController PseudocontactShiftEnergyController PseudocontactShiftEnergyController_Ts1 PseudocontactShiftEnergyController_Ts2 PseudocontactShiftEnergyController_Ts3 PseudocontactShiftEnergyController_Ts4 RigidChunkClaimer SequenceClaimer MetalloClaimer SymmetryClaimer TMHTopologySamplerClaimer TopologyClaimerFactory rosetta.protocols.evaluation.EvaluatorCreator(builtins.object) ConstraintEvaluatorWrapperCreator rosetta.protocols.evaluation.PoseEvaluator(builtins.object) ConstraintEvaluatorWrapper rosetta.protocols.rigid.RigidBodyMover(rosetta.protocols.canonical_sampling.ThermodynamicMover) RigidBodyRandomTMHMover rosetta.utility.excn.EXCN_Msg_Exception(rosetta.utility.excn.EXCN_Exception) EXCN_TopologyBroker EXCN_FailedBroking EXCN_FilterFailed EXCN_Input EXCN_Unknown   class AsymFoldandDockClaimer(TopologyClaimer)       Method resolution order: AsymFoldandDockClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, input_pose : rosetta.core.pose.Pose) -> NoneType   3. __init__(handle, rosetta.protocols.topology_broker.AsymFoldandDockClaimer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.AsymFoldandDockClaimer, random_mover : rosetta.protocols.moves.RandomMover, pose : rosetta.core.pose.Pose, stageID : rosetta.protocols.abinitio.StageID, scorefxn : rosetta.core.scoring.ScoreFunction, progress : float) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.AsymFoldandDockClaimer,  : rosetta.protocols.topology_broker.AsymFoldandDockClaimer) -> rosetta.protocols.topology_broker.AsymFoldandDockClaimer clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.AsymFoldandDockClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer docking_jump(...) from builtins.PyCapsule docking_jump(self : rosetta.protocols.topology_broker.AsymFoldandDockClaimer, pose : rosetta.core.pose.Pose, chain_break_res : int) -> int generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.AsymFoldandDockClaimer, new_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.AsymFoldandDockClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.AsymFoldandDockClaimer) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from TopologyClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false   -- if you can't live without this claim being accepted. ( e.g., RigidChunks ... ) add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class BasicJumpClaimer(TopologyClaimer)       Method resolution order: BasicJumpClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.topology_broker.BasicJumpClaimer) -> 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.topology_broker.BasicJumpClaimer,  : rosetta.protocols.topology_broker.BasicJumpClaimer) -> rosetta.protocols.topology_broker.BasicJumpClaimer clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.BasicJumpClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer end_label(...) from builtins.PyCapsule end_label(*args, **kwargs) Overloaded function.   1. end_label(rosetta.protocols.topology_broker.BasicJumpClaimer) -> str   2. end_label(self : rosetta.protocols.topology_broker.BasicJumpClaimer, endLabel : str) -> NoneType end_position(...) from builtins.PyCapsule end_position(*args, **kwargs) Overloaded function.   1. end_position(rosetta.protocols.topology_broker.BasicJumpClaimer) -> int   2. end_position(self : rosetta.protocols.topology_broker.BasicJumpClaimer, endPosition : int) -> NoneType generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.BasicJumpClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.BasicJumpClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType shared_from_this(...) from builtins.PyCapsule shared_from_this(rosetta.protocols.topology_broker.BasicJumpClaimer) -> rosetta.protocols.topology_broker.BasicJumpClaimer start_label(...) from builtins.PyCapsule start_label(*args, **kwargs) Overloaded function.   1. start_label(rosetta.protocols.topology_broker.BasicJumpClaimer) -> str   2. start_label(self : rosetta.protocols.topology_broker.BasicJumpClaimer, startLabel : str) -> NoneType start_position(...) from builtins.PyCapsule start_position(*args, **kwargs) Overloaded function.   1. start_position(rosetta.protocols.topology_broker.BasicJumpClaimer) -> int   2. start_position(self : rosetta.protocols.topology_broker.BasicJumpClaimer, startPosition : int) -> NoneType type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.BasicJumpClaimer) -> str Methods inherited from TopologyClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false   -- if you can't live without this claim being accepted. ( e.g., RigidChunks ... ) add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class ClaimerMessage(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, label : str) -> NoneType   3. __init__(handle, rosetta.protocols.topology_broker.ClaimerMessage) -> 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.topology_broker.ClaimerMessage) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.ClaimerMessage,  : rosetta.protocols.topology_broker.ClaimerMessage) -> rosetta.protocols.topology_broker.ClaimerMessage label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.ClaimerMessage) -> str matches(...) from builtins.PyCapsule matches(self : rosetta.protocols.topology_broker.ClaimerMessage, label : str) -> bool nr_recepients(...) from builtins.PyCapsule nr_recepients(rosetta.protocols.topology_broker.ClaimerMessage) -> int received(...) from builtins.PyCapsule received(rosetta.protocols.topology_broker.ClaimerMessage) -> bool received_by_me(...) from builtins.PyCapsule received_by_me(self : rosetta.protocols.topology_broker.ClaimerMessage, me : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t) -> NoneType set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.ClaimerMessage, str : str) -> NoneType type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.ClaimerMessage) -> str   name of Claimer   class ConstraintClaimer(TopologyClaimer)       Method resolution order: ConstraintClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, str) -> NoneType   doc   3. __init__(self : handle, cst_file : str, tag : str) -> NoneType   4. __init__(handle, bool) -> NoneType   doc   5. __init__(handle, bool, bool) -> NoneType   doc   6. __init__(self : handle, CmdFlag : bool, centroid : bool, fullatom : bool) -> NoneType   7. __init__(handle, rosetta.protocols.topology_broker.ConstraintClaimer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.ConstraintClaimer,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.ConstraintClaimer,  : rosetta.protocols.topology_broker.ConstraintClaimer) -> rosetta.protocols.topology_broker.ConstraintClaimer clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.ConstraintClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer combine_ratio(...) from builtins.PyCapsule combine_ratio(rosetta.protocols.topology_broker.ConstraintClaimer) -> int drop_random_rate(...) from builtins.PyCapsule drop_random_rate(rosetta.protocols.topology_broker.ConstraintClaimer) -> float filter_name(...) from builtins.PyCapsule filter_name(rosetta.protocols.topology_broker.ConstraintClaimer) -> str filter_weight(...) from builtins.PyCapsule filter_weight(rosetta.protocols.topology_broker.ConstraintClaimer) -> float generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.ConstraintClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType new_decoy(...) from builtins.PyCapsule new_decoy(rosetta.protocols.topology_broker.ConstraintClaimer) -> NoneType set_centroid(...) from builtins.PyCapsule set_centroid(self : rosetta.protocols.topology_broker.ConstraintClaimer, setting : bool) -> NoneType set_combine_ratio(...) from builtins.PyCapsule set_combine_ratio(self : rosetta.protocols.topology_broker.ConstraintClaimer, setting : int) -> NoneType set_cst_file(...) from builtins.PyCapsule set_cst_file(self : rosetta.protocols.topology_broker.ConstraintClaimer,  : str) -> NoneType set_filter_weight(...) from builtins.PyCapsule set_filter_weight(self : rosetta.protocols.topology_broker.ConstraintClaimer, weight : float) -> NoneType set_fullatom(...) from builtins.PyCapsule set_fullatom(self : rosetta.protocols.topology_broker.ConstraintClaimer, setting : bool) -> NoneType set_skip_redundant(...) from builtins.PyCapsule set_skip_redundant(self : rosetta.protocols.topology_broker.ConstraintClaimer, setting : int) -> NoneType tag(...) from builtins.PyCapsule tag(rosetta.protocols.topology_broker.ConstraintClaimer) -> str type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.ConstraintClaimer) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from TopologyClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false   -- if you can't live without this claim being accepted. ( e.g., RigidChunks ... ) add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   initialize dofs -- e.g., torsions, jumps -- Claimer searches init_claims for claims owned by *this label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class ConstraintEvaluatorWrapper(rosetta.protocols.evaluation.PoseEvaluator)       Method resolution order: ConstraintEvaluatorWrapper rosetta.protocols.evaluation.PoseEvaluator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, name : str, claimer : rosetta.protocols.topology_broker.ConstraintClaimer) -> NoneType   2. __init__(handle, rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. apply(...) from builtins.PyCapsule apply(*args, **kwargs) Overloaded function.   1. apply(self : rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType   2. apply(self : rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper, pose : rosetta.core.pose.Pose) -> float assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper,  : rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper) -> rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper name(...) from builtins.PyCapsule name(self : rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper, i : int) -> str size(...) from builtins.PyCapsule size(rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper) -> int Methods inherited from rosetta.protocols.evaluation.PoseEvaluator: applicable(...) from builtins.PyCapsule applicable(self : rosetta.protocols.evaluation.PoseEvaluator,  : rosetta.core.pose.Pose) -> bool   class ConstraintEvaluatorWrapperCreator(rosetta.protocols.evaluation.EvaluatorCreator)     creator for the ConstraintsEvaluatorWrapperCreator class     Method resolution order: ConstraintEvaluatorWrapperCreator rosetta.protocols.evaluation.EvaluatorCreator 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. add_evaluators(...) from builtins.PyCapsule add_evaluators(self : rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator, eval : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator,  : rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator) -> rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator register_options(...) from builtins.PyCapsule register_options(rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator) -> NoneType type_name(...) from builtins.PyCapsule type_name(rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator) -> str   class CoordConstraintClaimer(TopologyClaimer)       Method resolution order: CoordConstraintClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, pdb_file : str) -> NoneType   3. __init__(handle, rosetta.protocols.topology_broker.CoordConstraintClaimer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.CoordConstraintClaimer,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.CoordConstraintClaimer,  : rosetta.protocols.topology_broker.CoordConstraintClaimer) -> rosetta.protocols.topology_broker.CoordConstraintClaimer clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.CoordConstraintClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.CoordConstraintClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.CoordConstraintClaimer) -> NoneType   2. new_decoy(self : rosetta.protocols.topology_broker.CoordConstraintClaimer,  : rosetta.core.pose.Pose) -> NoneType superimpose(...) from builtins.PyCapsule superimpose(self : rosetta.protocols.topology_broker.CoordConstraintClaimer,  : rosetta.core.pose.Pose) -> NoneType   superimpose xyz coords in constraints_ with pose type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.CoordConstraintClaimer) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from TopologyClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false   -- if you can't live without this claim being accepted. ( e.g., RigidChunks ... ) add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   initialize dofs -- e.g., torsions, jumps -- Claimer searches init_claims for claims owned by *this label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class CutBiasClaimer(TopologyClaimer)       Method resolution order: CutBiasClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle,  : rosetta.utility.vector1_double) -> NoneType   3. __init__(self : handle, ss_def : rosetta.core.fragment.SecondaryStructure) -> NoneType   4. __init__(self : handle, ss_def : rosetta.core.fragment.SecondaryStructure, label : str) -> NoneType   5. __init__(handle, rosetta.protocols.topology_broker.CutBiasClaimer) -> 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.topology_broker.CutBiasClaimer,  : rosetta.protocols.topology_broker.CutBiasClaimer) -> rosetta.protocols.topology_broker.CutBiasClaimer clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.CutBiasClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.CutBiasClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.CutBiasClaimer,  : rosetta.utility.vector1_double) -> NoneType shared_from_this(...) from builtins.PyCapsule shared_from_this(rosetta.protocols.topology_broker.CutBiasClaimer) -> rosetta.protocols.topology_broker.CutBiasClaimer type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.CutBiasClaimer) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from TopologyClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false   -- if you can't live without this claim being accepted. ( e.g., RigidChunks ... ) add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   initialize dofs -- e.g., torsions, jumps -- Claimer searches init_claims for claims owned by *this label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class DensityScoringClaimer(TopologyClaimer)       Method resolution order: DensityScoringClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.topology_broker.DensityScoringClaimer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.DensityScoringClaimer, was_declined : rosetta.protocols.topology_broker.claims.DofClaim) -> bool add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.DensityScoringClaimer,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.DensityScoringClaimer,  : rosetta.protocols.topology_broker.DensityScoringClaimer) -> rosetta.protocols.topology_broker.DensityScoringClaimer clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.DensityScoringClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.DensityScoringClaimer, dc : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.DensityScoringClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType shared_from_this(...) from builtins.PyCapsule shared_from_this(rosetta.protocols.topology_broker.DensityScoringClaimer) -> rosetta.protocols.topology_broker.DensityScoringClaimer type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.DensityScoringClaimer) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from TopologyClaimer: add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   initialize dofs -- e.g., torsions, jumps -- Claimer searches init_claims for claims owned by *this label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class DisulfJumpClaimer(FragmentClaimer)     Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type  [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore     Method resolution order: DisulfJumpClaimer FragmentClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.topology_broker.DisulfJumpClaimer) -> 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.topology_broker.DisulfJumpClaimer,  : rosetta.protocols.topology_broker.DisulfJumpClaimer) -> rosetta.protocols.topology_broker.DisulfJumpClaimer clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.DisulfJumpClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.DisulfJumpClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType generate_jump_frags(...) from builtins.PyCapsule generate_jump_frags(self : rosetta.protocols.topology_broker.DisulfJumpClaimer, lib : rosetta.protocols.jumping.DisulfPairingLibrary, all_frames : rosetta.core.fragment.FrameList) -> NoneType initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.DisulfJumpClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(self : rosetta.protocols.topology_broker.DisulfJumpClaimer,  : rosetta.core.pose.Pose) -> NoneType   2. new_decoy(rosetta.protocols.topology_broker.DisulfJumpClaimer) -> NoneType type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.DisulfJumpClaimer) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from FragmentClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.FragmentClaimer, was_declined : rosetta.protocols.topology_broker.claims.DofClaim) -> bool get_mover(...) from builtins.PyCapsule get_mover(self : rosetta.protocols.topology_broker.FragmentClaimer,  : rosetta.core.pose.Pose) -> rosetta.protocols.moves.Mover get_sequence_region(...) from builtins.PyCapsule get_sequence_region(self : rosetta.protocols.topology_broker.FragmentClaimer, start_region : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType mover_tag(...) from builtins.PyCapsule mover_tag(rosetta.protocols.topology_broker.FragmentClaimer) -> str set_bInitDofs(...) from builtins.PyCapsule set_bInitDofs(self : rosetta.protocols.topology_broker.FragmentClaimer, set : bool) -> NoneType set_mover(...) from builtins.PyCapsule set_mover(self : rosetta.protocols.topology_broker.FragmentClaimer, mover : rosetta.protocols.simple_moves.FragmentMover) -> NoneType set_mover_tag(...) from builtins.PyCapsule set_mover_tag(self : rosetta.protocols.topology_broker.FragmentClaimer, str : str) -> NoneType shared_from_this(...) from builtins.PyCapsule shared_from_this(rosetta.protocols.topology_broker.FragmentClaimer) -> rosetta.protocols.topology_broker.FragmentClaimer Methods inherited from TopologyClaimer: add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class EXCN_FailedBroking(EXCN_TopologyBroker)       Method resolution order: EXCN_FailedBroking EXCN_TopologyBroker rosetta.utility.excn.EXCN_Msg_Exception rosetta.utility.excn.EXCN_Exception rosetta.utility.excn.EXCN_Base builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, msg : str) -> NoneType   2. __init__(handle, rosetta.protocols.topology_broker.EXCN_FailedBroking) -> 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.topology_broker.EXCN_FailedBroking,  : rosetta.protocols.topology_broker.EXCN_FailedBroking) -> rosetta.protocols.topology_broker.EXCN_FailedBroking Methods inherited from rosetta.utility.excn.EXCN_Msg_Exception: add_msg(...) from builtins.PyCapsule add_msg(self : rosetta.utility.excn.EXCN_Msg_Exception, str : str) -> NoneType msg(...) from builtins.PyCapsule msg(rosetta.utility.excn.EXCN_Msg_Exception) -> str Methods inherited from rosetta.utility.excn.EXCN_Base: __str__(...) from builtins.PyCapsule __str__(rosetta.utility.excn.EXCN_Base) -> str   class EXCN_FilterFailed(EXCN_TopologyBroker)       Method resolution order: EXCN_FilterFailed EXCN_TopologyBroker rosetta.utility.excn.EXCN_Msg_Exception rosetta.utility.excn.EXCN_Exception rosetta.utility.excn.EXCN_Base builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, msg : str) -> NoneType   2. __init__(handle, rosetta.protocols.topology_broker.EXCN_FilterFailed) -> 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.topology_broker.EXCN_FilterFailed,  : rosetta.protocols.topology_broker.EXCN_FilterFailed) -> rosetta.protocols.topology_broker.EXCN_FilterFailed Methods inherited from rosetta.utility.excn.EXCN_Msg_Exception: add_msg(...) from builtins.PyCapsule add_msg(self : rosetta.utility.excn.EXCN_Msg_Exception, str : str) -> NoneType msg(...) from builtins.PyCapsule msg(rosetta.utility.excn.EXCN_Msg_Exception) -> str Methods inherited from rosetta.utility.excn.EXCN_Base: __str__(...) from builtins.PyCapsule __str__(rosetta.utility.excn.EXCN_Base) -> str   class EXCN_Input(EXCN_TopologyBroker)       Method resolution order: EXCN_Input EXCN_TopologyBroker rosetta.utility.excn.EXCN_Msg_Exception rosetta.utility.excn.EXCN_Exception rosetta.utility.excn.EXCN_Base builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, msg : str) -> NoneType   2. __init__(handle, rosetta.protocols.topology_broker.EXCN_Input) -> 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.topology_broker.EXCN_Input,  : rosetta.protocols.topology_broker.EXCN_Input) -> rosetta.protocols.topology_broker.EXCN_Input Methods inherited from rosetta.utility.excn.EXCN_Msg_Exception: add_msg(...) from builtins.PyCapsule add_msg(self : rosetta.utility.excn.EXCN_Msg_Exception, str : str) -> NoneType msg(...) from builtins.PyCapsule msg(rosetta.utility.excn.EXCN_Msg_Exception) -> str Methods inherited from rosetta.utility.excn.EXCN_Base: __str__(...) from builtins.PyCapsule __str__(rosetta.utility.excn.EXCN_Base) -> str   class EXCN_TopologyBroker(rosetta.utility.excn.EXCN_Msg_Exception)       Method resolution order: EXCN_TopologyBroker rosetta.utility.excn.EXCN_Msg_Exception rosetta.utility.excn.EXCN_Exception rosetta.utility.excn.EXCN_Base builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle, rosetta.protocols.topology_broker.EXCN_TopologyBroker) -> 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.topology_broker.EXCN_TopologyBroker,  : rosetta.protocols.topology_broker.EXCN_TopologyBroker) -> rosetta.protocols.topology_broker.EXCN_TopologyBroker Methods inherited from rosetta.utility.excn.EXCN_Msg_Exception: add_msg(...) from builtins.PyCapsule add_msg(self : rosetta.utility.excn.EXCN_Msg_Exception, str : str) -> NoneType msg(...) from builtins.PyCapsule msg(rosetta.utility.excn.EXCN_Msg_Exception) -> str Methods inherited from rosetta.utility.excn.EXCN_Base: __str__(...) from builtins.PyCapsule __str__(rosetta.utility.excn.EXCN_Base) -> str   class EXCN_Unknown(EXCN_TopologyBroker)       Method resolution order: EXCN_Unknown EXCN_TopologyBroker rosetta.utility.excn.EXCN_Msg_Exception rosetta.utility.excn.EXCN_Exception rosetta.utility.excn.EXCN_Base builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, msg : str) -> NoneType   2. __init__(handle, rosetta.protocols.topology_broker.EXCN_Unknown) -> 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.topology_broker.EXCN_Unknown,  : rosetta.protocols.topology_broker.EXCN_Unknown) -> rosetta.protocols.topology_broker.EXCN_Unknown Methods inherited from rosetta.utility.excn.EXCN_Msg_Exception: add_msg(...) from builtins.PyCapsule add_msg(self : rosetta.utility.excn.EXCN_Msg_Exception, str : str) -> NoneType msg(...) from builtins.PyCapsule msg(rosetta.utility.excn.EXCN_Msg_Exception) -> str Methods inherited from rosetta.utility.excn.EXCN_Base: __str__(...) from builtins.PyCapsule __str__(rosetta.utility.excn.EXCN_Base) -> str   class FibrilModelingClaimer(TopologyClaimer)       Method resolution order: FibrilModelingClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.pose.Pose, rosetta.protocols.loops.Loops) -> NoneType   doc   3. __init__(self : handle, input_pose : rosetta.core.pose.Pose, rigid : rosetta.protocols.loops.Loops, shift : int) -> NoneType   4. __init__(self : handle, input_pose : rosetta.core.pose.Pose, rigid : rosetta.protocols.loops.Loops, input_rigid : rosetta.protocols.loops.Loops) -> NoneType   5. __init__(handle, rosetta.protocols.topology_broker.FibrilModelingClaimer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.FibrilModelingClaimer, random_mover : rosetta.protocols.moves.RandomMover, pose : rosetta.core.pose.Pose, stageID : rosetta.protocols.abinitio.StageID, scorefxn : rosetta.core.scoring.ScoreFunction, progress : float) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.FibrilModelingClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   has to decline foreign BB claims for slave regions assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.FibrilModelingClaimer,  : rosetta.protocols.topology_broker.FibrilModelingClaimer) -> rosetta.protocols.topology_broker.FibrilModelingClaimer clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.FibrilModelingClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.FibrilModelingClaimer, new_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.FibrilModelingClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType make_fibril(...) from builtins.PyCapsule make_fibril(self : rosetta.protocols.topology_broker.FibrilModelingClaimer, pose : rosetta.core.pose.Pose) -> NoneType type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.FibrilModelingClaimer) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from TopologyClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false   -- if you can't live without this claim being accepted. ( e.g., RigidChunks ... ) add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class FoldandDockClaimer(TopologyClaimer)       Method resolution order: FoldandDockClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, input_pose : rosetta.core.pose.Pose) -> NoneType   3. __init__(handle, rosetta.protocols.topology_broker.FoldandDockClaimer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.FoldandDockClaimer, random_mover : rosetta.protocols.moves.RandomMover, pose : rosetta.core.pose.Pose, stageID : rosetta.protocols.abinitio.StageID, scorefxn : rosetta.core.scoring.ScoreFunction, progress : float) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.FoldandDockClaimer,  : rosetta.protocols.topology_broker.FoldandDockClaimer) -> rosetta.protocols.topology_broker.FoldandDockClaimer clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.FoldandDockClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.FoldandDockClaimer, new_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.FoldandDockClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.FoldandDockClaimer) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from TopologyClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false   -- if you can't live without this claim being accepted. ( e.g., RigidChunks ... ) add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class FragmentClaimer(TopologyClaimer)       Method resolution order: FragmentClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle,  : rosetta.protocols.simple_moves.FragmentMover, mover_tag : str, weight : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType   3. __init__(self : handle,  : rosetta.protocols.simple_moves.FragmentMover, mover_tag : str, weight : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight, label : str, fags : rosetta.core.fragment.FragSet) -> NoneType   4. __init__(self : handle,  : rosetta.protocols.simple_moves.FragmentMover) -> NoneType   5. __init__(handle, rosetta.protocols.topology_broker.FragmentClaimer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.FragmentClaimer, was_declined : rosetta.protocols.topology_broker.claims.DofClaim) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.FragmentClaimer,  : rosetta.protocols.topology_broker.FragmentClaimer) -> rosetta.protocols.topology_broker.FragmentClaimer clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.FragmentClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.FragmentClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType get_mover(...) from builtins.PyCapsule get_mover(self : rosetta.protocols.topology_broker.FragmentClaimer,  : rosetta.core.pose.Pose) -> rosetta.protocols.moves.Mover get_sequence_region(...) from builtins.PyCapsule get_sequence_region(self : rosetta.protocols.topology_broker.FragmentClaimer, start_region : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.FragmentClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType mover_tag(...) from builtins.PyCapsule mover_tag(rosetta.protocols.topology_broker.FragmentClaimer) -> str set_bInitDofs(...) from builtins.PyCapsule set_bInitDofs(self : rosetta.protocols.topology_broker.FragmentClaimer, set : bool) -> NoneType set_mover(...) from builtins.PyCapsule set_mover(self : rosetta.protocols.topology_broker.FragmentClaimer, mover : rosetta.protocols.simple_moves.FragmentMover) -> NoneType set_mover_tag(...) from builtins.PyCapsule set_mover_tag(self : rosetta.protocols.topology_broker.FragmentClaimer, str : str) -> NoneType shared_from_this(...) from builtins.PyCapsule shared_from_this(rosetta.protocols.topology_broker.FragmentClaimer) -> rosetta.protocols.topology_broker.FragmentClaimer type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.FragmentClaimer) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from TopologyClaimer: add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class FragmentJumpClaimer(FragmentClaimer)     Claimer that works with the old system of BaseJumpSetup it supports only JumpFrames of type  [ BBTorsion ] UpJump DownJump [ BBTorsion ] the class JumpSample is still used to transport the information jumps and jump_atoms, but cuts are ignored all functionality of JumpSample is not used anymore     Method resolution order: FragmentJumpClaimer FragmentClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.jumping.BaseJumpSetup) -> NoneType   doc   3. __init__(handle, rosetta.protocols.jumping.BaseJumpSetup, str) -> NoneType   doc   4. __init__(self : handle, jump_def : rosetta.protocols.jumping.BaseJumpSetup, mover_tag : str, weight : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType   5. __init__(handle, rosetta.protocols.topology_broker.FragmentJumpClaimer) -> 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.topology_broker.FragmentJumpClaimer,  : rosetta.protocols.topology_broker.FragmentJumpClaimer) -> rosetta.protocols.topology_broker.FragmentJumpClaimer clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.FragmentJumpClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.FragmentJumpClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.FragmentJumpClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(self : rosetta.protocols.topology_broker.FragmentJumpClaimer,  : rosetta.core.pose.Pose) -> NoneType   2. new_decoy(rosetta.protocols.topology_broker.FragmentJumpClaimer) -> NoneType type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.FragmentJumpClaimer) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from FragmentClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.FragmentClaimer, was_declined : rosetta.protocols.topology_broker.claims.DofClaim) -> bool get_mover(...) from builtins.PyCapsule get_mover(self : rosetta.protocols.topology_broker.FragmentClaimer,  : rosetta.core.pose.Pose) -> rosetta.protocols.moves.Mover get_sequence_region(...) from builtins.PyCapsule get_sequence_region(self : rosetta.protocols.topology_broker.FragmentClaimer, start_region : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType mover_tag(...) from builtins.PyCapsule mover_tag(rosetta.protocols.topology_broker.FragmentClaimer) -> str set_bInitDofs(...) from builtins.PyCapsule set_bInitDofs(self : rosetta.protocols.topology_broker.FragmentClaimer, set : bool) -> NoneType set_mover(...) from builtins.PyCapsule set_mover(self : rosetta.protocols.topology_broker.FragmentClaimer, mover : rosetta.protocols.simple_moves.FragmentMover) -> NoneType set_mover_tag(...) from builtins.PyCapsule set_mover_tag(self : rosetta.protocols.topology_broker.FragmentClaimer, str : str) -> NoneType shared_from_this(...) from builtins.PyCapsule shared_from_this(rosetta.protocols.topology_broker.FragmentClaimer) -> rosetta.protocols.topology_broker.FragmentClaimer Methods inherited from TopologyClaimer: add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class LoopFragmentClaimer(FragmentClaimer)       Method resolution order: LoopFragmentClaimer FragmentClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle,  : rosetta.core.fragment.FragSet) -> NoneType   2. __init__(self : handle,  : rosetta.core.fragment.FragSet, label : str) -> NoneType   3. __init__(handle, rosetta.protocols.topology_broker.LoopFragmentClaimer) -> 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.topology_broker.LoopFragmentClaimer,  : rosetta.protocols.topology_broker.LoopFragmentClaimer) -> rosetta.protocols.topology_broker.LoopFragmentClaimer get_mover(...) from builtins.PyCapsule get_mover(self : rosetta.protocols.topology_broker.LoopFragmentClaimer,  : rosetta.core.pose.Pose) -> rosetta.protocols.moves.Mover loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.LoopFragmentClaimer, movemap : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.LoopFragmentClaimer) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from FragmentClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.FragmentClaimer, was_declined : rosetta.protocols.topology_broker.claims.DofClaim) -> bool clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.FragmentClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.FragmentClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType get_sequence_region(...) from builtins.PyCapsule get_sequence_region(self : rosetta.protocols.topology_broker.FragmentClaimer, start_region : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.FragmentClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType mover_tag(...) from builtins.PyCapsule mover_tag(rosetta.protocols.topology_broker.FragmentClaimer) -> str set_bInitDofs(...) from builtins.PyCapsule set_bInitDofs(self : rosetta.protocols.topology_broker.FragmentClaimer, set : bool) -> NoneType set_mover(...) from builtins.PyCapsule set_mover(self : rosetta.protocols.topology_broker.FragmentClaimer, mover : rosetta.protocols.simple_moves.FragmentMover) -> NoneType set_mover_tag(...) from builtins.PyCapsule set_mover_tag(self : rosetta.protocols.topology_broker.FragmentClaimer, str : str) -> NoneType shared_from_this(...) from builtins.PyCapsule shared_from_this(rosetta.protocols.topology_broker.FragmentClaimer) -> rosetta.protocols.topology_broker.FragmentClaimer Methods inherited from TopologyClaimer: add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class MembraneTopologyClaimer(TopologyClaimer)       Method resolution order: MembraneTopologyClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, input_pose : rosetta.core.pose.Pose) -> NoneType   3. __init__(handle, rosetta.protocols.topology_broker.MembraneTopologyClaimer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. addVirtualResAsRootMembrane(...) from builtins.PyCapsule addVirtualResAsRootMembrane(self : rosetta.protocols.topology_broker.MembraneTopologyClaimer, pose : rosetta.core.pose.Pose) -> NoneType add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.MembraneTopologyClaimer, random_mover : rosetta.protocols.moves.RandomMover, pose : rosetta.core.pose.Pose, stageID : rosetta.protocols.abinitio.StageID, scorefxn : rosetta.core.scoring.ScoreFunction, progress : float) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.MembraneTopologyClaimer,  : rosetta.protocols.topology_broker.MembraneTopologyClaimer) -> rosetta.protocols.topology_broker.MembraneTopologyClaimer build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.MembraneTopologyClaimer, pose : rosetta.core.pose.Pose, fold_tree_in : rosetta.core.kinematics.FoldTree) -> NoneType claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.MembraneTopologyClaimer) -> bool clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.MembraneTopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.MembraneTopologyClaimer, dof_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.MembraneTopologyClaimer, pose : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.MembraneTopologyClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.MembraneTopologyClaimer, pose : rosetta.core.pose.Pose) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.MembraneTopologyClaimer, pose : rosetta.core.pose.Pose) -> NoneType type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.MembraneTopologyClaimer) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from TopologyClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false   -- if you can't live without this claim being accepted. ( e.g., RigidChunks ... ) add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class MetalloClaimer(SequenceClaimer)       Method resolution order: MetalloClaimer SequenceClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.topology_broker.MetalloClaimer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.MetalloClaimer,  : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.MetalloClaimer,  : rosetta.protocols.topology_broker.MetalloClaimer) -> rosetta.protocols.topology_broker.MetalloClaimer clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.MetalloClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.MetalloClaimer, dc : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.MetalloClaimer, dc : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.MetalloClaimer, pose : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType shared_from_this(...) from builtins.PyCapsule shared_from_this(rosetta.protocols.topology_broker.MetalloClaimer) -> rosetta.protocols.topology_broker.MetalloClaimer type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.MetalloClaimer) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from TopologyClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false   -- if you can't live without this claim being accepted. ( e.g., RigidChunks ... ) add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class PcsEnergyController(TopologyClaimer)       Method resolution order: PcsEnergyController TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.topology_broker.PcsEnergyController) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.PcsEnergyController,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType   This is called each time the stageID is changed assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.PcsEnergyController,  : rosetta.protocols.topology_broker.PcsEnergyController) -> rosetta.protocols.topology_broker.PcsEnergyController clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.PcsEnergyController) -> rosetta.protocols.topology_broker.TopologyClaimer init_after_reading(...) from builtins.PyCapsule init_after_reading(rosetta.protocols.topology_broker.PcsEnergyController) -> NoneType   Called Each time END CLAIMER is processed set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.topology_broker.PcsEnergyController) -> NoneType   Called any time the CLAIMER is being read (before any tag is read) type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.PcsEnergyController) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from TopologyClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false   -- if you can't live without this claim being accepted. ( e.g., RigidChunks ... ) add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate first round of DOF claims generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   initialize dofs -- e.g., torsions, jumps -- Claimer searches init_claims for claims owned by *this label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class PseudocontactShiftEnergyController(TopologyClaimer)       Method resolution order: PseudocontactShiftEnergyController TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.topology_broker.PseudocontactShiftEnergyController) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.PseudocontactShiftEnergyController,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.PseudocontactShiftEnergyController,  : rosetta.protocols.topology_broker.PseudocontactShiftEnergyController) -> rosetta.protocols.topology_broker.PseudocontactShiftEnergyController clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.PseudocontactShiftEnergyController) -> rosetta.protocols.topology_broker.TopologyClaimer init_after_reading(...) from builtins.PyCapsule init_after_reading(rosetta.protocols.topology_broker.PseudocontactShiftEnergyController) -> NoneType type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.PseudocontactShiftEnergyController) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from TopologyClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false   -- if you can't live without this claim being accepted. ( e.g., RigidChunks ... ) add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate first round of DOF claims generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   initialize dofs -- e.g., torsions, jumps -- Claimer searches init_claims for claims owned by *this label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class PseudocontactShiftEnergyController_Ts1(TopologyClaimer)       Method resolution order: PseudocontactShiftEnergyController_Ts1 TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1,  : rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1) -> rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1) -> rosetta.protocols.topology_broker.TopologyClaimer init_after_reading(...) from builtins.PyCapsule init_after_reading(rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1) -> NoneType set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1) -> NoneType type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from TopologyClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false   -- if you can't live without this claim being accepted. ( e.g., RigidChunks ... ) add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate first round of DOF claims generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   initialize dofs -- e.g., torsions, jumps -- Claimer searches init_claims for claims owned by *this label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class PseudocontactShiftEnergyController_Ts2(TopologyClaimer)       Method resolution order: PseudocontactShiftEnergyController_Ts2 TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2,  : rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2) -> rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2) -> rosetta.protocols.topology_broker.TopologyClaimer init_after_reading(...) from builtins.PyCapsule init_after_reading(rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2) -> NoneType set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2) -> NoneType type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from TopologyClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false   -- if you can't live without this claim being accepted. ( e.g., RigidChunks ... ) add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate first round of DOF claims generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   initialize dofs -- e.g., torsions, jumps -- Claimer searches init_claims for claims owned by *this label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class PseudocontactShiftEnergyController_Ts3(TopologyClaimer)       Method resolution order: PseudocontactShiftEnergyController_Ts3 TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3,  : rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3) -> rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3) -> rosetta.protocols.topology_broker.TopologyClaimer init_after_reading(...) from builtins.PyCapsule init_after_reading(rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3) -> NoneType set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3) -> NoneType type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from TopologyClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false   -- if you can't live without this claim being accepted. ( e.g., RigidChunks ... ) add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate first round of DOF claims generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   initialize dofs -- e.g., torsions, jumps -- Claimer searches init_claims for claims owned by *this label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class PseudocontactShiftEnergyController_Ts4(TopologyClaimer)       Method resolution order: PseudocontactShiftEnergyController_Ts4 TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4,  : rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4) -> rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4) -> rosetta.protocols.topology_broker.TopologyClaimer init_after_reading(...) from builtins.PyCapsule init_after_reading(rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4) -> NoneType set_defaults(...) from builtins.PyCapsule set_defaults(rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4) -> NoneType type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from TopologyClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false   -- if you can't live without this claim being accepted. ( e.g., RigidChunks ... ) add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate first round of DOF claims generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   initialize dofs -- e.g., torsions, jumps -- Claimer searches init_claims for claims owned by *this label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class RigidBodyRandomTMHMover(rosetta.protocols.rigid.RigidBodyMover)       Method resolution order: RigidBodyRandomTMHMover rosetta.protocols.rigid.RigidBodyMover rosetta.protocols.canonical_sampling.ThermodynamicMover 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, max_trans : float, rotation_mag : float, translation_mag : float, tmhelix : int, claimer : rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   3. __init__(handle, rosetta.protocols.topology_broker.RigidBodyRandomTMHMover) -> 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.topology_broker.RigidBodyRandomTMHMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.RigidBodyRandomTMHMover,  : rosetta.protocols.topology_broker.RigidBodyRandomTMHMover) -> rosetta.protocols.topology_broker.RigidBodyRandomTMHMover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.topology_broker.RigidBodyRandomTMHMover) -> str Methods inherited from rosetta.protocols.rigid.RigidBodyMover: freeze(...) from builtins.PyCapsule freeze(rosetta.protocols.rigid.RigidBodyMover) -> NoneType preserve_detailed_balance(...) from builtins.PyCapsule preserve_detailed_balance(rosetta.protocols.rigid.RigidBodyMover) -> bool rb_jump(...) from builtins.PyCapsule rb_jump(*args, **kwargs) Overloaded function.   1. rb_jump(rosetta.protocols.rigid.RigidBodyMover) -> int   2. rb_jump(self : rosetta.protocols.rigid.RigidBodyMover, jump_id : int) -> NoneType rot_center(...) from builtins.PyCapsule rot_center(self : rosetta.protocols.rigid.RigidBodyMover, rot_center_in : rosetta.numeric.xyzVector_double_t) -> NoneType   Manual override of rotation center. set_preserve_detailed_balance(...) from builtins.PyCapsule set_preserve_detailed_balance(self : rosetta.protocols.rigid.RigidBodyMover,  : bool) -> NoneType   set whether detailed balance is preserved (i.e. no branch angle optimization during moves) torsion_id_ranges(...) from builtins.PyCapsule torsion_id_ranges(self : rosetta.protocols.rigid.RigidBodyMover, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_core_id_TorsionID_Range   get the TorsionIDs perturbed by the mover during moves, along with their ranges unfreeze(...) from builtins.PyCapsule unfreeze(rosetta.protocols.rigid.RigidBodyMover) -> NoneType Methods inherited from rosetta.protocols.canonical_sampling.ThermodynamicMover: finalize_simulation(...) from builtins.PyCapsule finalize_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicMover, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType   Callback executed after all Monte Carlo trials are completed. initialize_simulation(...) from builtins.PyCapsule initialize_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicMover, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover, cycle : int) -> NoneType   Callback executed before any Monte Carlo trials are attempted. is_multi_trial(...) from builtins.PyCapsule is_multi_trial(rosetta.protocols.canonical_sampling.ThermodynamicMover) -> bool   Return true if the move performs multiple trials on each apply.      last_inner_score_delta_over_temperature()      metropolis_hastings_mover()      set_metropolis_hastings_mover() last_inner_score_delta_over_temperature(...) from builtins.PyCapsule last_inner_score_delta_over_temperature(rosetta.protocols.canonical_sampling.ThermodynamicMover) -> float   If this is a multi-trial move, return the change in internal  score/temperature caused by the last call to apply().      is_multi_trial() last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.canonical_sampling.ThermodynamicMover) -> float   Return the proposal density ratio for last apply method. metropolis_hastings_mover(...) from builtins.PyCapsule metropolis_hastings_mover(rosetta.protocols.canonical_sampling.ThermodynamicMover) -> rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t   If this is a multi-trial move, return the MetropolisHastingsMover  being used internally.      is_multi_trial() observe_after_metropolis(...) from builtins.PyCapsule observe_after_metropolis(self : rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType   Callback executed after the Metropolis criterion is evaluated. set_metropolis_hastings_mover(...) from builtins.PyCapsule set_metropolis_hastings_mover(self : rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover : rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) -> NoneType   If this is a multi-trial move, set the MetropolisHastingsMover to  be used internally.      is_multi_trial() 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 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 RigidChunkClaimer(TopologyClaimer)     defines a rigid part of structure... imagine a loop-relax application core structure is fixed via jumps and loops can move     the rigid chunk takes a definition of rigid regions in form of an instance of Loops (just taken as bunch of start-end residue numbers ---  here defining the rigid residues and not the loops). the rigid chunk to keep its integrity will need jumps, the claimer will reuse jumps if somebody else claims them, or submit in finalize_claims his own jumps, if not enough jumps are present. in "bExclusive_ mode" the RigidChunk will reclaim any jump claim that is useful and wihin the rigid region. (i.e., foreign claim is dissallowed but own claim with same residues is issued --- in this way the claimer uses e.g., beta-sheet jumps, where they are suggested the input pose is used to initialize the rigid region ( via copying of internal coordinates )  e.g., a hole in the structure shouldn't pose a problem, since we basically copy the atom-tree.     Method resolution order: RigidChunkClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, input_pose : rosetta.core.pose.Pose, rigid : rosetta.protocols.loops.Loops) -> NoneType   3. __init__(handle, rosetta.protocols.topology_broker.RigidChunkClaimer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.RigidChunkClaimer, was_declined : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   will fail if a BB torsion claim of the rigid region has been declined adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.RigidChunkClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType   disallow torsion moves in relax if bRigidInRelax allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.RigidChunkClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   has to decline foreign BB claims for rigid regions, reclaim jumps where appropriate assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.RigidChunkClaimer,  : rosetta.protocols.topology_broker.RigidChunkClaimer) -> rosetta.protocols.topology_broker.RigidChunkClaimer clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.RigidChunkClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.RigidChunkClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   issue jump-claims for jumps yet missing to keep rigid regions fixed generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.RigidChunkClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate DofClaims for BB initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.RigidChunkClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   initialize BB residues and rigid-internal jumps from starting structure --- copying atom-tree dofs manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.RigidChunkClaimer, cut_bias : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.RigidChunkClaimer) -> NoneType   2. new_decoy(self : rosetta.protocols.topology_broker.RigidChunkClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.RigidChunkClaimer, cm : rosetta.protocols.topology_broker.ClaimerMessage) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.RigidChunkClaimer,  : rosetta.core.pose.Pose, bNeedToRepack : rosetta.utility.vector1_bool) -> NoneType   rigid-chunk can probably provide some side-chain info from full-length model type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.RigidChunkClaimer) -> str   type() is specifying the output name of the TopologyClaimer use_loops_from_threading_job(...) from builtins.PyCapsule use_loops_from_threading_job(*args, **kwargs) Overloaded function.   1. use_loops_from_threading_job(rosetta.protocols.topology_broker.RigidChunkClaimer) -> bool   Returns true if we are using loop definitions from ThreadingJob   2. use_loops_from_threading_job(self : rosetta.protocols.topology_broker.RigidChunkClaimer, setting : bool) -> NoneType   Sets whether we should use loop definitions from ThreadingJob Methods inherited from TopologyClaimer: add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   class SequenceClaimer(TopologyClaimer)       Method resolution order: SequenceClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, sequence : str, label : str, rsd_type_set_identifier : str) -> NoneType   3. __init__(handle, rosetta.protocols.topology_broker.SequenceClaimer) -> 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.topology_broker.SequenceClaimer,  : rosetta.protocols.topology_broker.SequenceClaimer) -> rosetta.protocols.topology_broker.SequenceClaimer clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.SequenceClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.SequenceClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round if this Sequence has been moved from position 1 --- needs to issue a fixed CUT in the fold-tree generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.SequenceClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType shared_from_this(...) from builtins.PyCapsule shared_from_this(rosetta.protocols.topology_broker.SequenceClaimer) -> rosetta.protocols.topology_broker.SequenceClaimer type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.SequenceClaimer) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from TopologyClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false   -- if you can't live without this claim being accepted. ( e.g., RigidChunks ... ) add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   initialize dofs -- e.g., torsions, jumps -- Claimer searches init_claims for claims owned by *this label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class SequenceNumberResolver(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.topology_broker.SequenceNumberResolver) -> NoneType   2. __init__(self : rosetta.protocols.topology_broker.SequenceNumberResolver,  : rosetta.protocols.topology_broker.SequenceNumberResolver) -> 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.topology_broker.SequenceNumberResolver,  : rosetta.protocols.topology_broker.SequenceNumberResolver) -> rosetta.protocols.topology_broker.SequenceNumberResolver find_global_pose_number(...) from builtins.PyCapsule find_global_pose_number(*args, **kwargs) Overloaded function.   1. find_global_pose_number(self : rosetta.protocols.topology_broker.SequenceNumberResolver, label : str, resid : int) -> int   Returns global position of element at position resid in sequence claim with the specified label.   2. find_global_pose_number(self : rosetta.protocols.topology_broker.SequenceNumberResolver, pos_pair : (str, int)) -> int   3. find_global_pose_number(self : rosetta.protocols.topology_broker.SequenceNumberResolver, label : str) -> int   Returns global position of first element of sequence claim with the specified label. find_label(...) from builtins.PyCapsule find_label(self : rosetta.protocols.topology_broker.SequenceNumberResolver, pose_number : int) -> str   Returns label of sequence claim that corresponds to the global sequence position <pose_number> find_local_pose_number(...) from builtins.PyCapsule find_local_pose_number(self : rosetta.protocols.topology_broker.SequenceNumberResolver, pose_number : int) -> int   Returns position of global <pose_number> in corresponding sequence claim. offset(...) from builtins.PyCapsule offset(self : rosetta.protocols.topology_broker.SequenceNumberResolver, label : str) -> int   Returns offset of a given label. register_label_offset(...) from builtins.PyCapsule register_label_offset(self : rosetta.protocols.topology_broker.SequenceNumberResolver, label : str, offset : int) -> NoneType   EXCN_BadInput if label or offset is already taken terminal_pair(...) from builtins.PyCapsule terminal_pair(rosetta.protocols.topology_broker.SequenceNumberResolver) -> (int, str)   returns the map element with the largest offset = SequenceClaim at the end of the sequence   class StartStructClaimer(FragmentClaimer)       Method resolution order: StartStructClaimer FragmentClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle,  : rosetta.core.pose.Pose) -> NoneType   3. __init__(handle, rosetta.protocols.topology_broker.StartStructClaimer) -> 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.topology_broker.StartStructClaimer,  : rosetta.protocols.topology_broker.StartStructClaimer) -> rosetta.protocols.topology_broker.StartStructClaimer clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.StartStructClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.StartStructClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType get_mover(...) from builtins.PyCapsule get_mover(self : rosetta.protocols.topology_broker.StartStructClaimer,  : rosetta.core.pose.Pose) -> rosetta.protocols.moves.Mover initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.StartStructClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   overloaded to allow perturbation of start structure new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(self : rosetta.protocols.topology_broker.StartStructClaimer,  : rosetta.core.pose.Pose) -> NoneType   2. new_decoy(rosetta.protocols.topology_broker.StartStructClaimer) -> NoneType shared_from_this(...) from builtins.PyCapsule shared_from_this(rosetta.protocols.topology_broker.StartStructClaimer) -> rosetta.protocols.topology_broker.StartStructClaimer type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.StartStructClaimer) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from FragmentClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.FragmentClaimer, was_declined : rosetta.protocols.topology_broker.claims.DofClaim) -> bool get_sequence_region(...) from builtins.PyCapsule get_sequence_region(self : rosetta.protocols.topology_broker.FragmentClaimer, start_region : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType mover_tag(...) from builtins.PyCapsule mover_tag(rosetta.protocols.topology_broker.FragmentClaimer) -> str set_bInitDofs(...) from builtins.PyCapsule set_bInitDofs(self : rosetta.protocols.topology_broker.FragmentClaimer, set : bool) -> NoneType set_mover(...) from builtins.PyCapsule set_mover(self : rosetta.protocols.topology_broker.FragmentClaimer, mover : rosetta.protocols.simple_moves.FragmentMover) -> NoneType set_mover_tag(...) from builtins.PyCapsule set_mover_tag(self : rosetta.protocols.topology_broker.FragmentClaimer, str : str) -> NoneType Methods inherited from TopologyClaimer: add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class SuggestValueMessage(ClaimerMessage)       Method resolution order: SuggestValueMessage ClaimerMessage builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, label : str) -> NoneType   2. __init__(handle, rosetta.protocols.topology_broker.SuggestValueMessage) -> 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.topology_broker.SuggestValueMessage,  : rosetta.protocols.topology_broker.SuggestValueMessage) -> rosetta.protocols.topology_broker.SuggestValueMessage Data descriptors defined here: some_claim_ Methods inherited from ClaimerMessage: __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.topology_broker.ClaimerMessage) -> str label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.ClaimerMessage) -> str matches(...) from builtins.PyCapsule matches(self : rosetta.protocols.topology_broker.ClaimerMessage, label : str) -> bool nr_recepients(...) from builtins.PyCapsule nr_recepients(rosetta.protocols.topology_broker.ClaimerMessage) -> int received(...) from builtins.PyCapsule received(rosetta.protocols.topology_broker.ClaimerMessage) -> bool received_by_me(...) from builtins.PyCapsule received_by_me(self : rosetta.protocols.topology_broker.ClaimerMessage, me : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t) -> NoneType set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.ClaimerMessage, str : str) -> NoneType type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.ClaimerMessage) -> str   name of Claimer   class SymmetryClaimer(TopologyClaimer)       Method resolution order: SymmetryClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.topology_broker.SymmetryClaimer) -> 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.topology_broker.SymmetryClaimer,  : rosetta.protocols.topology_broker.SymmetryClaimer) -> rosetta.protocols.topology_broker.SymmetryClaimer clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.SymmetryClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer shared_from_this(...) from builtins.PyCapsule shared_from_this(rosetta.protocols.topology_broker.SymmetryClaimer) -> rosetta.protocols.topology_broker.SymmetryClaimer symmetry_duplicate(...) from builtins.PyCapsule symmetry_duplicate(self : rosetta.protocols.topology_broker.SymmetryClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t,  : rosetta.core.pose.Pose) -> NoneType type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.SymmetryClaimer) -> str Methods inherited from TopologyClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false   -- if you can't live without this claim being accepted. ( e.g., RigidChunks ... ) add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate first round of DOF claims generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   initialize dofs -- e.g., torsions, jumps -- Claimer searches init_claims for claims owned by *this label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class TMHTopologySamplerClaimer(TopologyClaimer)       Method resolution order: TMHTopologySamplerClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, broker : rosetta.protocols.topology_broker.TopologyBroker) -> NoneType   3. __init__(handle, rosetta.protocols.topology_broker.TMHTopologySamplerClaimer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.TMHTopologySamplerClaimer,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.TMHTopologySamplerClaimer,  : rosetta.protocols.topology_broker.TMHTopologySamplerClaimer) -> rosetta.protocols.topology_broker.TMHTopologySamplerClaimer build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TMHTopologySamplerClaimer, pose : rosetta.core.pose.Pose, fold_tree : rosetta.core.kinematics.FoldTree) -> NoneType   this claimer builds its own radial fold tree based on read-in spanfile claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TMHTopologySamplerClaimer) -> bool   the broker checks if the claimer builds its own fold tree to figure out if needs to build one itself clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.TMHTopologySamplerClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   TMHTopologySamplerClaimer has virtual functions... use this to obtain a new instance generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.TMHTopologySamplerClaimer, dof_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate DofClaims get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TMHTopologySamplerClaimer, pose : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TMHTopologySamplerClaimer) -> rosetta.core.pose.Pose initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.TMHTopologySamplerClaimer, pose : rosetta.core.pose.Pose, init_dofs : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   make move_map and add the DoF claims from generate_claims() to the movemap.  Now we can move certain parts with certain DOFs. pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TMHTopologySamplerClaimer, pose : rosetta.core.pose.Pose) -> NoneType   read in the pose's spans via the MembraneTopology store din the pose, determine jumps, TMHs, loops, etc. register_options(...) from builtins.PyCapsule register_options() -> NoneType   register cmd-line options in option system ( call before core::init ) set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TMHTopologySamplerClaimer, pose : rosetta.core.pose.Pose) -> NoneType   get the pose from the boker and set it as this object's pose type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.TMHTopologySamplerClaimer) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from TopologyClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false   -- if you can't live without this claim being accepted. ( e.g., RigidChunks ... ) add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class TemplateFragmentClaimer(FragmentClaimer)     hacky wrapper to keep the old Template code alive a bit longer this claimer deals with the Jumpy part of the Templates.     Method resolution order: TemplateFragmentClaimer FragmentClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, str, int) -> NoneType   doc   3. __init__(self : handle, config_file : str, fragsize : int, weight : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType   4. __init__(handle, rosetta.protocols.topology_broker.TemplateFragmentClaimer) -> 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.topology_broker.TemplateFragmentClaimer,  : rosetta.protocols.topology_broker.TemplateFragmentClaimer) -> rosetta.protocols.topology_broker.TemplateFragmentClaimer clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.TemplateFragmentClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer read_config_file(...) from builtins.PyCapsule read_config_file(self : rosetta.protocols.topology_broker.TemplateFragmentClaimer, file : str) -> NoneType type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.TemplateFragmentClaimer) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from FragmentClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.FragmentClaimer, was_declined : rosetta.protocols.topology_broker.claims.DofClaim) -> bool generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.FragmentClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType get_mover(...) from builtins.PyCapsule get_mover(self : rosetta.protocols.topology_broker.FragmentClaimer,  : rosetta.core.pose.Pose) -> rosetta.protocols.moves.Mover get_sequence_region(...) from builtins.PyCapsule get_sequence_region(self : rosetta.protocols.topology_broker.FragmentClaimer, start_region : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.FragmentClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType mover_tag(...) from builtins.PyCapsule mover_tag(rosetta.protocols.topology_broker.FragmentClaimer) -> str set_bInitDofs(...) from builtins.PyCapsule set_bInitDofs(self : rosetta.protocols.topology_broker.FragmentClaimer, set : bool) -> NoneType set_mover(...) from builtins.PyCapsule set_mover(self : rosetta.protocols.topology_broker.FragmentClaimer, mover : rosetta.protocols.simple_moves.FragmentMover) -> NoneType set_mover_tag(...) from builtins.PyCapsule set_mover_tag(self : rosetta.protocols.topology_broker.FragmentClaimer, str : str) -> NoneType shared_from_this(...) from builtins.PyCapsule shared_from_this(rosetta.protocols.topology_broker.FragmentClaimer) -> rosetta.protocols.topology_broker.FragmentClaimer Methods inherited from TopologyClaimer: add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class TemplateJumpClaimer(FragmentJumpClaimer)     hacky wrapper to keep the old Template code alive a bit longer this claimer deals with the Jumpy part of the Templates.     Method resolution order: TemplateJumpClaimer FragmentJumpClaimer FragmentClaimer TopologyClaimer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, str) -> NoneType   doc   3. __init__(self : handle, config_file : str, weight : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType   4. __init__(handle, rosetta.protocols.topology_broker.TemplateJumpClaimer) -> 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.topology_broker.TemplateJumpClaimer,  : rosetta.protocols.topology_broker.TemplateJumpClaimer) -> rosetta.protocols.topology_broker.TemplateJumpClaimer clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.TemplateJumpClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer read_config_file(...) from builtins.PyCapsule read_config_file(self : rosetta.protocols.topology_broker.TemplateJumpClaimer, file : str) -> NoneType read_topol_file(...) from builtins.PyCapsule read_topol_file(self : rosetta.protocols.topology_broker.TemplateJumpClaimer, file : str) -> NoneType type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.TemplateJumpClaimer) -> str   type() is specifying the output name of the TopologyClaimer Methods inherited from FragmentJumpClaimer: generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.FragmentJumpClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.FragmentJumpClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(self : rosetta.protocols.topology_broker.FragmentJumpClaimer,  : rosetta.core.pose.Pose) -> NoneType   2. new_decoy(rosetta.protocols.topology_broker.FragmentJumpClaimer) -> NoneType Methods inherited from FragmentClaimer: accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.FragmentClaimer, was_declined : rosetta.protocols.topology_broker.claims.DofClaim) -> bool get_mover(...) from builtins.PyCapsule get_mover(self : rosetta.protocols.topology_broker.FragmentClaimer,  : rosetta.core.pose.Pose) -> rosetta.protocols.moves.Mover get_sequence_region(...) from builtins.PyCapsule get_sequence_region(self : rosetta.protocols.topology_broker.FragmentClaimer, start_region : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType mover_tag(...) from builtins.PyCapsule mover_tag(rosetta.protocols.topology_broker.FragmentClaimer) -> str set_bInitDofs(...) from builtins.PyCapsule set_bInitDofs(self : rosetta.protocols.topology_broker.FragmentClaimer, set : bool) -> NoneType set_mover(...) from builtins.PyCapsule set_mover(self : rosetta.protocols.topology_broker.FragmentClaimer, mover : rosetta.protocols.simple_moves.FragmentMover) -> NoneType set_mover_tag(...) from builtins.PyCapsule set_mover_tag(self : rosetta.protocols.topology_broker.FragmentClaimer, str : str) -> NoneType shared_from_this(...) from builtins.PyCapsule shared_from_this(rosetta.protocols.topology_broker.FragmentClaimer) -> rosetta.protocols.topology_broker.FragmentClaimer Methods inherited from TopologyClaimer: add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue   class TopologyBroker(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.topology_broker.TopologyBroker) -> NoneType   2. __init__(self : rosetta.protocols.topology_broker.TopologyBroker,  : rosetta.protocols.topology_broker.TopologyBroker) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add(...) from builtins.PyCapsule add(self : rosetta.protocols.topology_broker.TopologyBroker, cl : protocols::topology_broker::TopologyClaimer) -> NoneType   ---------------- Application Setup ------------------------------------      add new Claimers to the broker ---- useful before a job is started add_chainbreak_variants(...) from builtins.PyCapsule add_chainbreak_variants(*args, **kwargs) Overloaded function.   1. add_chainbreak_variants(self : rosetta.protocols.topology_broker.TopologyBroker, pose : rosetta.core.pose.Pose) -> NoneType   add chainbreak variant residue to the unphysical chainbreaks   2. add_chainbreak_variants(self : rosetta.protocols.topology_broker.TopologyBroker, pose : rosetta.core.pose.Pose, max_dist : int) -> NoneType   add chainbreak variant residue to the unphysical chainbreaks   3. add_chainbreak_variants(self : rosetta.protocols.topology_broker.TopologyBroker, pose : rosetta.core.pose.Pose, max_dist : int, sp : rosetta.core.kinematics.ShortestPathInFoldTree) -> NoneType   add chainbreak variant residue to the unphysical chainbreaks adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyBroker,  : rosetta.core.kinematics.MoveMap) -> NoneType   if some claimer wants to influence the movemap for relax he can do it here: apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.topology_broker.TopologyBroker,  : rosetta.core.pose.Pose) -> NoneType   ----------------------- Job Setup ------------------------------------------      at the start of a job this is called, e.g., by the AbrelaxMover  it generates a pose with appropriate foldtree and initializes dofs, adds constraints, etc. apply_filter(...) from builtins.PyCapsule apply_filter(self : rosetta.protocols.topology_broker.TopologyBroker,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID, progress : float) -> NoneType   apply filter (TopologyClaimer::passes_filter() ) and raise exception EXCN_FILTER_FAILED if failed assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.TopologyBroker,  : rosetta.protocols.topology_broker.TopologyBroker) -> rosetta.protocols.topology_broker.TopologyBroker begin(...) from builtins.PyCapsule begin(rosetta.protocols.topology_broker.TopologyBroker) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::topology_broker::TopologyClaimer> const*, std::vector<std::shared_ptr<protocols::topology_broker::TopologyClaimer>, std::allocator<std::shared_ptr<protocols::topology_broker::TopologyClaimer> > > > check_chainbreak_variants(...) from builtins.PyCapsule check_chainbreak_variants(self : rosetta.protocols.topology_broker.TopologyBroker, pose : rosetta.core.pose.Pose) -> bool   check that each chainbreak residue has a chainbreak variant claimer(...) from builtins.PyCapsule claimer(self : rosetta.protocols.topology_broker.TopologyBroker, i : int) -> protocols::topology_broker::TopologyClaimer   Returns the ith topology claimer if it exists. current_pose(...) from builtins.PyCapsule current_pose(rosetta.protocols.topology_broker.TopologyBroker) -> rosetta.core.pose.Pose does_final_fold_tree_exist(...) from builtins.PyCapsule does_final_fold_tree_exist(rosetta.protocols.topology_broker.TopologyBroker) -> bool end(...) from builtins.PyCapsule end(rosetta.protocols.topology_broker.TopologyBroker) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::topology_broker::TopologyClaimer> const*, std::vector<std::shared_ptr<protocols::topology_broker::TopologyClaimer>, std::allocator<std::shared_ptr<protocols::topology_broker::TopologyClaimer> > > > final_fold_tree(...) from builtins.PyCapsule final_fold_tree(rosetta.protocols.topology_broker.TopologyBroker) -> rosetta.core.kinematics.FoldTree   access for hacky claimers get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyBroker) -> rosetta.protocols.topology_broker.TopologyBroker   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyBroker) -> rosetta.protocols.topology_broker.TopologyBroker get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyBroker) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyBroker) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyBroker_t has_chainbreaks_to_close(...) from builtins.PyCapsule has_chainbreaks_to_close(rosetta.protocols.topology_broker.TopologyBroker) -> bool   do we need to close loops ( unphysical chainbreaks have been introduced? ) has_sequence_claimer(...) from builtins.PyCapsule has_sequence_claimer(rosetta.protocols.topology_broker.TopologyBroker) -> bool   / ------------------------------- End Consulting -------------------------------------------- loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyBroker,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   the SlidingWindowLoopClosure needs pure fragments, because it changes the the residue number in the ShortLoopClosure part  thus extra hook for this --- > only some Claimers will answer mover(...) from builtins.PyCapsule mover(self : rosetta.protocols.topology_broker.TopologyBroker,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID, scorefxn : rosetta.core.scoring.ScoreFunction, progress : float) -> rosetta.protocols.moves.Mover   return a set of Movers ( RandomMover, i.e. container of movers ) num_claimers(...) from builtins.PyCapsule num_claimers(rosetta.protocols.topology_broker.TopologyBroker) -> int   Returns the number of claimers associated with the broker relay_message(...) from builtins.PyCapsule relay_message(self : rosetta.protocols.topology_broker.TopologyBroker, msg : protocols::topology_broker::ClaimerMessage) -> NoneType resolve_sequence_label(...) from builtins.PyCapsule resolve_sequence_label(self : rosetta.protocols.topology_broker.TopologyBroker, label : str) -> protocols::topology_broker::claims::SequenceClaim   get the sequence claim that is consistent with the label,  throws EXCN_Unknown_SequenceLabel if not found sequence_number_resolver(...) from builtins.PyCapsule sequence_number_resolver(rosetta.protocols.topology_broker.TopologyBroker) -> protocols::topology_broker::SequenceNumberResolver switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyBroker,  : rosetta.core.pose.Pose) -> NoneType   switch to fullatom --- some Claimers might help by providing template based side-chain information use_job_pose(...) from builtins.PyCapsule use_job_pose(*args, **kwargs) Overloaded function.   1. use_job_pose(self : rosetta.protocols.topology_broker.TopologyBroker, setting : bool) -> NoneType   use the input pose from the job (i.e., call new_decoy( pose ) )   2. use_job_pose(rosetta.protocols.topology_broker.TopologyBroker) -> bool   Returns true if we are using the input pose from the job  (i.e. new_decoy(pose)), false otherwise.   class TopologyClaimer(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   2. __init__(self : rosetta.protocols.topology_broker.TopologyClaimer, weight : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType   3. __init__(rosetta.protocols.topology_broker.TopologyClaimer, rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. accept_declined_claim(...) from builtins.PyCapsule accept_declined_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   notification of declined claims: update your internal representation (e.g., movemap ) to remember this ! / return false   -- if you can't live without this claim being accepted. ( e.g., RigidChunks ... ) add_constraints(...) from builtins.PyCapsule add_constraints(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   add constraints to pose...  might make this stage dependent as with movers... add_mover(...) from builtins.PyCapsule add_mover(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.moves.RandomMover,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ adjust_relax_movemap(...) from builtins.PyCapsule adjust_relax_movemap(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> NoneType allow_claim(...) from builtins.PyCapsule allow_claim(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.claims.DofClaim) -> bool   allow a claim from a foreign Claimer assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer broker(...) from builtins.PyCapsule broker(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyBroker   return the broker we are collaborating with build_fold_tree(...) from builtins.PyCapsule build_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.core.kinematics.FoldTree) -> NoneType claim_accepted(...) from builtins.PyCapsule claim_accepted(self : rosetta.protocols.topology_broker.TopologyClaimer, my_claim : rosetta.protocols.topology_broker.claims.DofClaim) -> NoneType   this claim of yours was accepted.... I so far haven't done anything with this... might go away. claimer_builds_own_fold_tree(...) from builtins.PyCapsule claimer_builds_own_fold_tree(rosetta.protocols.topology_broker.TopologyClaimer) -> bool clone(...) from builtins.PyCapsule clone(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   clone it! finalize_claims(...) from builtins.PyCapsule finalize_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   is called after all round1 claims have been approved or retracted -- additional claims can be issued in this round generate_claims(...) from builtins.PyCapsule generate_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate first round of DOF claims generate_sequence_claims(...) from builtins.PyCapsule generate_sequence_claims(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   generate claims that affect the sequence of the pose get_fold_tree(...) from builtins.PyCapsule get_fold_tree(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree   in case a claimer has its own fold_tree.  get_fold_tree() is called by the broker get_pose_from_claimer(...) from builtins.PyCapsule get_pose_from_claimer(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer   self pointers   2. get_self_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.TopologyClaimer get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t   2. get_self_weak_ptr(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t initialize_dofs(...) from builtins.PyCapsule initialize_dofs(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose, init_claims : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t, failed_to_init : rosetta.utility.vector1_std_shared_ptr_protocols_topology_broker_claims_DofClaim_t) -> NoneType   initialize dofs -- e.g., torsions, jumps -- Claimer searches init_claims for claims owned by *this label(...) from builtins.PyCapsule label(rosetta.protocols.topology_broker.TopologyClaimer) -> str loop_frags(...) from builtins.PyCapsule loop_frags(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.kinematics.MoveMap) -> rosetta.core.fragment.FragSet   return fragments that can be used for loop-sampling... unfortunately some loop-samplers need fragments, rather then fragmovers  (e.g. short-loop closure since it remaps them on a short pose containing only the loop-residues. )  overloaded e.g., by LoopFragmentClaimer.. returns a movemap and fragset good for loop-sampling manipulate_cut_bias(...) from builtins.PyCapsule manipulate_cut_bias(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.utility.vector1_double) -> NoneType   multiply your bias to this -- if its zero don't change that, i.e., multiply only  this is used during fold-tree generation to set the cut-points. it starts with 1.0 for all residues.  Fragments can add their loop-fraction mover_weight(...) from builtins.PyCapsule mover_weight(rosetta.protocols.topology_broker.TopologyClaimer) -> rosetta.protocols.topology_broker.weights.AbinitioMoverWeight new_decoy(...) from builtins.PyCapsule new_decoy(*args, **kwargs) Overloaded function.   1. new_decoy(rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   a new decoy --- random choices to be made ? make them here   2. new_decoy(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType   an input pose is given, i.e., a starting structure for resampling  don't make random choices, base choices on given pose passes_filter(...) from builtins.PyCapsule passes_filter(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.protocols.abinitio.StageID,  : float,  : rosetta.std.basic_ostringstream_char_std_char_traits_char_std_allocator_char_t) -> bool   claimers can add movers to the RandomMover (Container).  add your moves, make it dependent on stage if you want to. So far this is called only by abinitio...  if you don't want to do anything special --- don't overload this method!  default: adds mover given by virtual call get_mover()  with stage-dependent weight given by abinitio_mover_weight_ pre_process(...) from builtins.PyCapsule pre_process(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType receive_message(...) from builtins.PyCapsule receive_message(self : rosetta.protocols.topology_broker.TopologyClaimer,  : protocols::topology_broker::ClaimerMessage) -> NoneType set_broker(...) from builtins.PyCapsule set_broker(self : rosetta.protocols.topology_broker.TopologyClaimer, ptr : rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t) -> NoneType   don't use this --- it is called by TopologyBroker add_claim only set_label(...) from builtins.PyCapsule set_label(self : rosetta.protocols.topology_broker.TopologyClaimer, str : str) -> NoneType set_mover_weight(...) from builtins.PyCapsule set_mover_weight(self : rosetta.protocols.topology_broker.TopologyClaimer, wset : rosetta.protocols.topology_broker.weights.AbinitioMoverWeight) -> NoneType set_pose_from_broker(...) from builtins.PyCapsule set_pose_from_broker(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose) -> NoneType switch_to_fullatom(...) from builtins.PyCapsule switch_to_fullatom(self : rosetta.protocols.topology_broker.TopologyClaimer,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool) -> NoneType   has this Claimer some side chain conformations to add?  starts with bNeedToRepack true for all residues... if you have a sidechain ---> copy it to pose and set needtoRepack false for this residue type(...) from builtins.PyCapsule type(rosetta.protocols.topology_broker.TopologyClaimer) -> str   name of Claimer   class TopologyClaimerFactory(builtins.object)     A non-copyable factory for instantiating TopologyClaimers by name. Commonly used TopologyClaimers are registered in the constructor. Additional claimers can be registered after the fact using the add_type() method.     Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_type(...) from builtins.PyCapsule add_type(*args, **kwargs) Overloaded function.   1. add_type(self : rosetta.protocols.topology_broker.TopologyClaimerFactory, name : str, claimer : rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   Registers the TopologyClaimer with name <name>. Instances of this  class can be retrieved by calling newTopologyClaimer(<name>).   2. add_type(self : rosetta.protocols.topology_broker.TopologyClaimerFactory, claimer : rosetta.protocols.topology_broker.TopologyClaimer) -> NoneType   Registers the TopologyClaimer using the name returned by  claimer->type(). Instances of this class can be retrieved by calling  newTopologyClaimer(<name>). get_instance(...) from builtins.PyCapsule get_instance() -> rosetta.protocols.topology_broker.TopologyClaimerFactory   Returns an instance to the singleton newTopologyClaimer(...) from builtins.PyCapsule newTopologyClaimer(self : rosetta.protocols.topology_broker.TopologyClaimerFactory, name : str) -> rosetta.protocols.topology_broker.TopologyClaimer   Returns a new instance of the TopologyClaimer identified by <name>