Bindings for protocols::toolbox namespace

Modules
		rosetta.protocols.toolbox.match_enzdes_util rosetta.protocols.toolbox.pose_manipulation rosetta.protocols.toolbox.pose_metric_calculators rosetta.protocols.toolbox.rigid_body rosetta.protocols.toolbox.rotamer_set_operations rosetta.protocols.toolbox.sample_around rosetta.protocols.toolbox.task_operations

Classes
		builtins.object AtomID_Mapper AtomLevelDomainMap CalcInterNeighborGroup ClusterBase ClusterPhilStyle ClusterOptions DecoySetEvaluation DummyClass EnergyLandscapeEvaluator MulliganPNearEvaluator RotamerBoltzmannWeightEvaluator InteratomicVarianceMatrix KCluster GreedyKCenter KMedoid KClusterData KClusterElement Node ResidueNetwork CovalentResidueNetwork DistanceResidueNetwork SF_Replica ScoreRmsPoint rosetta.core.pack.task.IGEdgeReweighter(builtins.object) IGLigandDesignEdgeUpweighter ResidueGroupIGEdgeUpweighter rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint(builtins.object) ScoreRmsPoints   class AtomID_Mapper(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.toolbox.AtomID_Mapper, rosetta.core.pose.Pose) -> NoneType   doc   2. __init__(self : rosetta.protocols.toolbox.AtomID_Mapper, pose : rosetta.core.pose.Pose, map_to_vanilla_pose : bool) -> NoneType   3. __init__(self : rosetta.protocols.toolbox.AtomID_Mapper, src : rosetta.protocols.toolbox.AtomID_Mapper) -> 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.toolbox.AtomID_Mapper,  : rosetta.protocols.toolbox.AtomID_Mapper) -> rosetta.protocols.toolbox.AtomID_Mapper atom_ids_in_res(...) from builtins.PyCapsule atom_ids_in_res(self : rosetta.protocols.toolbox.AtomID_Mapper, n : int) -> rosetta.utility.vector1_core_id_AtomID calculate_atom_id_map(...) from builtins.PyCapsule calculate_atom_id_map(*args, **kwargs) Overloaded function.   1. calculate_atom_id_map(self : rosetta.protocols.toolbox.AtomID_Mapper, target_pose : rosetta.core.pose.Pose, res_map : rosetta.std.map_unsigned_long_unsigned_long, source_fold_tree : rosetta.core.kinematics.FoldTree) -> rosetta.std.map_core_id_AtomID_core_id_AtomID   2. calculate_atom_id_map(self : rosetta.protocols.toolbox.AtomID_Mapper, target_pose : rosetta.core.pose.Pose, res_map : rosetta.std.map_unsigned_long_unsigned_long, source_fold_tree : rosetta.core.kinematics.FoldTree, source_mapper_to_vanilla : rosetta.protocols.toolbox.AtomID_Mapper) -> rosetta.std.map_core_id_AtomID_core_id_AtomID clone(...) from builtins.PyCapsule clone(rosetta.protocols.toolbox.AtomID_Mapper) -> rosetta.protocols.toolbox.AtomID_Mapper has_atom_id(...) from builtins.PyCapsule has_atom_id(self : rosetta.protocols.toolbox.AtomID_Mapper, atom_id : rosetta.core.id.AtomID) -> bool map_from_reference(...) from builtins.PyCapsule map_from_reference(self : rosetta.protocols.toolbox.AtomID_Mapper, atom_id : rosetta.core.id.AtomID) -> rosetta.core.id.AtomID map_to_reference(...) from builtins.PyCapsule map_to_reference(self : rosetta.protocols.toolbox.AtomID_Mapper, atom_id : rosetta.core.id.AtomID) -> rosetta.core.id.AtomID nres(...) from builtins.PyCapsule nres(rosetta.protocols.toolbox.AtomID_Mapper) -> int renumber_after_variant_changes(...) from builtins.PyCapsule renumber_after_variant_changes(self : rosetta.protocols.toolbox.AtomID_Mapper, pose : rosetta.core.pose.Pose) -> NoneType   class AtomLevelDomainMap(builtins.object)     ///////////////////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle, rosetta.core.pose.Pose) -> NoneType   doc   2. __init__(handle, rosetta.core.pose.Pose, bool) -> NoneType   doc   3. __init__(self : handle, pose : rosetta.core.pose.Pose, map_to_vanilla_pose : bool, allow_insert_res : rosetta.utility.vector1_unsigned_long) -> NoneType   4. __init__(handle, rosetta.protocols.toolbox.AtomLevelDomainMap) -> 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.toolbox.AtomLevelDomainMap,  : rosetta.protocols.toolbox.AtomLevelDomainMap) -> rosetta.protocols.toolbox.AtomLevelDomainMap atom_id_mapper(...) from builtins.PyCapsule atom_id_mapper(rosetta.protocols.toolbox.AtomLevelDomainMap) -> protocols::toolbox::AtomID_Mapper calculate_atom_id_domain_map(...) from builtins.PyCapsule calculate_atom_id_domain_map(self : rosetta.protocols.toolbox.AtomLevelDomainMap, pose : rosetta.core.pose.Pose) -> rosetta.std.map_core_id_AtomID_unsigned_long clone(...) from builtins.PyCapsule clone(rosetta.protocols.toolbox.AtomLevelDomainMap) -> rosetta.protocols.toolbox.AtomLevelDomainMap disallow_movement_of_input_res(...) from builtins.PyCapsule disallow_movement_of_input_res(self : rosetta.protocols.toolbox.AtomLevelDomainMap, pose : rosetta.core.pose.Pose) -> NoneType get(...) from builtins.PyCapsule get(*args, **kwargs) Overloaded function.   1. get(self : rosetta.protocols.toolbox.AtomLevelDomainMap, i : int) -> bool   2. get(self : rosetta.protocols.toolbox.AtomLevelDomainMap, atom_id : rosetta.core.id.AtomID) -> bool   3. get(self : rosetta.protocols.toolbox.AtomLevelDomainMap, torsion_id : rosetta.core.id.TorsionID, conformation : rosetta.core.conformation.Conformation) -> bool get_domain(...) from builtins.PyCapsule get_domain(*args, **kwargs) Overloaded function.   1. get_domain(self : rosetta.protocols.toolbox.AtomLevelDomainMap, i : int) -> int   2. get_domain(self : rosetta.protocols.toolbox.AtomLevelDomainMap, atom_id : rosetta.core.id.AtomID) -> int   3. get_domain(self : rosetta.protocols.toolbox.AtomLevelDomainMap, named_atom_id : rosetta.core.id.NamedAtomID, pose : rosetta.core.pose.Pose) -> int get_jump(...) from builtins.PyCapsule get_jump(self : rosetta.protocols.toolbox.AtomLevelDomainMap, jump_number : int, conformation : rosetta.core.conformation.Conformation) -> bool has_domain(...) from builtins.PyCapsule has_domain(self : rosetta.protocols.toolbox.AtomLevelDomainMap, atom_id : rosetta.core.id.AtomID) -> bool renumber_after_variant_changes(...) from builtins.PyCapsule renumber_after_variant_changes(self : rosetta.protocols.toolbox.AtomLevelDomainMap, pose : rosetta.core.pose.Pose) -> NoneType set(...) from builtins.PyCapsule set(*args, **kwargs) Overloaded function.   1. set(self : rosetta.protocols.toolbox.AtomLevelDomainMap, i : int, setting : bool) -> NoneType   2. set(self : rosetta.protocols.toolbox.AtomLevelDomainMap, named_atom_id : rosetta.core.id.NamedAtomID, pose : rosetta.core.pose.Pose, setting : bool) -> NoneType   3. set(self : rosetta.protocols.toolbox.AtomLevelDomainMap, atom_id : rosetta.core.id.AtomID, setting : bool) -> NoneType   4. set(self : rosetta.protocols.toolbox.AtomLevelDomainMap, setting : bool) -> NoneType set_domain(...) from builtins.PyCapsule set_domain(*args, **kwargs) Overloaded function.   1. set_domain(self : rosetta.protocols.toolbox.AtomLevelDomainMap, i : int, setting : int) -> NoneType   2. set_domain(self : rosetta.protocols.toolbox.AtomLevelDomainMap, atom_id : rosetta.core.id.AtomID, setting : int) -> NoneType   3. set_domain(self : rosetta.protocols.toolbox.AtomLevelDomainMap, atom_id : rosetta.core.id.NamedAtomID, pose : rosetta.core.pose.Pose, setting : int) -> NoneType   4. set_domain(self : rosetta.protocols.toolbox.AtomLevelDomainMap, setting : int) -> NoneType set_fixed_if_moving(...) from builtins.PyCapsule set_fixed_if_moving(*args, **kwargs) Overloaded function.   1. set_fixed_if_moving(self : rosetta.protocols.toolbox.AtomLevelDomainMap, i : int) -> NoneType   2. set_fixed_if_moving(self : rosetta.protocols.toolbox.AtomLevelDomainMap, atom_id : rosetta.core.id.AtomID) -> NoneType set_phosphate(...) from builtins.PyCapsule set_phosphate(self : rosetta.protocols.toolbox.AtomLevelDomainMap, i : int, pose : rosetta.core.pose.Pose, setting : bool) -> NoneType set_phosphate_domain(...) from builtins.PyCapsule set_phosphate_domain(self : rosetta.protocols.toolbox.AtomLevelDomainMap, i : int, pose : rosetta.core.pose.Pose, setting : int) -> NoneType set_sugar(...) from builtins.PyCapsule set_sugar(self : rosetta.protocols.toolbox.AtomLevelDomainMap, i : int, pose : rosetta.core.pose.Pose, setting : bool) -> NoneType set_sugar_domain(...) from builtins.PyCapsule set_sugar_domain(self : rosetta.protocols.toolbox.AtomLevelDomainMap, i : int, pose : rosetta.core.pose.Pose, setting : int) -> NoneType setup_movemap(...) from builtins.PyCapsule setup_movemap(self : rosetta.protocols.toolbox.AtomLevelDomainMap, mm : rosetta.core.kinematics.MoveMap, pose : rosetta.core.pose.Pose) -> NoneType update_to_move_chunks_with_domain(...) from builtins.PyCapsule update_to_move_chunks_with_domain(self : rosetta.protocols.toolbox.AtomLevelDomainMap, domain : int) -> NoneType   class CalcInterNeighborGroup(builtins.object)     This is complicated, so pay attention.  You define groups of residues within a protein (say, the N and C terminal domains).  You then define which pairs of groups you are interested in.  This calculator returns the union of the sets of residues at the interfaces between these domains/groups.  Functionally it is intended for "interface design" at the non-chainbreak interface between domains of multidomain proteins.  It contains a superset of the functionality of some of the other calculators (so I'll be obsoleting them, maybe?).  The pose does NOT have to have been scored.   "groups" string returns the input groups; of type utility::vector1< std::pair< std::set< core::Size >, std::set< core::Size > > >  (not a calculated value)   "dist_cutoff" returns the input cutoff distance for neighbor finding (not a calculated value)   "neighbors" returns a std::set<core::Size> of the neighbors calculated between the group pairs.   "num_neighbors" returns the size of the neighbors set.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.toolbox.CalcInterNeighborGroup) -> NoneType   2. __init__(rosetta.protocols.toolbox.CalcInterNeighborGroup, rosetta.utility.vector1_std_pair_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType   doc   3. __init__(self : rosetta.protocols.toolbox.CalcInterNeighborGroup, groups : rosetta.utility.vector1_std_pair_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, dist_cutoff : float) -> NoneType   4. __init__(self : rosetta.protocols.toolbox.CalcInterNeighborGroup, calculator : rosetta.protocols.toolbox.CalcInterNeighborGroup) -> 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.toolbox.CalcInterNeighborGroup,  : rosetta.protocols.toolbox.CalcInterNeighborGroup) -> rosetta.protocols.toolbox.CalcInterNeighborGroup compute(...) from builtins.PyCapsule compute(self : rosetta.protocols.toolbox.CalcInterNeighborGroup, pose : rosetta.core.pose.Pose) -> NoneType dist_cutoff(...) from builtins.PyCapsule dist_cutoff(*args, **kwargs) Overloaded function.   1. dist_cutoff(self : rosetta.protocols.toolbox.CalcInterNeighborGroup, cutoff : float) -> NoneType   2. dist_cutoff(rosetta.protocols.toolbox.CalcInterNeighborGroup) -> float   return distance cutoff groups(...) from builtins.PyCapsule groups(*args, **kwargs) Overloaded function.   1. groups(rosetta.protocols.toolbox.CalcInterNeighborGroup) -> rosetta.utility.vector1_std_pair_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t   2. groups(self : rosetta.protocols.toolbox.CalcInterNeighborGroup, groups : rosetta.utility.vector1_std_pair_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType neighbors(...) from builtins.PyCapsule neighbors(rosetta.protocols.toolbox.CalcInterNeighborGroup) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t num_neighbors(...) from builtins.PyCapsule num_neighbors(rosetta.protocols.toolbox.CalcInterNeighborGroup) -> float   class ClusterBase(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.toolbox.ClusterBase, dim : int) -> NoneType   2. __init__(self : rosetta.protocols.toolbox.ClusterBase,  : rosetta.protocols.toolbox.ClusterBase) -> 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.toolbox.ClusterBase) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.toolbox.ClusterBase,  : rosetta.protocols.toolbox.ClusterBase) -> rosetta.protocols.toolbox.ClusterBase cluster(...) from builtins.PyCapsule cluster(self : rosetta.protocols.toolbox.ClusterBase, i : int) -> rosetta.std.deque_unsigned_long_std_allocator_unsigned_long_t clusterlist(...) from builtins.PyCapsule clusterlist(rosetta.protocols.toolbox.ClusterBase) -> rosetta.utility.vector1_std_deque_unsigned_long_std_allocator_unsigned_long_t dim(...) from builtins.PyCapsule dim(rosetta.protocols.toolbox.ClusterBase) -> int dist(...) from builtins.PyCapsule dist(*args, **kwargs) Overloaded function.   1. dist(self : rosetta.protocols.toolbox.ClusterBase, i : int, j : int) -> float   2. dist(self : rosetta.protocols.toolbox.ClusterBase, i : int, j : int) -> float distance_matrix(...) from builtins.PyCapsule distance_matrix(*args, **kwargs) Overloaded function.   1. distance_matrix(rosetta.protocols.toolbox.ClusterBase) -> ObjexxFCL::FArray2D<double>   2. distance_matrix(rosetta.protocols.toolbox.ClusterBase) -> ObjexxFCL::FArray2D<double> limit_groupsize(...) from builtins.PyCapsule limit_groupsize(self : rosetta.protocols.toolbox.ClusterBase, limit : int) -> NoneType print_summary(...) from builtins.PyCapsule print_summary(self : rosetta.protocols.toolbox.ClusterBase, tags : rosetta.utility.vector1_std_string, all_energies : rosetta.utility.vector1_double) -> NoneType size(...) from builtins.PyCapsule size(rosetta.protocols.toolbox.ClusterBase) -> int sort_each_group_by_energy(...) from builtins.PyCapsule sort_each_group_by_energy(*args, **kwargs) Overloaded function.   1. sort_each_group_by_energy(self : rosetta.protocols.toolbox.ClusterBase, all_energies : rosetta.utility.vector1_double) -> NoneType   2. sort_each_group_by_energy(self : rosetta.protocols.toolbox.ClusterBase, all_energies : rosetta.utility.vector1_double, keep_center : bool) -> NoneType   class ClusterOptions(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.toolbox.ClusterOptions) -> NoneType   doc   2. __init__(self : rosetta.protocols.toolbox.ClusterOptions, assign_new_cluster_tag : bool) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Data descriptors defined here: assign_new_cluster_tag cluster_radius keep_center limit_cluster_size   class ClusterPhilStyle(ClusterBase)       Method resolution order: ClusterPhilStyle ClusterBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.toolbox.ClusterPhilStyle, int) -> NoneType   doc   2. __init__(self : rosetta.protocols.toolbox.ClusterPhilStyle, dim : int, rad : float) -> NoneType   3. __init__(self : rosetta.protocols.toolbox.ClusterPhilStyle,  : rosetta.protocols.toolbox.ClusterPhilStyle) -> 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.toolbox.ClusterPhilStyle,  : rosetta.protocols.toolbox.ClusterPhilStyle) -> rosetta.protocols.toolbox.ClusterPhilStyle compute(...) from builtins.PyCapsule compute(rosetta.protocols.toolbox.ClusterPhilStyle) -> NoneType do_clustering(...) from builtins.PyCapsule do_clustering(rosetta.protocols.toolbox.ClusterPhilStyle) -> NoneType set_n_max_cluster(...) from builtins.PyCapsule set_n_max_cluster(self : rosetta.protocols.toolbox.ClusterPhilStyle, setting : int) -> NoneType set_radius(...) from builtins.PyCapsule set_radius(self : rosetta.protocols.toolbox.ClusterPhilStyle, setting : float) -> NoneType Methods inherited from ClusterBase: __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.toolbox.ClusterBase) -> str cluster(...) from builtins.PyCapsule cluster(self : rosetta.protocols.toolbox.ClusterBase, i : int) -> rosetta.std.deque_unsigned_long_std_allocator_unsigned_long_t clusterlist(...) from builtins.PyCapsule clusterlist(rosetta.protocols.toolbox.ClusterBase) -> rosetta.utility.vector1_std_deque_unsigned_long_std_allocator_unsigned_long_t dim(...) from builtins.PyCapsule dim(rosetta.protocols.toolbox.ClusterBase) -> int dist(...) from builtins.PyCapsule dist(*args, **kwargs) Overloaded function.   1. dist(self : rosetta.protocols.toolbox.ClusterBase, i : int, j : int) -> float   2. dist(self : rosetta.protocols.toolbox.ClusterBase, i : int, j : int) -> float distance_matrix(...) from builtins.PyCapsule distance_matrix(*args, **kwargs) Overloaded function.   1. distance_matrix(rosetta.protocols.toolbox.ClusterBase) -> ObjexxFCL::FArray2D<double>   2. distance_matrix(rosetta.protocols.toolbox.ClusterBase) -> ObjexxFCL::FArray2D<double> limit_groupsize(...) from builtins.PyCapsule limit_groupsize(self : rosetta.protocols.toolbox.ClusterBase, limit : int) -> NoneType print_summary(...) from builtins.PyCapsule print_summary(self : rosetta.protocols.toolbox.ClusterBase, tags : rosetta.utility.vector1_std_string, all_energies : rosetta.utility.vector1_double) -> NoneType size(...) from builtins.PyCapsule size(rosetta.protocols.toolbox.ClusterBase) -> int sort_each_group_by_energy(...) from builtins.PyCapsule sort_each_group_by_energy(*args, **kwargs) Overloaded function.   1. sort_each_group_by_energy(self : rosetta.protocols.toolbox.ClusterBase, all_energies : rosetta.utility.vector1_double) -> NoneType   2. sort_each_group_by_energy(self : rosetta.protocols.toolbox.ClusterBase, all_energies : rosetta.utility.vector1_double, keep_center : bool) -> NoneType   class CovalentResidueNetwork(ResidueNetwork)     Creates networks based on covalent connections between residues     Method resolution order: CovalentResidueNetwork ResidueNetwork builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.toolbox.CovalentResidueNetwork,  : rosetta.protocols.toolbox.CovalentResidueNetwork) -> rosetta.protocols.toolbox.CovalentResidueNetwork generate_edges(...) from builtins.PyCapsule generate_edges(self : rosetta.protocols.toolbox.CovalentResidueNetwork, pose : rosetta.core.pose.Pose) -> NoneType Methods inherited from ResidueNetwork: average_shortest_path_length(...) from builtins.PyCapsule average_shortest_path_length(rosetta.protocols.toolbox.ResidueNetwork) -> float   calculates the average shortest path length of the network clear_edges(...) from builtins.PyCapsule clear_edges(rosetta.protocols.toolbox.ResidueNetwork) -> NoneType   empties edges connectivity_index(...) from builtins.PyCapsule connectivity_index(self : rosetta.protocols.toolbox.ResidueNetwork, resi : int) -> float   calculates the connectivity index of residue resi in the context of the network create_from_pose(...) from builtins.PyCapsule create_from_pose(self : rosetta.protocols.toolbox.ResidueNetwork, pose : rosetta.core.pose.Pose) -> NoneType   create a network from a pose dijkstras(...) from builtins.PyCapsule dijkstras(self : rosetta.protocols.toolbox.ResidueNetwork, resi : int) -> NoneType   run Dijkstra's shortest path algorithm on the given list of nodes  after execution, the "distanceFromStart" variable of each node will contain the distance from residue resi nodes(...) from builtins.PyCapsule nodes(rosetta.protocols.toolbox.ResidueNetwork) -> rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_std_allocator_std_shared_ptr_protocols_toolbox_Node_t   class DecoySetEvaluation(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.toolbox.DecoySetEvaluation) -> NoneType   2. __init__(self : rosetta.protocols.toolbox.DecoySetEvaluation,  : rosetta.protocols.toolbox.DecoySetEvaluation) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. all_energies(...) from builtins.PyCapsule all_energies(rosetta.protocols.toolbox.DecoySetEvaluation) -> rosetta.utility.vector1_double assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.toolbox.DecoySetEvaluation,  : rosetta.protocols.toolbox.DecoySetEvaluation) -> rosetta.protocols.toolbox.DecoySetEvaluation center_all(...) from builtins.PyCapsule center_all(self : rosetta.protocols.toolbox.DecoySetEvaluation, weights : ObjexxFCL::FArray1<double>) -> NoneType center_structure(...) from builtins.PyCapsule center_structure(*args, **kwargs) Overloaded function.   1. center_structure(self : rosetta.protocols.toolbox.DecoySetEvaluation, i : int) -> NoneType   2. center_structure(self : rosetta.protocols.toolbox.DecoySetEvaluation, i : int, weights : ObjexxFCL::FArray1<double>) -> NoneType clear(...) from builtins.PyCapsule clear(rosetta.protocols.toolbox.DecoySetEvaluation) -> NoneType compute_average_structure(...) from builtins.PyCapsule compute_average_structure(self : rosetta.protocols.toolbox.DecoySetEvaluation, average_structure : rosetta.ObjexxFCL.FArray2_double_t) -> NoneType compute_distance_matrix(...) from builtins.PyCapsule compute_distance_matrix(self : rosetta.protocols.toolbox.DecoySetEvaluation,  : ObjexxFCL::FArray2D<double>) -> NoneType coords(...) from builtins.PyCapsule coords(*args, **kwargs) Overloaded function.   1. coords(rosetta.protocols.toolbox.DecoySetEvaluation) -> ObjexxFCL::FArray3D<double>   2. coords(self : rosetta.protocols.toolbox.DecoySetEvaluation, i : int) -> ObjexxFCL::FArray2P<double> create_dist_constraints(...) from builtins.PyCapsule create_dist_constraints(self : rosetta.protocols.toolbox.DecoySetEvaluation, cst_set : rosetta.core.scoring.constraints.ConstraintSet) -> NoneType create_dist_constraints_median(...) from builtins.PyCapsule create_dist_constraints_median(self : rosetta.protocols.toolbox.DecoySetEvaluation, cst_set : rosetta.core.scoring.constraints.ConstraintSet) -> NoneType create_xyz_constraints_median(...) from builtins.PyCapsule create_xyz_constraints_median(self : rosetta.protocols.toolbox.DecoySetEvaluation, cst_set : rosetta.core.scoring.constraints.ConstraintSet, ref_pose : rosetta.core.pose.Pose, root : int) -> NoneType find_closest_to_average(...) from builtins.PyCapsule find_closest_to_average(self : rosetta.protocols.toolbox.DecoySetEvaluation, average_structure : rosetta.ObjexxFCL.FArray2_double_t) -> int n_atoms(...) from builtins.PyCapsule n_atoms(rosetta.protocols.toolbox.DecoySetEvaluation) -> int n_decoys(...) from builtins.PyCapsule n_decoys(rosetta.protocols.toolbox.DecoySetEvaluation) -> int n_decoys_max(...) from builtins.PyCapsule n_decoys_max(rosetta.protocols.toolbox.DecoySetEvaluation) -> int pop_back_CA_xyz(...) from builtins.PyCapsule pop_back_CA_xyz(rosetta.protocols.toolbox.DecoySetEvaluation) -> NoneType push_back(...) from builtins.PyCapsule push_back(self : rosetta.protocols.toolbox.DecoySetEvaluation, pose : rosetta.core.pose.Pose) -> NoneType push_back_CA_xyz(...) from builtins.PyCapsule push_back_CA_xyz(self : rosetta.protocols.toolbox.DecoySetEvaluation,  : rosetta.ObjexxFCL.FArray2_double_t, nres : int) -> NoneType push_back_CA_xyz_from_silent_file(...) from builtins.PyCapsule push_back_CA_xyz_from_silent_file(self : rosetta.protocols.toolbox.DecoySetEvaluation, sfd : rosetta.core.io.silent.SilentFileData, store_energies : bool) -> NoneType ref_pose(...) from builtins.PyCapsule ref_pose(rosetta.protocols.toolbox.DecoySetEvaluation) -> rosetta.core.pose.Pose register_options(...) from builtins.PyCapsule register_options() -> NoneType reserve(...) from builtins.PyCapsule reserve(self : rosetta.protocols.toolbox.DecoySetEvaluation, n_decoys_ : int) -> NoneType rmsd(...) from builtins.PyCapsule rmsd(self : rosetta.protocols.toolbox.DecoySetEvaluation, weights : ObjexxFCL::FArray1<double>, xx_ref : rosetta.ObjexxFCL.FArray2_double_t, xx : rosetta.ObjexxFCL.FArray2_double_t) -> float rmsf(...) from builtins.PyCapsule rmsf(*args, **kwargs) Overloaded function.   1. rmsf(self : rosetta.protocols.toolbox.DecoySetEvaluation, results : rosetta.utility.vector1_double) -> NoneType   2. rmsf(self : rosetta.protocols.toolbox.DecoySetEvaluation, result : ObjexxFCL::FArray1<double>) -> NoneType set_all_energies(...) from builtins.PyCapsule set_all_energies(self : rosetta.protocols.toolbox.DecoySetEvaluation, all_energies : rosetta.utility.vector1_double) -> NoneType set_n_atom(...) from builtins.PyCapsule set_n_atom(self : rosetta.protocols.toolbox.DecoySetEvaluation, natoms : int) -> NoneType set_weights(...) from builtins.PyCapsule set_weights(self : rosetta.protocols.toolbox.DecoySetEvaluation, weights : ObjexxFCL::FArray1<double>) -> NoneType superimpose(...) from builtins.PyCapsule superimpose(*args, **kwargs) Overloaded function.   1. superimpose(rosetta.protocols.toolbox.DecoySetEvaluation) -> NoneType   2. superimpose(self : rosetta.protocols.toolbox.DecoySetEvaluation, icenter : int) -> NoneType wRMSD(...) from builtins.PyCapsule wRMSD(self : rosetta.protocols.toolbox.DecoySetEvaluation, sigma2 : float, tolerance : float, weights : ObjexxFCL::FArray1<double>) -> int   class DistanceResidueNetwork(ResidueNetwork)     Creates networks based on residue proximity in space     Method resolution order: DistanceResidueNetwork ResidueNetwork builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.toolbox.DistanceResidueNetwork,  : rosetta.protocols.toolbox.DistanceResidueNetwork) -> rosetta.protocols.toolbox.DistanceResidueNetwork generate_edges(...) from builtins.PyCapsule generate_edges(self : rosetta.protocols.toolbox.DistanceResidueNetwork, pose : rosetta.core.pose.Pose) -> NoneType Methods inherited from ResidueNetwork: average_shortest_path_length(...) from builtins.PyCapsule average_shortest_path_length(rosetta.protocols.toolbox.ResidueNetwork) -> float   calculates the average shortest path length of the network clear_edges(...) from builtins.PyCapsule clear_edges(rosetta.protocols.toolbox.ResidueNetwork) -> NoneType   empties edges connectivity_index(...) from builtins.PyCapsule connectivity_index(self : rosetta.protocols.toolbox.ResidueNetwork, resi : int) -> float   calculates the connectivity index of residue resi in the context of the network create_from_pose(...) from builtins.PyCapsule create_from_pose(self : rosetta.protocols.toolbox.ResidueNetwork, pose : rosetta.core.pose.Pose) -> NoneType   create a network from a pose dijkstras(...) from builtins.PyCapsule dijkstras(self : rosetta.protocols.toolbox.ResidueNetwork, resi : int) -> NoneType   run Dijkstra's shortest path algorithm on the given list of nodes  after execution, the "distanceFromStart" variable of each node will contain the distance from residue resi nodes(...) from builtins.PyCapsule nodes(rosetta.protocols.toolbox.ResidueNetwork) -> rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_std_allocator_std_shared_ptr_protocols_toolbox_Node_t   class DummyClass(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle,  : int) -> NoneType   3. __init__(handle, rosetta.protocols.toolbox.DummyClass) -> 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.toolbox.DummyClass,  : rosetta.protocols.toolbox.DummyClass) -> rosetta.protocols.toolbox.DummyClass clone(...) from builtins.PyCapsule clone(rosetta.protocols.toolbox.DummyClass) -> rosetta.protocols.toolbox.DummyClass create(...) from builtins.PyCapsule create() -> rosetta.protocols.toolbox.DummyClass test(...) from builtins.PyCapsule test(rosetta.protocols.toolbox.DummyClass) -> NoneType   class EnergyLandscapeEvaluator(builtins.object)     Evaluates a set of score/rms points     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.toolbox.EnergyLandscapeEvaluator) -> 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.toolbox.EnergyLandscapeEvaluator,  : rosetta.protocols.toolbox.EnergyLandscapeEvaluator) -> rosetta.protocols.toolbox.EnergyLandscapeEvaluator clone(...) from builtins.PyCapsule clone(rosetta.protocols.toolbox.EnergyLandscapeEvaluator) -> rosetta.protocols.toolbox.EnergyLandscapeEvaluator compute(...) from builtins.PyCapsule compute(self : rosetta.protocols.toolbox.EnergyLandscapeEvaluator, points : rosetta.protocols.toolbox.ScoreRmsPoints) -> float   class GreedyKCenter(KCluster)     Greedy K-Center Clustering Algorithm     "A Fast Geometric Clustering Method on Conformation Space of Biomolecules" Jian Sun, Yuan Yao, Xuhui Huang, Vijay Pande, Gunnar Carlsson, Leonidas J. Guibas     Method resolution order: GreedyKCenter KCluster builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(*args, **kwargs) Overloaded function.   1. assign(self : rosetta.protocols.toolbox.GreedyKCenter,  : rosetta.protocols.toolbox.KClusterElement,  : rosetta.protocols.toolbox.KClusterData) -> float   2. assign(self : rosetta.protocols.toolbox.GreedyKCenter,  : rosetta.protocols.toolbox.GreedyKCenter) -> rosetta.protocols.toolbox.GreedyKCenter get_threshold(...) from builtins.PyCapsule get_threshold(rosetta.protocols.toolbox.GreedyKCenter) -> float init(...) from builtins.PyCapsule init(*args, **kwargs) Overloaded function.   1. init(self : rosetta.protocols.toolbox.GreedyKCenter,  : rosetta.protocols.toolbox.KClusterElement) -> NoneType   2. init(self : rosetta.protocols.toolbox.GreedyKCenter,  : rosetta.protocols.toolbox.KClusterElement, first : int) -> NoneType set_threshold(...) from builtins.PyCapsule set_threshold(self : rosetta.protocols.toolbox.GreedyKCenter,  : float) -> NoneType update(...) from builtins.PyCapsule update(self : rosetta.protocols.toolbox.GreedyKCenter,  : rosetta.protocols.toolbox.KClusterElement,  : rosetta.protocols.toolbox.KClusterData) -> NoneType whoami(...) from builtins.PyCapsule whoami(rosetta.protocols.toolbox.GreedyKCenter) -> bool Methods inherited from KCluster: cluster(...) from builtins.PyCapsule cluster(*args, **kwargs) Overloaded function.   1. cluster(self : rosetta.protocols.toolbox.KCluster,  : rosetta.protocols.toolbox.KClusterElement,  : rosetta.protocols.toolbox.KClusterData) -> NoneType   2. cluster(self : rosetta.protocols.toolbox.KCluster,  : rosetta.protocols.toolbox.KClusterElement,  : rosetta.protocols.toolbox.KClusterData, first : int) -> NoneType set_ncluster(...) from builtins.PyCapsule set_ncluster(self : rosetta.protocols.toolbox.KCluster, nc : int) -> NoneType   class IGLigandDesignEdgeUpweighter(rosetta.core.pack.task.IGEdgeReweighter)       Method resolution order: IGLigandDesignEdgeUpweighter rosetta.core.pack.task.IGEdgeReweighter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, weight_factor : float) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. get_edge_reweight(...) from builtins.PyCapsule get_edge_reweight(self : rosetta.protocols.toolbox.IGLigandDesignEdgeUpweighter, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask, res1 : int, res2 : int) -> float   class InteratomicVarianceMatrix(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.toolbox.InteratomicVarianceMatrix, n_atoms : int, ivm : ObjexxFCL::FArray2D<double>) -> NoneType   2. __init__(rosetta.protocols.toolbox.InteratomicVarianceMatrix) -> NoneType   doc   3. __init__(self : rosetta.protocols.toolbox.InteratomicVarianceMatrix, n_atoms : int) -> NoneType   4. __init__(self : rosetta.protocols.toolbox.InteratomicVarianceMatrix,  : rosetta.protocols.toolbox.InteratomicVarianceMatrix) -> 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.toolbox.InteratomicVarianceMatrix,  : rosetta.protocols.toolbox.InteratomicVarianceMatrix) -> rosetta.protocols.toolbox.InteratomicVarianceMatrix init(...) from builtins.PyCapsule init(self : rosetta.protocols.toolbox.InteratomicVarianceMatrix, n_atoms : int, n_decoys : int, coords : rosetta.ObjexxFCL.FArray3_double_t) -> NoneType ivm(...) from builtins.PyCapsule ivm(rosetta.protocols.toolbox.InteratomicVarianceMatrix) -> ObjexxFCL::FArray2D<double> kurtosis(...) from builtins.PyCapsule kurtosis(self : rosetta.protocols.toolbox.InteratomicVarianceMatrix, T : ObjexxFCL::FArray1<double>) -> float n_atoms(...) from builtins.PyCapsule n_atoms(rosetta.protocols.toolbox.InteratomicVarianceMatrix) -> int optimize_kurtosis(...) from builtins.PyCapsule optimize_kurtosis(self : rosetta.protocols.toolbox.InteratomicVarianceMatrix, ngrid : int, lb : float, ub : float) -> NoneType order_parameter(...) from builtins.PyCapsule order_parameter(self : rosetta.protocols.toolbox.InteratomicVarianceMatrix, epsilon : float, T : ObjexxFCL::FArray1<double>) -> NoneType   class KCluster(builtins.object)     basic class for performing a K-style Clustering algorithm     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.toolbox.KCluster) -> NoneType   2. __init__(rosetta.protocols.toolbox.KCluster, rosetta.protocols.toolbox.KCluster) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(*args, **kwargs) Overloaded function.   1. assign(self : rosetta.protocols.toolbox.KCluster,  : rosetta.protocols.toolbox.KClusterElement,  : rosetta.protocols.toolbox.KClusterData) -> float   2. assign(self : rosetta.protocols.toolbox.KCluster,  : rosetta.protocols.toolbox.KCluster) -> rosetta.protocols.toolbox.KCluster cluster(...) from builtins.PyCapsule cluster(*args, **kwargs) Overloaded function.   1. cluster(self : rosetta.protocols.toolbox.KCluster,  : rosetta.protocols.toolbox.KClusterElement,  : rosetta.protocols.toolbox.KClusterData) -> NoneType   2. cluster(self : rosetta.protocols.toolbox.KCluster,  : rosetta.protocols.toolbox.KClusterElement,  : rosetta.protocols.toolbox.KClusterData, first : int) -> NoneType get_threshold(...) from builtins.PyCapsule get_threshold(rosetta.protocols.toolbox.KCluster) -> float init(...) from builtins.PyCapsule init(*args, **kwargs) Overloaded function.   1. init(self : rosetta.protocols.toolbox.KCluster,  : rosetta.protocols.toolbox.KClusterElement) -> NoneType   2. init(self : rosetta.protocols.toolbox.KCluster,  : rosetta.protocols.toolbox.KClusterElement, first : int) -> NoneType set_ncluster(...) from builtins.PyCapsule set_ncluster(self : rosetta.protocols.toolbox.KCluster, nc : int) -> NoneType set_threshold(...) from builtins.PyCapsule set_threshold(self : rosetta.protocols.toolbox.KCluster,  : float) -> NoneType update(...) from builtins.PyCapsule update(self : rosetta.protocols.toolbox.KCluster,  : rosetta.protocols.toolbox.KClusterElement,  : rosetta.protocols.toolbox.KClusterData) -> NoneType whoami(...) from builtins.PyCapsule whoami(rosetta.protocols.toolbox.KCluster) -> bool   class KClusterData(builtins.object)     database of a K-style Clustering algorithm     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.toolbox.KClusterData) -> NoneType   2. __init__(self : rosetta.protocols.toolbox.KClusterData,  : rosetta.protocols.toolbox.KClusterData) -> 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.toolbox.KClusterData,  : rosetta.protocols.toolbox.KClusterData) -> rosetta.protocols.toolbox.KClusterData coords(...) from builtins.PyCapsule coords(rosetta.protocols.toolbox.KClusterData) -> ObjexxFCL::FArray3P<double> dist_square(...) from builtins.PyCapsule dist_square(*args, **kwargs) Overloaded function.   1. dist_square(self : rosetta.protocols.toolbox.KClusterData,  : rosetta.ObjexxFCL.FArray2_double_t,  : rosetta.ObjexxFCL.FArray2_double_t) -> float   2. dist_square(self : rosetta.protocols.toolbox.KClusterData,  : int,  : int) -> float get_natom(...) from builtins.PyCapsule get_natom(rosetta.protocols.toolbox.KClusterData) -> int get_ndata(...) from builtins.PyCapsule get_ndata(rosetta.protocols.toolbox.KClusterData) -> int get_tag(...) from builtins.PyCapsule get_tag(self : rosetta.protocols.toolbox.KClusterData, i : int) -> str load_silent_file(...) from builtins.PyCapsule load_silent_file(self : rosetta.protocols.toolbox.KClusterData,  : str,  : int) -> NoneType load_silent_files(...) from builtins.PyCapsule load_silent_files(rosetta.protocols.toolbox.KClusterData) -> NoneType mark_tags(...) from builtins.PyCapsule mark_tags(self : rosetta.protocols.toolbox.KClusterData,  : rosetta.protocols.toolbox.KClusterElement,  : str) -> NoneType save_all_in_one(...) from builtins.PyCapsule save_all_in_one(rosetta.protocols.toolbox.KClusterData) -> NoneType save_cluster_tree(...) from builtins.PyCapsule save_cluster_tree(rosetta.protocols.toolbox.KClusterData) -> NoneType show_cluster_assignments(...) from builtins.PyCapsule show_cluster_assignments(rosetta.protocols.toolbox.KClusterData) -> NoneType source_filename(...) from builtins.PyCapsule source_filename(self : rosetta.protocols.toolbox.KClusterData, i : int) -> str   class KClusterElement(builtins.object)     /////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.toolbox.KClusterElement) -> NoneType   2. __init__(self : rosetta.protocols.toolbox.KClusterElement, nd : int) -> NoneType   3. __init__(self : rosetta.protocols.toolbox.KClusterElement,  : rosetta.protocols.toolbox.KClusterElement) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_new_cluster(...) from builtins.PyCapsule add_new_cluster(self : rosetta.protocols.toolbox.KClusterElement, ndx_data : int) -> NoneType   add a new cluster center's data_ndx add_new_data(...) from builtins.PyCapsule add_new_data(self : rosetta.protocols.toolbox.KClusterElement, ndx_data : int) -> NoneType   add a new struture ndx to the data_ndx_ assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.toolbox.KClusterElement,  : rosetta.protocols.toolbox.KClusterElement) -> rosetta.protocols.toolbox.KClusterElement assign_type_data(...) from builtins.PyCapsule assign_type_data(self : rosetta.protocols.toolbox.KClusterElement,  : int,  : int,  : float) -> NoneType   assign a data into a cluster check(...) from builtins.PyCapsule check(rosetta.protocols.toolbox.KClusterElement) -> NoneType   check the list, close edit mode clear(...) from builtins.PyCapsule clear(rosetta.protocols.toolbox.KClusterElement) -> NoneType   clean the subcluster's list, open edit mode clear_data(...) from builtins.PyCapsule clear_data(rosetta.protocols.toolbox.KClusterElement) -> NoneType   clean the data list get_center_ndx(...) from builtins.PyCapsule get_center_ndx(self : rosetta.protocols.toolbox.KClusterElement, ndx_cluster : int) -> int   return cluster center's data_ndx get_cur_ncluster(...) from builtins.PyCapsule get_cur_ncluster(rosetta.protocols.toolbox.KClusterElement) -> int   return current cluster number get_data_ndx(...) from builtins.PyCapsule get_data_ndx(self : rosetta.protocols.toolbox.KClusterElement, ndx_data : int) -> int   return current data number get_distance(...) from builtins.PyCapsule get_distance(self : rosetta.protocols.toolbox.KClusterElement, ndx_data : int) -> float   return distance between data and center get_max_dist_ndx(...) from builtins.PyCapsule get_max_dist_ndx(rosetta.protocols.toolbox.KClusterElement) -> int get_max_distance(...) from builtins.PyCapsule get_max_distance(rosetta.protocols.toolbox.KClusterElement) -> float get_ndata(...) from builtins.PyCapsule get_ndata(rosetta.protocols.toolbox.KClusterElement) -> int   return current data number get_ndx_list(...) from builtins.PyCapsule get_ndx_list(*args, **kwargs) Overloaded function.   1. get_ndx_list(rosetta.protocols.toolbox.KClusterElement) -> rosetta.utility.vector1_unsigned_long   return the data ndx list of this cluster   2. get_ndx_list(self : rosetta.protocols.toolbox.KClusterElement, c : int) -> rosetta.utility.vector1_unsigned_long   return the ndx list of sub-cluster get_subcluster(...) from builtins.PyCapsule get_subcluster(self : rosetta.protocols.toolbox.KClusterElement, nc : int) -> rosetta.protocols.toolbox.KClusterElement   return the subcluster get_type(...) from builtins.PyCapsule get_type(self : rosetta.protocols.toolbox.KClusterElement, ndx_data : int) -> int   return data's type(local cluster index) ncluster(...) from builtins.PyCapsule ncluster(rosetta.protocols.toolbox.KClusterElement) -> int set_cluster(...) from builtins.PyCapsule set_cluster(self : rosetta.protocols.toolbox.KClusterElement, ndx_cluster : int, ndx_data : int) -> NoneType   set a cluster center's data_ndx   class KMedoid(KCluster)     Typical K-Medoids Clustering Algorithm     Method resolution order: KMedoid KCluster builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(*args, **kwargs) Overloaded function.   1. assign(self : rosetta.protocols.toolbox.KMedoid,  : rosetta.protocols.toolbox.KClusterElement,  : rosetta.protocols.toolbox.KClusterData) -> float   2. assign(self : rosetta.protocols.toolbox.KMedoid,  : rosetta.protocols.toolbox.KMedoid) -> rosetta.protocols.toolbox.KMedoid get_threshold(...) from builtins.PyCapsule get_threshold(rosetta.protocols.toolbox.KMedoid) -> float init(...) from builtins.PyCapsule init(*args, **kwargs) Overloaded function.   1. init(self : rosetta.protocols.toolbox.KMedoid,  : rosetta.protocols.toolbox.KClusterElement) -> NoneType   2. init(self : rosetta.protocols.toolbox.KMedoid,  : rosetta.protocols.toolbox.KClusterElement, first : int) -> NoneType set_threshold(...) from builtins.PyCapsule set_threshold(self : rosetta.protocols.toolbox.KMedoid,  : float) -> NoneType update(...) from builtins.PyCapsule update(self : rosetta.protocols.toolbox.KMedoid,  : rosetta.protocols.toolbox.KClusterElement,  : rosetta.protocols.toolbox.KClusterData) -> NoneType whoami(...) from builtins.PyCapsule whoami(rosetta.protocols.toolbox.KMedoid) -> bool Methods inherited from KCluster: cluster(...) from builtins.PyCapsule cluster(*args, **kwargs) Overloaded function.   1. cluster(self : rosetta.protocols.toolbox.KCluster,  : rosetta.protocols.toolbox.KClusterElement,  : rosetta.protocols.toolbox.KClusterData) -> NoneType   2. cluster(self : rosetta.protocols.toolbox.KCluster,  : rosetta.protocols.toolbox.KClusterElement,  : rosetta.protocols.toolbox.KClusterData, first : int) -> NoneType set_ncluster(...) from builtins.PyCapsule set_ncluster(self : rosetta.protocols.toolbox.KCluster, nc : int) -> NoneType   class MulliganPNearEvaluator(EnergyLandscapeEvaluator)     Evaluates a set of score/rms points using Vikram's pnear method   PNear = SUM( e^(rms^2/lambda^2)*e^(-(score-bg_score)/temperature) ) / SUM( e^( -(score-bg_score)/temperature ) )     Method resolution order: MulliganPNearEvaluator EnergyLandscapeEvaluator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, temperature : float, lambda : float) -> 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.toolbox.MulliganPNearEvaluator,  : rosetta.protocols.toolbox.MulliganPNearEvaluator) -> rosetta.protocols.toolbox.MulliganPNearEvaluator clone(...) from builtins.PyCapsule clone(rosetta.protocols.toolbox.MulliganPNearEvaluator) -> rosetta.protocols.toolbox.EnergyLandscapeEvaluator compute(...) from builtins.PyCapsule compute(self : rosetta.protocols.toolbox.MulliganPNearEvaluator, points : rosetta.protocols.toolbox.ScoreRmsPoints) -> float   class Node(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.toolbox.Node, id : str, resi : int) -> NoneType   2. __init__(self : rosetta.protocols.toolbox.Node,  : rosetta.protocols.toolbox.Node) -> 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.toolbox.Node,  : rosetta.protocols.toolbox.Node) -> rosetta.protocols.toolbox.Node Data descriptors defined here: distanceFromStart id in_list neighbors resi   class ResidueGroupIGEdgeUpweighter(rosetta.core.pack.task.IGEdgeReweighter)       Method resolution order: ResidueGroupIGEdgeUpweighter rosetta.core.pack.task.IGEdgeReweighter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, weight_factor : float, group1_in : rosetta.utility.vector1_unsigned_long, group2_in : rosetta.utility.vector1_unsigned_long) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. get_edge_reweight(...) from builtins.PyCapsule get_edge_reweight(self : rosetta.protocols.toolbox.ResidueGroupIGEdgeUpweighter,  : rosetta.core.pose.Pose,  : rosetta.core.pack.task.PackerTask, res1 : int, res2 : int) -> float   class ResidueNetwork(builtins.object)     residuenetwork base class     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.toolbox.ResidueNetwork) -> NoneType   2. __init__(rosetta.protocols.toolbox.ResidueNetwork, rosetta.protocols.toolbox.ResidueNetwork) -> 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.toolbox.ResidueNetwork,  : rosetta.protocols.toolbox.ResidueNetwork) -> rosetta.protocols.toolbox.ResidueNetwork average_shortest_path_length(...) from builtins.PyCapsule average_shortest_path_length(rosetta.protocols.toolbox.ResidueNetwork) -> float   calculates the average shortest path length of the network clear_edges(...) from builtins.PyCapsule clear_edges(rosetta.protocols.toolbox.ResidueNetwork) -> NoneType   empties edges connectivity_index(...) from builtins.PyCapsule connectivity_index(self : rosetta.protocols.toolbox.ResidueNetwork, resi : int) -> float   calculates the connectivity index of residue resi in the context of the network create_from_pose(...) from builtins.PyCapsule create_from_pose(self : rosetta.protocols.toolbox.ResidueNetwork, pose : rosetta.core.pose.Pose) -> NoneType   create a network from a pose dijkstras(...) from builtins.PyCapsule dijkstras(self : rosetta.protocols.toolbox.ResidueNetwork, resi : int) -> NoneType   run Dijkstra's shortest path algorithm on the given list of nodes  after execution, the "distanceFromStart" variable of each node will contain the distance from residue resi generate_edges(...) from builtins.PyCapsule generate_edges(self : rosetta.protocols.toolbox.ResidueNetwork, pose : rosetta.core.pose.Pose) -> NoneType   generate a list of edges from the pose -- MUST be reimplemented for each type of network nodes(...) from builtins.PyCapsule nodes(rosetta.protocols.toolbox.ResidueNetwork) -> rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_std_allocator_std_shared_ptr_protocols_toolbox_Node_t   class RotamerBoltzmannWeightEvaluator(EnergyLandscapeEvaluator)     Evaluates a set of score/rms points using the RotamerBoltzmann original method     Method resolution order: RotamerBoltzmannWeightEvaluator EnergyLandscapeEvaluator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, temperature : float, include_bg_point_in_sum : bool) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator,  : rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator) -> rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator clone(...) from builtins.PyCapsule clone(rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator) -> rosetta.protocols.toolbox.EnergyLandscapeEvaluator compute(...) from builtins.PyCapsule compute(self : rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator, points : rosetta.protocols.toolbox.ScoreRmsPoints) -> float   class SF_Replica(builtins.object)       Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.protocols.toolbox.SF_Replica, pose : rosetta.core.pose.Pose) -> float __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.toolbox.SF_Replica) -> 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.toolbox.SF_Replica,  : rosetta.protocols.toolbox.SF_Replica) -> rosetta.protocols.toolbox.SF_Replica clone(...) from builtins.PyCapsule clone(rosetta.protocols.toolbox.SF_Replica) -> rosetta.protocols.toolbox.SF_Replica   class ScoreRmsPoint(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.toolbox.ScoreRmsPoint, score_val : float, rms_val : float) -> NoneType   2. __init__(self : rosetta.protocols.toolbox.ScoreRmsPoint,  : rosetta.protocols.toolbox.ScoreRmsPoint) -> 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.toolbox.ScoreRmsPoint) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.toolbox.ScoreRmsPoint,  : rosetta.protocols.toolbox.ScoreRmsPoint) -> rosetta.protocols.toolbox.ScoreRmsPoint rms(...) from builtins.PyCapsule rms(rosetta.protocols.toolbox.ScoreRmsPoint) -> float score(...) from builtins.PyCapsule score(rosetta.protocols.toolbox.ScoreRmsPoint) -> float   class ScoreRmsPoints(rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint)       Method resolution order: ScoreRmsPoints rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.protocols.toolbox.ScoreRmsPoints, bg_point : rosetta.protocols.toolbox.ScoreRmsPoint) -> 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.toolbox.ScoreRmsPoints,  : rosetta.protocols.toolbox.ScoreRmsPoints) -> rosetta.protocols.toolbox.ScoreRmsPoints bg(...) from builtins.PyCapsule bg(rosetta.protocols.toolbox.ScoreRmsPoints) -> rosetta.protocols.toolbox.ScoreRmsPoint Methods inherited from rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint: __bool__(...) from builtins.PyCapsule __bool__(rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint) -> bool   Check whether the list is nonempty __getitem__(...) from builtins.PyCapsule __getitem__(rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint, int) -> protocols::toolbox::ScoreRmsPoint __iter__(...) from builtins.PyCapsule __iter__(rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint) -> iterator __len__(...) from builtins.PyCapsule __len__(rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint) -> int __repr__(...) from builtins.PyCapsule __repr__(rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint) -> str __setitem__(...) from builtins.PyCapsule __setitem__(rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint, int, protocols::toolbox::ScoreRmsPoint) -> NoneType append(...) from builtins.PyCapsule append(rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint, protocols::toolbox::ScoreRmsPoint) -> NoneType   adds an element to the end back(...) from builtins.PyCapsule back(rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint) -> protocols::toolbox::ScoreRmsPoint   access the last element capacity(...) from builtins.PyCapsule capacity(std::vector<protocols::toolbox::ScoreRmsPoint, std::allocator<protocols::toolbox::ScoreRmsPoint> >) -> int   returns the number of elements that can be held in currently allocated storage clear(...) from builtins.PyCapsule clear(std::vector<protocols::toolbox::ScoreRmsPoint, std::allocator<protocols::toolbox::ScoreRmsPoint> >) -> NoneType   clears the contents erase(...) from builtins.PyCapsule erase(rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint, int) -> NoneType   erases element at index extend = _vector_extend_func(vec, othervec) # Vector compatibility: Adding 'extend' to all utility.vector* functions front(...) from builtins.PyCapsule front(rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint) -> protocols::toolbox::ScoreRmsPoint   access the first element l(...) from builtins.PyCapsule l(rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint) -> int   lower index max_size(...) from builtins.PyCapsule max_size(std::vector<protocols::toolbox::ScoreRmsPoint, std::allocator<protocols::toolbox::ScoreRmsPoint> >) -> int   returns the maximum possible number of elements pop(...) from builtins.PyCapsule pop(*args, **kwargs) Overloaded function.   1. pop(rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint) -> protocols::toolbox::ScoreRmsPoint   remove and return last item   2. pop(rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint, int) -> protocols::toolbox::ScoreRmsPoint   remove and return item at index reserve(...) from builtins.PyCapsule reserve(std::vector<protocols::toolbox::ScoreRmsPoint, std::allocator<protocols::toolbox::ScoreRmsPoint> >, int) -> NoneType   reserves storage shrink_to_fit(...) from builtins.PyCapsule shrink_to_fit(std::vector<protocols::toolbox::ScoreRmsPoint, std::allocator<protocols::toolbox::ScoreRmsPoint> >) -> NoneType   reduces memory usage by freeing unused memory u(...) from builtins.PyCapsule u(rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint) -> int   upper index

Functions
		AdjacentRemainingNodes(...) method of builtins.PyCapsule instance AdjacentRemainingNodes(node : protocols::toolbox::Node) -> rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_std_allocator_std_shared_ptr_protocols_toolbox_Node_t CA_superimpose(...) method of builtins.PyCapsule instance CA_superimpose(*args, **kwargs) Overloaded function.   1. CA_superimpose(weights : ObjexxFCL::FArray1<double>, ref_pose : rosetta.core.pose.Pose, fit_pose : rosetta.core.pose.Pose) -> NoneType   2. CA_superimpose(ref_pose : rosetta.core.pose.Pose, fit_pose : rosetta.core.pose.Pose) -> NoneType Contains(...) method of builtins.PyCapsule instance Contains(nodes : rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_std_allocator_std_shared_ptr_protocols_toolbox_Node_t, node : protocols::toolbox::Node) -> bool ExtractSmallest(...) method of builtins.PyCapsule instance ExtractSmallest(nodes : rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_std_allocator_std_shared_ptr_protocols_toolbox_Node_t) -> protocols::toolbox::Node PyReturnValuePolicyTest_DummyClassCOP(...) method of builtins.PyCapsule instance PyReturnValuePolicyTest_DummyClassCOP() -> rosetta.protocols.toolbox.DummyClass PyReturnValuePolicyTest_DummyClassOP(...) method of builtins.PyCapsule instance PyReturnValuePolicyTest_DummyClassOP() -> rosetta.protocols.toolbox.DummyClass PyReturnValuePolicyTest_PoseCOP(...) method of builtins.PyCapsule instance PyReturnValuePolicyTest_PoseCOP() -> rosetta.core.pose.Pose PyReturnValuePolicyTest_PoseOP(...) method of builtins.PyCapsule instance PyReturnValuePolicyTest_PoseOP() -> rosetta.core.pose.Pose PyReturnValuePolicyTest_SF_ReplicaCOP(...) method of builtins.PyCapsule instance PyReturnValuePolicyTest_SF_ReplicaCOP() -> rosetta.protocols.toolbox.SF_Replica PyReturnValuePolicyTest_SF_ReplicaOP(...) method of builtins.PyCapsule instance PyReturnValuePolicyTest_SF_ReplicaOP() -> rosetta.protocols.toolbox.SF_Replica PyReturnValuePolicyTest_ScoreFunctionCOP(...) method of builtins.PyCapsule instance PyReturnValuePolicyTest_ScoreFunctionCOP() -> rosetta.core.scoring.ScoreFunction PyReturnValuePolicyTest_ScoreFunctionCOP2(...) method of builtins.PyCapsule instance PyReturnValuePolicyTest_ScoreFunctionCOP2() -> rosetta.core.scoring.ScoreFunction PyReturnValuePolicyTest_ScoreFunctionOP(...) method of builtins.PyCapsule instance PyReturnValuePolicyTest_ScoreFunctionOP() -> rosetta.core.scoring.ScoreFunction apply_superposition_transform(...) method of builtins.PyCapsule instance apply_superposition_transform(pose : rosetta.core.pose.Pose, rotation : rosetta.numeric.xyzMatrix_double_t, to_init_center : rosetta.numeric.xyzVector_double_t, to_fit_center : rosetta.numeric.xyzVector_double_t) -> NoneType apply_superposition_transform_to_jump(...) method of builtins.PyCapsule instance apply_superposition_transform_to_jump(pose : rosetta.core.pose.Pose, jump_id : int, rotation : rosetta.numeric.xyzMatrix_double_t, to_init_center : rosetta.numeric.xyzVector_double_t, to_fit_center : rosetta.numeric.xyzVector_double_t) -> NoneType dump_as_pdb(...) method of builtins.PyCapsule instance dump_as_pdb(*args, **kwargs) Overloaded function.   1. dump_as_pdb(filename : str, n : int, coords : rosetta.ObjexxFCL.FArray2_double_t) -> NoneType   write a CA ALA pdb   2. dump_as_pdb(filename : str, n : int, coords : rosetta.ObjexxFCL.FArray2_double_t, transvec : ObjexxFCL::FArray1D<double>) -> NoneType   write a CA ALA pdb file_full_path(...) method of builtins.PyCapsule instance file_full_path( : str) -> str fill_CA_coords(...) method of builtins.PyCapsule instance fill_CA_coords(*args, **kwargs) Overloaded function.   1. fill_CA_coords(pose : rosetta.core.pose.Pose, natoms : int, coords : rosetta.ObjexxFCL.FArray2_double_t) -> NoneType   2. fill_CA_coords(pose : rosetta.core.pose.Pose, coords : rosetta.ObjexxFCL.FArray2_double_t) -> NoneType fit_centered_coords(...) method of builtins.PyCapsule instance fit_centered_coords(natoms : int, weights : ObjexxFCL::FArray1<double>, ref_coords : rosetta.ObjexxFCL.FArray2_double_t, coords : rosetta.ObjexxFCL.FArray2_double_t, R : rosetta.numeric.xyzMatrix_double_t) -> NoneType fix_tag_suffix(...) method of builtins.PyCapsule instance fix_tag_suffix( : str) -> str get_K_cluster_engine(...) method of builtins.PyCapsule instance get_K_cluster_engine( : str) -> rosetta.protocols.toolbox.KCluster reset_x(...) method of builtins.PyCapsule instance reset_x(n : int, x : rosetta.ObjexxFCL.FArray2_double_t, wts : ObjexxFCL::FArray1<double>, transvec : ObjexxFCL::FArray1<double>) -> NoneType superposition_transform(...) method of builtins.PyCapsule instance superposition_transform(*args, **kwargs) Overloaded function.   1. superposition_transform(init_coords : rosetta.utility.vector1_numeric_xyzVector_double_t, ref_coords : rosetta.utility.vector1_numeric_xyzVector_double_t, rotation : rosetta.numeric.xyzMatrix_double_t, to_init_center : rosetta.numeric.xyzVector_double_t, to_fit_center : rosetta.numeric.xyzVector_double_t) -> NoneType   2. superposition_transform(init_coords : rosetta.utility.vector1_numeric_xyzVector_double_t, ref_coords : rosetta.utility.vector1_numeric_xyzVector_double_t, coord_weights : rosetta.utility.vector1_double, rotation : rosetta.numeric.xyzMatrix_double_t, to_init_center : rosetta.numeric.xyzVector_double_t, to_fit_center : rosetta.numeric.xyzVector_double_t) -> NoneType   3. superposition_transform(natoms : int, weights : ObjexxFCL::FArray1<double>, ref_coords : rosetta.ObjexxFCL.FArray2_double_t, coords : rosetta.ObjexxFCL.FArray2_double_t, R : rosetta.numeric.xyzMatrix_double_t, toCenter : rosetta.numeric.xyzVector_double_t, toFitCenter : rosetta.numeric.xyzVector_double_t) -> NoneType