Index – N

N (pyrosetta.rosetta.basic.sampling.orientations.QuatDBMetadata property) (pyrosetta.rosetta.core.chemical.element.Elements attribute) n (pyrosetta.rosetta.core.io.raw_data.DisulfideFile.ResNum property) (pyrosetta.rosetta.core.scoring.fiber_diffraction.Hankel property) (pyrosetta.rosetta.core.scoring.TorsionParams property) N (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum attribute) (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueOrientEntry property) n() (pyrosetta.rosetta.core.energy_methods.FAElecContextData method) N() (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) n() (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) N1_NODE_H (pyrosetta.rosetta.protocols.sparta.ANN property) N1_NODE_I (pyrosetta.rosetta.protocols.sparta.ANN property) N1_NODE_O (pyrosetta.rosetta.protocols.sparta.ANN property) N2_NODE_H (pyrosetta.rosetta.protocols.sparta.ANN property) N2_NODE_I (pyrosetta.rosetta.protocols.sparta.ANN property) N2_NODE_O (pyrosetta.rosetta.protocols.sparta.ANN property) n2c (pyrosetta.rosetta.protocols.rigid.Direction attribute) n8 (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData property) n_acceptor (pyrosetta.rosetta.core.scoring.elec.ElecGroup property) N_ACETYLATION (pyrosetta.rosetta.core.chemical.VariantType attribute) n_active_score_types() (pyrosetta.rosetta.core.scoring.EnergyGraph method) n_anchor() (pyrosetta.rosetta.protocols.sic_dock.Rose method) n_ang_U1D2_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) n_ang_U2D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) n_assigned() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D.Spin method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D.Spin method) n_atom() (pyrosetta.rosetta.core.id.AtomID_Map_AtomID method) (pyrosetta.rosetta.core.id.AtomID_Map_bool method) (pyrosetta.rosetta.core.id.AtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_MP_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_Real method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_NamedAtomID method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) N_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) N_ATOM_PROPERTIES (pyrosetta.rosetta.core.chemical.AtomProperty attribute) n_atoms() (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) (pyrosetta.rosetta.protocols.toolbox.InteratomicVarianceMatrix method) n_atoms_for_restype() (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) n_atomtypes() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) n_attached_waters() (pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo method) (pyrosetta.rosetta.core.scoring.lkball.lkbtrie.LKBAtom method) (pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo method) N_BB_BINS (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t property) n_bin_transition_data() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculator method) n_bins() (pyrosetta.rosetta.numeric.MathNTensor_bool_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_1_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_2_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_4_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_5_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_6_t method) (pyrosetta.rosetta.numeric.MathNTensorBase_bool_t method) (pyrosetta.rosetta.numeric.MathNTensorBase_double_t method) n_bins_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) n_bins_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) n_bonded_neighbor_all_res() (pyrosetta.rosetta.core.conformation.Residue method) n_branches() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) n_build_sets() (pyrosetta.rosetta.protocols.match.upstream.ProteinUpstreamBuilder method) n_ca() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) n_ca_bond() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) n_ca_c() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) n_ca_c_angle() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) n_cacheable_types (pyrosetta.rosetta.core.conformation.residue_datacache.ResidueDataCacheIndex attribute) n_candidates_ (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker property) n_carbons() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) n_chain_directions (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ChainDirection attribute) n_children() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) n_ci_2b_score_types (pyrosetta.rosetta.core.scoring.ScoreType attribute) n_clusters_from_last_run() (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringProtocol method) n_collision_check_atoms() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) n_columns() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) n_connected_residues() (pyrosetta.rosetta.core.scoring.etable.etrie.CountPairDataGeneric method) n_connection_pairs() (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParam method) n_connpoints_for_entry() (pyrosetta.rosetta.core.scoring.trie.CPDataCorrespondence method) n_correctly_aligned_positions() (in module pyrosetta.rosetta.core.sequence) n_current_residue_connections() (pyrosetta.rosetta.core.conformation.Residue method) n_cut (pyrosetta.rosetta.core.scoring.TMscoreStore property) n_cycle() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) n_cycles() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) n_daemon_set_messages (pyrosetta.rosetta.protocols.pack_daemon.DaemonSetMessage attribute) n_decoys() (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) n_decoys_max() (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) n_default_value() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) n_dependencies() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) n_deriv_check_results() (pyrosetta.rosetta.core.optimization.NumericalDerivCheckResult method) n_derivs() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_float_t method) n_derivs_ (pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_5_t property) n_designed() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) n_dis_U1D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) n_disjoint_sets() (pyrosetta.rosetta.utility.graph.DisjointSets method) n_dof() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) n_dof_nodes() (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) n_dof_temp() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) n_donor (pyrosetta.rosetta.core.scoring.elec.ElecGroup property) n_dump() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) n_elements() (pyrosetta.rosetta.core.chemical.ElementSet method) n_energy_method_types (pyrosetta.rosetta.core.scoring.methods.EnergyMethodType attribute) n_energy_methods (pyrosetta.rosetta.core.scoring.methods.EnergyMethods attribute) n_entries() (pyrosetta.rosetta.core.scoring.trie.CPDataCorrespondence method) n_external_samplers() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) n_external_transforms (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalTransform attribute) n_flex (pyrosetta.rosetta.protocols.fold_from_loops.utils.NubSegment property) n_fold_types (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) N_FORMYLATION (pyrosetta.rosetta.core.chemical.VariantType attribute) n_fragment_eval() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) n_fragment_gen() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) n_frags_ (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker property) n_GDT05 (pyrosetta.rosetta.core.scoring.TMscoreStore property) n_GDT05_max (pyrosetta.rosetta.core.scoring.TMscoreStore property) n_GDT1 (pyrosetta.rosetta.core.scoring.TMscoreStore property) n_GDT1_max (pyrosetta.rosetta.core.scoring.TMscoreStore property) n_GDT2 (pyrosetta.rosetta.core.scoring.TMscoreStore property) n_GDT2_max (pyrosetta.rosetta.core.scoring.TMscoreStore property) n_GDT4 (pyrosetta.rosetta.core.scoring.TMscoreStore property) n_GDT4_max (pyrosetta.rosetta.core.scoring.TMscoreStore property) n_GDT8 (pyrosetta.rosetta.core.scoring.TMscoreStore property) n_GDT8_max (pyrosetta.rosetta.core.scoring.TMscoreStore property) n_geometric_constraints() (pyrosetta.rosetta.protocols.match.Matcher method) n_hb_atoms (pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond attribute) n_hbond_acceptors() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) n_hbond_donors() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) n_hbonds() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) n_helices() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) n_input_sources() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.standard.StandardInnerLarvalJob method) n_kept_matches() (pyrosetta.rosetta.protocols.match.output.BestMatchesCollection method) n_key() (pyrosetta.rosetta.utility.keys.AutoKey_utility_options_Option_utility_keys_Key_utility_keys_NoClient_t static method) (pyrosetta.rosetta.utility.keys.KeyLookup_utility_options_OptionKey_t static method) (pyrosetta.rosetta.utility.options.AnyOptionKey static method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey static method) (pyrosetta.rosetta.utility.options.BooleanOptionKey static method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey static method) (pyrosetta.rosetta.utility.options.FileOptionKey static method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey static method) (pyrosetta.rosetta.utility.options.IntegerOptionKey static method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey static method) (pyrosetta.rosetta.utility.options.OptionKey static method) (pyrosetta.rosetta.utility.options.PathOptionKey static method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey static method) (pyrosetta.rosetta.utility.options.RealOptionKey static method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey static method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey static method) (pyrosetta.rosetta.utility.options.ScalarOptionKey static method) (pyrosetta.rosetta.utility.options.StringOptionKey static method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey static method) (pyrosetta.rosetta.utility.options.VectorOptionKey static method) n_ligand_rots() (pyrosetta.rosetta.protocols.simple_moves.WaterRotsDB method) n_ligandchis() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) N_LINK_TYPES (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType attribute) n_linked_basic_enhanced (pyrosetta.rosetta.protocols.carbohydrates.GlycanSequon attribute) n_linked_best_enhanced (pyrosetta.rosetta.protocols.carbohydrates.GlycanSequon attribute) N_LINKED_GLYCOSYLATION (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes attribute) n_linked_typical (pyrosetta.rosetta.protocols.carbohydrates.GlycanSequon attribute) n_long_range_types (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) n_loops() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) n_lower() (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) n_mainchain_atoms() (pyrosetta.rosetta.core.conformation.Residue method) n_mainchain_torsions_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) n_mainchain_torsions_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) N_METHYLATED (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) N_METHYLATION (pyrosetta.rosetta.core.chemical.VariantType attribute) n_min_pair_data (pyrosetta.rosetta.core.scoring.min_pair_data attribute) n_min_single_data (pyrosetta.rosetta.core.scoring.min_single_data attribute) n_mode() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams method) N_MODES (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMoverMode attribute) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes attribute) n_mutants() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver method) n_mutations() (pyrosetta.rosetta.protocols.pmut_scan.Mutant method) n_nodes() (pyrosetta.rosetta.utility.graph.DisjointSets method) n_non_polymeric_residue_connections() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) n_nonchitip_atoms_for_chi() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) n_nonjump_children() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) n_npd_properties() (pyrosetta.rosetta.protocols.pack_daemon.DaemonSet method) n_nucleotide_mut_trials_corrected() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) n_nus() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) n_omega() (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) N_OMEGA_PREFERENCE_TYPES (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType attribute) n_optE_data_types (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType attribute) n_orbitals() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.conformation.Residue method) N_p_sp2 (pyrosetta.rosetta.core.chemical.orbitals.orbital_type_enum attribute) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics attribute) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics.orbital_type_name attribute) n_parameters() (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) n_parameters_sets() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) n_part() (pyrosetta.rosetta.utility.options.OptionCollection static method) n_part_prefix_match() (pyrosetta.rosetta.utility.options.OptionCollection static method) n_pdbs_ (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) n_phi_bins() (pyrosetta.rosetta.core.scoring.Ramachandran method) (pyrosetta.rosetta.core.scoring.Ramachandran2B method) n_phore_match() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo method) N_pi_sp2 (pyrosetta.rosetta.core.chemical.orbitals.orbital_type_enum attribute) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics attribute) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics.orbital_type_name attribute) n_polymeric_residue_connections() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) N_pos() (pyrosetta.rosetta.protocols.match.upstream.OriginalBackboneBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.ProteinBackboneBuildPoint method) n_possible_hits_per_at3frame() (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) n_possible_hits_per_upstream_conformation() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) n_possible_residue_connections() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParam method) n_ppo_torsion_bins (pyrosetta.rosetta.core.conformation.ppo_torsion_bin attribute) n_predecessors_w_outstanding_jobs() (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) n_primary_outputs (pyrosetta.rosetta.protocols.jd3.JobOutputIndex property) n_probe_radii (pyrosetta.rosetta.protocols.match.ProbeRadius attribute) n_prof_tags (pyrosetta.rosetta.basic.ProfTag attribute) N_PROPERTIES (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) n_property_sets() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) n_protein_rots() (pyrosetta.rosetta.protocols.simple_moves.WaterRotsDB method) n_proton_chi() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) n_protons() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) n_psi_bins() (pyrosetta.rosetta.core.scoring.Ramachandran method) (pyrosetta.rosetta.core.scoring.Ramachandran2B method) n_pssms() (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) n_real_dofs() (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) n_rebuild_tries() (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) N_RECORD_TYPES (pyrosetta.rosetta.core.io.pdb.RecordType attribute) n_reference_pose() (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) n_rerelaxed() (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) n_res_eq (pyrosetta.rosetta.core.simple_metrics.metrics.summary_type attribute) n_res_gt (pyrosetta.rosetta.core.simple_metrics.metrics.summary_type attribute) n_res_gt_or_eq (pyrosetta.rosetta.core.simple_metrics.metrics.summary_type attribute) n_res_lt (pyrosetta.rosetta.core.simple_metrics.metrics.summary_type attribute) n_res_lt_or_eq (pyrosetta.rosetta.core.simple_metrics.metrics.summary_type attribute) n_res_ne (pyrosetta.rosetta.core.simple_metrics.metrics.summary_type attribute) n_residue() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.id.AtomID_Map_AtomID method) (pyrosetta.rosetta.core.id.AtomID_Map_bool method) (pyrosetta.rosetta.core.id.AtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_MP_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_Real method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_NamedAtomID method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) n_residue_connections_for_atom() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) n_residues() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) n_residues_after_cutpoint() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) n_residues_before_cutpoint() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) n_residues_for_entity() (pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence method) n_resources_declared() (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) n_resources_in_memory() (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) n_restypes() (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) n_restypes_to_build() (pyrosetta.rosetta.protocols.match.upstream.ProteinUpstreamBuilder method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamBuilder method) n_ring_carbons() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) n_ring_conformer_sets() (pyrosetta.rosetta.core.chemical.ResidueType method) n_rings() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) n_rotamer_bins() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) n_rotamer_bins_for_aa() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary static method) n_rotamer_bins_for_aa_02() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary static method) n_rotameric_bins_for_aa() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t static method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary static method) n_rotamers_for_restype() (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) n_rots_total() (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) n_rounds() (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) n_rows() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) n_sample() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) n_sample_rotamers() (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets method) n_samples_per_chi() (pyrosetta.rosetta.protocols.match.upstream.FullChiSampleSet method) n_samples_per_side_of_nrchi_bin() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) n_samples_wi_sd_range() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) n_score_types (pyrosetta.rosetta.core.scoring.ScoreType attribute) n_scores() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) n_secondary_outputs (pyrosetta.rosetta.protocols.jd3.JobOutputIndex property) n_secondary_structure_types (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SecondaryStructureType attribute) n_segment() (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) n_seqs() (pyrosetta.rosetta.core.sequence.CompositeSequence method) n_sequence_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) n_shortranged_2b_score_types (pyrosetta.rosetta.core.scoring.ScoreType attribute) n_ss_types (pyrosetta.rosetta.protocols.comparative_modeling.features.SSType attribute) n_steps_passed_in_previous_run() (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) n_svms() (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) n_tables() (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) n_task_operations() (pyrosetta.rosetta.core.pack.task.TaskFactory method) n_temp_levels() (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) n_term_pose (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover.Design property) n_term_stack (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover.Design property) n_terminal_constraint_strength() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) N_terminal_count() (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) n_terminus_size() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) n_to_gen() (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) n_to_output_per_group() (pyrosetta.rosetta.protocols.match.MatcherTask method) n_to_rerelax() (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) n_top_natives_to_score() (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData method) n_tor_U1D3_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) n_tor_U2D2_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) n_tor_U3D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) n_torsion_bins (pyrosetta.rosetta.protocols.comparative_modeling.features.TorsionBin attribute) n_torsion_sets() (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) n_torsions() (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) n_torsions_total() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) n_trees() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) n_trial_min_stage1_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) n_trial_min_stage2_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) n_trial_min_stage3_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) n_trial_min_stage4_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) n_types() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) n_unassigned() (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) n_unsat_Hpols (pyrosetta.rosetta.protocols.hbnet.DecoratedNetworkState property) n_upper() (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) n_value() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) N_VARIANTS (pyrosetta.rosetta.core.chemical.VariantType attribute) n_virtual_atoms() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.conformation.Residue method) n_Vmin_assignments() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) n_waters() (pyrosetta.rosetta.core.scoring.lkball.WaterBuilderForRestype method) n_waters_for_atom() (pyrosetta.rosetta.core.scoring.lkball.WaterBuilderForRestype method) n_xyz() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) Na (pyrosetta.rosetta.core.chemical.element.Elements attribute) NA (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType attribute) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) na_ade (pyrosetta.rosetta.core.chemical.AA attribute) na_analogue() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.conformation.Residue method) na_cyt (pyrosetta.rosetta.core.chemical.AA attribute) NA_GREEK_DISTANCE (pyrosetta.rosetta.core.chemical.GreekDistance attribute) na_gua (pyrosetta.rosetta.core.chemical.AA attribute) na_lra (pyrosetta.rosetta.core.chemical.AA attribute) na_lrc (pyrosetta.rosetta.core.chemical.AA attribute) na_lrg (pyrosetta.rosetta.core.chemical.AA attribute) na_lur (pyrosetta.rosetta.core.chemical.AA attribute) na_rad (pyrosetta.rosetta.core.chemical.AA attribute) na_rcy (pyrosetta.rosetta.core.chemical.AA attribute) na_rgu (pyrosetta.rosetta.core.chemical.AA attribute) na_thy (pyrosetta.rosetta.core.chemical.AA attribute) na_ura (pyrosetta.rosetta.core.chemical.AA attribute) naccess (pyrosetta.rosetta.core.scoring.sasa.SasaRadii attribute) nactive_residues() (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) NAIVE (pyrosetta.rosetta.core.conformation.Strategy attribute) nali() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) nallocated() (pyrosetta.rosetta.utility.graph.ArrayPool_double_t method) name (pyrosetta.rosetta.basic.citation_manager.CitationFormat property) (pyrosetta.rosetta.basic.citation_manager.CitedModuleType property) (pyrosetta.rosetta.basic.mpi.listener_tags property) (pyrosetta.rosetta.basic.mpi.mpi_tags property) (pyrosetta.rosetta.basic.ProfTag property) (pyrosetta.rosetta.basic.sampling.orientations.QuatDBMetadata property) (pyrosetta.rosetta.basic.thread_manager.RosettaThreadRequestOriginatingLevel property) (pyrosetta.rosetta.basic.TracerPriority property) (pyrosetta.rosetta.core.chemical.AA property) (pyrosetta.rosetta.core.chemical.Ancestor property) (pyrosetta.rosetta.core.chemical.AtomProperty property) (pyrosetta.rosetta.core.chemical.BondAromaticity property) (pyrosetta.rosetta.core.chemical.BondConjugability property) (pyrosetta.rosetta.core.chemical.BondIsometry property) (pyrosetta.rosetta.core.chemical.BondName property) (pyrosetta.rosetta.core.chemical.BondOrder property) (pyrosetta.rosetta.core.chemical.BondRingness property) (pyrosetta.rosetta.core.chemical.ElectronConfiguration.AngularMomentumQuantumNumber property) (pyrosetta.rosetta.core.chemical.ElectronConfiguration.PrincipalQuantumNumber property) (pyrosetta.rosetta.core.chemical.element.Elements property) (pyrosetta.rosetta.core.chemical.Element.Properties property) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.AtomicOrbitalTypes property) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.HybridOrbitalType property) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType property) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties property) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference property) (pyrosetta.rosetta.core.chemical.GreekDistance property) (pyrosetta.rosetta.core.chemical.Hybridization property) (pyrosetta.rosetta.core.chemical.ICoordAtomIDType property) (pyrosetta.rosetta.core.chemical.io.merge_residue_behavior property) (pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus property) (pyrosetta.rosetta.core.chemical.orbitals.orbital_type_enum property) (pyrosetta.rosetta.core.chemical.ResidueProperty property) (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation property) (pyrosetta.rosetta.core.chemical.rings.CPParameter property) (pyrosetta.rosetta.core.chemical.rings.RingSaturationType property) (pyrosetta.rosetta.core.chemical.rna.BaseDoubletOrientation property) (pyrosetta.rosetta.core.chemical.rna.BaseEdge property) (pyrosetta.rosetta.core.chemical.rna.BaseStackWhichSide property) (pyrosetta.rosetta.core.chemical.rna.ChiState property) (pyrosetta.rosetta.core.chemical.rna.LW_BaseDoubletOrientation property) (pyrosetta.rosetta.core.chemical.rna.PuckerState property) (pyrosetta.rosetta.core.chemical.rna.RNA_Torsion property) (pyrosetta.rosetta.core.chemical.TypeSetMode property) (pyrosetta.rosetta.core.chemical.VariantType property) (pyrosetta.rosetta.core.conformation.membrane.MEM property) (pyrosetta.rosetta.core.conformation.membrane.MP_GEOMETRY_TRANSITION property) (pyrosetta.rosetta.core.conformation.membrane.Orientation property) (pyrosetta.rosetta.core.conformation.parametric.ParameterType property) (pyrosetta.rosetta.core.conformation.parametric.RealPerturbationType property) (pyrosetta.rosetta.core.conformation.ppo_torsion_bin property) (pyrosetta.rosetta.core.conformation.residue_datacache.ResidueDataCacheIndex property) (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum property) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent.Tag property) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag property) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag property) (pyrosetta.rosetta.core.conformation.Strategy property) (pyrosetta.rosetta.core.conformation.symmetry.dof_type property) (pyrosetta.rosetta.core.conformation.symmetry.SlideCriteriaType property) (pyrosetta.rosetta.core.conformation.symmetry.SlideType property) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType property) (pyrosetta.rosetta.core.fragment.rna._RNA_MatchType_ property) (pyrosetta.rosetta.core.fragment.rna.SYN_ANTI_RESTRICTION property) (pyrosetta.rosetta.core.id.DOF_Type property) (pyrosetta.rosetta.core.id.MainchainTorsionType property) (pyrosetta.rosetta.core.id.TorsionType property) (pyrosetta.rosetta.core.import_pose.FileType property) (pyrosetta.rosetta.core.io.AtomInformation property) (pyrosetta.rosetta.core.io.HeaderInformation.CompoundToken property) (pyrosetta.rosetta.core.io.mmtf.ExtraDataEnum property) (pyrosetta.rosetta.core.io.pdb.RecordType property) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile.NumberingSystem property) (pyrosetta.rosetta.core.io.rcsb.ExperimentalTechnique property) (pyrosetta.rosetta.core.io.silent.SharedSilentDataType property) (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine property) (pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobianTypeEnum property) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergyRamping property) (pyrosetta.rosetta.core.pack.interaction_graph.ResiduePairEvalType property) (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour property) (pyrosetta.rosetta.core.pack.rotamer_set.BumpSelectorDecision property) (pyrosetta.rosetta.core.pack.task.ExtraRotSample property) (pyrosetta.rosetta.core.pack.task.PackerTaskSymmetryStatus property) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum property) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType property) (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType property) (pyrosetta.rosetta.core.pose.PoseCoordPickMode property) (pyrosetta.rosetta.core.pose.rna.RNA_ReactivityType property) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment property) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo property) (pyrosetta.rosetta.core.pose.rna.StubStubType property) 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(pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.ElementSet method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.MMAtomType method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.modifications.ChemistryBase method) (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.orbitals.OrbitalType method) (pyrosetta.rosetta.core.chemical.orbitals.OrbitalTypeSet method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.RenameAtom method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom method) (pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule method) (pyrosetta.rosetta.core.chemical.Set_AA method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetBaseName method) (pyrosetta.rosetta.core.chemical.SetDisulfideAtomName method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.energy_methods.GoapRsdType method) (pyrosetta.rosetta.core.environment.EnvCore method) (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) (pyrosetta.rosetta.core.io.rna.RDAT method) (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric method) (pyrosetta.rosetta.core.pack.palette.CustomBaseTypePackerPalette method) (pyrosetta.rosetta.core.pack.palette.DefaultPackerPalette method) (pyrosetta.rosetta.core.pack.palette.NCAADefaultPackerPalette method) (pyrosetta.rosetta.core.pack.palette.NoDesignPackerPalette method) (pyrosetta.rosetta.core.pack.palette.PackerPalette method) (pyrosetta.rosetta.core.pack.task.ALLAA static method) (pyrosetta.rosetta.core.pack.task.ALLAAwc static method) (pyrosetta.rosetta.core.pack.task.ALLAAxc static method) (pyrosetta.rosetta.core.pack.task.APOLA static method) (pyrosetta.rosetta.core.pack.task.APOLAR static method) (pyrosetta.rosetta.core.pack.task.AROMATIC static method) (pyrosetta.rosetta.core.pack.task.AUTO static method) (pyrosetta.rosetta.core.pack.task.CHARGED static method) (pyrosetta.rosetta.core.pack.task.EX static method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF static method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER static method) (pyrosetta.rosetta.core.pack.task.NATAA static method) (pyrosetta.rosetta.core.pack.task.NATRO static method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS static method) (pyrosetta.rosetta.core.pack.task.NOTAA static method) (pyrosetta.rosetta.core.pack.task.PIKAA static method) (pyrosetta.rosetta.core.pack.task.PIKNA static method) (pyrosetta.rosetta.core.pack.task.POLAR static method) (pyrosetta.rosetta.core.pack.task.PROPERTY static method) (pyrosetta.rosetta.core.pack.task.SCAN static method) (pyrosetta.rosetta.core.pack.task.TARGET static method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC static method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.hbonds.Polynomial_1d method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.saxs.FormFactor method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.cppdb.result method) (pyrosetta.rosetta.numeric.expression_parser.FunctionToken method) (pyrosetta.rosetta.numeric.expression_parser.VariableExpression method) (pyrosetta.rosetta.numeric.expression_parser.VariableToken method) (pyrosetta.rosetta.numeric.Polynomial_1d method) (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover static method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover static method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover static method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover static method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover static method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover static method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM static method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover static method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover static method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer static method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM static method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM static method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM static method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer static method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM static method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio static method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler static method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly static method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio static method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints static method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler static method) (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper static method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio static method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl static method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst static method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio static method) (pyrosetta.rosetta.protocols.abinitio.Protocol static method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher static method) (pyrosetta.rosetta.protocols.abinitio.Template method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover static method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover static method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover static method) (pyrosetta.rosetta.protocols.analysis.PackStatMover static method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover static method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover static method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover static method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover static method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter static method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol static method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover static method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin static method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop static method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover static method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover static method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover static method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover static method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster static method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol static method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer static method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop static method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert static method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD static method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD static method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp static method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy static method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy static method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel static method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock static method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol static method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler static method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler static method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover static method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover static method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover static method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover static method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover static method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro static method) (pyrosetta.rosetta.protocols.backrub.BackrubMover static method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol static method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover static method) (pyrosetta.rosetta.protocols.buns.BuriedUnsatHbondFilter2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.ConservedPosMutationFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover static method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover static method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover static method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover static method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase static method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy static method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover static method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder static method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController static method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange static method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.Pool_Evaluator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder static method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover static method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering static method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder static method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver static method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover static method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder static method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering static method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController static method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase static method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover static method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver static method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder static method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver static method) (pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy static method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover static method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler static method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover static method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler static method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens static method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover static method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover static method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover static method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover static method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover static method) (pyrosetta.rosetta.protocols.chemistries.Chemistry method) (pyrosetta.rosetta.protocols.chemistries.PatchChemistry method) (pyrosetta.rosetta.protocols.chemistries.WrappedBaseChemistry method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover static method) (pyrosetta.rosetta.protocols.cluster.ClusterBase static method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle static method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop static method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter static method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints static method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple static method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover static method) (pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator method) (pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover static method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover static method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover static method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover static method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover static method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover static method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover static method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover static method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreCutoffFilter method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.constraint_filters.ShowConstraintsFilter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints static method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints static method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover static method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover static method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover static method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover static method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover static method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluator method) (pyrosetta.rosetta.protocols.contact_map.ContactMap static method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol static method) (pyrosetta.rosetta.protocols.cryst.CrystRMS static method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover static method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover static method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover static method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover static method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover static method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover static method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover static method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover static method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover static method) (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover static method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo static method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover static method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign static method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations static method) (pyrosetta.rosetta.protocols.ddg.ddGMover static method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected static method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover static method) (pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign static method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover static method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover static method) (pyrosetta.rosetta.protocols.design_opt.Supercharge static method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA static method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover static method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign static method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker static method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna static method) (pyrosetta.rosetta.protocols.dna_dock.DNAClashCheckFilter method) (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilter method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover static method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol static method) (pyrosetta.rosetta.protocols.docking.DockingHighRes static method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy static method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation static method) (pyrosetta.rosetta.protocols.docking.DockingLowRes static method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble static method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol static method) (pyrosetta.rosetta.protocols.docking.DockingProtocol static method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact static method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle static method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol static method) (pyrosetta.rosetta.protocols.docking.DockMinMover static method) (pyrosetta.rosetta.protocols.docking.DockSetupMover static method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover static method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover static method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact static method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover static method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover static method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover static method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover static method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately static method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover static method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact static method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol static method) (pyrosetta.rosetta.protocols.docking.TemperedDocking static method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints static method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover static method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover static method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer static method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover static method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover static method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover static method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetric method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover static method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover static method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores static method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover static method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover static method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC static method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities static method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover static method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover static method) (pyrosetta.rosetta.protocols.environment.ClientMover static method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.Environment method) (pyrosetta.rosetta.protocols.environment.EnvMover static method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts static method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf static method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler static method) (pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilter method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs static method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol static method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol static method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol static method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize static method) (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs static method) (pyrosetta.rosetta.protocols.enzdes.LigBurialFilter method) (pyrosetta.rosetta.protocols.enzdes.LigDSasaFilter method) (pyrosetta.rosetta.protocols.enzdes.LigInterfaceEnergyFilter method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs static method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs static method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy static method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover static method) (pyrosetta.rosetta.protocols.enzdes.RemoveLigandFilter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover static method) (pyrosetta.rosetta.protocols.enzdes.RepackWithoutLigandFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol static method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover static method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover static method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover static method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover static method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover static method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover static method) (pyrosetta.rosetta.protocols.esm_perplexity.EsmPerplexityTensorflowProtocol method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric method) (pyrosetta.rosetta.protocols.evaluation.AlignEvaluator method) (pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator method) (pyrosetta.rosetta.protocols.evaluation.PoseEvaluator method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_long_t method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_Size method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_SSize method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_unsigned_long_t method) (pyrosetta.rosetta.protocols.evaluation.TimeEvaluator method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover static method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation static method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover static method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover static method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover static method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover static method) (pyrosetta.rosetta.protocols.filters.CalculatorFilter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.ContingentFilter method) (pyrosetta.rosetta.protocols.filters.FalseFilter method) (pyrosetta.rosetta.protocols.filters.Filter method) (pyrosetta.rosetta.protocols.filters.FilterValueMetric method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.filters.ReplicateFilter method) (pyrosetta.rosetta.protocols.filters.StochasticFilter method) (pyrosetta.rosetta.protocols.filters.TimeFilter method) (pyrosetta.rosetta.protocols.filters.TrueFalseFilter method) (pyrosetta.rosetta.protocols.filters.TrueFilter method) (pyrosetta.rosetta.protocols.filters.VectorPoseFilter method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR static method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation static method) (pyrosetta.rosetta.protocols.fldsgn.filters.CoreDunbrackFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.FragQualFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.InterlockingAromaFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.NcontactsFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.ParallelBetaPairingPreferenceFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureCountFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureHasResidueFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover static method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential static method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies static method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator static method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker static method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio static method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes static method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol static method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover static method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign static method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack static method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma static method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ConstraintFulfilmentFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ScorePoseSegmentFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover static method) (pyrosetta.rosetta.protocols.forge.components.BDR static method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild static method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG static method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG static method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGenerator static method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts static method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover static method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG static method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover static method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC static method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol static method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement static method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement static method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol static method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover static method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover static method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase static method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover static method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover static method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover static method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover static method) (pyrosetta.rosetta.protocols.hbnet.HBNet static method) (pyrosetta.rosetta.protocols.hbnet.HBNetScore method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface static method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler static method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler static method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix static method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle static method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix static method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle static method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix static method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover static method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe static method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation static method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler static method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize static method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler static method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover static method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly static method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize static method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol static method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover static method) (pyrosetta.rosetta.protocols.hybridization.MRMover static method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover static method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover static method) (pyrosetta.rosetta.protocols.hydrate.Hydrate static method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover static method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover static method) (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilter method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover static method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover static method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover static method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover static method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen static method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens static method) (pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilter method) (pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilter method) (pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilter method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate static method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF static method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer static method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock static method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand static method) (pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker static method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble static method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator static method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol static method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign static method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol static method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone static method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand static method) (pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilter method) (pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilter method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble static method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover static method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers static method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover static method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate static method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates static method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether static method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom static method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand static method) (pyrosetta.rosetta.protocols.ligand_docking.Transform static method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble static method) (pyrosetta.rosetta.protocols.ligand_docking.Translate static method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover static method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile static method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover static method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper static method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow static method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension static method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower static method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler static method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler static method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder static method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover static method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol static method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner static method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner static method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner static method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler static method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck static method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter static method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup static method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid static method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom static method) (pyrosetta.rosetta.protocols.loophash.FastGapMover static method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier static method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary static method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper static method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol static method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine static method) (pyrosetta.rosetta.protocols.LoopRebuild static method) (pyrosetta.rosetta.protocols.LoopRefine static method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops static method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover static method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure static method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck1B method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure static method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure static method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover static method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover static method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper static method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover static method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM static method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover static method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD static method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC static method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD static method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial static method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater static method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer static method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo static method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder static method) (pyrosetta.rosetta.protocols.magnesium.MgScanner static method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker static method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover static method) (pyrosetta.rosetta.protocols.match.MatcherMover static method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilter method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover static method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover static method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover static method) (pyrosetta.rosetta.protocols.matdes.SymDofMover static method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.md.CartesianMD static method) (pyrosetta.rosetta.protocols.md.MDBase static method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover static method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover static method) (pyrosetta.rosetta.protocols.medal.MedalMover static method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover static method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint static method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint static method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover static method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder static method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix static method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles static method) (pyrosetta.rosetta.protocols.membrane.FlipMover static method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence static method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover static method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility static method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover static method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover static method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover static method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover static method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover static method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover static method) (pyrosetta.rosetta.protocols.membrane.RotationMover static method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover static method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover static method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover static method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover static method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover static method) (pyrosetta.rosetta.protocols.membrane.TiltMover static method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover static method) (pyrosetta.rosetta.protocols.membrane.TranslationMover static method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover static method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover static method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover static method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler static method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover static method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover static method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover static method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover static method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover static method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker static method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover static method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover static method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy static method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover static method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover static method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover static method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer static method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover static method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset static method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest static method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover static method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover static method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker static method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover static method) (pyrosetta.rosetta.protocols.moves.CompositionMover static method) (pyrosetta.rosetta.protocols.moves.CycleMover static method) (pyrosetta.rosetta.protocols.moves.CyclicMover static method) (pyrosetta.rosetta.protocols.moves.DsspMover static method) (pyrosetta.rosetta.protocols.moves.FilterMover static method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover static method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover static method) (pyrosetta.rosetta.protocols.moves.IfMover static method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover static method) (pyrosetta.rosetta.protocols.moves.JumpOutMover static method) (pyrosetta.rosetta.protocols.moves.MCShowMover static method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil static method) (pyrosetta.rosetta.protocols.moves.MoveMapMover static method) (pyrosetta.rosetta.protocols.moves.Mover static method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover static method) (pyrosetta.rosetta.protocols.moves.MoverContainer static method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList static method) (pyrosetta.rosetta.protocols.moves.NullMover static method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.ProfilerMover static method) (pyrosetta.rosetta.protocols.moves.PyMOLMover static method) (pyrosetta.rosetta.protocols.moves.RampingMover static method) (pyrosetta.rosetta.protocols.moves.RandomMover static method) (pyrosetta.rosetta.protocols.moves.RepeatMover static method) (pyrosetta.rosetta.protocols.moves.SequenceMover static method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor static method) (pyrosetta.rosetta.protocols.moves.SwitchMover static method) (pyrosetta.rosetta.protocols.moves.TrialMover static method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover static method) (pyrosetta.rosetta.protocols.moves.WhileMover static method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover static method) (pyrosetta.rosetta.protocols.multistate_design.PosType method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol static method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover static method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol static method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover static method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder static method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover static method) (pyrosetta.rosetta.protocols.network.UIMover static method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover static method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover static method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover static method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover static method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer static method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover static method) (pyrosetta.rosetta.protocols.optimize_weights.OptEVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.IterativeVectorExpression method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VariableVectorExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VectorExpression method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential static method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences static method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover static method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover static method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover static method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover static method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover static method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover.Overlap method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover static method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover static method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling static method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover static method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover static method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover static method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser static method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter static method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter static method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter static method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector static method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector static method) (pyrosetta.rosetta.protocols.pose_selectors.Filter static method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector static method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector static method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty static method) (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorer method) (pyrosetta.rosetta.protocols.pose_sewing.filters.HasDisulfideFilter method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover static method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover static method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover static method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover static method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover static method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AtomicContactCountFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AverageDegreeFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.ClashWithTargetFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FNatFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.InterfaceHolesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.IRmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.LRmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdSimpleFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SpecificResiduesNearInterfaceFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SSamountFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreLoopsFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.Torsion method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TryRotamers static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB static method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover static method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionTensorflowProtocol method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionTensorflowProtocolBase method) (pyrosetta.rosetta.protocols.qsar.qsarMover static method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage static method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader static method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax static method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover static method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl static method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover static method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any static method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb static method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop static method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion static method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler static method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler static method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite static method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump static method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar static method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite static method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer static method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover static method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence static method) (pyrosetta.rosetta.protocols.recon_design.FitnessFilter method) (pyrosetta.rosetta.protocols.recon_design.MSDMover static method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover static method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover static method) (pyrosetta.rosetta.protocols.relax.CentroidRelax static method) (pyrosetta.rosetta.protocols.relax.ClassicRelax static method) (pyrosetta.rosetta.protocols.relax.FastRelax static method) (pyrosetta.rosetta.protocols.relax.LocalRelax static method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover static method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover static method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover static method) (pyrosetta.rosetta.protocols.relax.MiniRelax static method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover static method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase static method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax static method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover static method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover static method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover static method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMotionMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover static method) (pyrosetta.rosetta.protocols.rigid.RollMover static method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover static method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover static method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover static method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover static method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover static method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser static method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover static method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover static method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover static method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover static method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover static method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer static method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer static method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover static method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter static method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol static method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo static method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol static method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover static method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify static method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify static method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer static method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser static method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover static method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover static method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor static method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor static method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor static method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper static method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper static method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover static method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol static method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporter static method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelector static method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover static method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover static method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover static method) (pyrosetta.rosetta.protocols.score_filters.GeometryFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreTypeFilter method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator static method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold static method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst static method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops static method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides static method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree static method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover static method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer static method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment static method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover static method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover static method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover static method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover static method) (pyrosetta.rosetta.protocols.simple_ddg.AlaScan method) (pyrosetta.rosetta.protocols.simple_ddg.ddG static method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScan method) (pyrosetta.rosetta.protocols.simple_ddg.InterfaceBindingEnergyDensityFilter method) (pyrosetta.rosetta.protocols.simple_ddg.SSElementBisectddGFilter method) (pyrosetta.rosetta.protocols.simple_filters.AbinitioBaseFilter method) (pyrosetta.rosetta.protocols.simple_filters.AngleToVector method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.AveragePathLengthFilter method) (pyrosetta.rosetta.protocols.simple_filters.BatchEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.BatchNrEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.COFilter method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter method) (pyrosetta.rosetta.protocols.simple_filters.DisulfideEntropyFilter method) (pyrosetta.rosetta.protocols.simple_filters.DomainInterfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.EnergyPerResidueFilter method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover static method) (pyrosetta.rosetta.protocols.simple_filters.ExpiryFilter method) (pyrosetta.rosetta.protocols.simple_filters.ExternalEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.FileExistFilter method) (pyrosetta.rosetta.protocols.simple_filters.FileRemoveFilter method) (pyrosetta.rosetta.protocols.simple_filters.HelixHelixAngleFilter method) (pyrosetta.rosetta.protocols.simple_filters.HolesFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHydrophobicResidueContactsFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceSasaFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterRepeatContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.IntraRepeatContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.JumpEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LoopRmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.MembAccesResidueLipophilicityFilter method) (pyrosetta.rosetta.protocols.simple_filters.MotifScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.MPSpanAngleFilter method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilter method) (pyrosetta.rosetta.protocols.simple_filters.NeighborTypeFilter method) (pyrosetta.rosetta.protocols.simple_filters.NetChargeFilter method) (pyrosetta.rosetta.protocols.simple_filters.NMerPSSMEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.NMerSVMEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.NonSequentialNeighborsFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackStatFilter method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.PDDFScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.RangeFilter method) (pyrosetta.rosetta.protocols.simple_filters.RDC_Evaluator method) (pyrosetta.rosetta.protocols.simple_filters.ReadPoseExtraScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.RepeatParameterFilter method) (pyrosetta.rosetta.protocols.simple_filters.ReportFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueBurialFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueChiralityFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueIEFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueLipophilicityFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSelectionDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSetChainEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResiduesInInterfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.RGFilter method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter method) (pyrosetta.rosetta.protocols.simple_filters.SAXSScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter method) (pyrosetta.rosetta.protocols.simple_filters.SelectGdtEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SelectMaxsubEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SelectRDC_Evaluator method) (pyrosetta.rosetta.protocols.simple_filters.SelectRmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) (pyrosetta.rosetta.protocols.simple_filters.SheetFilter method) (pyrosetta.rosetta.protocols.simple_filters.SidechainRmsdFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) (pyrosetta.rosetta.protocols.simple_filters.SpanTopologyMatchPoseFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSElementLengthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSElementMotifContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinder method) (pyrosetta.rosetta.protocols.simple_filters.StemFinder method) (pyrosetta.rosetta.protocols.simple_filters.StructuralSimilarityEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilter method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricRmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareSASAFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter method) (pyrosetta.rosetta.protocols.simple_filters.TerminusDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.TMsAACompFilter method) (pyrosetta.rosetta.protocols.simple_filters.TMsSpanMembraneFilter method) (pyrosetta.rosetta.protocols.simple_filters.TotalSasaFilter method) (pyrosetta.rosetta.protocols.simple_filters.TruncatedScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.Worst9merFilter method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher static method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover static method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover static method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData static method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover static method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint static method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover static method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover static method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover static method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover static method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover static method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover static method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover static method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover static method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover static method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover static method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover static method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins static method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins static method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover static method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover static method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover static method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover static method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover static method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover static method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover static method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover static method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover static method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover static method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover static method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover static method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover static method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover static method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover static method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond static method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover static method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover static method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover static method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover static method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover static method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb static method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers static method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover static method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile static method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence static method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif static method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover static method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher static method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover static method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover static method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover static method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology static method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover static method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover static method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue static method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover static method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover static method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover static method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher static method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover static method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover static method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover static method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover static method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover static method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover static method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover static method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover static method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover static method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover static method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover static method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover static method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo static method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover static method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA static method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ static method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover static method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree static method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover static method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover static method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover static method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover static method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities static method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover static method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover static method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover static method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover static method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion static method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover static method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover static method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover static method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase static method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover static method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover static method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover static method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover static method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover static method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot static method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover static method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover static method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover static method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover static method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover static method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover static method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover static method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover static method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover static method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover static method) (pyrosetta.rosetta.protocols.simple_moves.Tumble static method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover static method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover static method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover static method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover static method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose static method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover static method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluator method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover static method) (pyrosetta.rosetta.protocols.splice.RBInMover static method) (pyrosetta.rosetta.protocols.splice.RBOutMover static method) (pyrosetta.rosetta.protocols.splice.RotLibOut static method) (pyrosetta.rosetta.protocols.splice.Splice static method) (pyrosetta.rosetta.protocols.splice.SpliceIn static method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody static method) (pyrosetta.rosetta.protocols.splice.SpliceInTail static method) (pyrosetta.rosetta.protocols.splice.SpliceOut static method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody static method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail static method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover static method) (pyrosetta.rosetta.protocols.star.StarAbinitio static method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer static method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup static method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser static method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup static method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.ProteinAtrRepScreener method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.RNA_AtrRepScreener method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.SimplePoseSelection method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.SimpleRMSD_Screener method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.SideChainCopier static method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker static method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker static method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover static method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer static method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser static method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger static method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList static method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler static method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer static method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.FromScratchMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo static method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb static method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives static method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList static method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser static method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb static method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF static method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion static method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue static method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb static method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer static method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized static method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny static method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb static method) (pyrosetta.rosetta.protocols.stepwise.screener.AlignRMSD_Screener method) (pyrosetta.rosetta.protocols.stepwise.screener.AnchorSugarScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.BaseBinMapUpdater method) (pyrosetta.rosetta.protocols.stepwise.screener.BaseCentroidScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.BulgeApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.CentroidDistanceScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.FastForwardToNextResidueAlternative method) (pyrosetta.rosetta.protocols.stepwise.screener.FastForwardToNextRigidBody method) (pyrosetta.rosetta.protocols.stepwise.screener.IntegrationTestBreaker method) (pyrosetta.rosetta.protocols.stepwise.screener.O2PrimeScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PackScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PartitionContactScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PhosphateScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PoseSelectionScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.ProteinCCD_ClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.ResidueContactScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryResidueBasedScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryStubBasedScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.SampleApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.Scorer method) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseResiduePairScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.StubApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.StubDistanceScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.SugarInstantiator method) (pyrosetta.rosetta.protocols.stepwise.screener.TagDefinition method) (pyrosetta.rosetta.protocols.stepwise.screener.VDW_BinScreener method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover static method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover static method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover static method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol static method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover static method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover static method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover static method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry static method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover static method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover static method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether static method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover static method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover static method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover static method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation static method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact static method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover static method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover static method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover static method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover static method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover static method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover static method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover static method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus static method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover static method) (pyrosetta.rosetta.protocols.trRosetta.trRosettaProtocol_v1 method) (pyrosetta.rosetta.protocols.trRosetta.trRosettaProtocolBase method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover static method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler static method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover static method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover static method) (pyrosetta.rosetta.std.locale method) (pyrosetta.rosetta.std.type_info method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) name1 (pyrosetta.rosetta.core.io.LinkInformation property) (pyrosetta.rosetta.core.io.SSBondInformation property) (pyrosetta.rosetta.core.scoring.tableID property) name1() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) (pyrosetta.rosetta.core.conformation.Residue method) name2 (pyrosetta.rosetta.core.io.LinkInformation property) (pyrosetta.rosetta.core.io.SSBondInformation property) (pyrosetta.rosetta.core.scoring.tableID property) name2suite() (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) name3 (pyrosetta.rosetta.protocols.dna.DnaDesignDef property) name3() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.protocols.simple_moves.IonizableResidue method) name3_1 (pyrosetta.rosetta.core.io.HELIXInformation property) (pyrosetta.rosetta.core.io.SHEETInformation property) name3_2 (pyrosetta.rosetta.core.io.HELIXInformation property) (pyrosetta.rosetta.core.io.SHEETInformation property) name3_from_oneletter() (in module pyrosetta.rosetta.protocols.motifs) name3_generated_by_base_residue_name() (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) name_ (pyrosetta.rosetta.utility.json_spirit.Pair_impl_utility_json_spirit_Config_vector_std_string_t property) name_for_common_type() (in module pyrosetta.rosetta.utility.tag) name_for_filter() (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) name_from_aa() (in module pyrosetta.rosetta.core.chemical) name_from_acc_chem_type() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) name_from_database_mode() (in module pyrosetta.rosetta.utility.sql_database) name_from_deriv_type() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) name_from_don_chem_type() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) name_from_elements() (in module pyrosetta.rosetta.core.chemical.element) name_from_foldtype() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) name_from_geo_dim_type() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) name_from_hybridization_type() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) name_from_score_type() (in module pyrosetta.rosetta.core.scoring) (pyrosetta.rosetta.core.scoring.ScoreTypeManager static method) name_from_seq_sep_type() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) name_from_transaction_mode() (in module pyrosetta.rosetta.utility.sql_database) name_from_weight_type() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) name_map() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) name_map_or_null() (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) name_mapOP() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) name_of_hbond_calc() (pyrosetta.rosetta.protocols.pose_metric_calculators.SemiExplicitWaterUnsatisfiedPolarsCalculator method) (pyrosetta.rosetta.protocols.simple_pose_metric_calculators.BuriedUnsatisfiedPolarsCalculator method) name_of_sasa_calc() (pyrosetta.rosetta.protocols.simple_pose_metric_calculators.BuriedUnsatisfiedPolarsCalculator method) name_of_weak_bunsat_calc() (pyrosetta.rosetta.protocols.buns.BuriedUnsatisfiedPolarsCalculator2 method) name_static() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric static method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric static method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric static method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric static method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric static method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric static method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric static method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric static method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric static method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric static method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric static method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetric static method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric static method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric static method) (pyrosetta.rosetta.protocols.filters.FilterValueMetric static method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric static method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric static method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric static method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric static method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric static method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric static method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric static method) name_to_column() (pyrosetta.rosetta.cppdb.backend.result method) name_to_listener_tag() (in module pyrosetta.rosetta.basic.mpi) name_wo_rgstr() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) named_atom_id_to_atom_id() (in module pyrosetta.rosetta.core.conformation) (in module pyrosetta.rosetta.core.pose) named_stub_id_to_stub_id() (in module pyrosetta.rosetta.core.pose) NamedAngleConstraint (class in pyrosetta.rosetta.core.scoring.constraints) NamedAngleConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) NamedAtomID (class in pyrosetta.rosetta.core.id) NamedAtomID_Map_bool_t (class in pyrosetta.rosetta.core.id) NamedAtomID_Map_core_id_NamedAtomID_t (class in pyrosetta.rosetta.core.id) NamedAtomID_Map_NamedAtomID (class in pyrosetta.rosetta.core.id) NamedAtomPairConstraint (class in pyrosetta.rosetta.core.scoring.constraints) NamedAtomPairConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) (class in pyrosetta.rosetta.protocols.constraints_additional) NamedDihedralConstraint (class in pyrosetta.rosetta.core.scoring.constraints) NamedSegmentSelector (class in pyrosetta.rosetta.protocols.denovo_design.residue_selectors) NamedSegmentSelectorCreator (class in pyrosetta.rosetta.protocols.denovo_design.residue_selectors) NamedSolution (class in pyrosetta.rosetta.protocols.denovo_design.components) NamedSolutions (class in pyrosetta.rosetta.protocols.denovo_design.components) NamedStubID (class in pyrosetta.rosetta.core.id) names_ (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) (pyrosetta.rosetta.protocols.cluster.calibur.PreloadedPDB property) names_vector() (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) naming_func() (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) NAND (pyrosetta.rosetta.protocols.filters.boolean_operations attribute) (pyrosetta.rosetta.protocols.task_operations.boolean_operations attribute) nangles() (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.optimization.MinimizerMap method) (pyrosetta.rosetta.core.optimization.NumDerivCheckData method) (pyrosetta.rosetta.core.optimization.SimpleDerivCheckResult method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) nargs() (pyrosetta.rosetta.numeric.expression_parser.FunctionToken method) NaryExpression (class in pyrosetta.rosetta.numeric.expression_parser) nat_ro_map() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) NATAA (class in pyrosetta.rosetta.core.pack.task) natbias_hh (pyrosetta.rosetta.core.scoring.ScoreType attribute) natbias_hs (pyrosetta.rosetta.core.scoring.ScoreType attribute) natbias_ss (pyrosetta.rosetta.core.scoring.ScoreType attribute) natbias_stwist (pyrosetta.rosetta.core.scoring.ScoreType attribute) NatbiasHelicesSheetPotential (class in pyrosetta.rosetta.protocols.fldsgn.potentials.sspot) NatbiasHelixPairPotential (class in pyrosetta.rosetta.protocols.fldsgn.potentials.sspot) NatbiasSecondaryStructureEnergy (class in pyrosetta.rosetta.protocols.fldsgn.potentials.sspot) NatbiasSecondaryStructureEnergyCreator (class in pyrosetta.rosetta.protocols.fldsgn.potentials.sspot) NatbiasStrandPairPotential (class in pyrosetta.rosetta.protocols.fldsgn.potentials.sspot) native() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo method) native_aa() (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) native_alignment() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) NATIVE_ANTIBODY_SEQ (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) native_CA_gdtmm() (in module pyrosetta.rosetta.core.scoring) native_CA_rmsd() (in module pyrosetta.rosetta.core.scoring) native_coms_ (pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions property) (pyrosetta.rosetta.protocols.electron_density.SelectDensityPointsOptions property) native_distance_viol() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) native_edensity_score_cutoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) native_ensemble_best() (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) native_file() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) native_hbond_ratio (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfo property) native_loop_core_CA_rmsd() (in module pyrosetta.rosetta.protocols.loops) native_middle_cas_ (pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions property) (pyrosetta.rosetta.protocols.electron_density.SelectDensityPointsOptions property) native_pose() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup method) (pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator method) (pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator method) (pyrosetta.rosetta.protocols.evaluation.AlignEvaluator method) (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobResult method) native_positions() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) native_rotamers_map() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFile method) native_scores_ (pyrosetta.rosetta.core.energy_methods.ScoreCache property) native_secstruct() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) native_tag() (pyrosetta.rosetta.protocols.jobdist.BasicJob method) NativeAntibodySeq (class in pyrosetta.rosetta.protocols.antibody.design) NativeEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) nativeness() (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData method) nativeness_high() (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData static method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData static method) nativeness_low() (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData static method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData static method) natives_ (pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions property) (pyrosetta.rosetta.protocols.electron_density.SelectDensityPointsOptions property) natives_select() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) NativeSelector (class in pyrosetta.rosetta.protocols.residue_selectors) NativeSelectorCreator (class in pyrosetta.rosetta.protocols.residue_selectors) natm() (pyrosetta.rosetta.protocols.normalmode.NormalMode method) natom (pyrosetta.rosetta.core.scoring.packing.HolesResult property) (pyrosetta.rosetta.core.scoring.sc.Atom property) natom() (pyrosetta.rosetta.core.energy_methods.GoapRsdType method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.core.scoring.packstat.SimplePDB method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_double_t method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_float method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_float_t method) (pyrosetta.rosetta.protocols.sic_dock.xyzStripeHashPoseWithMeta method) natom_aligned() (in module pyrosetta.rosetta.protocols.hybridization) natoms (pyrosetta.rosetta.core.scoring.APBSConfig property) nAtoms (pyrosetta.rosetta.core.scoring.sc._RESULTS property) natoms() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.UltraLightResidue method) (pyrosetta.rosetta.core.optimization.CartesianMinimizerMap method) (pyrosetta.rosetta.core.optimization.DOF_DataPoint method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomToAxisConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraint method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedDihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueCouplingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.RTConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) natoms_ (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo property) (pyrosetta.rosetta.core.scoring.PQR property) natoms_rmsd() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner method) natoms_superimpose_rmsd() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner method) nAtomWaters (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.atmInfo property) NATRO (class in pyrosetta.rosetta.core.pack.task) natro_movemap_ (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) NatureStyle (pyrosetta.rosetta.basic.citation_manager.CitationFormat attribute) Nb (pyrosetta.rosetta.core.chemical.element.Elements attribute) nb_list() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) nb_weight() (pyrosetta.rosetta.core.scoring.packing.HolesParams method) nbackbone_conformations() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) nballs() (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) (pyrosetta.rosetta.core.scoring.packing.PoseBallsLite method) nbb() (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.fragment.BBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) nbbconfs_for_flexseg() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) nbbconfs_for_moltenres() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) nbbconfs_for_res() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) nbcount() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_double_t method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_float method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_float_t method) (pyrosetta.rosetta.protocols.sic_dock.xyzStripeHashPoseWithMeta method) nbcount_raw() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) nbhist() (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) nblist() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.methods.NeighborListData method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) nblist_auto_update() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.core.optimization.MinimizerOptions method) nblist_dis2_cutoff_HH() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) nblist_dis2_cutoff_XH() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) nblist_dis2_cutoff_XX() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) nblist_type() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) nblocks() (pyrosetta.rosetta.utility.graph.ArrayPool_double_t method) nbonds() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.conformation.PseudoBond method) nbonds_from_bb_atom() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) nbonds_from_bb_atom_ (pyrosetta.rosetta.protocols.match.upstream.BuildSet property) nbr_atom() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.atmInfo method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.hbAcc method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.hbDon method) nbr_atom_rmsd() (in module pyrosetta.rosetta.core.scoring) nbr_atom_xyz() (pyrosetta.rosetta.core.conformation.Residue method) nbr_dis2_threshold() (pyrosetta.rosetta.core.scoring.dna.DNA_EnvPairPotential method) nbr_e_threshold() (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) nbr_radius() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) nbr_vertex() (pyrosetta.rosetta.core.chemical.MutableResidueType method) nbrs() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) nbrs1() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) nbrs2() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) ncaa_rotlib_n_bin_per_rot() (pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification method) ncaa_rotlib_n_rotameric_bins() (pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification method) ncaa_rotlib_path() (pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification method) NCAADefaultPackerPalette (class in pyrosetta.rosetta.core.pack.palette) NCAADefaultPackerPaletteCreator (class in pyrosetta.rosetta.core.pack.palette) ncaaList (pyrosetta.rosetta.protocols.forge.remodel.LineObject property) NCAARotamerLibrarySpecification (class in pyrosetta.rosetta.core.chemical.rotamers) NCAARotamerLibrarySpecificationCreator (class in pyrosetta.rosetta.core.chemical.rotamers) NCAARotLibBBTorsions (class in pyrosetta.rosetta.core.chemical) NCAARotLibNumRotamerBins (class in pyrosetta.rosetta.core.chemical) NCAARotLibPath (class in pyrosetta.rosetta.core.chemical) NCaCaC_Dihedral_Func (class in pyrosetta.rosetta.core.scoring.disulfides) ncap_prob_from_svm() (pyrosetta.rosetta.protocols.helix_capper.HelixNCapperMover method) ncbb_design_main_loop() (in module pyrosetta.rosetta.protocols.ncbb) NcbbDockDesignProtocol (class in pyrosetta.rosetta.protocols.ncbb) NcbbDockDesignProtocolCreator (class in pyrosetta.rosetta.protocols.ncbb) nchi() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) nchi_ (pyrosetta.rosetta.protocols.loop_grower.ResTorsions property) ncluster() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) ncol() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) ncols() (pyrosetta.rosetta.numeric.MathTensor_double_t method) NcontactsCalculator (class in pyrosetta.rosetta.protocols.fldsgn) NcontactsFilter (class in pyrosetta.rosetta.protocols.fldsgn.filters) NcontactsFilterCreator (class in pyrosetta.rosetta.protocols.fldsgn.filters) nContinuousSegments() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) nCPCrossoverBehaviors (pyrosetta.rosetta.core.scoring.etable.count_pair.CPCrossoverBehavior attribute) nCPResidueConnectionTypes (pyrosetta.rosetta.core.scoring.etable.count_pair.CPResidueConnectionType attribute) NCS_RESIDUE_MAPPING (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) NCSResMapping (class in pyrosetta.rosetta.protocols.symmetry) ncst() (pyrosetta.rosetta.protocols.md.Rattle method) ncsts() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) ncyc_postmin() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) ncyc_premin() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) ncycle() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) Nd (pyrosetta.rosetta.core.chemical.element.Elements attribute) ndaemons() (pyrosetta.rosetta.protocols.pack_daemon.DaemonSet method) ndihe() (pyrosetta.rosetta.core.chemical.ResidueType method) ndim() (pyrosetta.rosetta.numeric.kdtree.HyperRectangle method) (pyrosetta.rosetta.numeric.kdtree.KDTree method) ndims() (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) (pyrosetta.rosetta.utility.LexicographicalIterator method) ndofs() (pyrosetta.rosetta.core.optimization.CartesianMinimizerMap method) nDoFs() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) ndots() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) Ne (pyrosetta.rosetta.core.chemical.element.Elements attribute) ne (pyrosetta.rosetta.protocols.simple_filters.comparison_type attribute) NE2_CONNECT (pyrosetta.rosetta.core.chemical.VariantType attribute) near_interface (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo.Type attribute) Near_Native_StepWiseSampler_Count (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) near_squared_size() (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilter method) near_wat() (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom method) nearby_atom_cut() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.protocols.simple_filters.DomainInterfaceFilter method) nearby_atom_cutoff() (pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) nearest_atom_for_constraint() (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) nearest_neighbor() (in module pyrosetta.rosetta.numeric.kdtree) nearest_neighbors() (in module pyrosetta.rosetta.numeric.kdtree) nearest_ssize() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.ObjexxFCL) nearest_to_entry_stop_on_pose() (in module pyrosetta.rosetta.protocols.splice) NearNativeLoopCloser (class in pyrosetta.rosetta.protocols.pose_length_moves) NearNativeLoopCloserCreator (class in pyrosetta.rosetta.protocols.pose_length_moves) NEED_TO_KNOW (pyrosetta.rosetta.protocols.topology_broker.claims.BBClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.BBClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.CutClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.CutClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.LegacyRootClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.LegacyRootClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.SequenceClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.SequenceClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.SymmetryClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.SymmetryClaim.ClaimRight attribute) needsUpdatePropertyCache() (pyrosetta.rosetta.RDKit.Atom method) (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) neg_space_element_allocation_error_message() (in module pyrosetta.rosetta.utility.graph) neg_Tds() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) negate() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) negated() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) negative_better() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) NEGATIVE_CHARGE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) negln_rotprob() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) NegSpaceElement_double_t (class in pyrosetta.rosetta.utility.graph) neigh (pyrosetta.rosetta.protocols.cluster.calibur.AdjacentList property) neigh_count (pyrosetta.rosetta.core.scoring.ScoreType attribute) neigh_ress (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData property) neigh_vect (pyrosetta.rosetta.core.scoring.ScoreType attribute) neigh_vect_raw (pyrosetta.rosetta.core.scoring.ScoreType attribute) neighbor_count (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom property) neighbor_count() (in module pyrosetta.rosetta.protocols.sic_dock) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) neighbor_cutoff() (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.simple_filters.NonSequentialNeighborsFilter method) neighbor_detection_dis() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) neighbor_dis() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) neighbor_distance() (pyrosetta.rosetta.protocols.simple_filters.StemFinder method) neighbor_hits() (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) neighbor_id() (pyrosetta.rosetta.core.scoring.constraints.CstResNeighbConstIterator method) (pyrosetta.rosetta.core.scoring.constraints.CstResNeighbIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.ResidueNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.ResidueNeighborIterator method) neighbor_iterator_begin() (pyrosetta.rosetta.core.scoring.constraints.CstEnergyContainer method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.LREnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) neighbor_iterator_end() (pyrosetta.rosetta.core.scoring.constraints.CstEnergyContainer method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.LREnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) neighbor_mass() (pyrosetta.rosetta.core.scoring.TenANeighborNode method) neighbor_min() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) neighbor_min_add() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) neighbor_min_clear() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) neighbor_separation() (pyrosetta.rosetta.protocols.simple_filters.StemFinder method) neighbor_strands() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) neighbor_weight() (pyrosetta.rosetta.core.scoring.nv.NVscore method) NeighborDependentTabooSamplingKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) NeighborDependentTorsionSamplingKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) Neighborhood (class in pyrosetta.rosetta.protocols.neighbor) neighborhood_buns_polar_calc_name() (pyrosetta.rosetta.protocols.forge.components.BDR static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover static method) neighborhood_calc() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) neighborhood_calc_name() (pyrosetta.rosetta.protocols.forge.components.BDR static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover static method) NeighborhoodByDistanceCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) NeighborhoodResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) NeighborhoodResidueSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) neighboring_atoms() (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) NeighborList (class in pyrosetta.rosetta.core.scoring) (pyrosetta.rosetta.protocols.sparta.PDB property) NeighborListData (class in pyrosetta.rosetta.core.scoring.methods) neighbors (pyrosetta.rosetta.core.scoring.sc.Atom property) (pyrosetta.rosetta.protocols.toolbox.Node property) neighbors() (pyrosetta.rosetta.protocols.simple_filters.ResidueBurialFilter method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.FindEndpointsOperation method) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) neighbors_in_vector() (in module pyrosetta.rosetta.protocols.splice) NeighborsByDistanceCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) NeighborTypeFilter (class in pyrosetta.rosetta.protocols.simple_filters) NeighborTypeFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) NeighTeller (class in pyrosetta.rosetta.protocols.constel) NEITHER (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation attribute) NelderMeadSimplex (class in pyrosetta.rosetta.core.optimization) Nend_orient() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) Nend_pos() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) NestedEnergyTermDDGMutationOptEData (class in pyrosetta.rosetta.protocols.optimize_weights) NestedEnergyTermPNatAAOptEPositionData (class in pyrosetta.rosetta.protocols.optimize_weights) net_clash() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) net_formal_charge() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) net_indices (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) netcharge (pyrosetta.rosetta.core.scoring.ScoreType attribute) netcharge_energy_setup() (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) netcharge_setup_file() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) netcharge_setup_file_count() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) NetChargeConstraint (class in pyrosetta.rosetta.core.scoring.netcharge_energy) NetChargeEnergy (class in pyrosetta.rosetta.core.energy_methods) NetChargeEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) NetChargeEnergySetup (class in pyrosetta.rosetta.core.scoring.netcharge_energy) NetChargeFilter (class in pyrosetta.rosetta.protocols.simple_filters) NetChargeFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) netTargetPocketVolume() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) network_allow_same_residue_connect_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) network_analysis() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) network_analysis2() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) network_anchoring() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) network_anchoring_per_residue() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) network_atom_min_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) network_contains_aa() (in module pyrosetta.rosetta.protocols.hbnet) network_include_reverse_dir_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) network_meets_final_criteria() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) network_meets_initial_criteria() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) network_mode_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) network_pdb_written (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) network_reswise_high_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) network_reswise_min_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) network_spans_all_helices() (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) network_use_all_covalent_atoms_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) NetworkState (class in pyrosetta.rosetta.protocols.hbnet) NetworkStateScoreComparator (class in pyrosetta.rosetta.protocols.hbnet) NeuralNetwork (pyrosetta.rosetta.basic.citation_manager.CitedModuleType attribute) Neutral (pyrosetta.rosetta.protocols.antibody.H3BaseTypeEnum attribute) neutral_restypes() (pyrosetta.rosetta.protocols.simple_moves.IonizableResidue method) neutralize (pyrosetta.rosetta.core.chemical.rdkit.RestypeToRDMolOptions property) neutralize_rdmol() (in module pyrosetta.rosetta.core.chemical.rdkit) NEUTRON_DIFFRACTION (pyrosetta.rosetta.core.io.rcsb.ExperimentalTechnique attribute) new_array() (pyrosetta.rosetta.utility.graph.ArrayPool_double_t method) new_cache_ (pyrosetta.rosetta.core.fragment.CacheWrapper_protocols_simple_moves_GunnTuple_core_fragment_MapCacheUnit_protocols_simple_moves_GunnTuple_t property) (pyrosetta.rosetta.core.fragment.FragCache_protocols_simple_moves_GunnTuple_t property) new_calculator() (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculatorCreator method) new_chain() (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) new_chain_order() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) new_chemical_bond() (pyrosetta.rosetta.core.kinematics.FoldTree method) new_chemistry() (pyrosetta.rosetta.protocols.chemistries.ChemistryFactory method) new_chunk_library_inputter() (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputterFactory method) new_cluster_metric() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricFactory method) new_constraint_generator() (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorFactory method) new_data_instance() (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataFactory method) new_decoy() (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) new_entity() (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) (pyrosetta.rosetta.protocols.multistate_design.PosTypeCreator method) new_fold_tree_initializer() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) new_full_model_inputter() (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputterFactory method) new_func() (pyrosetta.rosetta.core.scoring.func.FuncFactory method) new_grid() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridFactory method) new_icoor() (pyrosetta.rosetta.core.chemical.Orbital method) NEW_JOB_ID_TAG (pyrosetta.rosetta.basic.mpi.mpi_tags attribute) new_jump() (pyrosetta.rosetta.core.kinematics.FoldTree method) new_jump_selector() (pyrosetta.rosetta.core.select.jump_selector.JumpSelectorFactory method) new_kinematics() (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) new_level_begins_ (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.DataBuffer property) new_move_selector() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) new_name() (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) new_orbital_icoor_data() (pyrosetta.rosetta.core.chemical.ResidueType method) new_pose_inputter() (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterFactory method) new_pose_outputter() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory method) new_positions() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) new_residue_selector() (pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorFactory method) new_secondary_outputter() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory method) new_secondary_structure_override() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) new_segment_name() (pyrosetta.rosetta.protocols.denovo_design.components.SegmentCounts method) new_sequence_override() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) new_sfr() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) new_simple_metric() (pyrosetta.rosetta.core.simple_metrics.SimpleMetricFactory method) new_sym_min() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) new_tasks() (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) new_terminal_pos() (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) new_vrts (pyrosetta.rosetta.protocols.environment.EnvClaimBroker.BrokerResult property) newClusteringTreeNode() (pyrosetta.rosetta.numeric.ClusteringTreeNode static method) newConstraint() (pyrosetta.rosetta.core.scoring.constraints.ConstraintFactory method) newDataLoader() (pyrosetta.rosetta.protocols.parser.DataLoaderFactory method) newFilter() (pyrosetta.rosetta.protocols.filters.FilterFactory method) newick_tree() (pyrosetta.rosetta.protocols.jd3.JobGenealogist method) newMover() (pyrosetta.rosetta.protocols.moves.MoverFactory method) newNode() (pyrosetta.rosetta.core.environment.FoldTreeSketch.Node static method) newPackerPalette() (pyrosetta.rosetta.core.pack.palette.PackerPaletteFactory method) newPatchOperation() (pyrosetta.rosetta.core.chemical.PatchOperationFactory method) newPosePropertyReporter() (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterFactory method) newPoseSelector() (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorFactory method) newResFilter() (pyrosetta.rosetta.core.pack.task.operation.ResFilterFactory method) newRLTO() (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory method) newTaskOperation() (pyrosetta.rosetta.core.pack.task.operation.TaskOperationFactory method) newTaskOperations() (pyrosetta.rosetta.core.pack.task.operation.TaskOperationFactory method) newTopologyClaimer() (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory method) next() (pyrosetta.rosetta.core.chemical.AutomorphismIterator method) (pyrosetta.rosetta.core.sequence.Cell method) (pyrosetta.rosetta.cppdb.backend.result method) (pyrosetta.rosetta.cppdb.result method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.GridSearchIterator method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.GridSearchIterator_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.GridSearchIterator_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.GridSearchIterator_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.GridSearchIterator_Ts4 method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue_Swapped method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) (pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t method) next_angle() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) next_center() (pyrosetta.rosetta.protocols.scoring.methods.pcs.GridSearchIterator method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.GridSearchIteratorCA method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.GridSearchIterator_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.GridSearchIterator_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.GridSearchIterator_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.GridSearchIterator_Ts4 method) next_child() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) next_circle() (pyrosetta.rosetta.core.scoring.packstat.trace method) next_exchange_schedule() (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) next_hb_res() (in module pyrosetta.rosetta.core.scoring.hbonds) next_job() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) next_level() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) next_random_job() (pyrosetta.rosetta.protocols.jd2.BOINCJobDistributor method) (pyrosetta.rosetta.protocols.jd2.ShuffleFileSystemJobDistributor method) next_resnum() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) next_row_exists (pyrosetta.rosetta.cppdb.backend.result attribute) (pyrosetta.rosetta.cppdb.backend.result.next_row attribute) next_row_unknown (pyrosetta.rosetta.cppdb.backend.result attribute) (pyrosetta.rosetta.cppdb.backend.result.next_row attribute) next_segment_id() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) next_struct() (pyrosetta.rosetta.core.import_pose.pose_stream.SilentFilePoseInputStream method) NEXT_Tab (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) next_torsion_string() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) nextFileName (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) nfev (pyrosetta.rosetta.numeric.nls.lm_status_struct property) nfft() (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fft_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) nflexible_segments() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) nFrags_ (pyrosetta.rosetta.protocols.frag_picker.QuotaDebug property) ngaussians() (pyrosetta.rosetta.core.scoring.SmoothScoreTermCoeffs method) ngroups() (pyrosetta.rosetta.protocols.symmetry.NCSResMapping method) nh1_wants_1 (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.UnsatCorrectionOptions property) nh2_wants_2 (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.UnsatCorrectionOptions property) nhashlookups() (pyrosetta.rosetta.protocols.sic_dock.scores.MotifHashRigidScore method) nhbonds() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) nheavyatoms() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.conformation.Residue method) Ni (pyrosetta.rosetta.core.chemical.element.Elements attribute) nint() (in module pyrosetta.rosetta.ObjexxFCL) nions (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) nirotamers() (pyrosetta.rosetta.protocols.motifs.IRCollection method) NIT (pyrosetta.rosetta.protocols.match.ProbeRadius attribute) niter() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) njobs (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor.CompletionMessage property) njumps() (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) nl_if() (in module pyrosetta.rosetta.ObjexxFCL.format) nlayers() (pyrosetta.rosetta.numeric.MathTensor_double_t method) nlev (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) nlevels() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) nlevels_ (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.PoolData property) nlevels_per_dim() (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) nloop() (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) nlr_gaussians() (pyrosetta.rosetta.core.scoring.CenHBPotential method) NLS (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet attribute) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet.COMPUTATION_TYPE attribute) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet attribute) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet.COMPUTATION_TYPE attribute) NLSAX (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet attribute) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet.COMPUTATION_TYPE attribute) NLSAXRH (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet attribute) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet.COMPUTATION_TYPE attribute) NLSDA (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet attribute) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet.COMPUTATION_TYPE attribute) NLSDAR (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet attribute) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet.COMPUTATION_TYPE attribute) NLSR (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet attribute) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet.COMPUTATION_TYPE attribute) NLSRH (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet attribute) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet.COMPUTATION_TYPE attribute) NM() (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) nmax_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) nmer_length() (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) nmer_pssm (pyrosetta.rosetta.core.scoring.ScoreType attribute) nmer_pssm_scorecut() (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) nmer_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) nmer_ref_seq_length() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) nmer_svm (pyrosetta.rosetta.core.scoring.ScoreType attribute) nmer_svm() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) nmer_svm_aa_matrix() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) nmer_svm_aa_matrix_defined() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) nmer_svm_avg_rank_as_energy() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) nmer_svm_defined() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) nmer_svm_list() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) nmer_svm_list_defined() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) nmer_svm_pssm_feat() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) nmer_svm_rank() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) nmer_svm_rank_defined() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) nmer_svm_rank_list() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) nmer_svm_rank_list_defined() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) nmer_svm_scorecut() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) nmer_svm_scorecut_defined() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) nmer_svm_term_length() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) NMerPSSMEnergy (class in pyrosetta.rosetta.core.scoring.methods) NMerPSSMEnergyCreator (class in pyrosetta.rosetta.core.scoring.methods) NMerPSSMEnergyFilter (class in pyrosetta.rosetta.protocols.simple_filters) NMerPSSMEnergyFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) NMerRefEnergy (class in pyrosetta.rosetta.core.scoring.methods) NMerRefEnergyCreator (class in pyrosetta.rosetta.core.scoring.methods) NMerSVMEnergy (class in pyrosetta.rosetta.core.scoring.methods) NMerSVMEnergyCreator (class in pyrosetta.rosetta.core.scoring.methods) NMerSVMEnergyFilter (class in pyrosetta.rosetta.protocols.simple_filters) NMerSVMEnergyFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) nmissing() (pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph method) nmode() (pyrosetta.rosetta.protocols.normalmode.NormalMode method) nmodes() (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) nmolten_res() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) nmoltenres() (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) (pyrosetta.rosetta.core.pack_basic.RotamerSetsBase method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) nmotifs() (pyrosetta.rosetta.protocols.motifs.MotifLibrary method) nmoves() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) NMR (pyrosetta.rosetta.core.io.rcsb.ExperimentalTechnique attribute) nmr2rosetta() (pyrosetta.rosetta.protocols.noesy_assign.MethylNames method) nmr_pcs (pyrosetta.rosetta.core.scoring.ScoreType attribute)

NMR_PCS_DATA (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) nmr_pre (pyrosetta.rosetta.core.scoring.ScoreType attribute) NMR_PRE_DATA (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) nmr_rdc (pyrosetta.rosetta.core.scoring.ScoreType attribute) NMR_RDC_DATA (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) NMR_VALUE_AVERAGING_TYPE (class in pyrosetta.rosetta.core.scoring.nmr) NMRDataFactory (class in pyrosetta.rosetta.core.scoring.nmr) NMRDummySpinlabelAtom (class in pyrosetta.rosetta.core.scoring.nmr) NMRDummySpinlabelConformer (class in pyrosetta.rosetta.core.scoring.nmr) NMRDummySpinlabelEnsemble (class in pyrosetta.rosetta.core.scoring.nmr) NMRDummySpinlabelVoxelGrid (class in pyrosetta.rosetta.core.scoring.nmr) NMRGridSearch (class in pyrosetta.rosetta.core.scoring.nmr) NMRSpinlabel (class in pyrosetta.rosetta.core.scoring.nmr) NMRSpinlabel.CONFORMER_FILTER (class in pyrosetta.rosetta.core.scoring.nmr) NMRTensor (class in pyrosetta.rosetta.core.scoring.nmr) nmtr() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) nmtr_ (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo property) No (pyrosetta.rosetta.core.chemical.element.Elements attribute) NO_ADDUCTS (class in pyrosetta.rosetta.core.pack.task) NO_ATOM_PROPERTY (pyrosetta.rosetta.core.chemical.AtomProperty attribute) NO_ATTACHMENT (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AttachmentType attribute) no_block (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.BlockParam property) no_chainend_ter() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) NO_CHI (pyrosetta.rosetta.core.chemical.rna.ChiState attribute) no_crosslinker (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker attribute) NO_DERIVATIVES_FOR_ATOM (pyrosetta.rosetta.core.scoring.disulfides.DisulfideDerivativeAtom attribute) NO_DESIGN (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation attribute) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation.LayerOperationType attribute) no_design() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) no_detect_pseudobonds() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) no_dis_dep_die() (pyrosetta.rosetta.core.scoring.etable.coulomb.Coulomb method) no_effect (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) NO_EXTRA_CHI_SAMPLES (pyrosetta.rosetta.core.pack.task.ExtraRotSample attribute) no_filter (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.filter_type attribute) no_lk_polar_desolvation (pyrosetta.rosetta.core.scoring.etable.EtableOptions property) NO_METAPATCHES (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) no_metapatches() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) no_min (pyrosetta.rosetta.protocols.antibody.design.MinTypeEnum attribute) no_modified_ddG() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) NO_MOVE (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.MoveType attribute) no_network_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) no_observer (pyrosetta.rosetta.protocols.moves.PyMOLObserver attribute) (pyrosetta.rosetta.protocols.moves.PyMOLObserver.ObserverType attribute) no_optH() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) no_output_cen() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) NO_OVERLAP (pyrosetta.rosetta.core.scoring.motif.MotifMatchOverlapReq attribute) no_prepack1 (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) no_prepack2 (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) NO_PROPERTY (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) NO_PUCKER (pyrosetta.rosetta.core.chemical.rna.PuckerState attribute) no_ranked_frags() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) NO_REACTIVITY (pyrosetta.rosetta.core.pose.rna.RNA_ReactivityType attribute) no_relax() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) NO_ROTAMER_TYPE (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) no_samples (pyrosetta.rosetta.protocols.match.upstream.ChiStrategy attribute) no_selector (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.selector_type attribute) no_stats (pyrosetta.rosetta.protocols.moves.StatsType attribute) NO_STRANDS (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) NO_SYMMETRIZATION_REQUEST (pyrosetta.rosetta.core.pack.task.PackerTaskSymmetryStatus attribute) NO_TYPE (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) NO_VARIANT (pyrosetta.rosetta.core.chemical.VariantType attribute) nobjs() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) NoBondIsometry (pyrosetta.rosetta.core.chemical.BondIsometry attribute) NoClient (class in pyrosetta.rosetta.utility.keys) Node (class in pyrosetta.rosetta.protocols.toolbox) (class in pyrosetta.rosetta.utility.graph) node() (pyrosetta.rosetta.protocols.jd3.JGJobNode method) (pyrosetta.rosetta.utility.graph.DisjointSets method) node1_ (pyrosetta.rosetta.numeric.ClusterOptions property) node2_ (pyrosetta.rosetta.numeric.ClusterOptions property) node_index_ (pyrosetta.rosetta.core.pack.interaction_graph.exposed_hydrophobic_data property) NodeBase (class in pyrosetta.rosetta.core.pack.interaction_graph) NoDefault() (pyrosetta.rosetta.utility.options.BooleanOption static method) nodeidx() (pyrosetta.rosetta.protocols.denovo_design.components.FoldGraph method) nodeindex_to_residue_memory_address() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) NodeManager (class in pyrosetta.rosetta.protocols.jd3.dag_node_managers) NodeManagerStorageMatrix (class in pyrosetta.rosetta.protocols.jd3.dag_node_managers) nodes() (pyrosetta.rosetta.protocols.hbnet.NetworkState method) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) nodes_from_same_flexseg() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) nodes_in_set() (pyrosetta.rosetta.utility.graph.DisjointSets method) NoDesignPackerPalette (class in pyrosetta.rosetta.core.pack.palette) NoDesignPackerPaletteCreator (class in pyrosetta.rosetta.core.pack.palette) NOESY_ASSIGN_CALIBRATE (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_CHEMSHIFT (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_CP_GEN_CST (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_DECOY_COMP (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_DIAGONAL (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_DIST_APPLY (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_DIST_CST_CAST (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_DIST_CST_EVAL (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_DIST_INIT (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_DIST_MAKE_POSE (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_DIST_PREP_SCORE (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_DIST_SET_COMPABILITY_SCORE (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_DISTANCE (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_ELIMINATE (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_GEN_CST (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_INITIAL (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_MAP2CB (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_MAP2CB_NEW (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_NETWORK (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_NETWORK_COMPUTE_NK (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_NETWORK_FILL_COV_GAMMA (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_NETWORK_FIND_RAW_ASSIGN (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_NETWORK_INVALIDATE_SEQ_NOE (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_NETWORK_PEAK_COUNT (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_NETWORK_PEAK_COUNT_EVAL (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_NETWORK_RETRIEVE_ASSIGN (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_NETWORK_TOTAL (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_NMR_STRING (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_PA_GEN_CST (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_READ_INPUT (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_REQUIRES_CB_MAPPING (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_SYMMETRY (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_TOTAL (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_UPDATE_PEAK_VOL (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_WRITE_ASSIGNMENTS (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_ASSIGN_WRITE_CST (pyrosetta.rosetta.basic.ProfTag attribute) NOESY_PHASEII_S2_RESAMPLING (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax.IterationStage attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeBase attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeBase.IterationStage attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid.IterationStage attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom.IterationStage attribute) NOESY_PHASEII_TOPO (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax.IterationStage attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeBase attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeBase.IterationStage attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid.IterationStage attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom.IterationStage attribute) NoesyModule (class in pyrosetta.rosetta.protocols.noesy_assign) NoFailDataMap (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts) noImplicitHs (pyrosetta.rosetta.core.chemical.rdkit.RestypeToRDMolOptions property) noise() (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDecayData method) NomenclatureManager (class in pyrosetta.rosetta.core.io) non_clash_sugar (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) non_const_pose() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) non_hbonding_atom() (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom method) non_helix_in_membrane_penalty() (pyrosetta.rosetta.core.scoring.MembranePotential method) non_ideal() (pyrosetta.rosetta.protocols.loophash.FastGapMover method) non_interface (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo.Type attribute) non_main_chain_sugar_coords (pyrosetta.rosetta.core.fragment.rna.TorsionSet property) non_main_chain_sugar_coords() (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) non_main_chain_sugar_coords_defined (pyrosetta.rosetta.core.fragment.rna.TorsionSet property) non_main_chain_sugar_coords_defined() (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) non_peptide_heavy_atom_RMSD() (in module pyrosetta.rosetta.core.scoring) non_polymer_bond() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) non_polymer_bond_exists() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) non_square_transpose() (in module pyrosetta.rosetta.numeric.linear_algebra) non_standard_residue_map() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) non_standard_residue_map_nonconst() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) non_virtual_score() (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) nonadduct_variants_match() (in module pyrosetta.rosetta.core.chemical) NonaromaticBond (pyrosetta.rosetta.core.chemical.BondAromaticity attribute) noncanonical_atom_count() (in module pyrosetta.rosetta.core.pose) noncanonical_chi_count() (in module pyrosetta.rosetta.core.pose) noncanonical_disulfide() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) noncanonical_residue_count() (in module pyrosetta.rosetta.core.pose) nonchitip_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) nonchitip_atoms() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) nonconst_atom() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) nonconst_atom_numbers_for_mg_calculation() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) nonconst_atom_numbers_for_vdw_calculation() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) nonconst_atoms() (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) nonconst_begin() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragSetCollection method) (pyrosetta.rosetta.core.fragment.MinimalFragSet method) (pyrosetta.rosetta.core.fragment.OrderedFragSet method) nonconst_cenlist_from_pose() (pyrosetta.rosetta.core.scoring.EnvPairPotential static method) (pyrosetta.rosetta.core.scoring.membrane.MembraneData static method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential static method) (pyrosetta.rosetta.core.scoring.MembranePotential static method) nonconst_circle() (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) nonconst_data() (pyrosetta.rosetta.core.conformation.Residue method) nonconst_data_ptr() (pyrosetta.rosetta.core.conformation.Residue method) nonconst_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_direction() (pyrosetta.rosetta.core.scoring.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) nonconst_downstream_algorithms() (pyrosetta.rosetta.protocols.match.Matcher method) nonconst_end() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragSetCollection method) (pyrosetta.rosetta.core.fragment.MinimalFragSet method) (pyrosetta.rosetta.core.fragment.OrderedFragSet method) nonconst_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) nonconst_generators() (pyrosetta.rosetta.core.scoring.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) nonconst_id() (pyrosetta.rosetta.core.scoring.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) nonconst_induced_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_induced_rf_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_inner_job() (pyrosetta.rosetta.protocols.jd3.LarvalJob method) nonconst_interface_from_pose() (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) nonconst_is_buried() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) nonconst_is_interface() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) nonconst_is_magnesium() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) nonconst_long_range_container() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) nonconst_Membrane_FAEmbed_from_pose() (in module pyrosetta.rosetta.core.scoring) nonconst_MembraneEmbed_from_pose() (in module pyrosetta.rosetta.core.scoring) nonconst_MembraneTopology_from_pose() (in module pyrosetta.rosetta.core.scoring) nonconst_monopole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_mp_param() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_other_struct_list() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) nonconst_partners() (pyrosetta.rosetta.core.scoring.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) nonconst_pose() (pyrosetta.rosetta.protocols.multistate_design.PackingState method) (pyrosetta.rosetta.protocols.multistate_design.SingleState method) nonconst_power() (pyrosetta.rosetta.core.scoring.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) nonconst_quadrupole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_rad() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) nonconst_rad2() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) nonconst_res() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) nonconst_resA() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) nonconst_resB() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) nonconst_residue_task() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) nonconst_rKirkwood() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_rna_scoring_info_from_pose() (in module pyrosetta.rosetta.core.scoring.rna) nonconst_rna_task() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) nonconst_rosetta_res_type() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_rotamer() (pyrosetta.rosetta.core.conformation.RotamerSetBase method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) nonconst_stored_induced_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_stored_induced_rf_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) nonconst_vdw_cached_rep_screen_info_from_pose() (in module pyrosetta.rosetta.protocols.scoring) nonconst_vdw_type() (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) nonconst_xyz() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) NonContinuousFrame (class in pyrosetta.rosetta.core.fragment) None (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference attribute) NONE (pyrosetta.rosetta.core.pose.rna.StubStubType attribute) none (pyrosetta.rosetta.core.scoring.MultipoleAxisType attribute) NONE (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingSchemeEnum attribute) None (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover attribute) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover.StructureOutputMode attribute) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe attribute) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe.StructureOutputMode attribute) NONE (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum attribute) none (pyrosetta.rosetta.protocols.network.UIObserver.ObserverType attribute) NONE (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol.FilterReportTime attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateTerminus attribute) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) none (pyrosetta.rosetta.utility.sql_database.TransactionMode attribute) (pyrosetta.rosetta.utility.sql_database.TransactionMode.e attribute) nonlocal_pairs() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) NonlocalContactsCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) nonmatching_residues() (in module pyrosetta.rosetta.core.io.external) nonmonotone() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) nonnegative_principal_angle_degrees() (in module pyrosetta.rosetta.numeric) NONOSE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) nonpivot_residues() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) NonPlaidFingerprint (class in pyrosetta.rosetta.protocols.pockets) nonprot_intrares_evaluator() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) NonResidueTypeConstraint (class in pyrosetta.rosetta.core.scoring.constraints) nonrotameric_chi_sample_wi_nrchi_bin (pyrosetta.rosetta.protocols.match.upstream.ChiStrategy attribute) nonrotameric_chi_sample_wi_nrchi_bin_to_lower_boundary (pyrosetta.rosetta.protocols.match.upstream.ChiStrategy attribute) NonSequentialNeighborsFilter (class in pyrosetta.rosetta.protocols.simple_filters) NonSequentialNeighborsFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) NonTerminalStartingSegmentRequirement (class in pyrosetta.rosetta.protocols.sewing.requirements) NonTerminalStartingSegmentRequirementCreator (class in pyrosetta.rosetta.protocols.sewing.requirements) nonzero_deltas() (pyrosetta.rosetta.core.kinematics.Jump method) nonzero_hbond_weight() (in module pyrosetta.rosetta.core.scoring.hbonds) nonzero_weight_score_types() (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) nonzero_weights() (in module pyrosetta.bindings.energies) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) nonzero_weights_dtype() (in module pyrosetta.bindings.energies) nook_finder() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) nooutput() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) NoOutputJobOutputter (class in pyrosetta.rosetta.protocols.jd2) NoOutputJobOutputterCreator (class in pyrosetta.rosetta.protocols.jd2) NOR (pyrosetta.rosetta.protocols.filters.boolean_operations attribute) (pyrosetta.rosetta.protocols.task_operations.boolean_operations attribute) NoRepackDisulfides (class in pyrosetta.rosetta.core.pack.task.operation) NoRepackDisulfidesCreator (class in pyrosetta.rosetta.core.pack.task.operation) NoResFilter (class in pyrosetta.rosetta.core.pack.task.operation) NoResFilterCreator (class in pyrosetta.rosetta.core.pack.task.operation) norm() (in module pyrosetta.rosetta.numeric.kinematic_closure) (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.MathVector_double_t method) (pyrosetta.rosetta.numeric.Quaternion_double_t method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) norm_error() (pyrosetta.rosetta.numeric.Quaternion_double_t method) norm_factor() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) norm_motif_score() (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyCalciumMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyInterModelMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyPartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorer method) norm_neg() (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter method) norm_prod (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder property) norm_squared() (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.Quaternion_double_t method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) norm_squared_error() (pyrosetta.rosetta.numeric.Quaternion_double_t method) NORM_TYPE_CH (pyrosetta.rosetta.core.scoring.nmr.RDC_NORM_TYPE attribute) NORM_TYPE_NH (pyrosetta.rosetta.core.scoring.nmr.RDC_NORM_TYPE attribute) NORM_TYPE_NONE (pyrosetta.rosetta.core.scoring.nmr.RDC_NORM_TYPE attribute) normal (pyrosetta.rosetta.core.conformation.membrane.MEM attribute) normal() (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) normal_to_ellipsoid() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) normalization() (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) Normalize() (pyrosetta.rosetta.basic.sampling.orientations.Quaternion method) normalize() (pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule method) (pyrosetta.rosetta.core.scoring.epr_deer.EPRSpinLabel method) (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.Quaternion_double_t method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams method) (pyrosetta.rosetta.RDGeom.Point method) (pyrosetta.rosetta.RDGeom.Point3D method) normalize_any() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) normalize_if_needed() (pyrosetta.rosetta.numeric.Quaternion_double_t method) normalize_or_zero() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) normalize_position_in_helix_given_length() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) normalize_to_thk() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) normalized() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) normalized_any() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) normalized_data() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingleSet method) normalized_distance (pyrosetta.rosetta.protocols.antibody.CDRDBPose property) (pyrosetta.rosetta.protocols.antibody.CDRDBSequence property) normalized_distance_in_degrees() (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) normalized_or_zero() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) normalized_peak_volume() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) NORMALIZED_SUM (pyrosetta.rosetta.protocols.calc_taskop_filters.Operation attribute) NormalizedEvaluatedArchive (class in pyrosetta.rosetta.protocols.jd2.archive) normalizing_area() (in module pyrosetta.rosetta.core.scoring) normalizing_area_total() (in module pyrosetta.rosetta.core.scoring) normalizing_area_total_hydrophobic_atoms_only() (in module pyrosetta.rosetta.core.scoring) normalizing_area_total_polar_atoms_only() (in module pyrosetta.rosetta.core.scoring) NormalMode (class in pyrosetta.rosetta.protocols.normalmode) NormalModeMinimizer (class in pyrosetta.rosetta.protocols.normalmode) NormalModeMinimizerCreator (class in pyrosetta.rosetta.protocols.normalmode) NormalModeMultifunc (class in pyrosetta.rosetta.protocols.normalmode) NormalModeRelaxMover (class in pyrosetta.rosetta.protocols.normalmode) NormalModeRelaxMoverCreator (class in pyrosetta.rosetta.protocols.normalmode) NORTH (pyrosetta.rosetta.core.chemical.rna.PuckerState attribute) North (pyrosetta.rosetta.protocols.antibody.CDRDefinitionEnum attribute) NOSETTING (pyrosetta.rosetta.protocols.cryst.SpacegroupSetting attribute) NOT (pyrosetta.rosetta.protocols.filters.boolean_operations attribute) (pyrosetta.rosetta.protocols.task_operations.boolean_operations attribute) not_already_connected() (in module pyrosetta.rosetta.protocols.dna) not_blank() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) not_done() (pyrosetta.rosetta.protocols.jd3.job_distributors.JobExtractor method) NOT_ELIMINATED (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.EliminationReason attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D.EliminationReason attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D.EliminationReason attribute) not_empty() (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) not_end() (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) not_equal_length() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) not_in_pose() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache method) not_normalized() (pyrosetta.rosetta.numeric.Quaternion_double_t method) NOT_SYMBOL (pyrosetta.rosetta.numeric.expression_parser.TokenType attribute) not_token() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTFactor method) not_unbounded() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) not_universal_main() (in module pyrosetta.rosetta.protocols.jobdist) not_using() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) not_valid() (pyrosetta.rosetta.core.conformation.membrane.Span method) not_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) NOTAA (class in pyrosetta.rosetta.core.pack.task) NotConjugableBond (pyrosetta.rosetta.core.chemical.BondConjugability attribute) note_coordinate_change_registered() (pyrosetta.rosetta.core.kinematics.AtomTree method) note_designed_residues() (pyrosetta.rosetta.protocols.dna.PDBOutput method) note_has_pseudobonds() (pyrosetta.rosetta.core.scoring.trie.CPDataCorrespondence method) note_hit_geometry() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) note_job_completed() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobQueen method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.EvenlyPartitionedNodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen method) (pyrosetta.rosetta.protocols.jd3.JobGenealogist method) (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) note_job_completed_and_track() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobQueen method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen method) (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) note_job_no_longer_running() (pyrosetta.rosetta.protocols.jd3.job_distributors.JobExtractor method) note_long_range_interactions_exist() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) note_long_range_interactions_exist_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) note_match_accepted() (pyrosetta.rosetta.protocols.match.output.LimitHitsPerRotamerFilter method) (pyrosetta.rosetta.protocols.match.output.StateAccumulatingMatchFilter method) note_output_match() (pyrosetta.rosetta.protocols.match.MatchOutputTracker method) note_preliminary_job_node_is_complete() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) note_rpe_calculated() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) note_short_range_interactions_exist() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) note_short_range_interactions_exist_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) note_state_substitution_accepted() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) note_submatrix_accessed() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) note_submatrix_added() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) note_vertex_reached() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) notes() (pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleAuthor method) NotExpression (class in pyrosetta.rosetta.numeric.expression_parser) Nothing (pyrosetta.rosetta.utility.CSI.CSI_Enum attribute) notify() (in module pyrosetta.rosetta.ObjexxFCL.internal.ObserverMediator) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) notify_destructed() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) notify_energy_change() (pyrosetta.rosetta.core.pose.metrics.EnergyDependentCalculator method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.InterfaceDefinitionCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.InterfaceDeltaEnergeticsCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.InterfaceNeighborDefinitionCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.InterfaceSasaDefinitionCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.SasaCalculator2 method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.SasaCalculatorLegacy method) (pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator method) (pyrosetta.rosetta.protocols.buns.BuriedUnsatisfiedPolarsCalculator2 method) (pyrosetta.rosetta.protocols.denovo_design.calculators.CavityCalculator method) (pyrosetta.rosetta.protocols.fldsgn.NcontactsCalculator method) (pyrosetta.rosetta.protocols.mean_field.EnergiesByTaskCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.CatPiCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.ChargeCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.ClashCountCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.FragQualCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.HPatchCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborsByDistanceCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NonlocalContactsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.PackstatCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.PiPiCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.ResidueDecompositionByChainCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.ResidueDecompositionCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.RotamerBoltzCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SaltBridgeCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SemiExplicitWaterUnsatisfiedPolarsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SHOBuriedUnsatisfiedPolarsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SurfaceCalculator method) (pyrosetta.rosetta.protocols.simple_pose_metric_calculators.BuriedUnsatisfiedPolarsCalculator method) (pyrosetta.rosetta.protocols.simple_pose_metric_calculators.NumberHBondsCalculator method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDistSasaCalculator method) notify_structure_change() (pyrosetta.rosetta.core.pose.metrics.EnergyDependentCalculator method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.InterfaceDefinitionCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.InterfaceDeltaEnergeticsCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.InterfaceNeighborDefinitionCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.InterfaceSasaDefinitionCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.SasaCalculator2 method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.SasaCalculatorLegacy method) (pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator method) (pyrosetta.rosetta.protocols.buns.BuriedUnsatisfiedPolarsCalculator2 method) (pyrosetta.rosetta.protocols.denovo_design.calculators.CavityCalculator method) (pyrosetta.rosetta.protocols.fldsgn.NcontactsCalculator method) (pyrosetta.rosetta.protocols.mean_field.EnergiesByTaskCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.CatPiCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.ChargeCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.ClashCountCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.FragQualCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.HPatchCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborsByDistanceCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NonlocalContactsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.PackstatCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.PiPiCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.ResidueDecompositionByChainCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.ResidueDecompositionCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.RotamerBoltzCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SaltBridgeCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SemiExplicitWaterUnsatisfiedPolarsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SHOBuriedUnsatisfiedPolarsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SurfaceCalculator method) (pyrosetta.rosetta.protocols.simple_pose_metric_calculators.BuriedUnsatisfiedPolarsCalculator method) (pyrosetta.rosetta.protocols.simple_pose_metric_calculators.NumberHBondsCalculator method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDistSasaCalculator method) NotJumpSelector (class in pyrosetta.rosetta.core.select.jump_selector) NotJumpSelectorCreator (class in pyrosetta.rosetta.core.select.jump_selector) NotResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) NotResidueSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) noutstanding() (pyrosetta.rosetta.utility.graph.ArrayPool_double_t method) Np (pyrosetta.rosetta.core.chemical.element.Elements attribute) nparams (pyrosetta.rosetta.protocols.denovo_design.movers.RelaxScriptCommand property) (pyrosetta.rosetta.protocols.relax.RelaxScriptCommand property) nparams() (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) npd_hb_eval_type_weight() (in module pyrosetta.rosetta.core.scoring.hbonds) npd_hb_weight() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) npd_hbond (pyrosetta.rosetta.core.scoring.ScoreType attribute) npd_hbond_bb_sc (pyrosetta.rosetta.core.scoring.ScoreType attribute) npd_hbond_intra (pyrosetta.rosetta.core.scoring.ScoreType attribute) npd_hbond_lr_bb (pyrosetta.rosetta.core.scoring.ScoreType attribute) npd_hbond_lr_bb_sc (pyrosetta.rosetta.core.scoring.ScoreType attribute) npd_hbond_sc (pyrosetta.rosetta.core.scoring.ScoreType attribute) NPD_HBOND_SET (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) npd_hbond_set() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) npd_hbond_sr_bb (pyrosetta.rosetta.core.scoring.ScoreType attribute) npd_hbond_sr_bb_sc (pyrosetta.rosetta.core.scoring.ScoreType attribute) npd_properties() (pyrosetta.rosetta.protocols.pack_daemon.MPIMultistateFitnessFunction method) (pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction method) NPDHBond (class in pyrosetta.rosetta.core.pack.interaction_graph) NPDHBondEnergy (class in pyrosetta.rosetta.core.energy_methods) NPDHBondEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) NPDHBondSet (class in pyrosetta.rosetta.core.scoring.hbonds) NPDHBSimpleEdge (class in pyrosetta.rosetta.core.pack.interaction_graph) NPDHBSimpleInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) NPDHBSimpleNode (class in pyrosetta.rosetta.core.pack.interaction_graph) NPDPropCalculator (class in pyrosetta.rosetta.protocols.pack_daemon) NPDPropCalculatorCreator (class in pyrosetta.rosetta.protocols.pack_daemon) npEnergy (pyrosetta.rosetta.core.scoring.APBSResult property) nperrun (pyrosetta.rosetta.protocols.mpi_refinement.MethodParams property) npick_per_iter() (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) npoints() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbAcc_t method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbDon_t method) (pyrosetta.rosetta.protocols.simple_moves.AtomHash method) npos() (pyrosetta.rosetta.core.sequence.SequenceCoupling method) nposes() (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) npr() (pyrosetta.rosetta.core.scoring.packstat.PackingScore method) (pyrosetta.rosetta.core.scoring.packstat.PackingScoreResData method) nproc() (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) npx (pyrosetta.rosetta.core.scoring.APBSResult property) npy (pyrosetta.rosetta.core.scoring.APBSResult property) npz (pyrosetta.rosetta.core.scoring.APBSResult property) nr_conformers_violatable_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) nr_fragments() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ShortLoopClosure method) nr_frags() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) nr_frames() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragSetCollection method) (pyrosetta.rosetta.core.fragment.MinimalFragSet method) (pyrosetta.rosetta.core.fragment.OrderedFragSet method) nr_models() (pyrosetta.rosetta.protocols.abinitio.PairingStatistics method) nr_moves() (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) nr_open_slaves() (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.WriteFileSFB method) nr_recepients() (pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer.CM_SuggestFixResidue method) (pyrosetta.rosetta.protocols.topology_broker.SuggestValueMessage method) nr_res_affected() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) nr_residues() (pyrosetta.rosetta.protocols.loops.Loops method) nrad() (pyrosetta.rosetta.core.scoring.packstat.PackingScore method) (pyrosetta.rosetta.core.scoring.packstat.PackingScoreResData method) NRbisafe() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) nrchi_bin_ (pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t property) (pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_float_t property) nrchi_lower_boundary() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) nrchi_mean_ (pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t property) (pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_float_t property) nrchi_prob_minimum_for_extra_samples() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) nrchi_probability() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) nrchi_sample() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) nrchi_sd_ (pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t property) (pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_float_t property) nrchi_start_angle() (pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification method) nrchi_symmetric() (pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification method) nrchi_upper_boundary() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) nread_limit_for_file() (pyrosetta.rosetta.utility.io.FileContentsMap method) nreads_for_file() (pyrosetta.rosetta.utility.io.FileContentsMap method) nremain_reset() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) nres (pyrosetta.rosetta.core.io.external.PsiPredResult property) nres() (pyrosetta.rosetta.core.environment.FoldTreeSketch method) (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.raw_data.DecoyFileData method) (pyrosetta.rosetta.core.io.raw_data.DecoyStruct method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreFileData method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructJSON method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.toolbox.AtomID_Mapper method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) nres_for_graphics (pyrosetta.rosetta.protocols.viewer.GraphicsState property) nres_protein() (in module pyrosetta.rosetta.core.pose) nres_scored (pyrosetta.rosetta.core.energy_methods.RG_Local_MinData property) (pyrosetta.rosetta.core.energy_methods.RG_MinData property) nres_topo() (pyrosetta.rosetta.core.conformation.membrane.SpanningTopology method) nresidue (pyrosetta.rosetta.core.scoring.sc.Atom property) nrot() (pyrosetta.rosetta.protocols.mean_field.AAProb method) nrotamer_offset_for_moltenres() (pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.core.pack_basic.RotamerSetsBase method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) nrotamers() (pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.core.pack_basic.RotamerSetsBase method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) nrotamers_for_moltenres() (pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.core.pack_basic.RotamerSetsBase method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) nrotamers_for_moltenres_in_bbconf() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) nrotamers_for_res() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) nrotamers_for_resid_in_bbconf() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) nrots() (pyrosetta.rosetta.numeric.AxisRotationSampler method) (pyrosetta.rosetta.numeric.UniformRotationSampler method) nrows() (pyrosetta.rosetta.numeric.MathTensor_double_t method) (pyrosetta.rosetta.protocols.frag_picker.LAMBEGO_IO method) (pyrosetta.rosetta.protocols.frag_picker.TorsionBinIO method) nRsteps_ (pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions property) (pyrosetta.rosetta.protocols.electron_density.PoseSphericalSamplesOptions property) (pyrosetta.rosetta.protocols.electron_density.SelectDensityPointsOptions property) nrun (pyrosetta.rosetta.protocols.mpi_refinement.MethodParams property) nsdie (pyrosetta.rosetta.core.scoring.APBSConfig.R_PARAM property) nseq_ (pyrosetta.rosetta.core.scoring.TMscoreStore property) nseq_ref_ (pyrosetta.rosetta.core.scoring.TMscoreStore property) nshells_for_atom() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) nsigmoids() (pyrosetta.rosetta.core.scoring.SmoothScoreTermCoeffs method) nsims (pyrosetta.rosetta.core.scoring.APBSConfig property) nsol() (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) nspans() (pyrosetta.rosetta.core.conformation.membrane.SpanningTopology method) (pyrosetta.rosetta.protocols.membrane.geometry.Embedding method) nsr_gaussians() (pyrosetta.rosetta.core.scoring.CenHBPotential method) nstep (pyrosetta.rosetta.protocols.md.MDscheduleData property) nstep() (pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) nstep_per_update() (pyrosetta.rosetta.protocols.md.Thermostat method) nsteps() (pyrosetta.rosetta.core.optimization.NumDerivCheckData method) (pyrosetta.rosetta.core.optimization.SimpleDerivCheckResult method) nstrand_values() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) nstruct() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) nstruct_centroid() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) nstruct_for_job() (in module pyrosetta.rosetta.protocols.jd3) nstruct_index() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) nstruct_max() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.InnerMultiThreadingJob method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) (pyrosetta.rosetta.protocols.jd3.standard.StandardInnerLarvalJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) nstruct_mode() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) nstruct_repeats() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) nsub_bblock() (pyrosetta.rosetta.protocols.matdes.ClashCheckFilter method) nsymmops() (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) NTERM_CONNECT (pyrosetta.rosetta.core.chemical.VariantType attribute) nterm_included() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) Nterm_offset() (pyrosetta.rosetta.protocols.splice.FindEndpointsOperation method) NTerminalAcetyltransferaseMover (class in pyrosetta.rosetta.protocols.enzymatic_movers) NTerminalAcetyltransferaseMoverCreator (class in pyrosetta.rosetta.protocols.enzymatic_movers) nth_dna_base() (pyrosetta.rosetta.protocols.dna.DNAParameters method) NtoCConstraintGenerator (class in pyrosetta.rosetta.protocols.forge.constraints) NtoCConstraintGeneratorCreator (class in pyrosetta.rosetta.protocols.forge.constraints) nton3_hbond_score() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) ntor() (pyrosetta.rosetta.protocols.normalmode.NormalMode method) ntorsions() (pyrosetta.rosetta.core.optimization.CartesianMinimizerMap method) ntrials() (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) ntries() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) NU (pyrosetta.rosetta.core.id.TorsionType attribute) nu() (pyrosetta.rosetta.core.conformation.Residue method) nu0_components() (pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential method) NU1 (pyrosetta.rosetta.core.chemical.rna.RNA_Torsion attribute) nu1_components() (pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential method) nu1_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) nu1_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) NU2 (pyrosetta.rosetta.core.chemical.rna.RNA_Torsion attribute) nu2_components() (pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential method) nu2_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) nu2_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) nu3_components() (pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential method) nu4_components() (pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential method) nu_angles (pyrosetta.rosetta.core.chemical.rings.RingConformer property) NU_ATOM (pyrosetta.rosetta.core.chemical.GreekDistance attribute) nu_atoms() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) Nub (class in pyrosetta.rosetta.protocols.fold_from_loops.utils) nub() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) NubInitioLoopClosureMover (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) NubInitioLoopClosureMoverCreator (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) NubInitioMover (class in pyrosetta.rosetta.protocols.fold_from_loops) NubInitioMoverCreator (class in pyrosetta.rosetta.protocols.fold_from_loops) NubSegment (class in pyrosetta.rosetta.protocols.fold_from_loops.utils) nucleation_prob() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix method) NUCLEOTIDE_DIPHOSPHATE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) NucleotideMutation (class in pyrosetta.rosetta.protocols.evolution) NucleotideMutationCreator (class in pyrosetta.rosetta.protocols.evolution) nudge_distance_bound() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) Null (class in pyrosetta.rosetta.utility.json_spirit) null_bfs_prune_visitor (class in pyrosetta.rosetta.utility.graph) null_type (pyrosetta.rosetta.utility.json_spirit.Value_type attribute) NullMover (class in pyrosetta.rosetta.protocols.moves) NullPerturber (class in pyrosetta.rosetta.protocols.denovo_design.components) NullPointerError (class in pyrosetta.rosetta.utility.excn) NullPoseFolder (class in pyrosetta.rosetta.protocols.denovo_design.components) NullResourceLocator (class in pyrosetta.rosetta.basic.resource_manager.locator) NullResourceLocatorCreator (class in pyrosetta.rosetta.basic.resource_manager.locator) NullStream (class in pyrosetta.rosetta.basic.resource_manager.locator) num (pyrosetta.rosetta.core.io.RemarkInfo property) (pyrosetta.rosetta.core.scoring.packstat.SimplePDB_Atom property) num_aa_types (pyrosetta.rosetta.core.chemical.AA attribute) num_aa_types() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) num_accepted() (pyrosetta.rosetta.protocols.moves.MoverStatistics method) num_accepted_scores() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) num_accepts() (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) num_atoms() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) num_base_rotamers_total() (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet method) num_bb_clones() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) num_bbconfs() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) num_bins() (pyrosetta.rosetta.core.scoring.motif.XformScore method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.protocols.simple_moves.DOFHistogramRecorder method) num_bondangles() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParam method) num_boundary_res() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) num_boundary_residues (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) num_bulge() (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepSequence method) num_by_cut (pyrosetta.rosetta.core.scoring.motif.XformSummary property) num_bytes() (pyrosetta.rosetta.utility.DenseBoolMap_5_0_t static method) num_cacheable_data_types (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType attribute) (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) num_canonical_aas (pyrosetta.rosetta.core.chemical.AA attribute) num_cav_ball_layers (pyrosetta.rosetta.core.scoring.packstat.SasaOptions property) num_cdr_loops (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) num_chains() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.frags.VallData method) num_chi_angles() (in module pyrosetta.rosetta.core.pose) num_chi_clones() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) num_chi_samples_total() (pyrosetta.rosetta.protocols.match.upstream.FullChiSampleSet method) num_chunk_sets() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) num_chunks() (pyrosetta.rosetta.core.import_pose.libraries.ChunkSet method) (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) num_claimers() (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) num_coef1() (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) num_coef2() (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) num_components() (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) num_considered_muliple_origins (pyrosetta.rosetta.protocols.match.MatcherOutputStats property) num_contact_types (pyrosetta.rosetta.protocols.frag_picker.ContactType attribute) num_context_graph_types (pyrosetta.rosetta.core.scoring.ContextGraphType attribute) num_core_res() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) num_core_residues (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) num_cstType (pyrosetta.rosetta.protocols.jumping.cstType attribute) num_current_pose_loops() (pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph method) num_cutpoint() (pyrosetta.rosetta.core.kinematics.FoldTree method) num_cuts() (pyrosetta.rosetta.core.environment.FoldTreeSketch method) NUM_CYCLIZATION_METHODS (pyrosetta.rosetta.protocols.peptide_deriver.CyclizationMethod attribute) num_deriv() (pyrosetta.rosetta.core.optimization.DerivCheckDataPoint method) (pyrosetta.rosetta.core.optimization.DOF_DataPoint method) num_designable() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) num_dimensions() (pyrosetta.rosetta.numeric.MathNTensor_bool_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_1_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_2_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_4_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_5_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_6_t method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) num_dofs() (pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobians method) num_dofType (pyrosetta.rosetta.protocols.jumping.dofType attribute) num_domains() (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) num_donor_acceptor_groups() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) num_ds_hit_incompatible (pyrosetta.rosetta.protocols.match.MatcherOutputStats property) num_edges() (pyrosetta.rosetta.core.conformation.PointGraphPy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintGraph method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.protocols.jd3.JobDigraph method) (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.DirectedNode method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t method) (pyrosetta.rosetta.utility.graph.LowMemNode method) (pyrosetta.rosetta.utility.graph.Node method) (pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) num_elements() (pyrosetta.rosetta.utility.recent_history_queue method) num_empty_uplist (pyrosetta.rosetta.protocols.match.MatcherOutputStats property) num_entities() (pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence method) NUM_ENTRIES (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolBackboneMinimizationMode attribute) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolBackboneRandomizationMode attribute) num_enz_cst_template_res() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo method) num_features_proq2() (pyrosetta.rosetta.core.scoring.ProQPotential method) num_features_proqm() (pyrosetta.rosetta.core.scoring.ProQPotential method) num_fragments_ (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore property) num_fragpick() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) num_geom_cst() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) num_hbond_acceptors() (in module pyrosetta.rosetta.core.pose) num_hbond_donors() (in module pyrosetta.rosetta.core.pose) num_heavy_atoms() (in module pyrosetta.rosetta.core.pose) num_heavy_unsat (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) num_helices_w_hbond() (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) num_hits() (pyrosetta.rosetta.core.scoring.motif.MotifHits method) num_hits1() (pyrosetta.rosetta.core.scoring.motif.MotifHits method) num_hits2() (pyrosetta.rosetta.core.scoring.motif.MotifHits method) num_independent_residues() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) num_input_structs() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) num_interactions() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions method) num_interfaces() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) num_intermolecular_hbonds() (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) num_intermolecular_hbs (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) num_iterations() (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) num_jobs() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.EvenlyPartitionedNodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) num_jobs_completed() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.EvenlyPartitionedNodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) num_jobs_submitted() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.EvenlyPartitionedNodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) num_jump() (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) num_jump_clones() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) num_jumps() (pyrosetta.rosetta.core.environment.FoldTreeSketch method) num_lines_in_file() (in module pyrosetta.rosetta.protocols.cluster.calibur) num_loop() (pyrosetta.rosetta.protocols.loops.Loops method) num_loops() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) num_lower_neighbors() (pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) num_mcfi_lists() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) num_mcfis() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) num_motifs() (pyrosetta.rosetta.core.scoring.motif.MotifHash method) num_moving_chunks() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) num_negative_states() (pyrosetta.rosetta.protocols.multistate_design.MultiStateFitnessFunction method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) num_neighbors() (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) (pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) num_neighbors_ (pyrosetta.rosetta.protocols.cluster.calibur.AdjacentList property) (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) (pyrosetta.rosetta.protocols.legacy_sewing.SewResidue property) num_neighbors_counting_self() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.utility.graph.DirectedNode method) (pyrosetta.rosetta.utility.graph.Node method) (pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) num_neighbors_counting_self_static() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.utility.graph.Node method) num_new_neighbors_ (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.DataBuffer property) num_nodes() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintGraph method) (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) (pyrosetta.rosetta.protocols.jd3.JobDigraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t method) num_non_up_only_incompatible (pyrosetta.rosetta.protocols.match.MatcherOutputStats property) num_npd_properties() (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction method) (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunctionDriver method) num_npd_properties_for_state() (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction method) (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunctionDriver method) num_orbital_types (pyrosetta.rosetta.core.chemical.orbitals.orbital_type_enum attribute) num_origins() (pyrosetta.rosetta.protocols.pockets.FingerprintBase method) (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) num_packed() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) num_pairings() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) num_parameters() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) num_partitions() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManagerStorageMatrix method) num_pose_minimize() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) num_poses() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) num_positions() (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) num_positive_states() (pyrosetta.rosetta.protocols.multistate_design.MultiStateFitnessFunction method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) num_possible_bins() (pyrosetta.rosetta.core.scoring.motif.XformScore method) num_potential_matches (pyrosetta.rosetta.protocols.match.MatcherOutputStats property) num_pts() (pyrosetta.rosetta.protocols.cluster.APCluster method) num_random_samples() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) (pyrosetta.rosetta.protocols.stepwise.StepWiseSampleAndScreen method) num_random_samples_ (pyrosetta.rosetta.protocols.stepwise.StepWiseSampleAndScreen property) num_rejections() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) num_residue_ (pyrosetta.rosetta.protocols.cluster.calibur.PreloadedPDB property) (pyrosetta.rosetta.protocols.cluster.calibur.SimPDB property) num_residues() (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence method) num_results_to_keep() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.EvenlyPartitionedNodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) num_results_to_keep_for_stage() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) num_results_total() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.EvenlyPartitionedNodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) num_rings() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) NUM_RM_TYPES (pyrosetta.rosetta.core.scoring.motif.RM_Type attribute) num_rotamers() (pyrosetta.rosetta.core.conformation.RotamerSetBase method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) NUM_RPM_TYPES (pyrosetta.rosetta.core.scoring.motif.RPM_Type attribute) num_samples() (pyrosetta.rosetta.basic.sampling.orientations.QuaternionGrid method) num_sampling_rotamers_total() (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet method) num_screeners() (pyrosetta.rosetta.protocols.stepwise.StepWiseSampleAndScreen method) NUM_SEGMENT_TYPES (pyrosetta.rosetta.protocols.denovo_design.components.SegmentCounts attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentCounts.SegmentType attribute) num_segments() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) num_selectors() (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) num_sent_to_proc (pyrosetta.rosetta.protocols.match.MatcherOutputStats property) num_seqpos_lists() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) num_sets() (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) num_sheets() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet method) num_simulated_annealing_rounds_centroid() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) num_slidablejumps() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) num_stages() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) num_states() (pyrosetta.rosetta.protocols.multistate_design.MultiStateFitnessFunction method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction method) (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunctionDriver method) num_states_for_aa_for_bb() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) num_states_for_bb() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) num_states_per_backbone_for_moltenres() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) num_states_total() (pyrosetta.rosetta.utility.LexicographicalIterator method) num_steps() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) num_steps_per_simulated_annealing_round_centroid() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) num_strands (pyrosetta.rosetta.core.io.SHEETInformation property) num_strands() (in module pyrosetta.rosetta.protocols.denovo_design.components) (pyrosetta.rosetta.protocols.fldsgn.topology.Sheet method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) num_strings() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) num_successes() (pyrosetta.rosetta.protocols.stepwise.StepWiseSampleAndScreen method) num_surrounding_sasa_bins (pyrosetta.rosetta.core.scoring.packstat.SasaOptions property) num_target_states() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) num_to_be_packed() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) num_to_dock() (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) num_total_residues() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) num_total_residues_with_pseudo() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) num_total_residues_without_pseudo() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) num_trials() (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) num_tries() (pyrosetta.rosetta.protocols.stepwise.StepWiseSampleAndScreen method) num_triggers() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) num_try_div() (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) num_types (pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobianTypeEnum attribute) num_undefined_coef1() (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) num_undefined_coef2() (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) num_unsat_Hpol (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) num_up_only_incompatible (pyrosetta.rosetta.protocols.match.MatcherOutputStats property) num_upper_neighbors() (pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) num_vertices() (pyrosetta.rosetta.core.conformation.PointGraphPy method) (pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) num_virtuals() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) num_water() (pyrosetta.rosetta.core.scoring.packstat.SimplePDB method) numAtomRings() (pyrosetta.rosetta.RDKit.RingInfo method) number (pyrosetta.rosetta.protocols.canonical_sampling.TorsionSpec property) Number() (pyrosetta.rosetta.basic.sampling.orientations.Permute method) (pyrosetta.rosetta.basic.sampling.orientations.QuatSet method) number() (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer method) number_bonded_heavyatoms() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) number_bonded_hydrogens() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) number_heavy_chain() (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) number_light_chain() (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) number_of_atoms() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) number_of_basepairs() (pyrosetta.rosetta.protocols.dna.DNAParameters method) number_of_bases() (pyrosetta.rosetta.protocols.dna.DNAParameters method) number_of_basesteps() (pyrosetta.rosetta.protocols.dna.DNAParameters method) number_of_configuration_keywords (pyrosetta.rosetta.protocols.loops.LoopConfiguration attribute) number_of_high_resolution_cycles() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) number_of_loop_refine_inner_cycle_names (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleName attribute) number_of_moves() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) number_of_patchdock_entries() (pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader method) number_of_ramachandran_hashes (pyrosetta.rosetta.protocols.features.RamachandranHash attribute) number_of_residue_identifiers (pyrosetta.rosetta.protocols.loops.ResidueIdentifier attribute) number_of_residues() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.chromophore.ChromophoreDataReader method) (pyrosetta.rosetta.protocols.chromophore.ReadResidueCoordinatesFromPDB method) number_to_propagate() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) NumberBondingPOrbitals (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference attribute) NumberBondingSOrbitals (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference attribute) Numberer (class in pyrosetta.rosetta.protocols.antibody.grafting) NumberHBondsCalculator (class in pyrosetta.rosetta.protocols.simple_pose_metric_calculators) NumberHybridOrbitalType (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.HybridOrbitalType attribute) numbering_scheme (pyrosetta.rosetta.protocols.antibody.AntibodyNumbering property) numbering_scheme() (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) numbering_scheme_ (pyrosetta.rosetta.protocols.antibody.design.MutantPosition property) numbering_scheme_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) numbering_scheme_is_present() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) numbering_scheme_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) numbering_scheme_transform (pyrosetta.rosetta.protocols.antibody.AntibodyNumbering property) NumberLonePairOrbitals (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference attribute) NumberOfAtomicOrbitalTypes (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.AtomicOrbitalTypes attribute) numberOfAtoms() (pyrosetta.rosetta.protocols.pockets.SmallMol method) NumberOfProperties (pyrosetta.rosetta.core.chemical.Element attribute) (pyrosetta.rosetta.core.chemical.Element.Properties attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) NumberTypeDifferences (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference attribute) numBondRings() (pyrosetta.rosetta.RDKit.RingInfo method) numchanges() (in module pyrosetta.rosetta.numeric.kinematic_closure) NumDerivCheckData (class in pyrosetta.rosetta.core.optimization) numeric_properties() (pyrosetta.rosetta.core.chemical.ResidueProperties method) numerical_derivative_check() (in module pyrosetta.rosetta.core.optimization) (in module pyrosetta.rosetta.core.optimization.symmetry) NumericalDerivCheckResult (class in pyrosetta.rosetta.core.optimization) NumericTraits_double_t (class in pyrosetta.rosetta.numeric) NumericTraits_float_t (class in pyrosetta.rosetta.numeric) NumericTraits_long_double_t (class in pyrosetta.rosetta.numeric) numGaussians() (pyrosetta.rosetta.core.scoring.func.USOGFunc method) NUMMD (pyrosetta.rosetta.core.io.pdb.RecordType attribute) NumNeighborsMPM (class in pyrosetta.rosetta.protocols.match) NumNeighborsSelector (class in pyrosetta.rosetta.core.select.residue_selector) NumNeighborsSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) numRings() (pyrosetta.rosetta.RDKit.RingInfo method) numroots() (in module pyrosetta.rosetta.numeric.kinematic_closure) nus() (pyrosetta.rosetta.core.conformation.Residue method) nusing() (pyrosetta.rosetta.core.energy_methods.GoapRsdType method) nvar() (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) NVlookup (class in pyrosetta.rosetta.core.scoring.nv) NVscore (class in pyrosetta.rosetta.core.scoring.nv) NVscoreCreator (class in pyrosetta.rosetta.core.scoring.nv) NWAligner (class in pyrosetta.rosetta.core.sequence) NWDP_TM() (pyrosetta.rosetta.protocols.hybridization.TMalign method) nwrites (pyrosetta.rosetta.core.scoring.APBSResult property) Nx_ (pyrosetta.rosetta.core.scoring.packstat.Array2D property) Ny_ (pyrosetta.rosetta.core.scoring.packstat.Array2D property)