Index – C

C() (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) c0() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) c1() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) c1prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) c2() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) c2prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) c3() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) c3prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) c4prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) c5prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) c_alpha_index() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) c_array_mult() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) C_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) c_beta_index() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) c_mult_ip() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) c_n() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) c_n_bond() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) c_n_ca() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) c_n_ca_angle() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) c_segment() (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) c_str() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) c_terminal_constraint_strength() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) c_terminus_size() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) c_xyz() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) CA() (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) CA_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) ca_c() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) ca_c_bond() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) ca_c_n() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) ca_c_n_angle() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) Ca_coords() (in module pyrosetta.rosetta.protocols.protein_interface_design.filters) CA_gdtmm() (in module pyrosetta.rosetta.core.scoring) CA_gdttm() (in module pyrosetta.rosetta.core.scoring) CA_maxsub() (in module pyrosetta.rosetta.core.scoring) CA_or_equiv_rmsd() (in module pyrosetta.rosetta.core.scoring) CA_rmsd() (in module pyrosetta.rosetta.core.scoring) CA_rmsd_symmetric() (in module pyrosetta.rosetta.core.scoring) CA_Sscore() (in module pyrosetta.rosetta.protocols.mpi_refinement) CA_superimpose() (in module pyrosetta.rosetta.protocols.toolbox) ca_xyz() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) CaCbCb_Angle_Func (class in pyrosetta.rosetta.core.scoring.disulfides) CaCbCbCa_Dihedral_Func (class in pyrosetta.rosetta.core.scoring.disulfides) cache() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) cache_fragments() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) cache_limit() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) cache_pose() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) cache_profile() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) cache_resfile() (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) cache_tag() (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) cache_task() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) CacheableAtomID_MapVector (class in pyrosetta.rosetta.core.id) CacheableData (class in pyrosetta.rosetta.basic.datacache) CacheableObserver (class in pyrosetta.rosetta.core.pose.datacache) CacheableObserverType (class in pyrosetta.rosetta.core.pose.datacache) CacheablePoseRawPtr (class in pyrosetta.rosetta.core.pose.datacache) CacheableResidueTypeSets (class in pyrosetta.rosetta.core.chemical) CacheableString (class in pyrosetta.rosetta.basic.datacache) CacheableStringFloatMap (class in pyrosetta.rosetta.basic.datacache) CacheableStringMap (class in pyrosetta.rosetta.basic.datacache) cached_score() (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) cal_delta_internal_coordinates() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) cal_delta_internal_coordinates_squared() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) cal_dis_angle_to_find_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) cal_distance() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) cal_distance_squared() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) cal_min_avg_dis_between_sheets_by_cen_res() (in module pyrosetta.rosetta.protocols.features.strand_assembly) cal_min_avg_dis_between_two_sheets_by_cen_res() (in module pyrosetta.rosetta.protocols.features.strand_assembly) cal_min_dis_between_sheets_by_all_res() (in module pyrosetta.rosetta.protocols.features.strand_assembly) cal_min_dis_between_two_sheets_by_all_res() (in module pyrosetta.rosetta.protocols.features.strand_assembly) cal_num_of_sheets_that_surround_this_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) cal_shortest_dis_between_facing_aro_in_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) Calc() (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) calc_all_averages() (in module pyrosetta.rosetta.protocols.unfolded_state_energy_calculator) calc_all_dist() (in module pyrosetta.rosetta.protocols.make_rot_lib) calc_angle_rmsd() (in module pyrosetta.rosetta.protocols.membrane) calc_bb_boltz_probs() (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) calc_boltz_score() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) calc_CA_Irmsd() (in module pyrosetta.rosetta.protocols.docking) calc_centroids() (in module pyrosetta.rosetta.protocols.make_rot_lib) calc_delta_sasa() (in module pyrosetta.rosetta.protocols.fldsgn.topology) calc_dihedral() (in module pyrosetta.rosetta.protocols.denovo_design.movers) (in module pyrosetta.toolbox.numpy_utils) calc_dist() (in module pyrosetta.rosetta.protocols.make_rot_lib) calc_exp_value_rot_matrix() (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) calc_Fnat() (in module pyrosetta.rosetta.protocols.docking) calc_Fnonnat() (in module pyrosetta.rosetta.protocols.docking) calc_geometry() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) calc_helix_axis() (in module pyrosetta.rosetta.protocols.membrane) calc_helix_tilt_angle() (in module pyrosetta.rosetta.protocols.membrane) calc_interacting_vector() (in module pyrosetta.rosetta.core.select.util) calc_interaction_energy() (in module pyrosetta.rosetta.protocols.docking) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) calc_interface_vector() (in module pyrosetta.rosetta.core.select.util) calc_intf_score() (in module pyrosetta.rosetta.protocols.docking) calc_Irmsd() (in module pyrosetta.rosetta.protocols.docking) calc_kl_divergence() (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) calc_Lrmsd() (in module pyrosetta.rosetta.protocols.docking) calc_P1rmsd() (in module pyrosetta.rosetta.protocols.docking) calc_P2rmsd() (in module pyrosetta.rosetta.protocols.docking) calc_per_atom_sasa() (in module pyrosetta.rosetta.core.scoring) calc_per_atom_sasa_sc() (in module pyrosetta.rosetta.core.scoring) calc_per_res_hydrophobic_sasa() (in module pyrosetta.rosetta.core.scoring) calc_quadratic() (in module pyrosetta.rosetta.basic) calc_res_contact() (in module pyrosetta.rosetta.protocols.docking) calc_rms() (in module pyrosetta.rosetta.numeric.model_quality) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) calc_rms_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) calc_rotamer_clusters() (in module pyrosetta.rosetta.protocols.make_rot_lib) calc_rsd_sasa() (in module pyrosetta.rosetta.protocols.forge.methods) calc_std_dev() (in module pyrosetta.rosetta.protocols.make_rot_lib) calc_strand_helix_angle() (in module pyrosetta.rosetta.protocols.fldsgn.topology) calc_strand_pairing_set() (in module pyrosetta.rosetta.protocols.fldsgn.topology) calc_total_sasa() (in module pyrosetta.rosetta.core.scoring) calc_vector_boltzmann() (in module pyrosetta.rosetta.protocols.unfolded_state_energy_calculator) calc_vector_mean() (in module pyrosetta.rosetta.protocols.unfolded_state_energy_calculator) calc_vector_median() (in module pyrosetta.rosetta.protocols.unfolded_state_energy_calculator) calc_vector_mode() (in module pyrosetta.rosetta.protocols.unfolded_state_energy_calculator) CalcInterNeighborGroup (class in pyrosetta.rosetta.protocols.toolbox) CalcSc() (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) calculate() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) calculate_atom_id_domain_map() (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap method) calculate_axes() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) calculate_center_xyz() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) calculate_chi2_free() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) calculate_dihedral_distance() (in module pyrosetta.rosetta.protocols.antibody.clusters) calculate_dihedral_w_4_resnums() (in module pyrosetta.rosetta.protocols.features.strand_assembly) calculate_energy() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) calculate_frh_frl() (in module pyrosetta.rosetta.protocols.antibody.grafting) calculate_geometry() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) calculate_highres_ref_energy() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) calculate_I_of_E() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) calculate_interface_score() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) calculate_intra_res_hbonds() (in module pyrosetta.rosetta.core.scoring.hbonds) calculate_inverting_virtuals() (in module pyrosetta.rosetta.core.conformation.symmetry) calculate_jacobians() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) calculate_lowres_ref_energy() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) calculate_neighbor_table() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) calculate_per_residue_interface_score() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) calculate_plane_axes() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) calculate_rigid_matrix() (in module pyrosetta.rosetta.core.chemical) calculate_stability_metric() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) calculate_statistics() (in module pyrosetta.rosetta.protocols.ncbb) calculate_total_cst_score() (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) calculate_tracer_visibilities() (pyrosetta.rosetta.basic.Tracer method) calculate_water_overcoordinated_hb_correction() (in module pyrosetta.rosetta.protocols.hydrate) calculated() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) calculator_id() (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 method) calibration_atom_type() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) call_output_observers() (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) call_setup() (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) calpha_superimpose_pose() (in module pyrosetta.rosetta.core.scoring) calpha_superimpose_with_mapping() (in module pyrosetta.rosetta.core.sequence) CamShiftEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) can_be_deleted() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) can_hold_another() (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.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) cancel_batches_previous_to() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) candidate_res_atoms_reqd_near_target_atom() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) CandidatesCollector (class in pyrosetta.rosetta.protocols.frag_picker) canonical() (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary method) canonical_atom_count() (in module pyrosetta.rosetta.core.pose) canonical_base_pair_step_library() (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_LibraryManager method) canonical_residue_count() (in module pyrosetta.rosetta.core.pose) canonical_sampling_main() (in module pyrosetta.rosetta.protocols.canonical_sampling) canonicalize() (in module pyrosetta.rosetta.protocols.denovo_design.components) capacity() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) carbohydrate_info() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) CarbohydrateInfoManager (class in pyrosetta.rosetta.core.chemical.carbohydrates) carry_out_filtering() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) cart_min() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) cart_numerical_derivative_check() (in module pyrosetta.rosetta.core.optimization) cartesian() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) cartesian_collect_atompairE_deriv() (in module pyrosetta.rosetta.core.optimization) cartesian_collect_torsional_deriv() (in module pyrosetta.rosetta.core.optimization) cartesian_dfunc() (in module pyrosetta.rosetta.core.optimization) CartesianBondedEnergy (class in pyrosetta.rosetta.core.scoring.methods) CartesianMinimizer (class in pyrosetta.rosetta.core.optimization) CartesianMultifunc (class in pyrosetta.rosetta.core.optimization) case_from_lines() (in module pyrosetta.rosetta.core.chemical) catalog() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) catalytic_res() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) CB() (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) CB_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) cb_dist_cut() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) CB_dist_cutoff() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation method) Cb_Distance_Func (class in pyrosetta.rosetta.core.scoring.disulfides) cb_force() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) cb_weight() (in module pyrosetta.rosetta.protocols.sic_dock) cb_weight_map_from_pose() (in module pyrosetta.rosetta.protocols.sic_dock) cb_weights_from_map() (in module pyrosetta.rosetta.protocols.sic_dock) cb_weights_from_pose() (in module pyrosetta.rosetta.protocols.sic_dock) cbx() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) cby() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) cbz() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) ccd_angle() (in module pyrosetta.rosetta.numeric) ccd_close() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) ccd_close_loops() (in module pyrosetta.rosetta.protocols.loops) CCDEndsGraftMover (class in pyrosetta.rosetta.protocols.grafting) CCDLoopClosureMover (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) CCDLoopClosureMoverCreator (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) CCluster (class in pyrosetta.rosetta.protocols.pockets) CClusterSet (class in pyrosetta.rosetta.protocols.pockets) CD (class in pyrosetta) cd_1b_types() (pyrosetta.rosetta.core.scoring.ScoreFunction method) cd_2b_begin() (pyrosetta.rosetta.core.scoring.ScoreFunction method) cd_2b_end() (pyrosetta.rosetta.core.scoring.ScoreFunction method) cd_2b_intrares_begin() (pyrosetta.rosetta.core.scoring.ScoreFunction method) cd_2b_intrares_end() (pyrosetta.rosetta.core.scoring.ScoreFunction method) cd_2b_types() (pyrosetta.rosetta.core.scoring.ScoreFunction method) cd_lr_2b_methods_begin() (pyrosetta.rosetta.core.scoring.ScoreFunction method) cd_lr_2b_methods_end() (pyrosetta.rosetta.core.scoring.ScoreFunction method) cd_lr_2b_types() (pyrosetta.rosetta.core.scoring.ScoreFunction method) cdr() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) cdr1_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) cdr2_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) cdr3_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) cdr_cluster_enum_to_string() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) cdr_cluster_is_present() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) cdr_cluster_string_to_enum() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) cdr_CN_anchor_distance() (in module pyrosetta.rosetta.protocols.antibody) cdr_definition_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_definition_is_present() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_definition_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) CDR_Detector (class in pyrosetta.rosetta.protocols.antibody.grafting) cdr_energy() (in module pyrosetta.rosetta.protocols.antibody) CDR_H3_cter_filter() (in module pyrosetta.rosetta.protocols.antibody) CDR_H3_filter() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) CDR_H3_filter_legacy_code_with_old_rule() (in module pyrosetta.rosetta.protocols.antibody) cdr_has_res_constraints() (in module pyrosetta.rosetta.protocols.antibody.constraints) cdr_landmark_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_landmark_is_present() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_landmark_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_name_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_name_is_present() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_name_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_overhang() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) CDRCluster (class in pyrosetta.rosetta.protocols.antibody.clusters) CDRClusterEnum (class in pyrosetta.rosetta.protocols.antibody.clusters) CDRClusterEnumManager (class in pyrosetta.rosetta.protocols.antibody.clusters) CDRClusterMatcher (class in pyrosetta.rosetta.protocols.antibody.clusters) CDRClusterSet (class in pyrosetta.rosetta.protocols.antibody.clusters) CDRDihedralConstraintMover (class in pyrosetta.rosetta.protocols.antibody.constraints) CDRGraftDesignOptions (class in pyrosetta.rosetta.protocols.antibody.design) CDRH3Modeler (class in pyrosetta.rosetta.protocols.antibody_legacy) CDRLandmarkEnum (class in pyrosetta.rosetta.protocols.antibody) CDRResidueSelector (class in pyrosetta.rosetta.protocols.antibody.residue_selector) CDRSetOptions (class in pyrosetta.rosetta.protocols.antibody) CDRSetOptionsParser (class in pyrosetta.rosetta.protocols.antibody) cen_dist10_pad() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist10_pad_hinv() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist10_pad_minus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist10_pad_plus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist12_pad() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist12_pad_hinv() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist12_pad_minus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist12_pad_plus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist5_pad() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist5_pad_hinv() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist5_pad_minus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist5_pad_plus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist6_pad() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist6_pad_hinv() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist6_pad_plus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist7_pad() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist7_pad_hinv() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist7_pad_minus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist7_pad_plus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) Cen_Distance_Func (class in pyrosetta.rosetta.core.scoring.disulfides) Cend_orient() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) Cend_pos() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) cenlist_from_pose() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) CenListInfo (class in pyrosetta.rosetta.core.scoring) CenrotLibrary (class in pyrosetta.rosetta.core.pack.dunbrack.cenrot) center() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.core.id.NamedStubID method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.kinematics.Stub method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) center_of_geom() (in module pyrosetta.rosetta.protocols.sic_dock) center_of_mass() (in module pyrosetta.rosetta.core.pose) (in module pyrosetta.rosetta.protocols.geometry) (pyrosetta.rosetta.protocols.loops.Loops method) center_residues() (in module pyrosetta.rosetta.protocols.cluster.calibur) centered() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) central_residue() (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator method) central_residue_group_selector() (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) central_residues() (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator method) centroid() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) centroid_by_chain() (in module pyrosetta.rosetta.protocols.geometry) centroid_by_chains() (in module pyrosetta.rosetta.protocols.geometry) centroid_by_residues() (in module pyrosetta.rosetta.protocols.geometry) centroid_dist() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) centroid_output() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) centroid_pair_by_jump() (in module pyrosetta.rosetta.protocols.geometry) centroid_pose_from_pdb() (in module pyrosetta.rosetta.core.import_pose) centroid_scatter() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) centroid_score_diff_cut() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) centroid_scorefxn() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) centroid_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) centroid_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) centroid_weights() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) CentroidDisulfideEnergyComponents (class in pyrosetta.rosetta.core.scoring.disulfides) CentroidDisulfideNeighborConstIterator (class in pyrosetta.rosetta.core.scoring.disulfides) CentroidDisulfideNeighborIterator (class in pyrosetta.rosetta.core.scoring.disulfides) CentroidDisulfidePotential (class in pyrosetta.rosetta.core.scoring.disulfides) CentroidRelax (class in pyrosetta.rosetta.protocols.relax) CentroidRotamerSampleData (class in pyrosetta.rosetta.core.pack.dunbrack.cenrot) centroids_by_jump() (in module pyrosetta.rosetta.protocols.geometry) centroids_by_jump_int() (in module pyrosetta.rosetta.protocols.geometry) CentroidScatter (class in pyrosetta.rosetta.core.scoring.fiber_diffraction) cenx() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) ceny() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) cenz() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) cfg_nd() (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) cfg_r() (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) chain() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation method) chain_begin() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) chain_com() (in module pyrosetta.rosetta.protocols.membrane) chain_cut() (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) chain_end() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) chain_end_res() (in module pyrosetta.rosetta.core.pose) chain_endings() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) chain_gws_string() (in module pyrosetta.rosetta.core.io.carbohydrates) chain_id() (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) chain_lt (class in pyrosetta.rosetta.protocols.pose_length_moves) chain_num() (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) chain_pair_pose_prepared() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) chain_sequence() (pyrosetta.rosetta.core.pose.Pose method) chain_sequences() (pyrosetta.rosetta.core.io.StructFileRep method) chain_tm_com() (in module pyrosetta.rosetta.protocols.membrane) ChainBreak (class in pyrosetta.rosetta.protocols.simple_filters) ChainbreakEnergy (class in pyrosetta.rosetta.core.scoring.methods) chainbreaks() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) ChainedSolutionList (class in pyrosetta.rosetta.protocols.kinematic_closure) chainID() (pyrosetta.rosetta.core.io.ResidueInformation method) chains() (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) chains_from_termini() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) chains_in_full_model() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) chains_whose_residues_are_separate_chemical_entities() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) ChainSplitMover (class in pyrosetta.rosetta.protocols.simple_moves) chainXYZ() (in module pyrosetta.rosetta.numeric.kinematic_closure) (in module pyrosetta.rosetta.numeric.kinematic_closure.radians) change_bond_type() (pyrosetta.rosetta.core.chemical.ResidueType method) change_chi_without_replacing_residue() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) change_cys_state() (in module pyrosetta.rosetta.core.conformation) change_foldtree() (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) change_sheet_id_if_possible() (in module pyrosetta.rosetta.protocols.features.strand_assembly) change_weight() (pyrosetta.rosetta.protocols.moves.MonteCarlo method) ChangeAndResetFoldTreeMover (class in pyrosetta.rosetta.protocols.simple_moves) ChangeBondType (class in pyrosetta.rosetta.core.chemical) changed() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) changes_connections_on() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (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.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase 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.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.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius 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) channel() (pyrosetta.rosetta.basic.Tracer method) channel_color() (pyrosetta.rosetta.basic.Tracer method) channel_name_color() (pyrosetta.rosetta.basic.Tracer method) CHAR() (in module pyrosetta.rosetta.ObjexxFCL.Fortran) char_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) char_to_int() (in module pyrosetta.rosetta.core.io.carbohydrates) char_type() (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) char_valid_as_torsion_bin() (in module pyrosetta.rosetta.core.conformation) charge() (pyrosetta.rosetta.core.chemical.Atom method) ChargeAtom (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) ChargeChargeFeaturesCreator (class in pyrosetta.rosetta.protocols.features) charged() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) CharmmPeriodicFunc (class in pyrosetta.rosetta.core.scoring.func) check() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) check_all_ligand_atoms() (in module pyrosetta.rosetta.protocols.ligand_docking.ligand_options) check_all_residues_sampled() (in module pyrosetta.rosetta.core.pose.full_model_info) check_and_correct_sister_atom_based_on_chirality() (in module pyrosetta.rosetta.core.io.pose_from_sfr) check_and_correct_sister_atom_based_on_outgroup() (in module pyrosetta.rosetta.core.io.pose_from_sfr) check_and_correct_sister_atoms() (in module pyrosetta.rosetta.core.io.pose_from_sfr) check_base_pair() (in module pyrosetta.rosetta.protocols.rna.denovo) check_binary_chars() (in module pyrosetta.rosetta.core.io.serialization) check_binary_unsigned_int() (in module pyrosetta.rosetta.core.io.serialization) check_bounds() (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) check_can_append() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) check_can_prepend() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) check_canonicalness_of_LR() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_canonicalness_of_PA() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_canonicalness_of_parallel_EE() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_cb() (in module pyrosetta.rosetta.protocols.antibody.design) check_clear_for_stacking() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) check_closure() (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) check_consistency() (pyrosetta.rosetta.core.conformation.signals.LengthEvent method) check_deprecated_flags() (in module pyrosetta.rosetta.core.init) check_domain_map() (pyrosetta.rosetta.core.scoring.NeighborList method) check_edges_for_atom_info() (pyrosetta.rosetta.core.kinematics.FoldTree method) check_extra_minimize_res_are_input() (in module pyrosetta.rosetta.core.import_pose) check_fa_dun() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) check_filters() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) check_fix_aho_cdr_numbering() (in module pyrosetta.rosetta.protocols.antibody) check_fold_tree() (pyrosetta.rosetta.core.kinematics.FoldTree method) check_fold_tree_OK() (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) check_for_base_neighbor() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) check_for_input_domain() (in module pyrosetta.rosetta.protocols.stepwise.modeler) check_for_messed_up_structure() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) check_for_symmetric_peaks() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) check_forming_base_pair() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) check_forward_backward() (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary method) check_frequency() (pyrosetta.rosetta.protocols.moves.MonteCarlo method) check_full_model_info_OK() (in module pyrosetta.rosetta.core.pose.full_model_info) check_good_cutpoint_neighbour() (in module pyrosetta.rosetta.core.conformation) check_hairpin() (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) check_heading_direction() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_helix_existence() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_if_connected_residues_belong_to_regions() (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) check_if_pose_renumbered_for_clusters() (in module pyrosetta.rosetta.protocols.antibody.clusters) check_if_proton_chi_atom() (in module pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens) check_if_residues_are_Ctermini() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) check_if_residues_are_Ntermini() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) check_in_base_pair_list() (in module pyrosetta.rosetta.core.pose.rna) check_instantiated_O2Prime_hydrogen() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) check_is_working_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) check_jump_to_next_residue_in_chain() (in module pyrosetta.rosetta.protocols.stepwise.modeler) check_jump_to_previous_residue_in_chain() (in module pyrosetta.rosetta.protocols.stepwise.modeler) check_key() (pyrosetta.rosetta.utility.options.OptionCollection method) check_kink_helix() (in module pyrosetta.rosetta.protocols.fldsgn.topology) check_loops() (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) check_LR() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_membrane_fold_tree() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) check_methods_in_right_order() (pyrosetta.rosetta.core.scoring.ScoreFunction method) check_mmt() (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) check_neighbor_ligand_atom() (in module pyrosetta.rosetta.protocols.ligand_docking.ligand_options) check_overlap() (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) check_PA() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_phosphate_contacts_donor() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) check_pleat() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) check_pose_tree_compatibility() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) check_rama() (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) check_rama2() (pyrosetta.rosetta.core.sequence.ABEGO method) check_rama_scores() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) check_range() (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) check_relevant_residues() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) check_relevant_residues_range() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) check_restricted_access() (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.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) check_rna_loop() (in module pyrosetta.rosetta.core.scoring.rna) check_sample_sugar_in_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) check_score() (in module pyrosetta.rosetta.protocols.ligand_docking) check_score_function_sanity() (in module pyrosetta.rosetta.core.init) check_scorefxn_has_constraint_terms_if_pose_has_constraints() (in module pyrosetta.rosetta.protocols.stepwise.modeler) check_setup() (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) check_specs() (pyrosetta.rosetta.utility.options.OptionCollection method) check_ss() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) check_stack() (in module pyrosetta.rosetta.core.scoring.rna) check_statement_sanity() (in module pyrosetta.rosetta.basic.database) check_status() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) check_strand_too_closeness() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_surface_area_leerichards_deriv() (in module pyrosetta.rosetta.core.scoring.packstat) check_sw_by_dis() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_valid_membrane() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) check_validity_and_get_working_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) check_value() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) check_values() (pyrosetta.rosetta.utility.options.OptionCollection method) check_vector() (in module pyrosetta.rosetta.protocols.membrane) check_watson_crick_sequence() (in module pyrosetta.rosetta.core.scoring.rna) check_whether_hairpin_connects_short_strand() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_same_direction_strands_connect_two_sheets_or_a_loop() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_sheets_are_connected_with_near_bb_atoms() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_strand_i_is_in_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_sw_by_sh_id_still_alive() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_sw_is_not_connected_with_continuous_atoms() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_this_pdb_should_be_excluded() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_this_sheet_is_too_short() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_working_res() (in module pyrosetta.rosetta.core.import_pose) checkpoint() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) checkpoint_cleanup() (in module pyrosetta.rosetta.protocols.dna) checkpoint_exists() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) checkpoint_file() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) checkpoint_with_interval() (in module pyrosetta.rosetta.protocols.checkpoint) ChemicalManager (class in pyrosetta.rosetta.core.chemical) ChemicalShiftAnisotropy (class in pyrosetta.rosetta.core.scoring) ChemicalShiftData (class in pyrosetta.rosetta.core.scoring.rna.chemical_shift) ChemicalShiftEvaluatorCreator (class in pyrosetta.rosetta.protocols.sparta) chemshift_compliance() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) CheshireCell (class in pyrosetta.rosetta.protocols.cryst) chi() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) chi1_torsion_atom() (in module pyrosetta.rosetta.core.chemical.rna) chi1_torsion_atom_index() (in module pyrosetta.rosetta.core.chemical.rna) chi2max() (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation method) chi2min() (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation method) chi_2_proton_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) chi_atom_vds() (pyrosetta.rosetta.core.chemical.ResidueType method) chi_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) chi_north_anti() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) chi_north_syn() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) chi_number_pseudoalpha() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) chi_number_pseudobeta() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) chi_number_pseudoepsilon() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) chi_number_pseudogamma() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) chi_number_pseudozeta() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) chi_rotamers() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) chi_south_anti() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) chi_south_syn() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) CHIDihedralSamplingData (class in pyrosetta.rosetta.core.scoring.carbohydrates) CHIEnergyFunction (class in pyrosetta.rosetta.core.scoring.carbohydrates) CHIEnergyFunctionLinkageType (class in pyrosetta.rosetta.core.scoring.carbohydrates) 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) child_index() (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) chinum() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) ChiralFlipAtoms (class in pyrosetta.rosetta.core.chemical) ChiralFlipNaming (class in pyrosetta.rosetta.core.chemical) chitip_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) chitip_atoms() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) ChiWellRmsdEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) choices() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) choose() (pyrosetta.rosetta.protocols.nonlocal.Chunk method) (pyrosetta.rosetta.protocols.nonlocal.Policy method) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy method) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy method) choose_best_solution_based_on_score_function() (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) choose_canonical() (in module pyrosetta.rosetta.protocols.denovo_design.components) choose_cutpoint() (pyrosetta.rosetta.protocols.loops.Loop method) choose_cutpoints() (pyrosetta.rosetta.protocols.loops.Loops method) choose_effective_sequence_separation() (in module pyrosetta.rosetta.core.scoring.constraints) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint 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.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) choose_fragment() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) choose_hbond_parameter_set() (in module pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators) choose_least_perturb_solution() (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) choose_n_best() (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) choose_random() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) choose_random_if_unspecified_nucleotide() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) choose_randomly_from_allowed_at_position() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) choose_window_length() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) choose_window_start() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) chop_fragments() (in module pyrosetta.rosetta.core.fragment) Chothia_Numberer (class in pyrosetta.rosetta.protocols.antibody.grafting) chr_chains_nonrepeated() (in module pyrosetta.rosetta.utility.tag) Chunk (class in pyrosetta.rosetta.protocols.nonlocal) chunk_coverage() (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) chunk_key() (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) chunk_probabilities() (in module pyrosetta.rosetta.protocols.medal) chunk_set() (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) ChunkExponent (class in pyrosetta.rosetta.ObjexxFCL) chunks_by_CA_CA_distance() (in module pyrosetta.rosetta.protocols.nonlocal) Ci() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) ci_1b_types() (pyrosetta.rosetta.core.scoring.ScoreFunction method) ci_2b_begin() (pyrosetta.rosetta.core.scoring.ScoreFunction method) ci_2b_end() (pyrosetta.rosetta.core.scoring.ScoreFunction method) ci_2b_intrares_begin() (pyrosetta.rosetta.core.scoring.ScoreFunction method) ci_2b_intrares_end() (pyrosetta.rosetta.core.scoring.ScoreFunction method) ci_2b_types() (pyrosetta.rosetta.core.scoring.ScoreFunction method) ci_lr_2b_methods_begin() (pyrosetta.rosetta.core.scoring.ScoreFunction method) ci_lr_2b_methods_end() (pyrosetta.rosetta.core.scoring.ScoreFunction method) ci_lr_2b_types() (pyrosetta.rosetta.core.scoring.ScoreFunction method) circle() (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) CircularGeneral1D_Func (class in pyrosetta.rosetta.core.scoring.func) CircularHarmonicFunc (class in pyrosetta.rosetta.core.scoring.func) CircularPermuteFreePeptideMover (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers) CircularPowerFunc (class in pyrosetta.rosetta.core.scoring.func) CircularSigmoidalFunc (class in pyrosetta.rosetta.core.scoring.func) cis_omega() (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) cis_omega_torsion_bin() (in module pyrosetta.rosetta.core.conformation) cis_peptide_bonds() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) cis_trans_match() (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) cispep_map() (pyrosetta.rosetta.core.io.StructFileRep method) CisPeptideInformation (class in pyrosetta.rosetta.core.io) cl_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.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) claim_accepted() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) claimer_builds_own_fold_tree() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) clashes() (pyrosetta.rosetta.protocols.hbnet.HBondNode method) class_name() (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter 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.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.simple_filters.Operator method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) ClassicAbinitio (class in pyrosetta.rosetta.protocols.abinitio) ClassicFragmentMover (class in pyrosetta.rosetta.protocols.simple_moves) ClassicMatchAlgorithm (class in pyrosetta.rosetta.protocols.match.downstream) ClassicRelax (class in pyrosetta.rosetta.protocols.relax) classification() (pyrosetta.rosetta.core.io.HeaderInformation method) classify_base_pairs() (in module pyrosetta.rosetta.core.pose.rna) classify_base_pairs_lores() (in module pyrosetta.rosetta.protocols.rna.denovo) clean_for_storage() (in module pyrosetta.rosetta.protocols.denovo_design.components) clean_from_storage() (in module pyrosetta.rosetta.protocols.denovo_design.components) clean_jumps() (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) clean_residue_task() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) clean_up() (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) cleanATOM() (in module pyrosetta.toolbox) (in module pyrosetta.toolbox.cleaning) cleanCRYS() (in module pyrosetta.toolbox) (in module pyrosetta.toolbox.cleaning) cleaned() (pyrosetta.rosetta.utility.options.OptionCollection method) cleaned_alignment_file() (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) cleanup() (in module pyrosetta.rosetta.core.import_pose) clear() (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.NeighborList method) (pyrosetta.rosetta.core.scoring.Strands method) (pyrosetta.rosetta.core.scoring.TMscoreStore method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter 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.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.simple_filters.Operator method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.io.FileContentsMap method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream 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.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.recent_history_queue method) clear_() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) clear_all() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) clear_blacklist() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) clear_checkpoints() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) clear_chi_rotamers() (pyrosetta.rosetta.core.chemical.ResidueType method) clear_comments() (pyrosetta.rosetta.core.io.silent.SilentStruct method) clear_compounds() (pyrosetta.rosetta.core.io.HeaderInformation method) clear_conformation_viewers() (in module pyrosetta.rosetta.protocols.viewer) clear_connected_resonances() (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) clear_connections() (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) clear_data() (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) clear_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) clear_design_taskset() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) clear_edges() (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) clear_energies() (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) clear_evaluators() (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) clear_events() (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) clear_experimental_techniques() (pyrosetta.rosetta.core.io.HeaderInformation method) clear_extent_eval() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) clear_extent_gen() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) clear_external_geom_samplers() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) clear_filters() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) clear_fragment_eval() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) clear_fragment_gen() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) clear_fragments() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) clear_free_peptide_movers() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) clear_from_pose() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) clear_glycan_trees() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) clear_hash_map() (pyrosetta.rosetta.protocols.match.HitHasher method) clear_info() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) clear_inverse_rotamers() (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) clear_jumps() (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) clear_keywords() (pyrosetta.rosetta.core.io.HeaderInformation method) clear_movers() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) clear_movers_and_refiners() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) clear_mutation_sets() (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation method) clear_no_notify() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) clear_observers() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) clear_orbitals() (pyrosetta.rosetta.core.chemical.ResidueType method) clear_other_pose_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) clear_output() (pyrosetta.rosetta.protocols.jd2.Job method) clear_overall_prob_set() (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation method) clear_parameters_list() (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) clear_parameters_set_list() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) clear_perturbers() (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) clear_poses() (pyrosetta.rosetta.protocols.moves.MonteCarlo method) clear_positions() (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation method) clear_postfold_movers() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) clear_prefold_movers() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) clear_prob_set() (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation method) clear_properties() (pyrosetta.rosetta.core.chemical.AtomType method) clear_rcgs() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) clear_refiners() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) clear_res_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) clear_reset_filters() (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) clear_residue_connections() (pyrosetta.rosetta.core.conformation.Residue method) clear_residues() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) clear_reslabel() (pyrosetta.rosetta.core.pose.PDBInfo method) clear_rms() (pyrosetta.rosetta.numeric.model_quality.RmsData method) clear_rna_scoring_info() (in module pyrosetta.rosetta.core.scoring.rna) clear_rna_secstruct_legacy_info() (in module pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy) clear_rnl_pose() (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) clear_rv_infos() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) clear_segments() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) clear_sequence_constraints() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) clear_serial_data() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) clear_setup_movers() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) clear_shared_silent_data() (pyrosetta.rosetta.core.io.silent.SilentFileData method) clear_structure_map() (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) clear_task() (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) clear_task_factory() (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) clear_title() (pyrosetta.rosetta.core.io.HeaderInformation method) clear_torsion_string_stack() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) clear_user_provided_movers() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) clear_Vall() (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager method) ClearChiRotamers (class in pyrosetta.rosetta.core.chemical) clearPoseExtraScore() (in module pyrosetta.rosetta.core.pose) clearPoseExtraScores() (in module pyrosetta.rosetta.core.pose) clearSmallPockets() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) clockwise() (in module pyrosetta.rosetta.core.membrane) clone() (pyrosetta.rosetta.basic.datacache.CacheableData method) (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) Clone() (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) clone() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.MoveMap 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) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.EMPTY method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NC method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.PIKRNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.RESET method) (pyrosetta.rosetta.core.pack.task.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.DipolarCoupling method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.NeighborList method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint 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.ConstraintSet 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.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover 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 method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.SegmentedAtomPairConstraintGenerator method) (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.CountFromLeft 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.RelativeSequencePosition method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (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.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover 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.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter 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.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.sewing.ReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.sewing.ReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.simple_filters.Operator method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator method) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator method) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.pose_metric_calculators.NeighborsByDistanceCalculator method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) (pyrosetta.rosetta.protocols.toolbox.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) clone_as_base_class() (pyrosetta.rosetta.core.scoring.ScoreFunction method) clone_cache_data() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) clone_flipping_chirality() (pyrosetta.rosetta.core.conformation.Residue method) clone_info() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) clone_scorefxn() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) clone_shifted() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) clone_with_frags() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) clone_with_template() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) close() (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ozstream method) close_chainbreaks() (in module pyrosetta.rosetta.protocols.jumping) close_loops() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) close_one_loop_stem() (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) close_one_loop_stem_helper() (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) close_to_dna() (in module pyrosetta.rosetta.protocols.dna) CloseContactResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) closed_loop() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) CloseOneCDRLoop (class in pyrosetta.rosetta.protocols.antibody)

CloseOneMover (class in pyrosetta.rosetta.protocols.antibody_legacy) closest_by_dist4() (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) closest_interface_residue() (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) closest_larger_peptide_vertex() (in module pyrosetta.rosetta.protocols.forge.methods) closest_orient_atoms_msd() (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) closest_smaller_peptide_vertex() (in module pyrosetta.rosetta.protocols.forge.methods) closest_suite() (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) closure_fragments() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) ClosureProblem (class in pyrosetta.rosetta.protocols.kinematic_closure) ClosureSolution (class in pyrosetta.rosetta.protocols.kinematic_closure) CloudPDBWriter (class in pyrosetta.rosetta.protocols.match.output) cluster() (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.cluster.APCluster method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) cluster_by_all_atom_rmsd() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) Cluster_Member (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) cluster_rmsd() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) cluster_sampling_cutoff() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) clusterCPockets() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) ClusterData (class in pyrosetta.rosetta.protocols.antibody.clusters) clustered_pose_list() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) clusterPockets() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) ClusterPoseSelector (class in pyrosetta.rosetta.protocols.pose_selectors) cm_main() (in module pyrosetta.rosetta.protocols.comparative_modeling) cmdline_options_activated() (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) CoarseRNA_Fragments (class in pyrosetta.rosetta.protocols.rna.denovo.coarse) CoarseRNA_LoopCloser (class in pyrosetta.rosetta.protocols.rna.denovo.coarse) code() (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) code_from_6bit() (in module pyrosetta.rosetta.utility) code_to_6bit() (in module pyrosetta.rosetta.utility) codon2aa() (in module pyrosetta.rosetta.core.chemical.NucleotideTools) collapse() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) collect_all_inverse_rotamers() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) com() (in module pyrosetta.rosetta.protocols.membrane) combine_and_trim() (in module pyrosetta.rosetta.protocols.nonlocal) combine_constraints() (in module pyrosetta.rosetta.core.scoring.constraints) combine_long_loop_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) combine_movemaps_post_insertion() (in module pyrosetta.rosetta.protocols.grafting) combine_names() (in module pyrosetta.rosetta.utility.file) combine_sequence_mappings() (in module pyrosetta.rosetta.core.id) Combine_Tags_Info (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna) combine_two_poses() (in module pyrosetta.rosetta.protocols.seeded_abinitio) CombinedConstraintEvaluatorCreator (class in pyrosetta.rosetta.protocols.constraints_additional) CombinedFilter (class in pyrosetta.rosetta.protocols.filters) command_string() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) comment_begin() (in module pyrosetta.rosetta.core.pack.task) comment_exists() (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) comment_from_line() (pyrosetta.rosetta.core.io.silent.SilentStruct method) comment_line() (pyrosetta.rosetta.core.io.silent.SilentFileData method) comment_lines() (pyrosetta.rosetta.core.io.silent.SilentFileData method) comment_name() (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) comment_value() (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) commit_change() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) commit_considered_substitution() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) common_type() (pyrosetta.rosetta.utility.tag.XMLSchemaType method) comparable() (in module pyrosetta.rosetta.utility.keys) compare_atom_coordinates() (in module pyrosetta.rosetta.core.pose) compare_binary_protein_silent_struct() (in module pyrosetta.rosetta.core.pose) compare_motif2scaffold_data_by_scaffold_low2high() (in module pyrosetta.rosetta.protocols.motif_grafting.movers) compare_RNA_char() (in module pyrosetta.rosetta.protocols.rna.denovo) compare_RNA_secstruct() (in module pyrosetta.rosetta.protocols.rna.denovo) compare_to_native() (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison method) compare_to_ref() (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) CompareByScoreCombination (class in pyrosetta.rosetta.protocols.frag_picker) compareCoverage() (pyrosetta.rosetta.protocols.pockets.ComparisonGrid method) CompareQueryPosition (class in pyrosetta.rosetta.protocols.frag_picker) CompareScoreComponent (class in pyrosetta.rosetta.protocols.frag_picker) CompareTotalScore (class in pyrosetta.rosetta.protocols.frag_picker) ComparisonGrid (class in pyrosetta.rosetta.protocols.pockets) compatibility_check() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) compatible_restype() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) compatible_with() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction 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) completed() (pyrosetta.rosetta.protocols.jd2.Job method) complex_ring_detection() (in module pyrosetta.rosetta.core.chemical) complex_type_generator_for_anchored_graft_mover() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) complex_type_generator_for_backbone_mover() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) complex_type_generator_for_logical_selector() (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) complex_type_generator_for_min_mover() (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) complex_type_generator_for_pack_rotamers_mover() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) complex_type_name_for_architect() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) complex_type_name_for_features_reporter() (in module pyrosetta.rosetta.protocols.features) complex_type_name_for_filter() (in module pyrosetta.rosetta.protocols.filters) complex_type_name_for_jump_selector() (in module pyrosetta.rosetta.core.select.jump_selector) complex_type_name_for_loop_definer() (in module pyrosetta.rosetta.protocols.loops.loops_definers) complex_type_name_for_mover() (in module pyrosetta.rosetta.protocols.moves) complex_type_name_for_res_filter() (in module pyrosetta.rosetta.core.pack.task.operation) complex_type_name_for_res_lvl_task_op() (in module pyrosetta.rosetta.core.pack.task.operation) complex_type_name_for_residue_selector() (in module pyrosetta.rosetta.core.select.residue_selector) complex_type_name_for_scoring_grid() (in module pyrosetta.rosetta.protocols.qsar.scoring_grid) complex_type_name_for_task_op() (in module pyrosetta.rosetta.core.pack.task.operation) complex_typename_for_element() (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) CompositeFragmentSelector (class in pyrosetta.rosetta.protocols.frag_picker) compound_in_progress() (pyrosetta.rosetta.core.io.HeaderInformation method) compound_token_to_string() (pyrosetta.rosetta.core.io.HeaderInformation method) CompoundArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) CompoundFilter (class in pyrosetta.rosetta.protocols.filters) CompoundPerturber (class in pyrosetta.rosetta.protocols.denovo_design.components) compounds() (pyrosetta.rosetta.core.io.HeaderInformation method) compress() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) compressed() (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) compute() (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.simple_filters.Operator method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator method) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator method) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator method) compute_alt_weights_for_npd_hbonds() (in module pyrosetta.rosetta.core.pack.interaction_graph) compute_atom_packing_scores() (in module pyrosetta.rosetta.core.scoring.packstat) compute_avge_scores() (in module pyrosetta.rosetta.protocols.sasa_scores) compute_bb_centroid() (in module pyrosetta.rosetta.core.scoring) compute_bb_radius() (in module pyrosetta.rosetta.core.scoring) compute_cav_ball_neighbor_count() (in module pyrosetta.rosetta.core.scoring.packstat) compute_cav_ball_volumes() (in module pyrosetta.rosetta.core.scoring.packstat) compute_center_of_mass() (in module pyrosetta.rosetta.protocols.forge.remodel) compute_centroid_environment() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) compute_csascore() (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) compute_dcentroid_environment() (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) compute_dcscore() (pyrosetta.rosetta.core.scoring.DipolarCoupling method) compute_dec15_score() (in module pyrosetta.rosetta.core.scoring.packing) compute_designable_neighbors() (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) compute_dipscore() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) compute_dipscore_nls() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) compute_dipscore_nlsDa() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) compute_dipscore_nlsDaR() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) compute_dipscore_nlsR() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) compute_embeddings_by_chain() (in module pyrosetta.rosetta.protocols.membrane) compute_exact_geosol() (in module pyrosetta.rosetta.core.scoring.geometric_solvation) compute_fa_projection() (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) compute_folding_energies() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) compute_func() (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) compute_holes_deriv() (in module pyrosetta.rosetta.core.scoring.packing) compute_holes_deriv_res() (in module pyrosetta.rosetta.core.scoring.packing) compute_holes_score() (in module pyrosetta.rosetta.core.scoring.packing) compute_holes_score_res() (in module pyrosetta.rosetta.core.scoring.packing) compute_interface() (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) compute_matching_energy() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential method) compute_membrane_embedding() (pyrosetta.rosetta.core.scoring.MembranePotential method) compute_mpair_score() (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) compute_mpcbeta_score() (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) compute_mpenv_score() (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) compute_nonhelix_penalty() (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) compute_nres_in_asymmetric_unit() (in module pyrosetta.rosetta.protocols.constraint_generator) compute_one_and_two_body_energies() (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) compute_one_body_energies() (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) compute_one_body_energy_maps() (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) compute_packing_score() (in module pyrosetta.rosetta.core.scoring.packstat) compute_packing_score_leerichards() (in module pyrosetta.rosetta.core.scoring.packstat) compute_pairwise_score() (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) compute_per_residue_coverage() (in module pyrosetta.rosetta.core.fragment) compute_pose_hpatch_score() (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) compute_pose_surface_energy() (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) compute_proposal_density() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) compute_proton_chi_samplings() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) compute_residue_packing_score() (in module pyrosetta.rosetta.core.scoring.packstat) compute_residue_packing_scores() (in module pyrosetta.rosetta.core.scoring.packstat) compute_residue_sasas_for_sasa_scores() (in module pyrosetta.rosetta.protocols.sasa_scores) compute_residue_surface_energy() (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) compute_rosettaholes_score() (in module pyrosetta.rosetta.core.scoring.packing) compute_rotdensities() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) compute_sasa() (in module pyrosetta.rosetta.core.scoring.packstat) compute_sasapack_scores() (in module pyrosetta.rosetta.protocols.sasa_scores) compute_sc_centroid() (in module pyrosetta.rosetta.core.scoring) compute_sc_radius() (in module pyrosetta.rosetta.core.scoring) compute_size() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) compute_ss_regions() (in module pyrosetta.rosetta.protocols.loops) compute_structure_based_embedding() (in module pyrosetta.rosetta.protocols.membrane) compute_surface_area_leerichards() (in module pyrosetta.rosetta.core.scoring.packstat) compute_surface_area_leerichards_deriv() (in module pyrosetta.rosetta.core.scoring.packstat) compute_surrounding_sasa() (in module pyrosetta.rosetta.core.scoring.packstat) compute_tensor_stats() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) compute_termini_penalty() (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) compute_tmproj_penalty() (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) compute_total_score() (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) compute_unique_chains() (in module pyrosetta.rosetta.core.pose) concave_shell() (in module pyrosetta.rosetta.core.membrane) concavity_direction() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) concavity_reference_residue() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) ConcurrencyTestCreator (class in pyrosetta.rosetta.protocols.features.helixAssembly) cond_exit() (in module pyrosetta.rosetta.utility) conditional_erase() (pyrosetta.rosetta.core.pose.PDBPoseMap method) conf2pdb_chain() (in module pyrosetta.rosetta.core.pose) conf_size() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) confidence() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) Conformation (class in pyrosetta.rosetta.core.conformation) conformation() (pyrosetta.rosetta.core.pose.Pose method) conformation_ptr() (pyrosetta.rosetta.core.pose.Pose method) ConformationEvent (class in pyrosetta.rosetta.core.pose.signals) conformer_found() (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) conformers_for_ring_size() (pyrosetta.rosetta.core.chemical.rings.RingConformerManager method) ConformerSwitchMover (class in pyrosetta.rosetta.protocols.docking) conj_map_times() (in module pyrosetta.rosetta.core.scoring.electron_density) conjugability() (pyrosetta.rosetta.core.chemical.Bond method) connect_atom() (pyrosetta.rosetta.core.conformation.Residue method) connect_info_cutoff() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) connect_map() (pyrosetta.rosetta.core.conformation.Residue method) connect_map_size() (pyrosetta.rosetta.core.conformation.Residue method) connected() (pyrosetta.rosetta.core.kinematics.FoldTree method) connected_by_twobonds() (pyrosetta.rosetta.core.scoring.methods.GoapRsdType method) connected_residue_at_lower() (pyrosetta.rosetta.core.conformation.Residue method) connected_residue_at_resconn() (pyrosetta.rosetta.core.conformation.Residue method) connected_residue_at_upper() (pyrosetta.rosetta.core.conformation.Residue method) connected_resonance_ids() (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) connected_resonances() (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) connection_distance() (pyrosetta.rosetta.core.conformation.Residue method) connection_incomplete() (pyrosetta.rosetta.core.conformation.Residue method) ConnectionArchitect (class in pyrosetta.rosetta.protocols.denovo_design.connection) ConnectionEvent (class in pyrosetta.rosetta.core.conformation.signals) ConnectionEvent.Tag (class in pyrosetta.rosetta.core.conformation.signals) ConnectionPerturber (class in pyrosetta.rosetta.protocols.denovo_design.components) connections_match() (pyrosetta.rosetta.core.conformation.Residue method) connections_to_residue() (pyrosetta.rosetta.core.conformation.Residue method) connectivity_index() (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) ConnectRight (class in pyrosetta.rosetta.protocols.forge.build) ConnectSulfurAndMakeVirtualProton (class in pyrosetta.rosetta.core.chemical) connid() (pyrosetta.rosetta.core.chemical.ResConnID method) ConsensusDesignMover (class in pyrosetta.rosetta.protocols.simple_moves) ConsensusSequenceType (class in pyrosetta.rosetta.core.enzymes) conservation_cutoff_aligned_segments() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) conservation_cutoff_protein_interface_design() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) ConservativeDesignOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) consider_mainchain_only() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) consider_substitution() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) const_access_Real_MathNTensor() (in module pyrosetta.rosetta.numeric) const_begin() (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) const_data_cache() (pyrosetta.rosetta.core.pose.Pose method) const_edge() (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) const_edge_list_begin() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) const_edge_list_end() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) const_end() (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) const_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) const_last() (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) const_lower_edge_list_begin() (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) const_lower_edge_list_end() (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) const_my_group() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) const_neighbor_iterator_begin() (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) const_neighbor_iterator_end() (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) const_next() (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) const_pose_apply() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) const_previous() (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) const_residues() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) const_upper_edge_list_begin() (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) const_upper_edge_list_end() (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) const_upper_neighbor_iterator_begin() (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) const_upper_neighbor_iterator_end() (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) const_vdw_cached_rep_screen_info_from_pose() (in module pyrosetta.rosetta.protocols.scoring) constant() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) ConstantConstraint (class in pyrosetta.rosetta.core.scoring.constraints) ConstantFunc (class in pyrosetta.rosetta.core.scoring.func) ConstantLengthFragSet (class in pyrosetta.rosetta.core.fragment) ConstDataMap (class in pyrosetta.rosetta.basic.datacache) constrain_coords() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) constrain_ligand_torsions() (in module pyrosetta.rosetta.protocols.ligand_docking) constrain_linker() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) constrain_pose_res_to_invrots() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) constrain_relax_segments() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) constrain_relax_to_native_coords() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) constrain_relax_to_start_coords() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) constrain_residue() (in module pyrosetta.rosetta.protocols.mpi_refinement) constrain_ring_atoms() (in module pyrosetta.rosetta.core.pose.ncbb) constrain_to_antigen_chains() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) constrain_to_epitope_residues() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) constrain_to_paratope_cdrs() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) constrain_to_paratope_residues() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) ConstrainHBondNetwork (class in pyrosetta.rosetta.protocols.hbnet) Constraint (class in pyrosetta.rosetta.core.scoring.constraints) constraint_set() (pyrosetta.rosetta.core.pose.Pose method) constraint_set_slice() (in module pyrosetta.rosetta.protocols.stepwise.modeler) ConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) ConstraintEvaluatorCreator (class in pyrosetta.rosetta.protocols.constraints_additional) ConstraintEvaluatorWrapperCreator (class in pyrosetta.rosetta.protocols.topology_broker) ConstraintFragmentSampler (class in pyrosetta.rosetta.protocols.abinitio) ConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) ConstraintGeneratorLoader (class in pyrosetta.rosetta.protocols.parser) ConstraintIO (class in pyrosetta.rosetta.core.scoring.constraints) ConstrainToIdealMover (class in pyrosetta.rosetta.protocols.simple_moves) constraints() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) constraints_from_link_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) constraints_NtoC() (in module pyrosetta.rosetta.protocols.flxbb) constraints_only() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) constraints_sheet() (in module pyrosetta.rosetta.protocols.flxbb) ConstraintScoreFilter (class in pyrosetta.rosetta.protocols.simple_filters) ConstraintSet (class in pyrosetta.rosetta.core.scoring.constraints) ConstraintsManager (class in pyrosetta.rosetta.protocols.constraint_generator) ConstraintsMap (class in pyrosetta.rosetta.protocols.constraint_generator) construct_and_dump_outpose() (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination method) construct_dummy_pose() (in module pyrosetta.rosetta.protocols.denovo_design) construct_from_pose() (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) construct_kd_tree() (in module pyrosetta.rosetta.numeric.kdtree) construct_poly_ala_pose() (in module pyrosetta.rosetta.protocols.denovo_design) (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) construct_poly_beta_ala_pose() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) construct_poly_d_ala_pose() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) construct_poly_d_beta_ala_pose() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) construct_poly_uniq_restype_pose() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) construct_poly_XXX_pose() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) ConstScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) Contact (class in pyrosetta.rosetta.protocols.contact_map) contact_distance2() (in module pyrosetta.rosetta.protocols.dna) contact_name() (in module pyrosetta.rosetta.protocols.frag_picker) contact_order() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) contact_type() (in module pyrosetta.rosetta.protocols.frag_picker) ContactMapEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) ContactPartner (class in pyrosetta.rosetta.protocols.contact_map) contain() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) contain_nic() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) contains() (in module pyrosetta.rosetta.protocols.sparta) Contains() (in module pyrosetta.rosetta.protocols.toolbox) contains() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.forge.build.Interval method) contains_atom_type() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) contains_bond_length() (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) contains_carbohydrate_residues() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) contains_element_type() (pyrosetta.rosetta.core.chemical.ElementSet method) contains_position() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) contains_protein() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) contains_seqpos() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) context_derivative_empty() (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) context_graph() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) continue_if_silent() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) continuous() (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) ContinuousAssembly (class in pyrosetta.rosetta.protocols.sewing) controlling_chi_for_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) conventional_chains() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) conventional_numbering() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) converge() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) ConvergenceTest (class in pyrosetta.rosetta.core.optimization) convert_acgu_to_1234() (in module pyrosetta.rosetta.core.chemical.rna) convert_atom_name() (in module pyrosetta.rosetta.core.io.pose_from_sfr) convert_based_on_match_type() (in module pyrosetta.rosetta.protocols.rna.denovo) convert_cartesian_to_grid() (in module pyrosetta.rosetta.protocols.pockets) convert_cartesian_to_spherical_coor_triplet() (in module pyrosetta.rosetta.protocols.pockets) convert_from_std_map() (in module pyrosetta.rosetta.core.pose) convert_GeomSampleInfo_to_FuncOP() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) convert_grid_to_cartesian() (in module pyrosetta.rosetta.protocols.pockets) convert_inorder_table_to_original_order() (in module pyrosetta.rosetta.core.scoring.trie) convert_inorder_vector_to_original_order() (in module pyrosetta.rosetta.core.scoring.trie) convert_res_name() (in module pyrosetta.rosetta.core.io.pose_from_sfr) convert_residue_names_into_linkage_map_key() (in module pyrosetta.rosetta.core.chemical.carbohydrates) convert_scores_to_probabilities() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) convert_spherical_coor_triplet_to_cartesian() (in module pyrosetta.rosetta.protocols.pockets) convert_sugar_modeling_to_residue_alternative_set() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) convert_to_BondName() (in module pyrosetta.rosetta.core.chemical) convert_to_working_res() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) ConvertRealToVirtualMover (class in pyrosetta.rosetta.protocols.simple_moves) ConvertVirtualToRealMover (class in pyrosetta.rosetta.protocols.simple_moves) convolute_maps() (in module pyrosetta.rosetta.core.scoring.electron_density) coord() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) coord_constrain_sidechains() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) coord_frame_ref() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) coordinate_constrain_selection() (in module pyrosetta.rosetta.protocols.relax) coordinate_constraint_weight() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) coordinate_constraints_during_minimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) coordinate_for_nonchi_atom_in_ideal_frame() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) CoordinateConstraint (class in pyrosetta.rosetta.core.scoring.constraints) CoordinateConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) CoordinateConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) coordinates() (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) coords() (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.protocols.toolbox.KClusterData method) copy() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pose.PDBInfo method) copy_all_o2prime_torsions() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) copy_bb_donor_acceptor_arrays() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) copy_bulge_res_and_sugar_torsion() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) copy_clone() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) copy_connectivity() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) copy_coords() (pyrosetta.rosetta.core.kinematics.AtomTree 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) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) copy_data() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) copy_dna_chains() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) copy_dofs() (in module pyrosetta.rosetta.core.pose.copydofs) copy_dofs_from_pose() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) copy_dofs_match_atom_names() (in module pyrosetta.rosetta.core.pose.copydofs) copy_dofs_sort_criterion() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) copy_dofs_to_pose() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) copy_fragments() (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) copy_from() (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.protocols.hbnet.HBondEdge method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.sewing.HashEdge method) (pyrosetta.rosetta.protocols.sewing.ModelNode 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.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) copy_helix_bondangles() (in module pyrosetta.rosetta.protocols.helical_bundle) copy_helix_bondlengths() (in module pyrosetta.rosetta.protocols.helical_bundle) copy_helix_dihedrals() (in module pyrosetta.rosetta.protocols.helical_bundle) copy_loop_pose_to_original() (in module pyrosetta.rosetta.protocols.generalized_kinematic_closure) copy_next_pose_segment() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) copy_over_phosphate_variants() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) copy_pdbinfo() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) copy_pose_crd() (in module pyrosetta.rosetta.protocols.mpi_refinement) copy_residue_connections() (pyrosetta.rosetta.core.conformation.Residue method) copy_residue_connections_from() (pyrosetta.rosetta.core.conformation.Residue method) copy_residue_coordinates_and_rebuild_missing_atoms() (in module pyrosetta.rosetta.core.conformation) copy_scores() (pyrosetta.rosetta.core.io.silent.SilentStruct method) copy_segment() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) copy_targeted_dna() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) copy_values() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) copy_without_output() (pyrosetta.rosetta.protocols.jd2.Job method) CopyRotamerMover (class in pyrosetta.rosetta.protocols.simple_moves) copysign() (in module pyrosetta.rosetta.utility) COradius2() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) corrcoef() (in module pyrosetta.rosetta.numeric.statistics) corrcoef_with_provided_mean_and_std_dev() (in module pyrosetta.rosetta.numeric.statistics) correct_polymer_dependent_atoms_in_pose_segment() (in module pyrosetta.rosetta.protocols.generalized_kinematic_closure) correctly_add_cutpoint_variants() (in module pyrosetta.rosetta.core.pose) correctly_remove_variants_incompatible_with_lower_cutpoint_variant() (in module pyrosetta.rosetta.core.pose) correctly_remove_variants_incompatible_with_upper_cutpoint_variant() (in module pyrosetta.rosetta.core.pose) corresponding_res_block() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) corresponding_residue_in_current() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) cos_theta() (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) COSFXN() (in module pyrosetta.rosetta.numeric.crick_equations) could_be_accepted() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) could_not_create_resource_error_message() (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration method) CouldHaveHybridization() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) count() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.numeric.model_quality.RmsData method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) count_AA_w_direction() (in module pyrosetta.rosetta.protocols.features.strand_assembly) count_AA_wo_direction() (in module pyrosetta.rosetta.protocols.features.strand_assembly) count_accepted() (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) count_bb_atoms() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) count_bb_atoms_in_residue() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) count_bulges() (in module pyrosetta.rosetta.protocols.denovo_design) count_candidates() (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) count_CBs() (in module pyrosetta.rosetta.protocols.sic_dock) count_components() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) count_connected_components_and_initialize_vertex_groups() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) count_cutpoints() (in module pyrosetta.rosetta.protocols.forge.methods) count_dynamic_memory() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.protocols.hbnet.HBondEdge method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.sewing.HashEdge method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) count_energy_drop() (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) count_ff() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) count_fixed_residues() (pyrosetta.rosetta.core.kinematics.FoldTree method) count_gly_as_polar() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) count_linkers() (in module pyrosetta.rosetta.protocols.sic_dock) count_n_matches() (pyrosetta.rosetta.protocols.match.MatchCounter method) count_num_covered() (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) count_pools() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) count_query_ss() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) count_selected() (in module pyrosetta.rosetta.core.select.residue_selector) count_static_memory() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.protocols.hbnet.HBondEdge method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.sewing.HashEdge method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) count_trial() (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) count_uniq_char() (in module pyrosetta.rosetta.protocols.ncbb) CountFromLeft (class in pyrosetta.rosetta.protocols.forge.build) CountPairRepMap (class in pyrosetta.rosetta.core.scoring.elec) counts() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) CoupledMover (class in pyrosetta.rosetta.protocols.simple_moves) cov() (in module pyrosetta.rosetta.numeric.statistics) cov_with_provided_mean() (in module pyrosetta.rosetta.numeric.statistics) covalent_compliance() (in module pyrosetta.rosetta.protocols.noesy_assign) CovalentCompliance (class in pyrosetta.rosetta.protocols.noesy_assign) CovalentConnectionReplaceInfo (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) CovalentResidueNetwork (class in pyrosetta.rosetta.protocols.toolbox) CPParameter (class in pyrosetta.rosetta.core.chemical.rings) crankshaft_alpha_gamma() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) create() (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover method) (pyrosetta.rosetta.protocols.nonlocal.HelixRotate method) (pyrosetta.rosetta.protocols.nonlocal.SheetTranslate method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) create_acc_orientation_vector() (in module pyrosetta.rosetta.core.scoring.hbonds) create_alignment_id_map_legacy() (in module pyrosetta.rosetta.protocols.stepwise.modeler.align) create_alpha_beta_models_table() (in module pyrosetta.rosetta.protocols.sewing) create_assembly() (pyrosetta.rosetta.protocols.sewing.AssemblyFactory method) create_atom_tree() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) create_blank_file() (in module pyrosetta.rosetta.utility.file) create_bond_length() (in module pyrosetta.rosetta.core.chemical) create_cache() (in module pyrosetta.rosetta.protocols.frag_picker.scores) create_chimera_segment() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) create_comparer() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator method) create_complex_type_generator() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) create_consensus_design_task() (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover method) create_constraint() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator method) create_cpdata_correspondence_for_rotamer() (in module pyrosetta.rosetta.core.scoring.trie) create_cpdata_correspondence_for_rotamerset() (in module pyrosetta.rosetta.core.scoring.trie) create_data() (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator method) create_directed_dependency() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) create_directory() (in module pyrosetta.rosetta.utility.file) create_directory_recursive() (in module pyrosetta.rosetta.utility.file) create_docking_high_res_mover() (pyrosetta.rosetta.protocols.docking.DockingHighResFactory method) create_don_orientation_vector() (in module pyrosetta.rosetta.core.scoring.hbonds) create_empty_map() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) create_energy_method() (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergyCreator method) create_entity_resfile_contents() (in module pyrosetta.rosetta.protocols.pack_daemon) create_euler_rotation() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) create_ExactSHOEnergy_from_cmdline() (in module pyrosetta.rosetta.core.scoring.geometric_solvation) create_expression_tree() (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) create_extra_output() (in module pyrosetta.rosetta.protocols.floppy_tail) create_fallback_configuration() (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationCreator method) (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfigurationCreator method) create_features_reporter() (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator method) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator method) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator method) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator method) create_filter() (pyrosetta.rosetta.protocols.filters.FilterCreator method) create_fragment_set() (in module pyrosetta.rosetta.protocols.hybridization) create_fragment_set_no_ssbias() (in module pyrosetta.rosetta.protocols.hybridization) create_from_cacheable_data() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) create_from_motifs() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) create_from_pose() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) create_from_remarks() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) create_from_tag() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) create_from_xml() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) create_full_to_input_res_map() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) create_func() (in module pyrosetta.rosetta.protocols.constraint_generator) create_glycan_movemap_from_residue_selector() (in module pyrosetta.rosetta.core.pose.carbohydrates) create_grid() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator method) create_info() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) create_inner_cycle() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory method) create_instance() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) create_JobInputter() (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator method) create_JobOutputter() (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator method) create_jump_fragments() (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) create_jump_sample() (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) create_loader() (pyrosetta.rosetta.protocols.parser.DataLoaderCreator method) create_long_range_energy_container() (in module pyrosetta.rosetta.core.scoring.methods) create_loop_mover() (pyrosetta.rosetta.protocols.loops.LoopMoverFactory method) create_loops_definer() (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator method) create_match_position_modifier() (in module pyrosetta.rosetta.protocols.match) create_membrane_docking_foldtree_from_partners() (in module pyrosetta.rosetta.protocols.membrane) create_membrane_foldtree_anchor_com() (in module pyrosetta.rosetta.protocols.membrane) create_membrane_foldtree_anchor_pose_tmcom() (in module pyrosetta.rosetta.protocols.membrane) create_membrane_foldtree_anchor_tmcom() (in module pyrosetta.rosetta.protocols.membrane) create_membrane_foldtree_from_anchors() (in module pyrosetta.rosetta.protocols.membrane) create_membrane_multi_partner_foldtree_anchor_tmcom() (in module pyrosetta.rosetta.protocols.membrane) create_model_from_pose() (in module pyrosetta.rosetta.protocols.sewing) create_mover() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.SplitAndMixPoseMoverCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator method) (pyrosetta.rosetta.protocols.moves.MoverCreator method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator method) create_new_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) create_new_node() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) create_new_parameters_set() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) create_options() (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator method) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator method) create_oriented_water_rotamer() (in module pyrosetta.rosetta.core.pack.rotamer_set) create_output_upstream_pose() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) create_packer_graph() (in module pyrosetta.rosetta.core.pack) create_packer_task() (pyrosetta.rosetta.core.pack.task.TaskFactory method) create_pdb_contents_from_sfr() (in module pyrosetta.rosetta.core.io.pdb) create_protocol() (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator method) create_rdf_function() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator method) create_remark_headers_from_cstcache() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) create_reporter() (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator method) create_requirement() (pyrosetta.rosetta.protocols.sewing.sampling.requirements.GlobalRequirementCreator method) create_res_filter() (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator method) create_res_level_task_operation() (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) create_residue() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.ResidueFactory method) create_resource_loader() (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.core.io.silent.SilentFileLoaderCreator method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator method) create_resource_locator() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator method) create_resource_manager() (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator method) create_resource_manager_from_options_system() (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory method) create_resource_options() (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory method) create_resources() (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) create_rna_vall_torsions() (in module pyrosetta.rosetta.protocols.rna.denovo) create_rotamer() (pyrosetta.rosetta.core.conformation.Residue method) create_rotamer_string() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) create_sample_vector() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) create_sasa_method() (in module pyrosetta.rosetta.core.scoring.sasa) create_score_function() (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory method) create_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) create_scores() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) create_scoring_method() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) create_SecMatchResiduePairEvaluatorOP() (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory method) create_selector() (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator method) create_sequence() (pyrosetta.rosetta.core.sequence.SequenceCreator method) create_sequence_profile_constraints() (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover method) create_sfr_from_cif_file_op() (in module pyrosetta.rosetta.core.io.mmcif) create_sfr_from_pdb_file_contents() (in module pyrosetta.rosetta.core.io.pdb) create_shuffle_map_recursive_rms() (in module pyrosetta.rosetta.core.scoring) create_silent_struct() (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.SilentStructCreator method) create_SilentStructOP() (pyrosetta.rosetta.core.io.silent.SilentFileData method) create_specific_membrane_foldtree() (in module pyrosetta.rosetta.protocols.membrane) create_standard_o2prime_pack_task() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) create_subpose() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) create_tag() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) create_tag_from_xml() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) create_tag_from_xml_string() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) create_task_and_apply_taskoperations() (pyrosetta.rosetta.core.pack.task.TaskFactory method) create_task_for_allhotspot_packing() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) create_task_for_hotspot_packing() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) create_task_operation() (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator method) create_temp_filename() (in module pyrosetta.rosetta.utility.file) create_torsion_value_string() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) create_working_data() (in module pyrosetta.rosetta.core.io.pose_from_sfr) creates_undefined_backbone() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction 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) cross() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.numeric.kinematic_closure) CrossLinker (class in pyrosetta.rosetta.protocols.cyclic_peptide) CrosslinkerMover (class in pyrosetta.rosetta.protocols.cyclic_peptide) CrosslinkerMoverHelper (class in pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) crossover() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) crosspeak() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) CrossPeakInfo (class in pyrosetta.rosetta.protocols.noesy_assign) crosspeaks() (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) crystinfo() (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.pose.PDBInfo method) crystRMS() (in module pyrosetta.rosetta.protocols.cryst) crystRMSfast() (in module pyrosetta.rosetta.protocols.cryst) CSA (class in pyrosetta.rosetta.core.scoring) CSAcomputed() (pyrosetta.rosetta.core.scoring.CSA method) CSAerr() (pyrosetta.rosetta.core.scoring.CSA method) CSAval() (pyrosetta.rosetta.core.scoring.CSA method) CSI_bgBlack() (in module pyrosetta.rosetta.utility) CSI_bgBlue() (in module pyrosetta.rosetta.utility) CSI_bgCyan() (in module pyrosetta.rosetta.utility) CSI_bgDefault() (in module pyrosetta.rosetta.utility) CSI_bgGreen() (in module pyrosetta.rosetta.utility) CSI_bgMagenta() (in module pyrosetta.rosetta.utility) CSI_bgRed() (in module pyrosetta.rosetta.utility) CSI_bgWhite() (in module pyrosetta.rosetta.utility) CSI_bgYellow() (in module pyrosetta.rosetta.utility) CSI_Black() (in module pyrosetta.rosetta.utility) CSI_Blue() (in module pyrosetta.rosetta.utility) CSI_Bold() (in module pyrosetta.rosetta.utility) CSI_Cyan() (in module pyrosetta.rosetta.utility) CSI_Default() (in module pyrosetta.rosetta.utility) CSI_Green() (in module pyrosetta.rosetta.utility) CSI_Magenta() (in module pyrosetta.rosetta.utility) CSI_Nothing() (in module pyrosetta.rosetta.utility) CSI_Red() (in module pyrosetta.rosetta.utility) CSI_Reset() (in module pyrosetta.rosetta.utility) CSI_Sequence (class in pyrosetta.rosetta.utility) CSI_Underline() (in module pyrosetta.rosetta.utility) CSI_White() (in module pyrosetta.rosetta.utility) CSI_Yellow() (in module pyrosetta.rosetta.utility) CSScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) cst_block() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) cst_file() (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) cst_gen_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader method) cst_io() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) cst_max_seq_sep() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) cst_residue_in_pose() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) cst_type() (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) cstAtoms() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) cstAtoms_defined() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) cstfile() (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) cstfile_name() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) CstInfoMover (class in pyrosetta.rosetta.protocols.simple_moves) Cstring (class in pyrosetta.rosetta.ObjexxFCL) cterm_included() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) cube() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.ObjexxFCL) cubic_interpolation() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) cubic_polynomial_deriv() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) cubic_polynomial_from_spline() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) cubic_roots1() (in module pyrosetta.rosetta.protocols.cluster.calibur) cubic_roots2() (in module pyrosetta.rosetta.protocols.cluster.calibur) cull_violators() (in module pyrosetta.rosetta.core.scoring.constraints) cumulate_jobs() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) cumulate_replicas() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) curr_num_in_recent_history() (pyrosetta.rosetta.utility.recent_history_queue method) curr_rot() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) current_acceptance_ratio() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) current_batch() (in module pyrosetta.rosetta.protocols.jd2) current_batch_id() (in module pyrosetta.rosetta.protocols.jd2) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) current_input_tag() (in module pyrosetta.rosetta.protocols.jd2) current_job() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) current_job_id() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) current_nstruct_index() (in module pyrosetta.rosetta.protocols.jd2) current_output_filename() (in module pyrosetta.rosetta.protocols.jd2) current_output_name() (in module pyrosetta.rosetta.protocols.jd2) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) current_replica() (in module pyrosetta.rosetta.protocols.jd2) current_rotamer() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) current_score() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) current_scorefxn() (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) current_size() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) current_trial() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) custom_angle() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) custom_rama_table() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) custom_type_name() (pyrosetta.rosetta.utility.tag.XMLSchemaType method) custom_variant_types() (pyrosetta.rosetta.core.chemical.ResidueType method) CustomScoreSelector (class in pyrosetta.rosetta.protocols.frag_picker) cut() (pyrosetta.rosetta.protocols.loops.Loop method) cut_bond() (pyrosetta.rosetta.core.chemical.Bond method) cut_bond_neighbor() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) cut_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) cut_residue() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) CutChainMover (class in pyrosetta.rosetta.protocols.simple_moves) cutoff() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) cutoff_buried_surface_area() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) cutoff_distance() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors method) cutpoint() (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) cutpoint_by_jump() (pyrosetta.rosetta.core.kinematics.FoldTree method) cutpoint_map() (pyrosetta.rosetta.core.kinematics.FoldTree method) cutpoint_open_in_full_model() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) cutpoint_probabilities() (in module pyrosetta.rosetta.protocols.medal) cutpoint_segment() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) cutpoint_separation() (in module pyrosetta.rosetta.protocols.antibody) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) cutpoints() (pyrosetta.rosetta.core.kinematics.FoldTree method) cutpoints_separation() (in module pyrosetta.rosetta.protocols.antibody) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) cutpos_list() (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) cwd() (in module pyrosetta.rosetta.utility.file) CycleMover (class in pyrosetta.rosetta.protocols.moves) cycles() (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) CyclicMover (class in pyrosetta.rosetta.protocols.moves) CyclizationMover (class in pyrosetta.rosetta.protocols.simple_moves) cyclize_pose() (in module pyrosetta.rosetta.protocols.relax) CycpepSymmetryFilter (class in pyrosetta.rosetta.protocols.cyclic_peptide)