Index – F

F() (in module pyrosetta.rosetta.ObjexxFCL.format) f0() (pyrosetta.rosetta.core.scoring.electron_density.KromerMann method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann method) f1() (pyrosetta.rosetta.core.scoring.DerivVectorPair method) f1ij() (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) f2() (pyrosetta.rosetta.core.scoring.DerivVectorPair method) f2ij() (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) f3ij() (pyrosetta.rosetta.core.scoring.CSA method) fa_center() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_depth() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_dun_cutoff() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) fa_hatr() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) Fa_Membed_update() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_penalty() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_proj() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_proj_coord() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_proj_deriv() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_stack_base_all() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) FabConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) factorA() (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) factorB() (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) factorsLTE19() (in module pyrosetta.rosetta.core.scoring.electron_density) (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) factorsLTE5() (in module pyrosetta.rosetta.core.scoring.electron_density) (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) factory_name() (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory method) factory_register() (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsFactory method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory method) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory method) (pyrosetta.rosetta.protocols.sewing.sampling.requirements.RequirementFactory method) FACTSPoseInfo (class in pyrosetta.rosetta.core.scoring) FACTSPotential (class in pyrosetta.rosetta.core.scoring) FACTSResidueInfo (class in pyrosetta.rosetta.core.scoring) FACTSRotamerSetInfo (class in pyrosetta.rosetta.core.scoring) FACTSRsdTypeInfo (class in pyrosetta.rosetta.core.scoring) FACTSRsdTypeMap (class in pyrosetta.rosetta.core.scoring) fade_energy() (in module pyrosetta.rosetta.core.scoring.hbonds) FadeInterval (class in pyrosetta.rosetta.core.scoring.hbonds) FaDockingSlideIntoContact (class in pyrosetta.rosetta.protocols.docking) fail() (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) fake_hit() (in module pyrosetta.rosetta.protocols.match) fallback_specified() (pyrosetta.rosetta.basic.resource_manager.FallbackConfiguration method) (pyrosetta.rosetta.protocols.loops.LoopsFileFallbackConfiguration method) FallbackConfiguration (class in pyrosetta.rosetta.basic.resource_manager) FallbackConfigurationCreator (class in pyrosetta.rosetta.basic.resource_manager) FallbackConfigurationFactory (class in pyrosetta.rosetta.basic.resource_manager) false_movemap() (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) FaMPEnvEnergy (class in pyrosetta.rosetta.core.scoring.membrane) FaMPEnvEnergyCreator (class in pyrosetta.rosetta.core.scoring.membrane) FaMPEnvSmoothEnergy (class in pyrosetta.rosetta.core.scoring.membrane) FaMPEnvSmoothEnergyCreator (class in pyrosetta.rosetta.core.scoring.membrane) FaMPSolvEnergy (class in pyrosetta.rosetta.core.scoring.membrane) FaMPSolvEnergyCreator (class in pyrosetta.rosetta.core.scoring.membrane) FAScatter (class in pyrosetta.rosetta.core.scoring.fiber_diffraction) fasol_cubic_poly_far_xhi() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) fasol_cubic_poly_far_xlo() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) fast() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) fast_ccd_close_loops() (in module pyrosetta.rosetta.protocols.loops.loop_mover.perturb) fast_forward() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) fast_forward_to_next_residue_pair() (in module pyrosetta.rosetta.protocols.stepwise.screener) fast_rmsd() (in module pyrosetta.rosetta.protocols.cluster.calibur) fast_scan() (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) FastGapMover (class in pyrosetta.rosetta.protocols.loophash) FaSymDockingSlideTogether (class in pyrosetta.rosetta.protocols.simple_moves.symmetry) FavorNativeResidue (class in pyrosetta.rosetta.protocols.protein_interface_design) FavorNonNativeResidue (class in pyrosetta.rosetta.protocols.protein_interface_design) fcen10() (pyrosetta.rosetta.core.scoring.CenListInfo method) fcen12() (pyrosetta.rosetta.core.scoring.CenListInfo method) fcen6() (pyrosetta.rosetta.core.scoring.CenListInfo method) features_reporter_dependencies() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) features_reporter_xml_schema_group_name() (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) FeaturesReporterCreator (class in pyrosetta.rosetta.protocols.features) FeaturesReporterFactory (class in pyrosetta.rosetta.protocols.features) featurizer_state() (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) fetch_stored_derivatives() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) fft3() (in module pyrosetta.rosetta.numeric.fourier) fft3_dynamic() (in module pyrosetta.rosetta.numeric.fourier) FiberDiffractionOptionsCreator (class in pyrosetta.rosetta.core.scoring.fiber_diffraction) figure_out_base_pair_partner() (in module pyrosetta.rosetta.protocols.rna.denovo) figure_out_chain_numbers_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) figure_out_chain_numbers_from_full_model_info_const() (in module pyrosetta.rosetta.core.pose.full_model_info) figure_out_conventional_chains_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) figure_out_dock_domain_map() (in module pyrosetta.rosetta.core.import_pose) figure_out_dock_domain_map_from_full_model_info_const() (in module pyrosetta.rosetta.core.pose.full_model_info) figure_out_fixed_domain_map() (in module pyrosetta.rosetta.core.import_pose) figure_out_motif_mode() (in module pyrosetta.rosetta.core.import_pose) figure_out_moving_chain_break_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_moving_chain_breaks() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_moving_cutpoints_closed() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_moving_cutpoints_closed_from_moving_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_moving_partition_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) figure_out_moving_partition_res_for_jump() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_moving_partition_res_for_suite() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_moving_rna_chain_breaks() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) figure_out_neighbors() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) figure_out_pose_domain_map() (in module pyrosetta.rosetta.core.pose.full_model_info) figure_out_pose_domain_map_const() (in module pyrosetta.rosetta.core.pose.full_model_info) figure_out_protein_modeling_info() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) figure_out_reasonable_rna_fold_tree() (in module pyrosetta.rosetta.core.pose.rna) figure_out_rebuild_bulge_mode() (in module pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters) figure_out_reference_res_for_jump() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) figure_out_reference_res_for_suite() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_repackable_residues() (in module pyrosetta.rosetta.core.pack) figure_out_residue_numbers_from_line() (in module pyrosetta.rosetta.core.io.silent) (pyrosetta.rosetta.core.io.silent.SilentStruct method) figure_out_root_and_moving_partition_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_root_partition_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_sample_both_sugar_base_rotamer() (in module pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters) figure_out_sample_res() (in module pyrosetta.rosetta.core.import_pose) figure_out_secstruct() (in module pyrosetta.rosetta.protocols.rna.denovo) figure_out_segment_ids_from_line() (pyrosetta.rosetta.core.io.silent.SilentStruct method) figure_out_stepwise_movemap() (in module pyrosetta.rosetta.protocols.stepwise.modeler.movemap) figure_out_working_interface_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler.packer) figure_out_working_res() (in module pyrosetta.rosetta.core.import_pose) fij() (pyrosetta.rosetta.core.scoring.RDC method) file() (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) file_basename() (in module pyrosetta.rosetta.utility) (in module pyrosetta.rosetta.utility.file) file_contents() (in module pyrosetta.rosetta.utility) file_delete() (in module pyrosetta.rosetta.utility.file) file_exists() (in module pyrosetta.rosetta.utility.file) file_extension() (in module pyrosetta.rosetta.utility.file) file_full_path() (in module pyrosetta.rosetta.protocols.toolbox) file_is_atom_tree_diff() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) file_name() (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) file_read() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) file_reading_token() (pyrosetta.rosetta.protocols.loops.Loops method) file_size() (in module pyrosetta.rosetta.utility.file) FileContentsMap (class in pyrosetta.rosetta.utility.io) FileJobOutputter (class in pyrosetta.rosetta.protocols.jd2) FileListResourceLocator (class in pyrosetta.rosetta.basic.resource_manager.locator) FileListResourceLocatorCreator (class in pyrosetta.rosetta.basic.resource_manager.locator) FileName (class in pyrosetta.rosetta.utility.file) filename() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (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.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ozstream method) FileOption (class in pyrosetta.rosetta.utility.options) FileOptionKey (class in pyrosetta.rosetta.utility.options) FileStream (class in pyrosetta.rosetta.basic.resource_manager.locator) FileSystemResourceLocator (class in pyrosetta.rosetta.basic.resource_manager.locator) FileSystemResourceLocatorCreator (class in pyrosetta.rosetta.basic.resource_manager.locator) filetype() (in module pyrosetta.rosetta.protocols.cluster.calibur) FileVectorOption (class in pyrosetta.rosetta.utility.options) FileVectorOptionKey (class in pyrosetta.rosetta.utility.options) fill() (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) fill_A_line() (in module pyrosetta.rosetta.protocols.scoring.methods.pcs) (in module pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) (in module pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) (in module pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) (in module pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) fill_A_line_fast() (in module pyrosetta.rosetta.protocols.scoring.methods.pcs2) fill_A_line_slow() (in module pyrosetta.rosetta.protocols.scoring.methods.pcs2) fill_CA_coords() (in module pyrosetta.rosetta.protocols.toolbox) fill_data() (in module pyrosetta.rosetta.protocols.recces) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) fill_energy_map() (pyrosetta.rosetta.core.scoring.EnergyEdge method) fill_f1_f2() (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) fill_from_string() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) fill_from_string_cs() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) fill_from_string_residue_depth_version1() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) fill_from_string_version1() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) fill_grid_with_backbone_heavyatom_spheres() (in module pyrosetta.rosetta.protocols.match) fill_grid_with_residue_heavyatom_spheres() (in module pyrosetta.rosetta.protocols.match) fill_grid_with_residue_spheres() (in module pyrosetta.rosetta.protocols.match) fill_h2o_hbond_set() (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) fill_hbond_bb_pair_score_dssp() (in module pyrosetta.rosetta.core.scoring.dssp) fill_hbond_set() (in module pyrosetta.rosetta.core.scoring.hbonds) fill_hbond_set_by_AHdist_threshold() (in module pyrosetta.rosetta.core.scoring.hbonds) fill_ideal_xyz_from_icoor() (pyrosetta.rosetta.core.chemical.ResidueType method) fill_in_default_jump_atoms() (in module pyrosetta.rosetta.protocols.rna.denovo) fill_in_gaps() (in module pyrosetta.rosetta.protocols.frags) fill_intra_res_hbond_set() (in module pyrosetta.rosetta.core.scoring.hbonds) fill_jobs() (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) fill_missing_atoms() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) fill_mutations_list() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) fill_neighbor_residues() (in module pyrosetta.rosetta.core.select) fill_non_loop_cst_set() (in module pyrosetta.rosetta.protocols.forge.methods) fill_other_struct_list() (pyrosetta.rosetta.core.io.silent.SilentStruct method) fill_pose() (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) fill_rna_data_info() (pyrosetta.rosetta.core.io.rna.RNA_DataReader method) fill_rotamer_vector() (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) fill_solution() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) fill_struct() (pyrosetta.rosetta.core.io.silent.SilentStruct method) fill_struct_with_residue_numbers() (pyrosetta.rosetta.core.io.silent.SilentStruct method) fill_struct_with_submotif_info_list() (pyrosetta.rosetta.core.io.silent.SilentStruct method) fill_template_frames_from_pdb() (in module pyrosetta.rosetta.core.fragment) fill_tenA_neighbor_residues() (in module pyrosetta.rosetta.core.select) fill_upstream_children_res_and_tips() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) fill_vdw_cached_rep_screen_info_from_command_line() (in module pyrosetta.rosetta.protocols.scoring) fill_vdw_cached_rep_screen_info_from_options() (in module pyrosetta.rosetta.protocols.scoring) FillAUTOTaskOperation (class in pyrosetta.rosetta.core.pack.task.operation) fillTargetPockets() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) Filter (class in pyrosetta.rosetta.protocols.pose_selectors) filter() (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) filter_acceptor_ligands() (in module pyrosetta.rosetta.protocols.magnesium) filter_by_constraints_energy_asymmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) filter_by_constraints_energy_symmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) filter_by_lj() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) filter_by_sidechain_distance_asymmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) filter_by_sidechain_distance_symmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) filter_loop_neighbors_by_distance() (in module pyrosetta.rosetta.protocols.loops) filter_max_bend() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) filter_max_dist() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) filter_max_orthoangle() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) filter_max_planeangle() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) filter_max_twist() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) filter_min_bend() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) filter_min_dist() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) filter_min_orthoangle() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) filter_min_planeangle() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) filter_min_twist() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) filter_motifs() (in module pyrosetta.rosetta.core.scoring.motif) filter_name() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) filter_native_big_bins() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) filter_neighbors_by_distance() (in module pyrosetta.rosetta.core.select) filter_on() (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) filter_out_high() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) filter_out_low() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) filter_structs() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) FilterCollection (class in pyrosetta.rosetta.protocols.filters) FilterCreator (class in pyrosetta.rosetta.protocols.filters) filtered_base_axis_array() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) filtered_base_pair_array() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) filtered_base_stack_array() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) filtered_base_stack_axis_array() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) filtered_base_stagger_array() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) FilteredSolutions (class in pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers) FilterReportAsPoseExtraScoresMover (class in pyrosetta.rosetta.protocols.moves) FilterReporter (class in pyrosetta.rosetta.protocols.pose_reporters) FilterReporterMover (class in pyrosetta.rosetta.protocols.moves) filters() (pyrosetta.rosetta.protocols.simple_filters.Operator method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) FilterStructs (class in pyrosetta.rosetta.protocols.flxbb) FilterStructs_Packstat (class in pyrosetta.rosetta.protocols.flxbb) FilterStructs_TotalCharge (class in pyrosetta.rosetta.protocols.flxbb) final_cleanup() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) final_design_min() (in module pyrosetta.rosetta.protocols.ncbb) final_frlx_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) final_pose() (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) final_repack() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) final_stream() (pyrosetta.rosetta.basic.Tracer method) Finalize() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) finalize() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) finalize_after_derivatives() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy 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.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_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) finalize_batch() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) finalize_claims() (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) finalize_compound_records() (pyrosetta.rosetta.core.io.HeaderInformation method) finalize_experimental_technique_records() (pyrosetta.rosetta.core.io.HeaderInformation method) finalize_keyword_records() (pyrosetta.rosetta.core.io.HeaderInformation method) finalize_parse() (pyrosetta.rosetta.core.io.HeaderInformation method) finalize_scoring() (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) finalize_simulation() (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.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver 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.kinematic_closure.BalancedKicMover 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.UniformSphereTransMover 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.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover 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.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) finalize_total_energy() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy 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.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_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) FinalizeAromatic() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) finalized() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) finalized_energies() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) FinalizeUnhybridized() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) find() (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) find_attach_pt() (in module pyrosetta.rosetta.protocols.ligand_docking) find_automatically() (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) find_basepairs() (in module pyrosetta.rosetta.core.scoring.dna) (in module pyrosetta.rosetta.protocols.dna) find_best_match() (in module pyrosetta.rosetta.core.chemical) find_bonds_in_rings() (in module pyrosetta.rosetta.core.chemical) find_bound_waters_that_are_daughters_in_fold_tree() (in module pyrosetta.rosetta.protocols.magnesium) find_cache_file() (in module pyrosetta.rosetta.basic.database) find_char_location_in_string() (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) find_chi_bonds() (in module pyrosetta.rosetta.core.chemical) find_chunk() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) find_closest_atom() (in module pyrosetta.rosetta.protocols.metal_interface) Find_Closest_Intersect_SQ() (in module pyrosetta.rosetta.protocols.pockets) find_common_intersection_atoms() (in module pyrosetta.rosetta.core.scoring.power_diagram) find_connected_components() (in module pyrosetta.rosetta.utility.graph) find_connecting_jump() (in module pyrosetta.rosetta.protocols.forge.methods) find_cutpoint() (in module pyrosetta.rosetta.protocols.forge.methods) find_cutpoint_variants() (in module pyrosetta.rosetta.core.scoring.methods) find_database_path() (in module pyrosetta.rosetta.basic.database) find_design_interface() (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) find_design_interface_arg_sweep() (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) find_downstream_connection_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) find_edge() (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.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) find_energy_edge() (pyrosetta.rosetta.core.scoring.EnergyGraph method) find_existing_residues() (in module pyrosetta.rosetta.protocols.evaluation) find_filter_or_die() (in module pyrosetta.rosetta.protocols.moves) find_first_interface_residue() (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) find_first_not_of() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_first_of() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_glycan_sequence_file() (in module pyrosetta.rosetta.core.chemical.carbohydrates) find_hash_edge() (pyrosetta.rosetta.protocols.sewing.SewGraph method) find_hbond_res_struct() (in module pyrosetta.rosetta.protocols.hbnet) find_helices_over_length() (in module pyrosetta.rosetta.protocols.aa_composition) find_hits() (pyrosetta.rosetta.protocols.match.Matcher method) find_in_pose_if_missing_from_header() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) find_index_in_other_pose_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) find_intersections() (in module pyrosetta.rosetta.core.scoring.power_diagram) find_jump_number_at_suite() (in module pyrosetta.rosetta.protocols.stepwise.modeler) find_jump_rec() (in module pyrosetta.rosetta.protocols.denovo_design) find_key_cl() (pyrosetta.rosetta.utility.options.OptionCollection method)

find_key_file() (pyrosetta.rosetta.utility.options.OptionCollection method) find_last() (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_last_non_whitespace() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_last_not_of() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_last_of() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_last_whitespace() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_length() (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) find_ligands() (in module pyrosetta.rosetta.protocols.flxbb) find_lowest_constraint_energy_residue() (in module pyrosetta.rosetta.protocols.protein_interface_design) find_max_r() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) find_metalbinding_atoms() (in module pyrosetta.rosetta.core.util) find_metalbinding_atoms_for_complex() (in module pyrosetta.rosetta.core.util) find_metalbinding_atoms_helper() (in module pyrosetta.rosetta.core.util) find_min_xyz() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) find_minimization_edge() (pyrosetta.rosetta.core.scoring.MinimizationGraph method) find_nbr_dist() (in module pyrosetta.rosetta.core.chemical) find_nearest_disulfide() (in module pyrosetta.rosetta.protocols.rosetta_scripts) find_nearest_res() (in module pyrosetta.rosetta.protocols.rosetta_scripts) find_nearest_residue() (in module pyrosetta.rosetta.protocols.protein_interface_design) find_nearest_residue_to_coord() (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) find_neighbors() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) find_neighbors_restricted() (in module pyrosetta.rosetta.core.conformation) find_new_jump_residue() (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) find_new_symmetric_jump_residues() (in module pyrosetta.rosetta.core.pose.symmetry) find_next_vertex_with_smallest_dist() (in module pyrosetta.rosetta.core.scoring.power_diagram) find_non_protein_chunks() (in module pyrosetta.rosetta.protocols.loops) find_non_whitespace() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_num_scattering_atoms() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) find_orientations_and_lengths() (in module pyrosetta.rosetta.protocols.denovo_design.components) find_pairing() (in module pyrosetta.rosetta.protocols.fldsgn.filters) find_pairing_idx() (in module pyrosetta.rosetta.protocols.fldsgn.filters) find_peptide_attach_pt() (in module pyrosetta.rosetta.protocols.ligand_docking) find_pitch() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) find_possible_orders() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) find_regions_with_minimum_size() (in module pyrosetta.rosetta.protocols.nonlocal) find_relevant_connections_onersd() (in module pyrosetta.rosetta.core.scoring.methods) find_residue_max_radii() (in module pyrosetta.rosetta.core.pack) find_resource_configuration() (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) find_resource_locator() (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) find_resource_options() (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) find_resource_tag_by_job_tag() (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) find_rosettascript_tag() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) find_seqpos_of_saccharides_child_residue_at() (in module pyrosetta.rosetta.core.conformation.carbohydrates) find_seqpos_of_saccharides_mainchain_child() (in module pyrosetta.rosetta.core.conformation.carbohydrates) find_seqpos_of_saccharides_parent_residue() (in module pyrosetta.rosetta.core.conformation.carbohydrates) find_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) find_SilentStructOPs (class in pyrosetta.rosetta.protocols.wum) find_start_of_next_interface_region() (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) find_stop_of_this_interface_region() (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) find_symmetric_basejump_anchor() (in module pyrosetta.rosetta.core.pose.symmetry) find_unconnected_residues() (in module pyrosetta.rosetta.protocols.ligand_docking) find_weights_file() (in module pyrosetta.rosetta.core.scoring) find_whitespace() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) findClusters() (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) findClustersByExemplars() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) findExemplars() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) findLoopFromDensity() (in module pyrosetta.rosetta.protocols.electron_density) findPockets() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) FindPossibleAtomTypesForAtom() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) findPSP() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) findSampling() (in module pyrosetta.rosetta.core.scoring.electron_density) (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) findSampling5() (in module pyrosetta.rosetta.core.scoring.electron_density) (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) findSPS() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) findUU() (in module pyrosetta.rosetta.numeric.model_quality) finer_sampling_at_chain_closure() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) FingerprintMultifunc (class in pyrosetta.rosetta.protocols.pockets) finish_pose() (pyrosetta.rosetta.core.io.silent.SilentStruct method) finished() (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) finished_simulation() (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) finite() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) first_adjacent_heavy_atom() (pyrosetta.rosetta.core.conformation.Residue method) first_base_atom() (in module pyrosetta.rosetta.core.chemical.rna) first_base_atom_index() (in module pyrosetta.rosetta.core.chemical.rna) first_connected_resonance() (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) first_residue() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) first_residue_index() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) first_sidechain_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) first_sidechain_hydrogen() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) fit_centered_coords() (in module pyrosetta.rosetta.protocols.toolbox) fit_layer_lines_with_splines() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) fitness() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) fitness_pbest() (pyrosetta.rosetta.core.optimization.Particle method) fitness_valid() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) fitnessCostPerATP() (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) FitSimpleHelixMultiFunc (class in pyrosetta.rosetta.protocols.helical_bundle) fiveprime_cap() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) fix_bfactorsH() (in module pyrosetta.rosetta.core.scoring.cryst) fix_bfactorsMissing() (in module pyrosetta.rosetta.core.scoring.cryst) fix_disulfides() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) fix_glycan_order() (in module pyrosetta.rosetta.core.io) FIX_HIS_TAUTOMER (class in pyrosetta.rosetta.core.pack.task) fix_his_tautomer() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) fix_pdbinfo_damaged_by_insertion() (in module pyrosetta.rosetta.core.pose) fix_protein_jump_atom() (in module pyrosetta.rosetta.protocols.stepwise.modeler) fix_reference_energies() (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) fix_sugar_coords() (in module pyrosetta.rosetta.core.pose.rna) fix_tag_suffix() (in module pyrosetta.rosetta.protocols.toolbox) fix_up_jump_atoms() (in module pyrosetta.rosetta.protocols.stepwise.modeler) fix_up_jump_atoms_and_residue_type_variants() (in module pyrosetta.rosetta.protocols.stepwise.modeler) fix_up_residue_type_variants() (in module pyrosetta.rosetta.core.pose) fix_up_residue_type_variants_at_strand_beginning() (in module pyrosetta.rosetta.core.pose) fix_up_residue_type_variants_at_strand_end() (in module pyrosetta.rosetta.core.pose) fix_with_coord_cst() (in module pyrosetta.rosetta.protocols.loops) fix_worst_bad_ramas() (in module pyrosetta.rosetta.protocols.relax) fixed() (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) fixed_dist() (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) fixed_domain_map() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) fixed_energies() (pyrosetta.rosetta.core.scoring.MinimizationGraph method) fixed_energy_terms() (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) fixed_size() (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) FixedOffsetPivots (class in pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers) FixedOffsetsPivots (class in pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers) FixedPivots (class in pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers) FixedTemperatureController (class in pyrosetta.rosetta.protocols.canonical_sampling) fixEigenvector() (in module pyrosetta.rosetta.numeric.model_quality) fixH() (in module pyrosetta.rosetta.protocols.relax) fixResidue() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) fixup_magnesiums() (in module pyrosetta.rosetta.protocols.magnesium) fixup_patches() (in module pyrosetta.rosetta.core.chemical) flag_file() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) flag_for_calculation() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) flanking_left_aa() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) flanking_left_nres() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) flanking_left_ss() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) flanking_right_aa() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) flanking_right_nres() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) flanking_right_ss() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) flexbb() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) FlexBBMeanField (class in pyrosetta.rosetta.protocols.mean_field) flip_atom_xyz() (in module pyrosetta.rosetta.core.io.pose_from_sfr) flip_HNQ() (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) flip_subset() (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) flip_upstream_downstream_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) FlipMover (class in pyrosetta.rosetta.protocols.membrane) FlipMoverCreator (class in pyrosetta.rosetta.protocols.membrane) float_ambiguity() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) float_label() (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) float_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) FloatingResonance (class in pyrosetta.rosetta.protocols.noesy_assign) flood_fill3D() (in module pyrosetta.rosetta.protocols.sic_dock) FloppyTailMover (class in pyrosetta.rosetta.protocols.floppy_tail) flush() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.YamlEmitter method) (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.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) flush_all_channels() (pyrosetta.rosetta.basic.Tracer method) flush_all_tracers() (pyrosetta.rosetta.basic.Tracer method) flush_finalize() (pyrosetta.rosetta.utility.io.ozstream method) FlxbbDesign (class in pyrosetta.rosetta.protocols.flxbb) FlxbbDesign_main() (in module pyrosetta.rosetta.protocols.flxbb) FlxbbDesignPack (class in pyrosetta.rosetta.protocols.flxbb) fmt_real() (in module pyrosetta.rosetta.utility) fname() (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) focused_edge() (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) fold() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) fold_in_rb_deltas() (pyrosetta.rosetta.core.kinematics.Jump method) fold_label_resonance() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) fold_proton_resonance() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) fold_tree() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) fold_tree_from_loops() (in module pyrosetta.rosetta.protocols.forge.methods) (in module pyrosetta.rosetta.protocols.loops) fold_tree_from_pose() (in module pyrosetta.rosetta.protocols.forge.methods) fold_tree_io() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) FoldConstraints (class in pyrosetta.rosetta.protocols.abinitio) foldInChanges() (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) FoldTree (class in pyrosetta.rosetta.core.kinematics) foldTree() (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) foldtree_string() (pyrosetta.rosetta.core.io.StructFileRep method) FoldTreeFromFoldGraphMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) FoldTreeRequest (class in pyrosetta.rosetta.protocols.loop_modeling) foldtype_from_name() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) foldtype_from_spairs() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) follow_edge() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) foo_all() (in module pyrosetta.rosetta.utility.py) foo_all_sp() (in module pyrosetta.rosetta.utility.py) foo_int() (pyrosetta.rosetta.utility.py.Base method) foo_string() (pyrosetta.rosetta.utility.py.Base method) foo_value() (pyrosetta.rosetta.utility.py.Base method) foo_value_sp() (pyrosetta.rosetta.utility.py.Base method) force_aa_neighbors_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) force_all_aa_neighbors_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) force_bitflip() (pyrosetta.rosetta.core.io.silent.SilentStruct method) force_centroid_interaction() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) force_const() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) force_fold_tree() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) force_job_purging() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) force_nbr_atom_orient() (pyrosetta.rosetta.core.chemical.ResidueType method) force_phosphate_instantiation() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) ForceDisulfidesMover (class in pyrosetta.rosetta.protocols.simple_moves) form_disulfide() (in module pyrosetta.rosetta.core.conformation) form_disulfide_helper() (in module pyrosetta.rosetta.core.conformation) formal_charge() (pyrosetta.rosetta.core.chemical.Atom method) formatted_icoord_tree() (in module pyrosetta.rosetta.core.chemical) FormFactorManager (class in pyrosetta.rosetta.core.scoring.saxs) forward_connections() (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) FourAtomsConstraintData (class in pyrosetta.rosetta.protocols.frag_picker.scores) FourPointsFunc (class in pyrosetta.rosetta.core.scoring.func) frac_atoms_within() (in module pyrosetta.rosetta.protocols.ligand_docking) fract_property_penalty() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) frag_files() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) frag_id() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) frag_libs() (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) frag_set_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.FragSetLoader method) frag_sizes() (pyrosetta.rosetta.protocols.frags.FragLib method) FragInsertAndAlignMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) FragLib (class in pyrosetta.rosetta.protocols.frags) fragment() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) fragment_as_pose() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) fragment_contacts() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) fragment_ptr() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) fragment_set_slice() (in module pyrosetta.rosetta.core.fragment) FragmentAllAtomCrmsd (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentCandidate (class in pyrosetta.rosetta.protocols.frag_picker) FragmentChunkCrms (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentCrmsd (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentCrmsdResDepth (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentDME (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentJumpClaimer (class in pyrosetta.rosetta.protocols.topology_broker) FragmentLibraryManager (class in pyrosetta.rosetta.core.fragment.picking_old) FragmentMover (class in pyrosetta.rosetta.protocols.simple_moves) FragmentPerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) FragmentPicker (class in pyrosetta.rosetta.protocols.frag_picker) fragments() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.nonlocal.Policy method) (pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy method) (pyrosetta.rosetta.protocols.nonlocal.UniformPolicy method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) fragments_for_permutation() (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) fragments_for_permutation_take_X_from_pose() (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) FragmentSampler (class in pyrosetta.rosetta.protocols.abinitio) FragmentScoreManager (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentScoreMap (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentScoringMethod (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentSelectingRule (class in pyrosetta.rosetta.protocols.frag_picker) frags_per_pos() (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector method) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector method) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector method) FragSet (class in pyrosetta.rosetta.core.fragment) FragSetLoader (class in pyrosetta.rosetta.protocols.parser) Frame (class in pyrosetta.rosetta.core.fragment) frame() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) frames() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) framework_dependant_clusters() (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) framework_dependant_mutations() (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) framework_dependant_positions() (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) free_dof_options() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) free_resource_by_job_tag() (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) free_resource_by_tag() (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) free_rsd() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) FreePeptide (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover) FreePeptideMover (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers) freeze() (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.UniformSphereTransMover method) freeze_sugar_torsions() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) freq() (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) frequency_in_taboo_map() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) fresh_instance() (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.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter 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.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.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.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter 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.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.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.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.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.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.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.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.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.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_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.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) from_bond_cst() (pyrosetta.rosetta.core.kinematics.Jump method) from_four_points() (pyrosetta.rosetta.core.kinematics.Stub method) from_other_chains() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) from_same_chain() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) from_span() (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) from_span_positive_z() (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) from_stubs() (pyrosetta.rosetta.core.kinematics.Jump method) front() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface 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.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) Fstring (class in pyrosetta.rosetta.ObjexxFCL) Fstring_of() (in module pyrosetta.rosetta.ObjexxFCL) Fsubstring (class in pyrosetta.rosetta.ObjexxFCL) ft_mover() (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) ftoa() (in module pyrosetta.rosetta.protocols.sparta) full_cache_name() (in module pyrosetta.rosetta.basic.database) full_definition() (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) full_hit() (in module pyrosetta.rosetta.protocols.match) full_length_rmsd_over_residue_list() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) full_model_info_defined() (in module pyrosetta.rosetta.core.pose.full_model_info) full_model_info_into_pose() (pyrosetta.rosetta.core.io.silent.SilentStruct method) full_model_parameter_type_from_string() (in module pyrosetta.rosetta.core.pose.full_model_info) full_model_parameters() (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) full_model_size() (in module pyrosetta.rosetta.core.pose.full_model_info) full_name() (in module pyrosetta.rosetta.basic.database) full_sequence() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) full_to_sub() (in module pyrosetta.rosetta.core.pose.full_model_info) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) fullatom_scorefxn() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) fullatom_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) FullAtomRNA_Fragments (class in pyrosetta.rosetta.protocols.rna.denovo.fragments) FullModelInfo (class in pyrosetta.rosetta.core.pose.full_model_info) Func (class in pyrosetta.rosetta.core.scoring.func) func() (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc 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.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.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.protocols.moves.GeometricFunc method) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc method) func_() (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) function_tag() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method)