Index – R

r (pyrosetta.rosetta.core.optimization.EItem property) (pyrosetta.rosetta.core.scoring.packstat.Circle property) R (pyrosetta.rosetta.numeric.Py_xyzTransform_double property) (pyrosetta.rosetta.numeric.xyzTransform_double_t property) (pyrosetta.rosetta.numeric.xyzTransform_float_t property) r() (pyrosetta.rosetta.core.scoring.packing.Ball method) R() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) R0() (pyrosetta.rosetta.core.scoring.lDDT_Calculator method) r0_range() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters method) r1 (pyrosetta.rosetta.protocols.sparta.PDB property) (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) R1_PARA (pyrosetta.rosetta.core.scoring.nmr.PRE_RATE_TYPE attribute) r21 (pyrosetta.rosetta.protocols.normalmode.ContactStruct property) R2_PARA (pyrosetta.rosetta.core.scoring.nmr.PRE_RATE_TYPE attribute) R2quat() (in module pyrosetta.rosetta.protocols.simple_filters) R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) r_alpha() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) r_alpha_m() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) r_alpha_p_x() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) r_alpha_p_y() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) r_alpha_p_z() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) r_ik (pyrosetta.rosetta.protocols.cluster.Exemplar property) r_kk (pyrosetta.rosetta.protocols.cluster.DataPoint property) r_param (pyrosetta.rosetta.core.scoring.APBSConfig property) R_PEPTOID (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) r_vectors (pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1.screw_construct_struct property) Ra (pyrosetta.rosetta.core.chemical.element.Elements attribute) rad (pyrosetta.rosetta.protocols.sparta.RingData property) rad() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) rad2() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) rad2deg() (pyrosetta.rosetta.numeric.NumericTraits_double_t static method) (pyrosetta.rosetta.numeric.NumericTraits_float_t static method) (pyrosetta.rosetta.numeric.NumericTraits_long_double_t static method) radial_bin_index() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) radial_count() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) radial_disp() (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) radial_lookup() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) radial_lookup_withkey() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) RADIANS (pyrosetta.rosetta.numeric.conversions.AngleUnit attribute) radians() (in module pyrosetta.rosetta.numeric.conversions) radians_to_degrees() (pyrosetta.rosetta.numeric.NumericTraits_double_t static method) (pyrosetta.rosetta.numeric.NumericTraits_float_t static method) (pyrosetta.rosetta.numeric.NumericTraits_long_double_t static method) radical_atom() (pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry method) radius (pyrosetta.rosetta.basic.sampling.orientations.QuatDBMetadata property) (pyrosetta.rosetta.core.scoring.packstat.SimplePDB_Atom property) (pyrosetta.rosetta.core.scoring.packstat.Sphere property) (pyrosetta.rosetta.core.scoring.PQR property) (pyrosetta.rosetta.core.scoring.sc._ATOM_RADIUS property) (pyrosetta.rosetta.core.scoring.sc.Atom property) radius() (pyrosetta.rosetta.core.pose.xyzStripeHashPose.const_iterator method) (pyrosetta.rosetta.core.scoring.packing.Ball method) (pyrosetta.rosetta.core.scoring.packstat.CavityBall method) (pyrosetta.rosetta.numeric.geometry.hashing.Ball method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash.const_iterator method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) radius_ (pyrosetta.rosetta.core.scoring.packstat.CavityBall property) (pyrosetta.rosetta.numeric.geometry.hashing.Ball property) radius_for_attype() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) radius_of_gyration() (in module pyrosetta.rosetta.core.pose) RadiusOfGyrationFeatures (class in pyrosetta.rosetta.protocols.features) RadiusOfGyrationFeaturesCreator (class in pyrosetta.rosetta.protocols.features) RAINBOW_COLOR (pyrosetta.rosetta.protocols.viewer.graphics_states_param.ColorMode attribute) RAINBOW_CPK_COLOR (pyrosetta.rosetta.protocols.viewer.graphics_states_param.ColorMode attribute) rama (pyrosetta.rosetta.core.scoring.ScoreType attribute) rama() (pyrosetta.rosetta.protocols.hybridization.FragmentBiasAssigner method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) rama2b (pyrosetta.rosetta.core.scoring.ScoreType attribute) rama2b_lr (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) Rama2bPerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) rama_bin_probability_left() (pyrosetta.rosetta.core.scoring.Ramachandran2B method) rama_bin_probability_right() (pyrosetta.rosetta.core.scoring.Ramachandran2B method) rama_cutoff_energy() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) rama_delta() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) rama_power() (pyrosetta.rosetta.core.scoring.Ramachandran method) rama_prepro (pyrosetta.rosetta.core.scoring.ScoreType attribute) rama_prepro_check (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.filter_type attribute) rama_prepro_multiplier() (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) rama_probability() (pyrosetta.rosetta.core.scoring.Ramachandran method) rama_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) Rama_Table_Type (class in pyrosetta.rosetta.core.scoring) Ramachandran (class in pyrosetta.rosetta.core.scoring) ramachandran (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolBackboneRandomizationMode attribute) Ramachandran2B (class in pyrosetta.rosetta.core.scoring) ramachandran_method (pyrosetta.rosetta.core.scoring.methods.EnergyMethods attribute) RamachandranEnergy (class in pyrosetta.rosetta.core.energy_methods) RamachandranEnergy2B (class in pyrosetta.rosetta.core.energy_methods) RamachandranEnergy2BCreator (class in pyrosetta.rosetta.core.energy_methods) RamachandranEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) RamachandranHash (class in pyrosetta.rosetta.protocols.features) RamaCheck1B (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) RamaCheck2B (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) RamaCheckBase (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) RamaE() (pyrosetta.rosetta.core.scoring.Ramachandran2B method) RamaE_Lower() (pyrosetta.rosetta.core.scoring.Ramachandran2B method) RamaE_Upper() (pyrosetta.rosetta.core.scoring.Ramachandran2B method) RamaMutationSelector (class in pyrosetta.rosetta.protocols.cyclic_peptide) RamaMutationSelectorCreator (class in pyrosetta.rosetta.protocols.cyclic_peptide) RamaPerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) RamaPrePro (class in pyrosetta.rosetta.core.scoring) ramaprepro_lr (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) RamaPreProEnergy (class in pyrosetta.rosetta.core.energy_methods) RamaPreProEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) RamaPreproFilename (class in pyrosetta.rosetta.core.chemical) RamaPreproResname (class in pyrosetta.rosetta.core.chemical) RamaScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) ramp_chainbreak() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ShortLoopClosure method) ramp_down_constraints() (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) ramp_fa_rep (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) ramp_minpack_loop() (in module pyrosetta.rosetta.protocols.mpi_refinement) ramp_minpack_pose() (in module pyrosetta.rosetta.protocols.mpi_refinement) ramp_rama (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) ramp_rnp_vdw() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) ramp_schedule (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GADockStageParams property) RampingFunc (class in pyrosetta.rosetta.protocols.moves) RampingMover (class in pyrosetta.rosetta.protocols.moves) RampingMoverCreator (class in pyrosetta.rosetta.protocols.moves) rand_sleep() (in module pyrosetta.rosetta.utility) RANDOM (pyrosetta.rosetta.core.conformation.symmetry.SlideType attribute) random (pyrosetta.rosetta.protocols.rigid.Direction attribute) random() (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) random_access() (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) random_angle() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) random_basepair() (pyrosetta.rosetta.protocols.dna.DNAParameters method) random_basestep() (pyrosetta.rosetta.protocols.dna.DNAParameters method) random_bin() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculator method) random_bin_based_on_prev_and_next() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculator method) random_bin_based_on_previous() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculator method) random_bin_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) random_bin_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) random_bin_iplus1_given_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) random_chunk (pyrosetta.rosetta.protocols.hybridization.AlignOption attribute) random_chunk_insertion() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) random_connection() (in module pyrosetta.rosetta.protocols.ligand_docking) random_delay() (in module pyrosetta.rosetta.core.init) random_device_name() (pyrosetta.rosetta.basic.random.RandomGeneratorSettings method) random_drop_rate() (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) random_entity() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.Mutate1Randomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) random_entry() (pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader method) random_fragment_insertion() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) random_jump_change() (pyrosetta.rosetta.core.import_pose.RNA_JumpMover method) random_limit_groupsize() (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) random_mainchain_torsions() (pyrosetta.rosetta.core.scoring.RamaPrePro method) random_mainchain_torsions_from_bin() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculator method) random_mainchain_torsions_from_bins() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculator method) random_mainchain_torsions_using_adjacent_bins() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculator method) random_mode() (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) random_mover() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) random_normal() (in module pyrosetta.rosetta.numeric.random) random_orientation_perturbation() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) RANDOM_PERMUTATION (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMoverMode attribute) random_perturbation() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) random_phi_psi_pert (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) random_phi_psi_pert_size (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) random_phipsi_from_rama() (pyrosetta.rosetta.core.scoring.Ramachandran method) random_phipsi_from_rama_by_torsion_bin() (pyrosetta.rosetta.core.scoring.Ramachandran method) random_phipsi_from_rama_by_torsion_bin_left() (pyrosetta.rosetta.core.scoring.Ramachandran2B method) random_phipsi_from_rama_by_torsion_bin_right() (pyrosetta.rosetta.core.scoring.Ramachandran2B method) random_phipsi_from_rama_left() (pyrosetta.rosetta.core.scoring.Ramachandran2B method) random_phipsi_from_rama_right() (pyrosetta.rosetta.core.scoring.Ramachandran2B method) random_point() (pyrosetta.rosetta.numeric.IntervalSet_Double method) (pyrosetta.rosetta.numeric.IntervalSet_double_t method) random_position_offset() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) random_range() (in module pyrosetta.rosetta.numeric.random) (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover method) random_range2() (pyrosetta.rosetta.numeric.random.RandomGenerator method) random_reorientation_matrix() (in module pyrosetta.rosetta.protocols.geometry) random_rotation() (in module pyrosetta.rosetta.core.scoring.motif) (in module pyrosetta.rosetta.numeric.random) random_sample() (pyrosetta.rosetta.numeric.random.WeightedSampler method) random_selector (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.selector_type attribute) RANDOM_SIDE (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum attribute) random_stub() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) random_torsion_move() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) random_trans() (pyrosetta.rosetta.core.kinematics.Jump method) random_tree_from_jump_points() (pyrosetta.rosetta.core.kinematics.FoldTree method) random_unit_quaternion() (in module pyrosetta.rosetta.numeric.random) random_vector() (in module pyrosetta.rosetta.numeric.random) random_vector_spherical() (in module pyrosetta.rosetta.numeric.random) random_vector_unit_cube() (in module pyrosetta.rosetta.numeric.random) random_xform() (in module pyrosetta.rosetta.numeric.random) randomAngle() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) RandomConformerMover (class in pyrosetta.rosetta.protocols.ligand_docking) RandomConformers (class in pyrosetta.rosetta.protocols.ligand_docking) RandomConformersCreator (class in pyrosetta.rosetta.protocols.ligand_docking) RandomGapSolutionPicker (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers) RandomGenerator (class in pyrosetta.rosetta.numeric.random) RandomGeneratorSettings (class in pyrosetta.rosetta.basic.random) RandomGlycanFoliageSelector (class in pyrosetta.rosetta.core.select.residue_selector) RandomGlycanFoliageSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) randomize (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GenKICPerturberEffect attribute) randomize() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) (pyrosetta.rosetta.protocols.splice.RBInMover method) randomize_alpha_backbone_by_rama (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) randomize_backbone_by_bins (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) randomize_backbone_by_rama_prepro (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) randomize_chis() (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) randomize_cut() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) randomize_dihedral (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) randomize_glycan_torsions() (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) randomize_init_rnp() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) randomize_input_sequence() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) randomize_ligand() (pyrosetta.rosetta.protocols.ligand_docking.Transform method) randomize_loop() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) randomize_loop_coords() (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) randomize_loops() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) randomize_missing_coords() (in module pyrosetta.rosetta.core.io.pose_from_sfr) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) randomize_pose_rigid_bodies() (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) randomize_selected_atoms() (in module pyrosetta.rosetta.protocols.comparative_modeling) randomize_stage() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) randomize_substrate_torsions() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) RandomizeBBByRamaPrePro (class in pyrosetta.rosetta.protocols.backbone_moves) RandomizeBBByRamaPreProCreator (class in pyrosetta.rosetta.protocols.backbone_moves) RandomMover (class in pyrosetta.rosetta.protocols.moves) RandomMoverCreator (class in pyrosetta.rosetta.protocols.moves) RandomMutation (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) RandomMutationCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) RandomOmegaFlipMover (class in pyrosetta.rosetta.protocols.simple_moves) RandomOmegaFlipMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) RandomPositionRotationMover (class in pyrosetta.rosetta.protocols.membrane) RandomPositionTranslationMover (class in pyrosetta.rosetta.protocols.membrane) randomRBstart (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) RandomResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) RandomResidueSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) RandomSheetBuilder (class in pyrosetta.rosetta.protocols.jumping) RandomSolutions (class in pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers) RandomSymmetrySlider (class in pyrosetta.rosetta.protocols.symmetry) RandomTorsionMover (class in pyrosetta.rosetta.protocols.simple_moves) RandomTorsionMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) RandomTorsionPoseFolder (class in pyrosetta.rosetta.protocols.denovo_design.components) range() (in module pyrosetta.rosetta.protocols.sic_dock) (pyrosetta.rosetta.core.scoring.PairEPotential method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc method) (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter method) range1_lower() (pyrosetta.rosetta.core.conformation.symmetry.SymDof method) range1_upper() (pyrosetta.rosetta.core.conformation.symmetry.SymDof method) range2_is_bound() (pyrosetta.rosetta.core.conformation.symmetry.SymDof method) range2_lower() (pyrosetta.rosetta.core.conformation.symmetry.SymDof method) range2_upper() (pyrosetta.rosetta.core.conformation.symmetry.SymDof method) range_check() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) range_pair_ (pyrosetta.rosetta.core.scoring.Hairpin property) RangeError (class in pyrosetta.rosetta.utility.excn) RangeFilter (class in pyrosetta.rosetta.protocols.simple_filters) RangeFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) RangeRelaxMover (class in pyrosetta.rosetta.protocols.relax) ranges() (pyrosetta.rosetta.numeric.DiscreteIntervalEncodingTree_unsigned_long_t method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) rank (pyrosetta.rosetta.utility.graph.DS_Node property) rank() (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) rank_score() (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) ranked_model() (pyrosetta.rosetta.protocols.abinitio.PairingStatistics method) ranking_cenfilter() (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) ranking_fafilter() (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) ranking_prerelax (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfo property) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfo property) rate_threshold() (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilter method) ratio() (pyrosetta.rosetta.core.optimization.DerivCheckDataPoint method) (pyrosetta.rosetta.core.optimization.DOF_DataPoint method) ratio_cutoff() (pyrosetta.rosetta.protocols.pose_metric_calculators.FragQualCalculator method) RationalLoopComparator (class in pyrosetta.rosetta.protocols.loops) RationalMonteCarlo (class in pyrosetta.rosetta.protocols.simple_moves.rational_mc) Rattle (class in pyrosetta.rosetta.protocols.md) raw_array() (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM method) (pyrosetta.rosetta.core.scoring.APBSConfig.R_PARAM method) raw_child_index() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_default_string() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) raw_get_nonjump_atom() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_input_stub_atom0() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_input_stub_atom1() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_input_stub_atom2() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_input_stub_atom3() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_msg() (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.environment.EXCN_Env_Exception method) (pyrosetta.rosetta.core.environment.EXCN_FTSketchGraph method) (pyrosetta.rosetta.core.id.EXCN_AtomNotFound method) (pyrosetta.rosetta.core.kinematics.EXCN_InvalidFoldTree method) (pyrosetta.rosetta.core.pack.task.ResfileReaderException method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.EXCN_CalcFailed method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.EXCN_InitFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_CalcFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_detection_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_undefined_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_grafting_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_invalid_cdr_region_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_json_cdr_detection_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_numbering_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_scs_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_unexpected_region_length_ method) (pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Heat_Converged method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Pool_Converged method) (pyrosetta.rosetta.protocols.constraint_generator.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.denovo_design.architects.EXCN_PreFilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_PoseInconsistent method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_RemarksNotPresent method) (pyrosetta.rosetta.protocols.denovo_design.connection.EXCN_ConnectionSetupFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_NothingToFold method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Passport method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Security_Exception method) (pyrosetta.rosetta.protocols.forge.remodel.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.jd2.archive.EXCN_Archive method) (pyrosetta.rosetta.protocols.jd2.JD2Failure method) (pyrosetta.rosetta.protocols.loophash.EXCN_bbdb_Merge_Failed method) (pyrosetta.rosetta.protocols.loophash.EXCN_DB_IO_Failed method) (pyrosetta.rosetta.protocols.loophash.EXCN_Invalid_Hashmap method) (pyrosetta.rosetta.protocols.loophash.EXCN_No_Extra_Data_To_Write method) (pyrosetta.rosetta.protocols.loophash.EXCN_Wrong_DB_Format method) (pyrosetta.rosetta.protocols.loops.EXCN_Loop_not_closed method) (pyrosetta.rosetta.protocols.moves.EXCN_Converged method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_AssignmentNotFound method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_FileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_NoesyAssign method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownAtomname method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownResonance method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_FailedBroking method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_Input method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_TopologyBroker method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_Unknown method) (pyrosetta.rosetta.utility.excn.BadInput method) (pyrosetta.rosetta.utility.excn.Exception method) (pyrosetta.rosetta.utility.excn.FileNotFound method) (pyrosetta.rosetta.utility.excn.IOError method) (pyrosetta.rosetta.utility.excn.KeyError method) (pyrosetta.rosetta.utility.excn.NullPointerError method) (pyrosetta.rosetta.utility.excn.RangeError method) (pyrosetta.rosetta.utility.excn.RosettaScriptsOptionError method) (pyrosetta.rosetta.utility.excn.UserCorrectableIssue method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) raw_parent() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_previous_child() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_previous_sibling() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_score() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup method) raw_select() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastPlus method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_LoopOverSCs method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrix method) raw_stub_atom1() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_stub_atom2() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_stub_atom3() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) raw_unfolded_state_energymap() (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential method) raw_value_string() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) RawFileData (class in pyrosetta.rosetta.core.io.raw_data) RawFileData.const_iterator (class in pyrosetta.rosetta.core.io.raw_data) RawFileData.iterator (class in pyrosetta.rosetta.core.io.raw_data) RawStruct (class in pyrosetta.rosetta.core.io.raw_data) ray_distance_derivs (class in pyrosetta.rosetta.protocols.pockets) Rb (pyrosetta.rosetta.core.chemical.element.Elements attribute) RB1 (pyrosetta.rosetta.core.id.DOF_Type attribute) RB2 (pyrosetta.rosetta.core.id.DOF_Type attribute) RB3 (pyrosetta.rosetta.core.id.DOF_Type attribute) RB4 (pyrosetta.rosetta.core.id.DOF_Type attribute) RB5 (pyrosetta.rosetta.core.id.DOF_Type attribute) RB6 (pyrosetta.rosetta.core.id.DOF_Type attribute) rb_adjust_template() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) rb_chain() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterface method) RB_dbase() (pyrosetta.rosetta.protocols.splice.RBInMover method) RB_DEFAULT (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType attribute) rb_grid_rotamer_trials_atr_rep() (in module pyrosetta.rosetta.protocols.ligand_docking) rb_grid_score_atr_rep() (in module pyrosetta.rosetta.protocols.ligand_docking) RB_HELIX (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType attribute) rb_jump() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover 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.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover 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_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterface method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) RB_lt (class in pyrosetta.rosetta.protocols.rbsegment_relax) rb_min_jumps() (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) rb_minimizable() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) rb_minimize_all_confs() (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) rb_rot_size (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) rb_sensitive() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) RB_SHEET (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentType attribute) rb_trans_size (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) RBDatabase_fname() (pyrosetta.rosetta.protocols.splice.RBInMover method) RBfitResult (class in pyrosetta.rosetta.protocols.electron_density) RBfitResultComparitor (class in pyrosetta.rosetta.protocols.electron_density) RBInMover (class in pyrosetta.rosetta.protocols.splice) RBInMoverCreator (class in pyrosetta.rosetta.protocols.splice) rbMCM (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) rbmin (pyrosetta.rosetta.protocols.electron_density.MinimizePoseIntoDensityOptions property) RBOutMover (class in pyrosetta.rosetta.protocols.splice) RBOutMoverCreator (class in pyrosetta.rosetta.protocols.splice) RBResidueRange (class in pyrosetta.rosetta.protocols.rbsegment_relax) RBSegment (class in pyrosetta.rosetta.protocols.rbsegment_relax) RBSegmentMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) RBSegmentRelax (class in pyrosetta.rosetta.protocols.rbsegment_relax) RBSegmentRelax_main() (in module pyrosetta.rosetta.protocols) RBSegmentRelaxImpl (class in pyrosetta.rosetta.protocols) RBSegmentType (class in pyrosetta.rosetta.protocols.rbsegment_relax) RC_Tab (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) rcFileName (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) rcl1 (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) rcl2 (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) rcl3 (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) RDAT (class in pyrosetta.rosetta.core.io.rna) rdbuf() (pyrosetta.rosetta.protocols.frag_picker.QuotaDebug method) (pyrosetta.rosetta.std.ifstream method) (pyrosetta.rosetta.std.istringstream method) (pyrosetta.rosetta.std.ofstream method) (pyrosetta.rosetta.std.ostringstream method) (pyrosetta.rosetta.std.stringstream method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_ostream_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_ostreambase_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) RDC (class in pyrosetta.rosetta.core.scoring) rdc (pyrosetta.rosetta.core.scoring.ScoreType attribute) RDC.RDC_TYPE (class in pyrosetta.rosetta.core.scoring) rdc_D_const() (in module pyrosetta.rosetta.core.scoring.nmr.rdc) rdc_D_max() (in module pyrosetta.rosetta.core.scoring.nmr.rdc) rdc_erf() (in module pyrosetta.rosetta.core.scoring.nmr.rdc) RDC_Evaluator (class in pyrosetta.rosetta.protocols.simple_filters) rdc_ideal_bond_length() (in module pyrosetta.rosetta.core.scoring.nmr.rdc) RDC_NORM_TYPE (class in pyrosetta.rosetta.core.scoring.nmr) RDC_Rohl (class in pyrosetta.rosetta.core.scoring) rdc_rohl (pyrosetta.rosetta.core.scoring.ScoreType attribute) rdc_scaling_factor_toCH() (in module pyrosetta.rosetta.core.scoring.nmr.rdc) rdc_scaling_factor_toNH() (in module pyrosetta.rosetta.core.scoring.nmr.rdc) rdc_segments (pyrosetta.rosetta.core.scoring.ScoreType attribute) RDC_TYPE (class in pyrosetta.rosetta.core.scoring.nmr) RDC_TYPE_CACB (pyrosetta.rosetta.core.scoring.nmr.RDC_TYPE attribute) RDC_TYPE_CACO (pyrosetta.rosetta.core.scoring.nmr.RDC_TYPE attribute) RDC_TYPE_CAHA (pyrosetta.rosetta.core.scoring.nmr.RDC_TYPE attribute) RDC_TYPE_CAHN (pyrosetta.rosetta.core.scoring.nmr.RDC_TYPE attribute) RDC_TYPE_CC (pyrosetta.rosetta.core.scoring.RDC attribute) (pyrosetta.rosetta.core.scoring.RDC.RDC_TYPE attribute) RDC_TYPE_CH (pyrosetta.rosetta.core.scoring.RDC attribute) (pyrosetta.rosetta.core.scoring.RDC.RDC_TYPE attribute) RDC_TYPE_CHN (pyrosetta.rosetta.core.scoring.RDC attribute) (pyrosetta.rosetta.core.scoring.RDC.RDC_TYPE attribute) RDC_TYPE_COHN (pyrosetta.rosetta.core.scoring.nmr.RDC_TYPE attribute) rdc_type_from_atom_names() (in module pyrosetta.rosetta.core.scoring.nmr) RDC_TYPE_NC (pyrosetta.rosetta.core.scoring.RDC attribute) (pyrosetta.rosetta.core.scoring.RDC.RDC_TYPE attribute) RDC_TYPE_NCA (pyrosetta.rosetta.core.scoring.nmr.RDC_TYPE attribute) (pyrosetta.rosetta.core.scoring.RDC attribute) (pyrosetta.rosetta.core.scoring.RDC.RDC_TYPE attribute) RDC_TYPE_NCO (pyrosetta.rosetta.core.scoring.nmr.RDC_TYPE attribute) RDC_TYPE_NH (pyrosetta.rosetta.core.scoring.nmr.RDC_TYPE attribute) (pyrosetta.rosetta.core.scoring.RDC attribute) (pyrosetta.rosetta.core.scoring.RDC.RDC_TYPE attribute) RDCData (class in pyrosetta.rosetta.core.scoring.nmr.rdc) RDCEnergy (class in pyrosetta.rosetta.protocols.nmr.rdc) RDCEnergyCreator (class in pyrosetta.rosetta.protocols.nmr.rdc) RdcEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) RDCMultiSet (class in pyrosetta.rosetta.core.scoring.nmr.rdc) RDCMultiSet.COMPUTATION_TYPE (class in pyrosetta.rosetta.core.scoring.nmr.rdc) RDCScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) RdcSelectEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) RDCSingle (class in pyrosetta.rosetta.core.scoring.nmr.rdc) RDCSingleSet (class in pyrosetta.rosetta.core.scoring.nmr.rdc) RdcTargetEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) RDCTensor (class in pyrosetta.rosetta.core.scoring.nmr.rdc) rdf_function_ct_namer() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory static method) rdf_function_group_name() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory static method) RDFBase (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFBase.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFBinaryHbondCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFBinaryHbondFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFBinaryHbondFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFBinaryOrbitalFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFBinaryOrbitalFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFBinaryOrbitalFunctionCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFChargeCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFChargeFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFChargeFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFElecCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFElecFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFElecFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFEtableCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFEtableFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFEtableFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFFunctionCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFFunctionFactory (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFHbondCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFHbondFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFHbondFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFOrbitalFunction (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFOrbitalFunction.FunctionSign (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) RDFOrbitalFunctionCreator (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) rdkit_metric() (in module pyrosetta.rosetta.core.chemical.rdkit) (pyrosetta.rosetta.protocols.drug_design.RDKitMetric method) RDKitMetric (class in pyrosetta.rosetta.protocols.drug_design) RDKitMetricCreator (class in pyrosetta.rosetta.protocols.drug_design) RDKitMetricsMover (class in pyrosetta.rosetta.protocols.drug_design) RDKitMetricsMoverCreator (class in pyrosetta.rosetta.protocols.drug_design) RDMolToRestype (class in pyrosetta.rosetta.core.chemical.rdkit) RDProps (class in pyrosetta.rosetta.RDKit) RDValue (class in pyrosetta.rosetta.RDKit) Re (pyrosetta.rosetta.core.chemical.element.Elements attribute) re_init() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameterManager method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameterManager method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenterManager method) reachable_buried_volume() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) reached_ (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange property) reactivity() (pyrosetta.rosetta.core.io.rna.RDAT method) reactivity_error() (pyrosetta.rosetta.core.io.rna.RDAT method) read() (in module pyrosetta.rosetta.ObjexxFCL) (in module pyrosetta.rosetta.utility.json_spirit) (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.core.conformation.symmetry.SymDof method) (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.fragment.DownJumpSRFD method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) (pyrosetta.rosetta.core.io.serialization.BUFFER method) (pyrosetta.rosetta.protocols.cluster.calibur.SimPDB method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) (pyrosetta.rosetta.protocols.frag_picker.CSTalosIO method) (pyrosetta.rosetta.protocols.frag_picker.JCouplingIO method) (pyrosetta.rosetta.protocols.frag_picker.LAMBEGO_IO method) (pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO method) (pyrosetta.rosetta.protocols.frag_picker.TorsionBinIO method) (pyrosetta.rosetta.protocols.toolbox.ClusterBase method) (pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) (pyrosetta.rosetta.std.ifstream method) (pyrosetta.rosetta.std.iostream method) (pyrosetta.rosetta.std.istream method) (pyrosetta.rosetta.std.istringstream method) (pyrosetta.rosetta.std.stringstream method) (pyrosetta.rosetta.std.wistream method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.tag.Tag method) read_aa_encoding_matrix() (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) read_aa_matrix() (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) read_additional_pdb_data() (in module pyrosetta.rosetta.core.import_pose) read_alignment_file() (in module pyrosetta.rosetta.core.sequence) read_alignments_from_file() (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) read_all_alignments() (in module pyrosetta.rosetta.core.sequence) read_all_poses() (in module pyrosetta.rosetta.core.import_pose) read_all_variables_from_input_file() (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction method) (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunctionDriver method) read_aln() (in module pyrosetta.rosetta.core.sequence) read_alternative_3_letter_codes_from_database_file() (in module pyrosetta.rosetta.core.io) read_anchorfile() (pyrosetta.rosetta.protocols.anchored_design.Anchor method) read_and_store_fragments() (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) read_assignments() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) read_atom_selection_from_string() (in module pyrosetta.rosetta.core.io.nmr) read_binary() (in module pyrosetta.rosetta.core.io.serialization) (pyrosetta.rosetta.core.scoring.motif.XformScore static method) read_biounit() (in module pyrosetta.rosetta.protocols.sic_dock) read_blueprint() (pyrosetta.rosetta.protocols.parser.BluePrint method) read_blueprint_stream() (pyrosetta.rosetta.protocols.parser.BluePrint method) read_bond_file() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) read_center_normal_from_cmd() (in module pyrosetta.rosetta.protocols.membrane) read_center_normal_from_tag() (in module pyrosetta.rosetta.protocols.membrane) read_checkpoint() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) (pyrosetta.rosetta.protocols.multistate_design.MultiStateEntity method) (pyrosetta.rosetta.protocols.multistate_design.SingleStateEntityData method) read_codes_and_roots_from_database_file() (in module pyrosetta.rosetta.core.chemical.carbohydrates) read_coef1() (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) read_coef1_default() (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) read_coef1_user() (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) read_coef2() (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) read_coef2_default() (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) read_coef2_user() (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) read_comment_pdb() (in module pyrosetta.rosetta.core.pose) read_config_file() (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) read_conformers_from_database_file_for_ring_size() (in module pyrosetta.rosetta.core.chemical.rings) read_constraint() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomToAxisConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraint method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedDihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueCouplingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.RTConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) read_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO static method) (pyrosetta.rosetta.protocols.abinitio.Template method) read_constraints_new() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO static method) read_coordfile() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) read_cp_tables_from_db() (in module pyrosetta.rosetta.core.scoring.elec) read_cst_file() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) read_data() (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.fragment.BBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.DownJumpSRFD method) (pyrosetta.rosetta.core.fragment.FragmentIO method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.SecstructSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.UpJumpSRFD method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomToAxisConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraint method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedDihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueCouplingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.RTConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.DistanceFunc method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CB_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CBSG_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.SG_Dist_Func method) (pyrosetta.rosetta.core.scoring.disulfides.SGSG_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.CircularSplineFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.CountViolFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.FadeFunc method) (pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianChainDoubleFunc method) (pyrosetta.rosetta.core.scoring.func.GaussianChainFunc method) (pyrosetta.rosetta.core.scoring.func.GaussianChainGeneralFunc method) (pyrosetta.rosetta.core.scoring.func.GaussianChainQuadrupleFunc method) (pyrosetta.rosetta.core.scoring.func.GaussianChainSingleFunc method) (pyrosetta.rosetta.core.scoring.func.GaussianChainTripleFunc method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.HarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.IdentityFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction method) (pyrosetta.rosetta.core.scoring.func.MinMultiHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.ScalarWeightedFunc method) (pyrosetta.rosetta.core.scoring.func.SigmoidFunc method) (pyrosetta.rosetta.core.scoring.func.SkipViolFunc method) (pyrosetta.rosetta.core.scoring.func.SmoothStepFunc method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SplineFunc method) (pyrosetta.rosetta.core.scoring.func.SquareWell2Func method) (pyrosetta.rosetta.core.scoring.func.SquareWellFunc method) (pyrosetta.rosetta.core.scoring.func.SumFunc method) (pyrosetta.rosetta.core.scoring.func.TopOutFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.core.sequence.ChemicalShiftScoringScheme method) (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.CompassScoringScheme method) (pyrosetta.rosetta.core.sequence.CompositeScoringScheme method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.DPScoringScheme method) (pyrosetta.rosetta.core.sequence.L1ScoringScheme method) (pyrosetta.rosetta.core.sequence.MatrixScoringScheme method) (pyrosetta.rosetta.core.sequence.PairScoringScheme method) (pyrosetta.rosetta.core.sequence.ProfSimScoringScheme method) (pyrosetta.rosetta.core.sequence.ScoringScheme method) (pyrosetta.rosetta.core.sequence.Sequence method) (pyrosetta.rosetta.core.sequence.SequenceAlignment method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) (pyrosetta.rosetta.core.sequence.SimpleScoringScheme method) (pyrosetta.rosetta.numeric.kdtree.KDPoint method) (pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint method) (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) (pyrosetta.rosetta.protocols.jumping.ChainbreakDistFunc method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions method) read_data_file() (pyrosetta.rosetta.core.scoring.packing.HolesParams method) (pyrosetta.rosetta.core.scoring.packing.HolesParamsRes method) read_data_from_stream() (pyrosetta.rosetta.core.fragment.FragmentIO method) read_database() (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) read_db() (pyrosetta.rosetta.protocols.loophash.BackboneDB method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) read_db_file() (pyrosetta.rosetta.core.scoring.epr_deer.EPRSpinLabel method) read_ddg_predictions_file() (in module pyrosetta.rosetta.core.io.PositionDdGInfo) read_def() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomToAxisConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraint method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedDihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueCouplingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.RTConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) read_depth() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_disulf_pairing_list() (in module pyrosetta.rosetta.protocols.jumping) read_disulfide_database() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingDatabase method) read_disulfides() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) read_edge_file() (pyrosetta.rosetta.protocols.sewing.hashing.EdgeMapGenerator method) read_eigvec_file() (pyrosetta.rosetta.protocols.evaluation.PCA method) read_entities_checkpoint() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) read_enzyme_cstfile() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) read_enzyme_data_from_file() (in module pyrosetta.rosetta.core.enzymes) read_exp_data() (pyrosetta.rosetta.protocols.ddG.ddGData method) read_fasta_file() (in module pyrosetta.rosetta.core.sequence) read_fasta_file_and_concatenate() (in module pyrosetta.rosetta.core.sequence) read_fasta_file_return_str() (in module pyrosetta.rosetta.core.sequence) read_fasta_file_section() (in module pyrosetta.rosetta.core.sequence) read_fasta_file_str() (in module pyrosetta.rosetta.core.sequence) read_file() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.ElementSet method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.orbitals.OrbitalTypeSet method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser method) (pyrosetta.rosetta.protocols.frags.RMSVallData method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) read_file_into_string() (in module pyrosetta.rosetta.protocols.cyclic_peptide_predict) read_files_for_base_residue_types() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) read_files_for_unpatchable_residue_types() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) read_fold_tree() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) read_fold_tree_from_file() (in module pyrosetta.rosetta.protocols.backrub) read_fragment_file() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.MinimalFragSet method) read_fragment_stream() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.MinimalFragSet method) read_frames_from_file() (pyrosetta.rosetta.core.fragment.FragmentIO method) read_frames_from_stream() (pyrosetta.rosetta.core.fragment.FragmentIO method) read_from_binary() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) read_from_binary_chk() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) read_from_binary_file() (pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc method) (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) read_from_checkpoint() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) read_from_cmd_line() (pyrosetta.rosetta.protocols.wum.SilentStructStore method) read_from_database() (pyrosetta.rosetta.core.sequence.MatrixScoringScheme method) read_from_disk() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) read_from_file() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.sequence.ChemicalShiftScoringScheme method) (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.CompassScoringScheme method) (pyrosetta.rosetta.core.sequence.CompositeScoringScheme method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.DPScoringScheme method) (pyrosetta.rosetta.core.sequence.L1ScoringScheme method) (pyrosetta.rosetta.core.sequence.MatrixScoringScheme method) (pyrosetta.rosetta.core.sequence.PairScoringScheme method) (pyrosetta.rosetta.core.sequence.ProfSimScoringScheme method) (pyrosetta.rosetta.core.sequence.ScoringScheme method) (pyrosetta.rosetta.core.sequence.Sequence method) (pyrosetta.rosetta.core.sequence.SequenceAlignment method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) (pyrosetta.rosetta.core.sequence.SimpleScoringScheme method) (pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.PairingLibrary method) (pyrosetta.rosetta.protocols.jumping.SpecificGeometryLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) (pyrosetta.rosetta.protocols.loop_grower.LoopComparator method) (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist method) (pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc method) (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) (pyrosetta.rosetta.protocols.wum.SilentStructStore method) read_from_file_no_filters() (pyrosetta.rosetta.protocols.jumping.PairingLibrary method) (pyrosetta.rosetta.protocols.jumping.SpecificGeometryLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) read_from_files() (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) read_from_global_options() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) read_from_options() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) read_from_pose() (pyrosetta.rosetta.protocols.loophash.BackboneSegment method) read_from_stream() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList method) (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) (pyrosetta.rosetta.protocols.wum.SilentStructStore method) read_from_string() (pyrosetta.rosetta.protocols.wum.SilentStructStore method) read_from_tag() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) read_Gaussian_parameters_from_database_file() (in module pyrosetta.rosetta.core.scoring.carbohydrates) read_general_aln() (in module pyrosetta.rosetta.core.sequence) read_general_aln_file() (in module pyrosetta.rosetta.core.sequence) read_generations_checkpoint() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) read_global_seq_info() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) read_glycan_sequence_file() (in module pyrosetta.rosetta.core.chemical.carbohydrates) read_gridsearch_values_from_string() (in module pyrosetta.rosetta.core.io.nmr) read_grishin_aln_file() (in module pyrosetta.rosetta.core.sequence) read_H3_cter_fragment() (in module pyrosetta.rosetta.protocols.antibody_legacy) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) read_H3_seq() (in module pyrosetta.rosetta.protocols.splice) read_header() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) read_homologs() (pyrosetta.rosetta.protocols.loophash.BackboneDB method) read_hyfile() (in module pyrosetta.rosetta.protocols.hydrate) read_in_amoeba_parameters() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) read_in_and_recursively_replace_includes() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) read_in_and_set_disulfides() (pyrosetta.rosetta.core.io.raw_data.DisulfideFile method) read_in_database_file() (in module pyrosetta.rosetta.core.io.nmr) read_in_multipole_parameters() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) read_in_points_to_search() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) read_in_spanfile() (pyrosetta.rosetta.core.scoring.MembraneTopology method) read_in_structures() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver method) read_in_VDW_rep_screen_pose() (pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo method) read_in_VDW_rep_screen_pose_from_command_line() (pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo method) read_in_VDW_rep_screen_pose_from_options() (pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo method) read_in_vdw_tinker_parameters() (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) read_individual_constraint_new() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO static method) read_info_file() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) read_input_pdbs() (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) read_inputs() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) read_key_value_pair_from_line() (in module pyrosetta.rosetta.core.io.nmr) read_legacydb() (pyrosetta.rosetta.protocols.loophash.BackboneDB method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) read_linkage_conformers_from_database_file() (in module pyrosetta.rosetta.core.chemical.carbohydrates) read_loop_file() (pyrosetta.rosetta.protocols.loops.JSONFormattedLoopsFileReader method) (pyrosetta.rosetta.protocols.loops.LoopsFileIO method) read_loop_file_stream() (pyrosetta.rosetta.protocols.loops.LoopsFileIO method) read_loop_fragments() (in module pyrosetta.rosetta.protocols.loops) read_loops_file() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) read_loops_file_block() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo method) read_loops_options() (pyrosetta.rosetta.protocols.loops.Loops method) read_many() (pyrosetta.rosetta.protocols.splice.SpliceSegment method) read_mArray() (in module pyrosetta.rosetta.utility.json_spirit) read_merge_behaviors_from_database_file() (in module pyrosetta.rosetta.core.chemical.io) read_meta_file() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) read_metric_value() (in module pyrosetta.rosetta.basic) read_minor_helix_params() (in module pyrosetta.rosetta.protocols.helical_bundle) read_mObject() (in module pyrosetta.rosetta.utility.json_spirit) read_model_file() (in module pyrosetta.rosetta.protocols.legacy_sewing) (pyrosetta.rosetta.protocols.sewing.hashing.ModelFileReader static method) read_motifs_binary() (in module pyrosetta.rosetta.core.scoring.motif) read_mover_weight() (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) read_mut_data() (pyrosetta.rosetta.protocols.ddG.ddGData method) read_native_residue_file() (in module pyrosetta.rosetta.protocols.legacy_sewing) read_nmer_fname_vector() (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) read_nmer_pssm() (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) read_nmer_pssm_fname_vector() (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) read_nmer_pssm_list() (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) read_nmer_svm() (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) read_nmer_svm_fname_vector() (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) read_nmer_svm_list() (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) read_nmer_svm_rank() (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) read_nmer_svm_rank_fname_vector() (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) read_nmer_svm_rank_list() (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) read_nomenclature_table_from_database_file() (in module pyrosetta.rosetta.core.chemical.carbohydrates) read_only_ATOM_entries() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) read_options() (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) read_or_throw() (in module pyrosetta.rosetta.utility.json_spirit) read_P_AA_ABEGO3() (pyrosetta.rosetta.core.scoring.P_AA_ABEGO3 method) read_P_AA_ss() (pyrosetta.rosetta.core.scoring.P_AA_ss method) read_P_AA_SS_cen6() (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) read_packer_problem_file() (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) read_pairing_list() (in module pyrosetta.rosetta.core.scoring.dssp) read_pairings() (pyrosetta.rosetta.protocols.abinitio.Templates method) read_params() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) read_partners_from_file() (pyrosetta.rosetta.protocols.splice.BBMatching method) read_patchdock() (pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader method) read_patchdock_entry() (pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader method) read_pcs_dataset_params_list() (in module pyrosetta.rosetta.core.io.nmr) read_pdb_header() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) read_pdb_profile() (pyrosetta.rosetta.protocols.splice.RotLibdb method) (pyrosetta.rosetta.protocols.splice.SpliceSegment method) read_pdb_profile_file() (pyrosetta.rosetta.protocols.splice.SpliceSegment method) read_pdb_seq() (in module pyrosetta.rosetta.protocols.splice) read_peak() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) read_peptide_design_file() (in module pyrosetta.rosetta.protocols.cyclic_peptide_predict) read_pose() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.protocols.hybridization.TMalign method) read_pose_from_file() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) read_pose_numbered_loops_file() (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader method) read_poses() (pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader method) read_potential() (pyrosetta.rosetta.core.scoring.methods.dfire.DFIRE_Potential method) read_pre_dataset_params_list() (in module pyrosetta.rosetta.core.io.nmr) read_probabilities_or_die() (in module pyrosetta.rosetta.numeric) read_profile() (pyrosetta.rosetta.protocols.splice.RotLibdb method) (pyrosetta.rosetta.protocols.splice.SpliceSegment method) read_psipred_ss2() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_psipred_ss2_file() (in module pyrosetta.rosetta.core.pose) read_pssm_features() (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) read_RBSegment_file() (in module pyrosetta.rosetta.protocols.rbsegment_relax) read_rdat_file() (pyrosetta.rosetta.core.io.rna.RDAT method) read_rdc_dataset_params_list() (in module pyrosetta.rosetta.core.io.nmr) read_RDC_file() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling_Rohl method) read_rdc_tensor_values_from_string() (in module pyrosetta.rosetta.core.io.nmr) read_record_definitions_from_file() (in module pyrosetta.rosetta.core.io.pdb) read_residuetype_from_database() (pyrosetta.rosetta.core.chemical.ResidueDatabaseIO method) read_resonances() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) read_resources_from_xml() (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) read_ring_sizes_and_morphemes_from_database_file() (in module pyrosetta.rosetta.core.chemical.carbohydrates) read_rotamer_selection_file() (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) read_score_headers() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) read_sequence() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) read_short_names_to_iupac_format_string() (in module pyrosetta.rosetta.core.chemical.carbohydrates) read_silent_struct() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) read_spine_x() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_splice_segments() (pyrosetta.rosetta.protocols.splice.Splice method) read_split_behaviors_from_database_file() (in module pyrosetta.rosetta.core.chemical.io) read_ss2() (in module pyrosetta.rosetta.protocols.mpi_refinement) read_ss_file() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_ss_files() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_std_frags_from_cmd() (in module pyrosetta.rosetta.core.fragment) read_stream() (pyrosetta.rosetta.core.io.silent.SilentFileData method) read_strength() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) read_structures() (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) read_subset_of_global_option_collection() (in module pyrosetta.rosetta.basic.options) read_symmetry_data_from_file() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) read_symmetry_data_from_stream() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) read_tag() (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) read_tags_fast() (pyrosetta.rosetta.core.io.raw_data.DecoyFileData method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.raw_data.ScoreFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) read_talos_ss() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_through_errors() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) read_topol_file() (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) read_topology_file() (in module pyrosetta.rosetta.core.chemical) read_torsion_database() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) read_undefined_coef1() (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) read_undefined_coef2() (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) read_vall() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) read_wt_data() (pyrosetta.rosetta.protocols.ddG.ddGData method) read_xfres_binary() (in module pyrosetta.rosetta.core.scoring.motif) readDecoyNames() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) readDecoys() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) readMRCandResize() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) (pyrosetta.rosetta.core.scoring.electron_density_atomwise.ElectronDensityAtomwise method) ReadPoseExtraScoreFilter (class in pyrosetta.rosetta.protocols.simple_filters) ReadPoseExtraScoreFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) ReadResfile (class in pyrosetta.rosetta.core.pack.task.operation) ReadResfileAndObeyLengthEvents (class in pyrosetta.rosetta.core.pack.task.operation) ReadResfileAndObeyLengthEventsCreator (class in pyrosetta.rosetta.core.pack.task.operation) ReadResfileCreator (class in pyrosetta.rosetta.core.pack.task.operation) ReadResfileFromDB (class in pyrosetta.rosetta.protocols.task_operations) ReadResfileFromDBCreator (class in pyrosetta.rosetta.protocols.task_operations) ReadResidueCoordinatesFromPDB (class in pyrosetta.rosetta.protocols.chromophore) readsome() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.std.ifstream method) (pyrosetta.rosetta.std.iostream method) (pyrosetta.rosetta.std.istream method) (pyrosetta.rosetta.std.istringstream method) (pyrosetta.rosetta.std.stringstream method) (pyrosetta.rosetta.std.wistream method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) readValueOrDie() (in module pyrosetta.rosetta.core.scoring.func) READY (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum attribute) ready() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) ready_for_batch() (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) ready_for_nonideal_scoring() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) ready_to_align() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) real2afteroption() (in module pyrosetta.rosetta.basic.options) Real2string() (in module pyrosetta.rosetta.utility) real3afteroption() (in module pyrosetta.rosetta.basic.options) real_data_ (pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct property) real_groups (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore property) REAL_OPTION (pyrosetta.rosetta.utility.options.OptionTypes attribute) real_parameter() (pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) real_parameter_cop() (pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) real_regex_pattern() (in module pyrosetta.rosetta.utility.tag) real_to_virtual() (in module pyrosetta.rosetta.core.chemical) (pyrosetta.rosetta.core.pose.Pose method) real_type (pyrosetta.rosetta.utility.json_spirit.Value_type attribute) real_value (pyrosetta.rosetta.protocols.features.MetricData property) REAL_VECTOR_OPTION (pyrosetta.rosetta.utility.options.OptionTypes attribute) realafteroption() (in module pyrosetta.rosetta.basic.options) RealAngleToShort() (in module pyrosetta.rosetta.protocols.loophash) realatomdata_index (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData property) RealFilter (class in pyrosetta.rosetta.core.chemical) realignDecoys() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) RealMetric (class in pyrosetta.rosetta.core.simple_metrics) RealOption (class in pyrosetta.rosetta.utility.options) RealOptionKey (class in pyrosetta.rosetta.utility.options) RealPerturbationType (class in pyrosetta.rosetta.core.conformation.parametric) RealValuedParameter (class in pyrosetta.rosetta.core.conformation.parametric) realVector_groups (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore property) realvector_parameter() (pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) realvector_parameter_cop() (pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) RealVectorOption (class in pyrosetta.rosetta.utility.options) RealVectorOptionKey (class in pyrosetta.rosetta.utility.options) RealVectorValuedParameter (class in pyrosetta.rosetta.core.conformation.parametric) reassign_atoms_for_intra_residue_stubs() (pyrosetta.rosetta.core.kinematics.FoldTree method) rebuild_all_in_dihedral_mode_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) rebuild_bulge_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) rebuild_disulfide() (in module pyrosetta.rosetta.core.util) rebuild_fa_disulfides() (in module pyrosetta.rosetta.core.util) rebuild_filter() (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) rebuild_loops_until_closed() (in module pyrosetta.rosetta.protocols.comparative_modeling) rebuild_missing_atoms() (in module pyrosetta.rosetta.protocols.denovo_design) rebuild_pdb2pose() (pyrosetta.rosetta.core.pose.PDBInfo method) rebuild_polymer_bond_dependent_atoms() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) rebuild_polymer_bond_dependent_atoms_this_residue_only() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) rebuild_residue_connection_dependent_atoms() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) rebuild_residue_selector() (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) recal_foldtree (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) recalculate_rmsd_and_output_silent_file() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) recalculate_transforms() (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) recalculate_z_coordinate() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) RECCES_Mover (class in pyrosetta.rosetta.protocols.recces) RECCES_Options (class in pyrosetta.rosetta.protocols.recces.options) RECCES_Parameters (class in pyrosetta.rosetta.protocols.recces.params) recces_pose_setup() (in module pyrosetta.rosetta.protocols.recces) recchis (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ChiInfo property) receive() (pyrosetta.rosetta.basic.mpi.DbMoverMessageListener method) (pyrosetta.rosetta.basic.mpi.MessageListener method) receive_char_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI static method) receive_double_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI static method) receive_doubles_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI static method) receive_integer_from_anyone() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI static method) receive_integer_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI static method) receive_integers_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI static method) receive_linkunits_from() (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_chemical_RestypeDestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_ConnectionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_IdentityEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_LengthEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_XYZEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_ConformationEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_DestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_EnergyEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.PausableSignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_chemical_RestypeDestructionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_ConnectionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_IdentityEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_LengthEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_XYZEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_ConformationEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_DestructionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_EnergyEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_GeneralEvent_t method) receive_message() (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) RECEIVE_MESSAGE_TAG (pyrosetta.rosetta.basic.mpi.mpi_tags attribute) receive_observers_from() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) receive_size_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI static method) receive_sizes_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI static method) receive_string_from_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI static method) received() (pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer.CM_SuggestFixResidue method) (pyrosetta.rosetta.protocols.topology_broker.SuggestValueMessage method) received_by_me() (pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer.CM_SuggestFixResidue method) (pyrosetta.rosetta.protocols.topology_broker.SuggestValueMessage method) recent_history_queue (class in pyrosetta.rosetta.utility) recent_score() (pyrosetta.rosetta.protocols.simple_filters.PDDFScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.SAXSScoreFilter method) recenter() (in module pyrosetta.rosetta.core.conformation.symmetry) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) receptor() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) receptor_anchor_pos (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) receptor_chain() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) receptor_first_res() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) receptor_last_res() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) receptor_nres() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) reciprocalSpaceFilter() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) recommended_box_size() (pyrosetta.rosetta.protocols.ligand_docking.Transform method) recommended_grid_size() (pyrosetta.rosetta.protocols.ligand_docking.Transform method) recompute_and_print() (pyrosetta.rosetta.protocols.pose_metric_calculators.SHOBuriedUnsatisfiedPolarsCalculator method) RecomputeDensityMapMover (class in pyrosetta.rosetta.protocols.cryst) RecomputeDensityMapMoverCreator (class in pyrosetta.rosetta.protocols.cryst) reconstitute_assembly_from_string() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) record() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist.DistanceRecord method) record_annealer_trajectory() (pyrosetta.rosetta.core.pack.annealer.FixbbSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SequenceSymmetricAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SmartFixbbSimAnnealer method) record_endpoint() (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) record_inv6() (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist.DistanceRecord method) record_match() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.OutputWriter method) (pyrosetta.rosetta.protocols.match.output.PDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter method) record_move() (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) record_new_pose() (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) record_new_score_function() (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) record_new_temperature() (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) record_pose_metrics() (in module pyrosetta.rosetta.protocols.glycopeptide_docking) record_statistics() (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) RecordCollection (class in pyrosetta.rosetta.core.io.pdb) RecordType (class in pyrosetta.rosetta.core.io.pdb) recover_and_pack_conformer_sidechains() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) recover_checkpoint() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.checkpoint.CheckPointer method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) recover_hit() (pyrosetta.rosetta.protocols.match.upstream.ProteinUpstreamBuilder method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamBuilder method) recover_low() (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MixedMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) recover_low_stages_ (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio property) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints property) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper property) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio property) recover_original_on_failure() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) recover_sidechains() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) RecoverSideChainsMover (class in pyrosetta.rosetta.protocols.comparative_modeling) recovery_rate() (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecovery method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSimple method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSQLite method) recreate_pose_for_entity() (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) recreate_task() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) recscore (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfo property) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfo property) recurse_revert_far_c_terminal_parent() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) recurse_revert_far_n_terminal_parent() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) recursive() (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) recursive_depth (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFGMSettings property) recursive_depth_ (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentSettings property) recursive_multiple_disulfide_former() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) recursive_residues_from_rbsegs() (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) recursively_write_ct_to_schema() (pyrosetta.rosetta.utility.tag.XMLSchemaRepeatableCTNode method) recyclable() (pyrosetta.rosetta.cppdb.backend.connection method) (pyrosetta.rosetta.cppdb.session method) (pyrosetta.rosetta.utility.sql_database.session method) Red (pyrosetta.rosetta.utility.CSI.CSI_Enum attribute) redefine_begin_end() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing method) redefine_chi() (pyrosetta.rosetta.core.chemical.MutableResidueType method) RedefineChi (class in pyrosetta.rosetta.core.chemical) redesign_loop_neighborhood() (pyrosetta.rosetta.protocols.forge.components.BDR method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) redimension() (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) redo() (pyrosetta.rosetta.protocols.jumping.SameStrand method) reduce (pyrosetta.rosetta.core.scoring.sasa.SasaRadii attribute) reduce_fa_rep() (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) reduce_task() (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) Reduced_Jdipolar() (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) reduced_scorefxn() (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) reducible() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) ref() (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) ref_atom (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator.MappedAtom property) ref_baseline() (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter method) ref_counted (class in pyrosetta.rosetta.cppdb) REF_CS_Tab (pyrosetta.rosetta.protocols.sparta.Sparta property) ref_nc (pyrosetta.rosetta.core.scoring.ScoreType attribute) ref_pKa() (pyrosetta.rosetta.protocols.simple_moves.IonizableResidue method) ref_pose() (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) ref_pose_for() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) ref_ptr_cppdb_backend_connection_t (class in pyrosetta.rosetta.cppdb) ref_ptr_cppdb_backend_loadable_driver_t (class in pyrosetta.rosetta.cppdb) ref_ptr_cppdb_backend_statement_t (class in pyrosetta.rosetta.cppdb) ref_ptr_cppdb_pool_t (class in pyrosetta.rosetta.cppdb) ref_shift (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData property) ref_start_struct() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) ref_xyz() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) refBound() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) RefConvert_std_string_t (class in pyrosetta.rosetta.core.chemical) RefConvert_unsigned_long_t (class in pyrosetta.rosetta.core.chemical) RefConvert_void__star__t (class in pyrosetta.rosetta.core.chemical) refCSFileName (pyrosetta.rosetta.protocols.sparta.Sparta property) reference() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) reference_conformation() (pyrosetta.rosetta.core.environment.DofPassport method) reference_copy() (pyrosetta.rosetta.ObjexxFCL.Dimension method) reference_e_method (pyrosetta.rosetta.core.scoring.methods.EnergyMethods attribute) reference_name() (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) reference_pdb_id() (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation method) reference_pose() (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.scoring.sc.ElectrostaticSimilarityCalculator method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.PDBOutput method) (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterface method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilter method) (pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation method) reference_pose_cop() (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) reference_pose_from_current() (pyrosetta.rosetta.core.pose.Pose method) reference_pose_name() (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) reference_pose_set() (pyrosetta.rosetta.core.pose.Pose method) reference_pose_set_cop() (pyrosetta.rosetta.core.pose.Pose method) reference_res (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarModeling property) reference_res() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) reference_residue() (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) reference_selector() (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) reference_structure() (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolReferenceStructure method) reference_stub() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) reference_xyz_consistency_check() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker method) ReferenceEnergy (class in pyrosetta.rosetta.core.energy_methods) ReferenceEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) ReferenceEnergyNoncanonical (class in pyrosetta.rosetta.core.energy_methods) ReferenceEnergyNoncanonicalCreator (class in pyrosetta.rosetta.core.energy_methods) ReferencePose (class in pyrosetta.rosetta.core.pose.reference_pose) ReferencePoseSet (class in pyrosetta.rosetta.core.pose.reference_pose) references_ (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) refine() (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) refine_all_cdr_loops() (in module pyrosetta.rosetta.protocols.tcr) refine_assembly() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) refine_cdr3_loops() (in module pyrosetta.rosetta.protocols.tcr) refine_cdr_loop() (in module pyrosetta.rosetta.protocols.tcr) refine_cycle() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) refine_input() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner method) refine_native_get_good_FT() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) refine_pose() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) refine_pose_list() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup method) refine_tcr_cdr_loops() (in module pyrosetta.rosetta.protocols.tcr) RefineBetaBarrel (class in pyrosetta.rosetta.protocols.antibody) RefinementResult (class in pyrosetta.rosetta.protocols.electron_density) RefinementResultComparitor (class in pyrosetta.rosetta.protocols.electron_density) refit_motif_sidechains() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) refpose_enabled_residue_number_string() (in module pyrosetta.rosetta.utility.tag) refpose_name() (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionRefPose method) refpose_number() (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionRefPose method) refpose_offset() (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionRefPose method) refresh() (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid method) refresh_bbstub_constraints() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) refresh_coordinate_constraints() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) refresh_energy_cache() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) refresh_normalmode() (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) refuse_unexpected_files() (pyrosetta.rosetta.utility.io.FileContentsMap method) refweight_arg() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) refweight_asp() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) refweight_glu() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) refweight_lys() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) refx() (pyrosetta.rosetta.protocols.simple_filters.AngleToVector method) refy() (pyrosetta.rosetta.protocols.simple_filters.AngleToVector method) refz() (pyrosetta.rosetta.protocols.simple_filters.AngleToVector method) regenerate_lattice() (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) regenerate_model() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) RegEx_based_CDR_Detector (class in pyrosetta.rosetta.protocols.antibody.grafting) regex_usable() (in module pyrosetta.rosetta.core.select.residue_selector) RegExManager (class in pyrosetta.rosetta.protocols.antibody.grafting) region (pyrosetta.rosetta.core.sequence.Line property) region() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragSetCollection method) (pyrosetta.rosetta.core.fragment.MinimalFragSet method) (pyrosetta.rosetta.core.fragment.OrderedFragSet method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) region1() (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) region2() (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) region_all() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragSetCollection method) (pyrosetta.rosetta.core.fragment.MinimalFragSet method) (pyrosetta.rosetta.core.fragment.OrderedFragSet method) region_simple() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragSetCollection method) (pyrosetta.rosetta.core.fragment.MinimalFragSet method) (pyrosetta.rosetta.core.fragment.OrderedFragSet method) regional_avg_per_residue_dG (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData property) regional_avg_per_residue_dSASA (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData property) regional_avg_per_residue_energy_int (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData property) regional_avg_per_residue_energy_sep (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData property) regional_avg_per_residue_SASA_int (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData property) regional_avg_per_residue_SASA_sep (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData property) RegionalConnections (class in pyrosetta.rosetta.protocols.simple_filters) register1() (in module pyrosetta.rosetta.protocols.init) register2() (in module pyrosetta.rosetta.protocols.init) register3() (in module pyrosetta.rosetta.protocols.init) register4() (in module pyrosetta.rosetta.protocols.init) register_calculator() (pyrosetta.rosetta.core.pose.metrics.CalculatorFactory method) register_clash() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) register_common_options() (in module pyrosetta.rosetta.protocols.abinitio) register_container_traversal() (in module pyrosetta.distributed.packed_pose) register_data_tags_for_input_pose_id() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.TagManager method) register_factory_prototypes() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser static method) register_ff() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) register_hbond() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) register_label_offset() (pyrosetta.rosetta.protocols.topology_broker.SequenceNumberResolver method) register_mover() (pyrosetta.rosetta.protocols.environment.Environment method) (pyrosetta.rosetta.protocols.wum.MoverList method) register_new_job() (pyrosetta.rosetta.protocols.jd3.JobGenealogist method) register_options() (in module pyrosetta.rosetta.protocols.evaluation) (in module pyrosetta.rosetta.protocols.jd2) (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover static method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover static method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover static method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover static method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover static method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication static method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover static method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM static method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover static method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover static method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer static method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM static method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM static method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM static method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer static method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM static method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio static method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler static method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly static method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio static method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints static method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler static method) (pyrosetta.rosetta.protocols.abinitio.HedgeArchive static method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax static method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase static method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid static method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom static method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper static method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio static method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl static method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst static method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio static method) (pyrosetta.rosetta.protocols.abinitio.PairingStatistics static method) (pyrosetta.rosetta.protocols.abinitio.Protocol static method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher static method) (pyrosetta.rosetta.protocols.abinitio.Template static method) (pyrosetta.rosetta.protocols.abinitio.Templates static method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover static method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover static method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover static method) (pyrosetta.rosetta.protocols.analysis.PackStatMover static method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover static method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover static method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover static method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover static method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter static method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol static method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover static method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin static method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop static method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover static method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover static method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover static method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover static method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster static method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol static method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer static method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop static method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert static method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD static method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD static method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp static method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy static method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy static method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel static method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock static method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol static method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler static method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler static method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover static method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover static method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover static method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover static method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover static method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro static method) (pyrosetta.rosetta.protocols.backrub.BackrubMover static method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol static method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover static method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover static method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover static method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover static method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover static method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase static method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy static method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover static method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder static method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController static method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange static method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder static method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover static method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering static method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder static method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver static method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover static method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder static method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering static method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController static method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase static method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover static method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver static method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder static method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver static method) (pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy static method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover static method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler static method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover static method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler static method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens static method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover static method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover static method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover static method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover static method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover static method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover static method) (pyrosetta.rosetta.protocols.cluster.ClusterBase static method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle static method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop static method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter static method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints static method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple static method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover static method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover static method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover static method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover static method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover static method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover static method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover static method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover static method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover static method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints static method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints static method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover static method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover static method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover static method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover static method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover static method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.contact_map.ContactMap static method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol static method) (pyrosetta.rosetta.protocols.cryst.CrystRMS static method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover static method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover static method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover static method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover static method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover static method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover static method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover static method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover static method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover static method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover static method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo static method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover static method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign static method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations static method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication static method) (pyrosetta.rosetta.protocols.ddg.ddGMover static method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected static method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign static method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover static method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover static method) (pyrosetta.rosetta.protocols.design_opt.Supercharge static method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA static method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover static method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign static method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker static method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna static method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover static method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol static method) (pyrosetta.rosetta.protocols.docking.DockingHighRes static method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy static method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation static method) (pyrosetta.rosetta.protocols.docking.DockingLowRes static method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble static method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol static method) (pyrosetta.rosetta.protocols.docking.DockingProtocol static method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact static method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle static method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol static method) (pyrosetta.rosetta.protocols.docking.DockMinMover static method) (pyrosetta.rosetta.protocols.docking.DockSetupMover static method) (pyrosetta.rosetta.protocols.docking.DockTaskFactory method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover static method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover static method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact static method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover static method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover static method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover static method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover static method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately static method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover static method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact static method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol static method) (pyrosetta.rosetta.protocols.docking.TemperedDocking static method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints static method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover static method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover static method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer static method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover static method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover static method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover static method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover static method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover static method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores static method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover static method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover static method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC static method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities static method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover static method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover static method) (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringProtocol static method) (pyrosetta.rosetta.protocols.environment.ClientMover static method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM static method) (pyrosetta.rosetta.protocols.environment.EnvMover static method) (pyrosetta.rosetta.protocols.environment.ScriptCM static method) (pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamers static method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts static method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf static method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler static method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface static method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs static method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol static method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol static method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol static method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize static method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs static method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs static method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs static method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy static method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover static method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter static method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover static method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol static method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover static method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover static method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover static method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover static method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover static method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover static method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover static method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation static method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover static method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover static method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter static method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter static method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover static method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover static method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR static method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation static method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover static method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential static method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies static method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator static method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker static method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio static method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes static method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol static method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover static method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign static method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack static method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover static method) (pyrosetta.rosetta.protocols.forge.components.BDR static method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild static method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG static method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG static method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGenerator static method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts static method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover static method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG static method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover static method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC static method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol static method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement static method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement static method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol static method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover static method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover static method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase static method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover static method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover static method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover static method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover static method) (pyrosetta.rosetta.protocols.hbnet.HBNet static method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface static method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler static method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler static method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix static method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle static method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix static method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle static method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix static method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions static method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover static method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe static method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation static method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler static method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize static method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler static method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover static method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly static method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize static method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol static method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover static method) (pyrosetta.rosetta.protocols.hybridization.MRMover static method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover static method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover static method) (pyrosetta.rosetta.protocols.hydrate.Hydrate static method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover static method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover static method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover static method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover static method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase static method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager static method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive static method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive static method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive static method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover static method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover static method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen static method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens static method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate static method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF static method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer static method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock static method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand static method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker static method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble static method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator static method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol static method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign static method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol static method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone static method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand static method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble static method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover static method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers static method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover static method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate static method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates static method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether static method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom static method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand static method) (pyrosetta.rosetta.protocols.ligand_docking.Transform static method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble static method) (pyrosetta.rosetta.protocols.ligand_docking.Translate static method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover static method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile static method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover static method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper static method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow static method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension static method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower static method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler static method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler static method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder static method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover static method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol static method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner static method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner static method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner static method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler static method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck static method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter static method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup static method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid static method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom static method) (pyrosetta.rosetta.protocols.loophash.FastGapMover static method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier static method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary static method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper static method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol static method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine static method) (pyrosetta.rosetta.protocols.LoopRebuild static method) (pyrosetta.rosetta.protocols.LoopRefine static method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops static method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover static method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure static method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck1B static method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B static method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase static method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure static method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure static method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover static method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover static method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper static method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover static method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM static method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover static method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD static method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC static method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD static method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial static method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater static method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer static method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo static method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder static method) (pyrosetta.rosetta.protocols.magnesium.MgScanner static method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker static method) (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions static method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover static method) (pyrosetta.rosetta.protocols.match.MatcherMover static method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover static method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover static method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover static method) (pyrosetta.rosetta.protocols.matdes.SymDofMover static method) (pyrosetta.rosetta.protocols.md.CartesianMD static method) (pyrosetta.rosetta.protocols.md.MDBase static method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover static method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover static method) (pyrosetta.rosetta.protocols.medal.MedalMover static method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover static method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint static method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint static method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover static method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder static method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix static method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles static method) (pyrosetta.rosetta.protocols.membrane.FlipMover static method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence static method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover static method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility static method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover static method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover static method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover static method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover static method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover static method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover static method) (pyrosetta.rosetta.protocols.membrane.RotationMover static method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover static method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover static method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover static method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover static method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover static method) (pyrosetta.rosetta.protocols.membrane.TiltMover static method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover static method) (pyrosetta.rosetta.protocols.membrane.TranslationMover static method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover static method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover static method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover static method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler static method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover static method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover static method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover static method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover static method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover static method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker static method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover static method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover static method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy static method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover static method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover static method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover static method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer static method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover static method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset static method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest static method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover static method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover static method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker static method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover static method) (pyrosetta.rosetta.protocols.moves.CompositionMover static method) (pyrosetta.rosetta.protocols.moves.CycleMover static method) (pyrosetta.rosetta.protocols.moves.CyclicMover static method) (pyrosetta.rosetta.protocols.moves.DsspMover static method) (pyrosetta.rosetta.protocols.moves.FilterMover static method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover static method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover static method) (pyrosetta.rosetta.protocols.moves.IfMover static method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover static method) (pyrosetta.rosetta.protocols.moves.JumpOutMover static method) (pyrosetta.rosetta.protocols.moves.MCShowMover static method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil static method) (pyrosetta.rosetta.protocols.moves.MoveMapMover static method) (pyrosetta.rosetta.protocols.moves.Mover static method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover static method) (pyrosetta.rosetta.protocols.moves.MoverContainer static method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList static method) (pyrosetta.rosetta.protocols.moves.NullMover static method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover static method) (pyrosetta.rosetta.protocols.moves.ProfilerMover static method) (pyrosetta.rosetta.protocols.moves.PyMOLMover static method) (pyrosetta.rosetta.protocols.moves.RampingMover static method) (pyrosetta.rosetta.protocols.moves.RandomMover static method) (pyrosetta.rosetta.protocols.moves.RepeatMover static method) (pyrosetta.rosetta.protocols.moves.SequenceMover static method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor static method) (pyrosetta.rosetta.protocols.moves.SwitchMover static method) (pyrosetta.rosetta.protocols.moves.TrialMover static method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover static method) (pyrosetta.rosetta.protocols.moves.WhileMover static method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover static method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol static method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover static method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol static method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover static method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder static method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover static method) (pyrosetta.rosetta.protocols.network.UIMover static method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover static method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover static method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover static method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover static method) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule static method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters static method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat static method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky static method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy static method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk static method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer static method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover static method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential static method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences static method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover static method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover static method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover static method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover static method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover static method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover static method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover static method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling static method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover static method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover static method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover static method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser static method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover static method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover static method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover static method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover static method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TryRotamers static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB static method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover static method) (pyrosetta.rosetta.protocols.qsar.qsarMover static method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage static method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader static method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax static method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover static method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl static method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover static method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any static method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb static method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop static method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion static method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler static method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler static method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite static method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump static method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar static method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite static method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer static method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover static method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence static method) (pyrosetta.rosetta.protocols.recon_design.MSDMover static method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover static method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover static method) (pyrosetta.rosetta.protocols.relax.CentroidRelax static method) (pyrosetta.rosetta.protocols.relax.ClassicRelax static method) (pyrosetta.rosetta.protocols.relax.FastRelax static method) (pyrosetta.rosetta.protocols.relax.LocalRelax static method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover static method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover static method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover static method) (pyrosetta.rosetta.protocols.relax.MiniRelax static method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover static method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase static method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax static method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover static method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover static method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover static method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMotionMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover static method) (pyrosetta.rosetta.protocols.rigid.RollMover static method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover static method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM static method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover static method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover static method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover static method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover static method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser static method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover static method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover static method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover static method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover static method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover static method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer static method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer static method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover static method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter static method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol static method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo static method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol static method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover static method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify static method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify static method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer static method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser static method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover static method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover static method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor static method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor static method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor static method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper static method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper static method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover static method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol static method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover static method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecovery method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover static method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator static method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold static method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst static method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops static method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides static method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree static method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover static method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer static method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment static method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover static method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover static method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover static method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover static method) (pyrosetta.rosetta.protocols.simple_ddg.ddG static method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover static method) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher static method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover static method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover static method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData static method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover static method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint static method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover static method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover static method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover static method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover static method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover static method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover static method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover static method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover static method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover static method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover static method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover static method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins static method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins static method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover static method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover static method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover static method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover static method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover static method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover static method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover static method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover static method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover static method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover static method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover static method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover static method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover static method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover static method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover static method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond static method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover static method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover static method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover static method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover static method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover static method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb static method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers static method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover static method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile static method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence static method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif static method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover static method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher static method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover static method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover static method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover static method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology static method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover static method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover static method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue static method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover static method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover static method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover static method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher static method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover static method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover static method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover static method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover static method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover static method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover static method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover static method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover static method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover static method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover static method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover static method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover static method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo static method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover static method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA static method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ static method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover static method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree static method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover static method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover static method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover static method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover static method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities static method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover static method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover static method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover static method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover static method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion static method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover static method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover static method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover static method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase static method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover static method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover static method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover static method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover static method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover static method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot static method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover static method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover static method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover static method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover static method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover static method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover static method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover static method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover static method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover static method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover static method) (pyrosetta.rosetta.protocols.simple_moves.Tumble static method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover static method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover static method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover static method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover static method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose static method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover static method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.sparta.Sparta static method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover static method) (pyrosetta.rosetta.protocols.splice.RBInMover static method) (pyrosetta.rosetta.protocols.splice.RBOutMover static method) (pyrosetta.rosetta.protocols.splice.RotLibOut static method) (pyrosetta.rosetta.protocols.splice.Splice static method) (pyrosetta.rosetta.protocols.splice.SpliceIn static method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody static method) (pyrosetta.rosetta.protocols.splice.SpliceInTail static method) (pyrosetta.rosetta.protocols.splice.SpliceOut static method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody static method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail static method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover static method) (pyrosetta.rosetta.protocols.star.StarAbinitio static method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer static method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup static method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser static method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup static method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.SideChainCopier static method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker static method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker static method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover static method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer static method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser static method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger static method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler static method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList static method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler static method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer static method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.FromScratchMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo static method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb static method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives static method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList static method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser static method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler static method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb static method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF static method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion static method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue static method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb static method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer static method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized static method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny static method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb static method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover static method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover static method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover static method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol static method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover static method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover static method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover static method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry static method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover static method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover static method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether static method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover static method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover static method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover static method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation static method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact static method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover static method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover static method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover static method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover static method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover static method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover static method) (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation static method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover static method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus static method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover static method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer static method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover static method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler static method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover static method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover static method) register_options_broker() (in module pyrosetta.rosetta.protocols.abinitio) register_options_universal_main() (in module pyrosetta.rosetta.protocols.jobdist) register_result() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.EvenlyPartitionedNodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) register_result_with_token() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) register_score_maker() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) register_store_provider() (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager method) (pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreManager method) register_variable_expression() (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) register_with_citation_manager() (in module pyrosetta.rosetta.protocols.cyclic_peptide_predict) register_work_unit() (pyrosetta.rosetta.protocols.wum.WorkUnitList method) register_work_units() (pyrosetta.rosetta.protocols.loophash.MPI_LoopHashRefine method) (pyrosetta.rosetta.protocols.loophash.MPI_LoopHashRefine_Emperor method) (pyrosetta.rosetta.protocols.loophash.MPI_LoopHashRefine_Master method) (pyrosetta.rosetta.protocols.mpi_refinement.MPI_Refine_Emperor method) (pyrosetta.rosetta.protocols.mpi_refinement.MPI_Refine_Master method) (pyrosetta.rosetta.protocols.mpi_refinement.MPI_Refinement method) (pyrosetta.rosetta.protocols.wum.MPI_WorkUnitManager method) (pyrosetta.rosetta.protocols.wum.MPI_WorkUnitManager_Slave method) (pyrosetta.rosetta.protocols.wum.WorkUnitManager method) rehash() (pyrosetta.rosetta.std.unordered_map_basic_datacache_ResRotPair_float_basic_datacache_ResRotPairHasher_std_equal_to_basic_datacache_ResRotPair_std_allocator_std_pair_const_basic_datacache_ResRotPair_float_t method) (pyrosetta.rosetta.std.unordered_map_std_pair_char_char_int_core_sequence_CharPairHash_std_equal_to_std_pair_char_char_std_allocator_std_pair_const_std_pair_char_char_int_t method) (pyrosetta.rosetta.std.unordered_map_unsigned_long_numeric_MathMatrix_float_t method) reindex_residues() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) reindex_sections() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) reinitialize() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) reinitialize_active_energy_methods() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) reinitialize_CCD_torsions() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) reinitialize_for_each_job() (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop 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.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler 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.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder 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.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover 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.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover 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.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize 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.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.forge.components.BDR 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.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) (pyrosetta.rosetta.protocols.hydrate.Hydrate method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler 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.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover 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.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM 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_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover 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.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover 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.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DsspMover method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.Mover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover 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.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot 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.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop 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.PrepackMover 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.SecretionOptimizationMover 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.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover 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.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover 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.IdealizeHelicesMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax 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.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover 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.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover 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_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover 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.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover 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.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover 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.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.star.StarAbinitio 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.SideChainCopier method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler 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.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover 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.monte_carlo.StepWiseMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) reinitialize_for_new_input() (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop 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.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler 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.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder 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.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover 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.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover 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.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize 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.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.forge.components.BDR 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.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) (pyrosetta.rosetta.protocols.hydrate.Hydrate method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler 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.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover 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.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM 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_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover 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.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover 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.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DsspMover method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.Mover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover 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.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot 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.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop 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.PrepackMover 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.SecretionOptimizationMover 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.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover 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.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover 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.IdealizeHelicesMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax 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.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover 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.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover 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_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover 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.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover 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.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover 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.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.star.StarAbinitio 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.SideChainCopier method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler 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.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover 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.monte_carlo.StepWiseMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) reinitialize_mingraph_neighborhood_for_residue() (in module pyrosetta.rosetta.core.pack) reinitialize_minnode_for_residue() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) reinstate_pose() (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) reject (pyrosetta.rosetta.protocols.hotspot_hashing.StubStatus attribute) reject_change() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) reject_change_npd() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) reject_mutant() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver method) reject_perturbation() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) REJECTED (pyrosetta.rosetta.protocols.monte_carlo.TrialResult attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.BBClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.BBClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.CutClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.CutClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.LegacyRootClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.LegacyRootClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.SequenceClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.SequenceClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.SymmetryClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.SymmetryClaim.ClaimRight attribute) rejection_thresh() (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter method) rel_deriv_dev() (pyrosetta.rosetta.core.optimization.NumDerivCheckData method) (pyrosetta.rosetta.core.optimization.SimpleDerivCheckResult method) rel_per_res_sc_sasa() (in module pyrosetta.rosetta.core.scoring.sasa) relative() (pyrosetta.rosetta.protocols.environment.claims.XYZClaim method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) relative_pose_filter() (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) relative_pose_names() (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) RelativeConnectRight (class in pyrosetta.rosetta.protocols.forge.build) RelativePoseFilter (class in pyrosetta.rosetta.protocols.calc_taskop_filters) RelativePoseFilterCreator (class in pyrosetta.rosetta.protocols.calc_taskop_filters) RelativeSegmentFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) RelativeSegmentFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) RelativeSequencePosition (class in pyrosetta.rosetta.protocols.forge.build) RELAX (pyrosetta.rosetta.protocols.abinitio.StageID attribute) relax (pyrosetta.rosetta.protocols.antibody.design.MinTypeEnum attribute) relax() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) relax_after_neighbors_perturbation() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) relax_bound() (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) relax_cdrs() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) relax_favorable_poses() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) relax_in_current_context() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) relax_induced_dipoles() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) relax_interface() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) Relax_main() (in module pyrosetta.rosetta.protocols.relax) relax_mover() (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter method) relax_neighbors() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) relax_optimized_CDR_grafts() (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) relax_pose() (in module pyrosetta.rosetta.protocols.relax) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) relax_protocol() (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) relax_rounds_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) relax_structure() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) relax_tcr_model() (in module pyrosetta.rosetta.protocols.tcr) relax_type (pyrosetta.rosetta.protocols.mpi_refinement.MethodParams property) relax_unbound() (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter method) relaxmode() (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) RelaxProtocolBase (class in pyrosetta.rosetta.protocols.relax) RelaxScriptCommand (class in pyrosetta.rosetta.protocols.denovo_design.movers) (class in pyrosetta.rosetta.protocols.relax) RelaxScriptFileContents (class in pyrosetta.rosetta.protocols.relax) RelaxScriptManager (class in pyrosetta.rosetta.protocols.relax) relay_message() (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) release() (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) release_buffers() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) release_file() (pyrosetta.rosetta.protocols.jd2.DebugOut_MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd2.MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd2.WriteOut_MpiFileBuffer method) release_specific() (pyrosetta.rosetta.cppdb.session method) (pyrosetta.rosetta.utility.sql_database.session method) release_threads() (pyrosetta.rosetta.basic.thread_manager.RosettaThreadManager method) ReleaseConstraintFromResidueMover (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) ReleaseConstraintFromResidueMoverCreator (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) reletter_chains() (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) relevant_downstream_atoms() (pyrosetta.rosetta.protocols.match.MatcherTask method) remainder() (in module pyrosetta.rosetta.numeric) (pyrosetta.rosetta.numeric.RemainderSelector_double_false_t static method) (pyrosetta.rosetta.numeric.RemainderSelector_int_true_t static method) RemainderSelector_double_false_t (class in pyrosetta.rosetta.numeric) RemainderSelector_int_true_t (class in pyrosetta.rosetta.numeric) remaining_list_ (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) remaining_list_index_ (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) remap() (pyrosetta.rosetta.protocols.comparative_modeling.features.ResidueFeature method) (pyrosetta.rosetta.protocols.comparative_modeling.features.SSFeature method) (pyrosetta.rosetta.protocols.comparative_modeling.features.TorsionFeature method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) remap_allowed_residues_to_template() (pyrosetta.rosetta.protocols.task_operations.LinkResidues method) remap_atom_vds() (pyrosetta.rosetta.core.chemical.MutableChiRecord method) (pyrosetta.rosetta.core.chemical.MutableResidueConnection method) remap_cis_omega_torsion_bins_to_trans() (in module pyrosetta.rosetta.core.conformation) remap_pdb_atom_names() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) remap_rb_segments() (in module pyrosetta.rosetta.protocols.rbsegment_relax) remap_resid() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomToAxisConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraint method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedDihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueCouplingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.RTConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache method) remap_residue() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) remap_residue_level_tasks() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) remap_residue_positions() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) remap_residues() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesSeqRecoveryCache method) remap_value() (pyrosetta.rosetta.core.fragment.BaseCacheUnit method) remapped_clone() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomToAxisConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraint method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedDihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueCouplingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.RTConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) REMARK (pyrosetta.rosetta.core.io.pdb.RecordType attribute) remark() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) RemarkInfo (class in pyrosetta.rosetta.core.io) Remarks (class in pyrosetta.rosetta.core.io) REMARKS (pyrosetta.rosetta.protocols.sparta.GDB property) remarks() (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.pose.PDBInfo method) remember_unrecognized_res() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) remember_unrecognized_water() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) remodel() (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) remodel_fold_tree_to_account_for_insertion() (in module pyrosetta.rosetta.core.kinematics) remodel_generic_taskfactory() (in module pyrosetta.rosetta.protocols.forge.methods) remodel_max_length() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) remodel_min_length() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) remodel_tcr_cdr_loops() (in module pyrosetta.rosetta.protocols.tcr) remodelable() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) RemodelAccumulator (class in pyrosetta.rosetta.protocols.forge.remodel) RemodelConstraintGenerator (class in pyrosetta.rosetta.protocols.forge.remodel) RemodelData (class in pyrosetta.rosetta.protocols.forge.remodel) remodelData() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) RemodelDesignMover (class in pyrosetta.rosetta.protocols.forge.remodel) RemodelEnzdesCstModule (class in pyrosetta.rosetta.protocols.forge.remodel) RemodelGlobalFrame (class in pyrosetta.rosetta.protocols.forge.remodel) RemodelLigandHandler (class in pyrosetta.rosetta.protocols.forge.remodel) RemodelLoopMover (class in pyrosetta.rosetta.protocols.forge.remodel) RemodelLoopMoverPoseFolder (class in pyrosetta.rosetta.protocols.denovo_design.components) RemodelMover (class in pyrosetta.rosetta.protocols.forge.remodel) RemodelMoverCreator (class in pyrosetta.rosetta.protocols.forge.remodel) RemodelRotamerLinks (class in pyrosetta.rosetta.protocols.forge.remodel) RemodelRotamerLinksCreator (class in pyrosetta.rosetta.protocols.forge.remodel) RemodelWorkingSet (class in pyrosetta.rosetta.protocols.forge.remodel) REMOVE (pyrosetta.rosetta.protocols.enzdes.CstAction attribute) remove() (pyrosetta.bindings.pose.ResidueLabelAccessor method) (pyrosetta.rosetta.core.fragment.FrameList method) (pyrosetta.rosetta.core.select.residue_selector.ResidueVector method) (pyrosetta.rosetta.numeric.Xforms method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultVector method) (pyrosetta.rosetta.protocols.cluster.calibur.AdjacentList method) (pyrosetta.rosetta.protocols.denovo_design.components.BuildPhases method) (pyrosetta.rosetta.protocols.denovo_design.components.EnumeratedVectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.denovo_design.components.NamedSolution method) (pyrosetta.rosetta.protocols.denovo_design.components.NamedSolutions method) (pyrosetta.rosetta.protocols.denovo_design.components.VectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairings method) (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.sewing.hashing.SegmentVector method) (pyrosetta.rosetta.protocols.topology_broker.claims.CutClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.LegacyRootClaim method) (pyrosetta.rosetta.std.list_const_protocols_match_Hit__star__t method) (pyrosetta.rosetta.std.list_core_id_AtomID_t method) (pyrosetta.rosetta.std.list_core_io_rcsb_ExperimentalTechnique_t method) (pyrosetta.rosetta.std.list_core_scoring_power_diagram_PDvertex__star__t method) (pyrosetta.rosetta.std.list_double_t method) (pyrosetta.rosetta.std.list_int_t method) (pyrosetta.rosetta.std.list_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.list_RDKit_Atom__star__t method) (pyrosetta.rosetta.std.list_RDKit_Bond__star__t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_double_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.list_std_set_std_string_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_operation_ResLvlTaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_chunk_library_inputters_ChunkLibraryInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_full_model_inputters_FullModelInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_inputters_PoseInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_PoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_SecondaryPoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_XMLSchemaParticle_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_interaction_graph_AnnealableGraphBase_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_rotamer_set_RotamerOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_task_operation_TaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_power_diagram_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_deallocation_DeallocationMessage_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_LarvalJob_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_output_OutputSpecification_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_pose_outputters_SecondaryPoseOutputter_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_CrossPeak_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.std.list_std_string_t method) (pyrosetta.rosetta.std.list_unsigned_long_t method) (pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t method) (pyrosetta.rosetta.std.list_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.list_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.std.vector_core_scoring_hbonds_graph_HBondInfo method) (pyrosetta.rosetta.std.vector_core_scoring_sc_Atom method) (pyrosetta.rosetta.std.vector_double method) (pyrosetta.rosetta.std.vector_float method) (pyrosetta.rosetta.std.vector_int method) (pyrosetta.rosetta.std.vector_numeric_xyzMatrix_double_t method) (pyrosetta.rosetta.std.vector_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.vector_std_list_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.vector_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t method) (pyrosetta.rosetta.std.vector_std_map_unsigned_long_unsigned_long_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_pair_std_shared_ptr_protocols_filters_Filter_protocols_filters_boolean_operations_t method) (pyrosetta.rosetta.std.vector_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_set_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_chemical_Orbital_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_fragment_FragSet_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_pose_Pose_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_cluster_calibur_Stru_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_hbnet_HBondNetStruct_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_std_list_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.vector_std_string method) (pyrosetta.rosetta.std.vector_std_vector_double_t method) (pyrosetta.rosetta.std.vector_std_vector_int_t method) (pyrosetta.rosetta.std.vector_std_vector_std_string_t method) (pyrosetta.rosetta.std.vector_std_vector_std_vector_double_t method) 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(pyrosetta.rosetta.utility.vector1_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_numeric_xyzVector_double_std_less_std_string_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_unsigned_long_std_less_std_string_std_allocator_std_pair_const_std_string_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_core_chemical_AA_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_core_chemical_AA_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_shared_ptr_protocols_frag_picker_CandidatesCollector_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_frag_picker_CandidatesCollector_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_unsigned_long_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_utility_keys_Key2Tuple_unsigned_long_unsigned_long_unsigned_long_std_less_utility_keys_Key2Tuple_unsigned_long_unsigned_long_std_allocator_std_pair_const_utility_keys_Key2Tuple_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_bool_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_core_id_AtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_core_kinematics_Jump_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_std_pair_core_id_AtomID_core_id_AtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_DOF_ID_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_NamedAtomID_core_id_NamedAtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_TorsionID_core_id_TorsionID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_TorsionID_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_io_HeaderInformation_CompoundToken_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_aa_composition_energy_TailFunction_core_scoring_aa_composition_energy_TailFunction_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_int_int_t method) 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(pyrosetta.rosetta.utility.vector1_utility_vector0_unsigned_short_std_allocator_unsigned_short_t method) (pyrosetta.rosetta.utility.vector1_utility_vector0_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_bool_std_allocator_bool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_char_std_allocator_char_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_chemical_BondName_std_allocator_core_chemical_BondName_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_chemical_BondRingness_std_allocator_core_chemical_BondRingness_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_chemical_VariantType_std_allocator_core_chemical_VariantType_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_id_AtomID_std_allocator_core_id_AtomID_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_id_DOF_ID_std_allocator_core_id_DOF_ID_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_id_NamedAtomID_std_allocator_core_id_NamedAtomID_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_id_TorsionID_std_allocator_core_id_TorsionID_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_scoring_packstat_Circle__star__std_allocator_core_scoring_packstat_Circle__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_scoring_power_diagram_PDsphere__star__std_allocator_core_scoring_power_diagram_PDsphere__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_scoring_ScoreType_std_allocator_core_scoring_ScoreType_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_float_std_allocator_float_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_int_std_allocator_int_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_long_std_allocator_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_interpolation_spline_CubicSpline_std_allocator_numeric_interpolation_spline_CubicSpline_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_xyzVector_float_std_allocator_numeric_xyzVector_float_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_ObjexxFCL_ubyte_std_allocator_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_denovo_design_components_StrandOrientation_std_allocator_protocols_denovo_design_components_StrandOrientation_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_denovo_design_components_StructureSlice_std_allocator_protocols_denovo_design_components_StructureSlice_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_loops_Loops_std_allocator_protocols_loops_Loops_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_std_allocator_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_int_int_std_allocator_std_pair_int_int_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_numeric_xyzVector_double_numeric_xyzVector_double_std_allocator_std_pair_numeric_xyzVector_double_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_std_allocator_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_std_string_std_string_std_allocator_std_pair_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_std_pair_std_pair_double_double_unsigned_long_std_allocator_std_pair_unsigned_long_std_pair_std_pair_double_double_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_unsigned_long_std_allocator_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_core_scoring_dna_TorsionFourierComponent_std_allocator_std_shared_ptr_const_core_scoring_dna_TorsionFourierComponent_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_std_allocator_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_match_upstream_ScaffoldBuildPoint_std_allocator_std_shared_ptr_const_protocols_match_upstream_ScaffoldBuildPoint_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_simple_filters_ResidueDepthData_std_allocator_std_shared_ptr_const_protocols_simple_filters_ResidueDepthData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_conformation_Residue_std_allocator_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_kinematics_tree_Atom_std_allocator_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_optimization_DOF_Node_std_allocator_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_pack_interaction_graph_NPDHBond_std_allocator_std_shared_ptr_core_pack_interaction_graph_NPDHBond_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_pack_task_ResfileCommand_std_allocator_std_shared_ptr_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_scoring_saxs_DistanceHistogram_std_allocator_std_shared_ptr_core_scoring_saxs_DistanceHistogram_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_sequence_Cell_std_allocator_std_shared_ptr_core_sequence_Cell_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_antibody_PDBLandmark_std_allocator_std_shared_ptr_protocols_antibody_PDBLandmark_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_fldsgn_topology_HelixPairing_std_allocator_std_shared_ptr_protocols_fldsgn_topology_HelixPairing_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_std_allocator_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_flexpack_rotamer_set_FlexbbRotamerSet_std_allocator_std_shared_ptr_protocols_flexpack_rotamer_set_FlexbbRotamerSet_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_quota_QuotaPool_std_allocator_std_shared_ptr_protocols_frag_picker_quota_QuotaPool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_AdaptiveScoreHistogram_std_allocator_std_shared_ptr_protocols_frag_picker_scores_AdaptiveScoreHistogram_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_AtomPairConstraintsData_std_allocator_std_shared_ptr_protocols_frag_picker_scores_AtomPairConstraintsData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_FourAtomsConstraintData_std_allocator_std_shared_ptr_protocols_frag_picker_scores_FourAtomsConstraintData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_Entity_std_allocator_std_shared_ptr_protocols_genetic_algorithm_Entity_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_std_allocator_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_jd3_JGJobNode_std_allocator_std_shared_ptr_protocols_jd3_JGJobNode_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_minimization_packing_MinimalRotamer_std_allocator_std_shared_ptr_protocols_minimization_packing_MinimalRotamer_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_pose_sewing_data_storage_SegmentEnvelope_std_allocator_std_shared_ptr_protocols_pose_sewing_data_storage_SegmentEnvelope_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_keys_Key2Tuple_unsigned_long_unsigned_long_std_allocator_utility_keys_Key2Tuple_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_keys_Key3Tuple_unsigned_long_unsigned_long_unsigned_long_std_allocator_utility_keys_Key3Tuple_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_std_allocator_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_std_allocator_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_std_allocator_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_void__star__std_allocator_void__star__t method) remove_all_anchors_and_ENF() (in module pyrosetta.rosetta.protocols.hydrate) remove_all_enzdes_constraints() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) remove_all_hotspot_constraints() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) remove_all_jump_atoms() (in module pyrosetta.rosetta.protocols.denovo_design) remove_all_variant_types() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) remove_all_virtual_phosphates() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) remove_and_store_bracketed() (in module pyrosetta.rosetta.core.pose.rna) remove_atom_info() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) remove_bad_inputs_from_job_list() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.BOINCJobDistributor method) (pyrosetta.rosetta.protocols.jd2.FileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.ShuffleFileSystemJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor method) remove_base_residue_type() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) remove_bracketed() (in module pyrosetta.rosetta.core.pose.rna) remove_calculator() (pyrosetta.rosetta.core.pose.metrics.CalculatorFactory method) remove_carbohydrate_branch_point_variants() (in module pyrosetta.rosetta.core.pose.carbohydrates) remove_chain_break_jump_point() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) remove_chain_break_variants() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) remove_chainbreaks() (pyrosetta.rosetta.protocols.jumping.JumpSample method) remove_chainbreaks_according_to_jumps() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) remove_checkpoint_file() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) remove_child() (pyrosetta.rosetta.protocols.jd3.JGResultNode method) remove_connection_inconsistencies() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) remove_constraint() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.constraints.Constraints method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) remove_constraints() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) remove_constraints_from_pose() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) remove_constraints_from_pose_for_block() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) remove_constraints_of_type() (in module pyrosetta.rosetta.core.scoring.constraints) remove_coordinate_constraints_from_pose() (in module pyrosetta.rosetta.protocols.protein_interface_design) remove_covalent_connection_from_pose() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo method) remove_covalent_connections_from_pose() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) remove_cut() (in module pyrosetta.rosetta.protocols.jumping) remove_cutpoint() (in module pyrosetta.rosetta.protocols.forge.methods) remove_cutpoint_closed() (in module pyrosetta.rosetta.core.import_pose) remove_cutpoint_variants() (in module pyrosetta.rosetta.core.util) (in module pyrosetta.rosetta.protocols.forge.methods) (in module pyrosetta.rosetta.protocols.loops) remove_cutpoint_variants_for_ccd() (in module pyrosetta.rosetta.protocols.grafting) remove_cutpoints() (in module pyrosetta.rosetta.protocols.forge.methods) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) remove_cutpoints_closed() (in module pyrosetta.rosetta.core.import_pose) remove_cycles() (pyrosetta.rosetta.core.environment.FoldTreeSketch method) remove_duplicate_phi_psi() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) remove_duplicates() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) remove_enzdes_constraints() (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) remove_evaluation() (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) remove_excess_protons() (in module pyrosetta.rosetta.core.chemical.rdkit) remove_existing() (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) remove_favor_native_constraints() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver method) remove_file() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) remove_from_string() (in module pyrosetta.rosetta.utility) remove_gapped_positions() (pyrosetta.rosetta.core.sequence.SequenceAlignment method) remove_hairpin() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) remove_high_energy_water_molecules() (in module pyrosetta.rosetta.protocols.hydrate) remove_highest_energy_member_of_each_group() (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) remove_hotspot_constraints_from_pose() (in module pyrosetta.rosetta.protocols.hotspot_hashing) remove_info() (pyrosetta.rosetta.protocols.dna.PDBOutput method) remove_inline_comments() (in module pyrosetta.rosetta.utility.io) remove_input_file() (pyrosetta.rosetta.utility.Inline_File_Provider method) remove_invrots_clashing_with_parent_res() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode method) remove_last_filter() (pyrosetta.rosetta.protocols.filters.FilterCollection method) remove_ligand_canonical_residues() (in module pyrosetta.rosetta.core.pose) remove_lower_terminus_type_from_conformation_residue() (in module pyrosetta.rosetta.core.conformation) remove_lower_terminus_type_from_pose_residue() (in module pyrosetta.rosetta.core.pose) remove_member() (pyrosetta.rosetta.protocols.cluster.Cluster method) remove_mg_bound_waters() (in module pyrosetta.rosetta.protocols.magnesium) remove_missing_density() (in module pyrosetta.rosetta.protocols.loops) remove_missing_jump_atoms() (in module pyrosetta.rosetta.protocols.denovo_design) remove_models_from_dssp() (in module pyrosetta.rosetta.protocols.legacy_sewing) remove_non_buried_wat() (in module pyrosetta.rosetta.protocols.hydrate) remove_non_protein_residues() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) remove_nonbb_constraints() (in module pyrosetta.rosetta.core.scoring.constraints) remove_nonprotein_residues() (in module pyrosetta.rosetta.core.pose) remove_observer() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) remove_occupied_density_from_density() (in module pyrosetta.rosetta.protocols.electron_density) remove_other_pose_at_idx() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) remove_pair() (pyrosetta.rosetta.core.pose.rna.RNA_SecStruct method) remove_parent() (pyrosetta.rosetta.protocols.jd3.JGJobNode method) remove_position_from_template_res() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) remove_position_from_template_res_for_block() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) remove_random_stubs_from_set() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) remove_redundant() (pyrosetta.rosetta.numeric.UniformRotationSampler method) remove_register_shifts() (in module pyrosetta.rosetta.protocols.fldsgn.filters) remove_remark_header_for_geomcst() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) remove_remodel_constraints_from_pose() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) remove_residue_selector() (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) remove_residue_type() (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) remove_seqpos() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache method) remove_seqpos_from_template_res() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache method) remove_short_chunks() (in module pyrosetta.rosetta.protocols.loops) remove_silent_file_if_it_exists() (in module pyrosetta.rosetta.core.io.silent) remove_singlet_base_pairs() (pyrosetta.rosetta.core.pose.rna.RNA_SecStruct method) remove_singletons() (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) remove_singletons_and_update_pose_focus() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) remove_small_gaps() (in module pyrosetta.rosetta.protocols.loops) remove_stub() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) remove_surface_waters() (pyrosetta.rosetta.core.scoring.packstat.SimplePDB method) remove_terminal_loops() (pyrosetta.rosetta.protocols.loops.Loops method) remove_terminal_phosphates() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) remove_trigger() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) remove_unpatchable_residue_type() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) remove_upper_lower_variants_from_RNA() (in module pyrosetta.rosetta.core.pose.rna) remove_upper_terminus_type_from_conformation_residue() (in module pyrosetta.rosetta.core.conformation) remove_upper_terminus_type_from_pose_residue() (in module pyrosetta.rosetta.core.pose) remove_variant_type() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) remove_variant_type_from_conformation_residue() (in module pyrosetta.rosetta.core.conformation) remove_variant_type_from_pose_residue() (in module pyrosetta.rosetta.core.pose) remove_variant_type_from_residue() (in module pyrosetta.rosetta.core.pose) remove_vector_exclude_residues() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 method) remove_virtual_O2Prime_hydrogen() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) remove_virtual_residues() (in module pyrosetta.rosetta.core.pose) remove_virtual_rna_residue_variant_type() (in module pyrosetta.rosetta.core.pose.rna) remove_waters_except_mg_bound() (in module pyrosetta.rosetta.protocols.magnesium) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) removeAtom() (pyrosetta.rosetta.RDKit.RWMol method) removeBond() (pyrosetta.rosetta.RDKit.RWMol method) removeConformer() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) RemoveConstraints (class in pyrosetta.rosetta.protocols.constraint_generator) RemoveConstraintsCreator (class in pyrosetta.rosetta.protocols.constraint_generator) removeDecoys() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) RemoveHybridization() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) RemoveLigandFilter (class in pyrosetta.rosetta.protocols.enzdes) RemoveLigandFilterCreator (class in pyrosetta.rosetta.protocols.enzdes) RemoveMetalConnectionsMover (class in pyrosetta.rosetta.protocols.metal_interface) RemoveMetalConnectionsMoverCreator (class in pyrosetta.rosetta.protocols.metal_interface) RemoveNorCTermMPM (class in pyrosetta.rosetta.protocols.match) RemoveRemodelCsts (class in pyrosetta.rosetta.protocols.forge.constraints) RemoveRemodelCstsCreator (class in pyrosetta.rosetta.protocols.forge.constraints) RemoveRotamerSpecifications (class in pyrosetta.rosetta.core.chemical) rename_atom() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.io.ResidueInformation method) rename_atoms() (in module pyrosetta.rosetta.core.chemical) rename_checkpoint_files() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) rename_energies() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) rename_segment() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) RenameAtom (class in pyrosetta.rosetta.core.chemical) render() (pyrosetta.rosetta.core.environment.FoldTreeSketch method) render_movemap() (pyrosetta.rosetta.core.environment.DofPassport method) RenderGridsToKinemage (class in pyrosetta.rosetta.protocols.qsar) RenderGridsToKinemageCreator (class in pyrosetta.rosetta.protocols.qsar) renew_trj_scratch() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) renormalize_quota_pools() (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) renormalize_weights() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) renumber_after_variant_changes() (pyrosetta.rosetta.core.pose.toolbox.AtomID_Mapper method) (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) renumber_all_decoys() (pyrosetta.rosetta.core.io.silent.SilentFileData method) renumber_decoys() (pyrosetta.rosetta.core.import_pose.pose_stream.SilentFilePoseInputStream method) renumber_jumps() (pyrosetta.rosetta.core.kinematics.FoldTree method) renumber_jumps_ordered() (pyrosetta.rosetta.core.kinematics.FoldTree method) renumber_movable_group() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) renumber_pdb() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter method) renumber_pdbinfo_based_on_conf_chains() (in module pyrosetta.rosetta.core.pose) renumber_rotamers() (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) renumber_with_pdb_info() (in module pyrosetta.rosetta.protocols.hybridization) reorder() (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) reorder_foldtree_around_mobile_regions() (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) reorder_full_model_info_after_append() (in module pyrosetta.rosetta.core.pose.full_model_info) reorder_full_model_info_after_delete() (in module pyrosetta.rosetta.core.pose.full_model_info) reorder_full_model_info_after_prepend() (in module pyrosetta.rosetta.core.pose.full_model_info) reorder_glycan_residues() (in module pyrosetta.rosetta.core.io) reorder_membrane_foldtree() (in module pyrosetta.rosetta.protocols.membrane) reorder_pose() (in module pyrosetta.rosetta.core.import_pose) reorder_randomly() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) reorder_root_partition_res() (in module pyrosetta.rosetta.core.pose) reorder_spans() (pyrosetta.rosetta.core.conformation.membrane.SpanningTopology method) reorder_tensor() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) reorder_with_first_non_mobile_as_root() (in module pyrosetta.rosetta.protocols.ligand_docking) reorient_extended_fibril() (in module pyrosetta.rosetta.protocols.fibril) rep (pyrosetta.rosetta.protocols.ligand_docking.Ligand_info property) rep_ramp_cycles (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) rep_weight() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) repack (pyrosetta.rosetta.protocols.antibody.design.MinTypeEnum attribute) repack() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.pack_daemon.BasicSimAnnealerRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.DenseIGRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.DoubleDenseIGRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.FASTER_IG_Repacker method) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.RotamerSubsetRepacker method) (pyrosetta.rosetta.protocols.simple_ddg.AlaScan method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) repack_antibody_interface() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) repack_antigen_ab_interface() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) repack_antigen_interface() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) repack_bound() (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) repack_cdrs() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) repack_chain1() (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) repack_chain2() (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) repack_connection_and_residues_in_movemap() (in module pyrosetta.rosetta.protocols.grafting) repack_connection_and_residues_in_movemap_and_piece() (in module pyrosetta.rosetta.protocols.grafting) repack_connection_and_residues_in_movemap_and_piece_and_neighbors() (in module pyrosetta.rosetta.protocols.grafting) repack_disulfides() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) repack_neighbors() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) repack_period() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) repack_query() (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) repack_shell() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) (pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) (pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) repack_tcr_model() (in module pyrosetta.rosetta.protocols.tcr) repack_tf_from_residue_sets() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) repack_these_residues() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) repack_this_residue() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) repack_to_matrix() (pyrosetta.rosetta.protocols.frag_picker.CSTalosIO method) repack_unbound() (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) repackable_residues() (in module pyrosetta.rosetta.core.pack) repacking_radius() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) repacking_residues() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) RepackingRefiner (class in pyrosetta.rosetta.protocols.loop_modeling.refiners) RepackingRefinerCreator (class in pyrosetta.rosetta.protocols.loop_modeling.refiners) RepackLigandSiteWithoutLigandMover (class in pyrosetta.rosetta.protocols.enzdes) RepackMinimize (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) RepackMinimizeCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) RepackSidechainsMover (class in pyrosetta.rosetta.protocols.minimization_packing) RepackSidechainsMoverCreator (class in pyrosetta.rosetta.protocols.minimization_packing) RepackTrial (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) RepackTrialCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) RepackWithoutLigandFilter (class in pyrosetta.rosetta.protocols.enzdes) RepackWithoutLigandFilterCreator (class in pyrosetta.rosetta.protocols.enzdes) repeat() (in module pyrosetta.rosetta.ObjexxFCL.format) repeat_generation_with_additional_residue() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) repeat_propagation() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) repeat_sync() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) repeat_to_preserve() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) RepeatMover (class in pyrosetta.rosetta.protocols.moves) RepeatParameterFilter (class in pyrosetta.rosetta.protocols.simple_filters) RepeatParameterFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) RepeatPropagationMover (class in pyrosetta.rosetta.protocols.simple_moves) RepeatPropagationMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) RepeatProteinRelax (class in pyrosetta.rosetta.protocols.relax) RepeatProteinRelaxCreator (class in pyrosetta.rosetta.protocols.relax) repeats (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GADockStageParams property) (pyrosetta.rosetta.protocols.ligand_docking.Transform_info property) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble_info property) repeats() (pyrosetta.rosetta.protocols.simple_ddg.AlaScan method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScan method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) repeats_ (pyrosetta.rosetta.protocols.simple_filters.PackStatFilter property) repeats_per_turn() (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) RepGrid (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) RepGridCreator (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) REPL_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) replace() (in module pyrosetta.rosetta.protocols.forge.methods) replace_atom() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) replace_char() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.Sequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) replace_col() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) replace_conformation_residue_copying_existing_coordinates() (in module pyrosetta.rosetta.core.conformation) replace_creator() (pyrosetta.rosetta.core.scoring.constraints.ConstraintFactory method) replace_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) replace_environment_variables() (in module pyrosetta.rosetta.utility) replace_file() (in module pyrosetta.rosetta.protocols.monte_carlo) replace_first_in() (in module pyrosetta.rosetta.utility) replace_in() (in module pyrosetta.rosetta.utility) replace_layer() (pyrosetta.rosetta.numeric.MathNTensor_double_1_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_2_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_4_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_5_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_6_t method) (pyrosetta.rosetta.numeric.MathTensor_double_t method) replace_option_namespace_colons_with_underscores() (in module pyrosetta.rosetta.basic.options) replace_parameter_via_clone() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) replace_pose_residue_copying_existing_coordinates() (in module pyrosetta.rosetta.core.pose) replace_region() (in module pyrosetta.rosetta.protocols.grafting) replace_res() (pyrosetta.rosetta.core.pose.PDBInfo method) replace_res_remap_bfactors() (pyrosetta.rosetta.core.pose.PDBInfo method) replace_residue() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) replace_residue_in_atom_tree() (in module pyrosetta.rosetta.core.conformation) replace_residue_keeping_all_atom_positions() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) replace_row() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) replace_segment() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) replace_spaces() (in module pyrosetta.rosetta.utility) replace_stub1() (pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData method) replace_stub2() (pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData method) replace_stub3() (pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData method) replace_tree() (pyrosetta.rosetta.core.kinematics.AtomTree method) replaceAtom() (pyrosetta.rosetta.RDKit.RWMol method) replaceAtomBookmark() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) replaceBond() (pyrosetta.rosetta.RDKit.RWMol method) replaced_symmetric_foldtree_with_new_monomer() (in module pyrosetta.rosetta.core.conformation.symmetry) ReplaceMainchainAtom (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithBromine (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithChlorine (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithEthyl (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithFluorine (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithHydroxyl (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithIodine (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithMethoxy (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithMethyl (class in pyrosetta.rosetta.core.chemical) ReplaceProtonWithTrifluoromethyl (class in pyrosetta.rosetta.core.chemical) ReplaceRegionMover (class in pyrosetta.rosetta.protocols.grafting.simple_movers) ReplaceRegionMoverCreator (class in pyrosetta.rosetta.protocols.grafting.simple_movers) replaces() (pyrosetta.rosetta.core.chemical.Patch method) replaces_residue_type() (pyrosetta.rosetta.core.chemical.Patch method) ReplaceString() (pyrosetta.rosetta.protocols.pockets.GenPharmacophore method) ReplicaExchangeMC (class in pyrosetta.rosetta.protocols.moves) ReplicateFilter (class in pyrosetta.rosetta.protocols.filters) ReplicateFilterCreator (class in pyrosetta.rosetta.protocols.filters) ReplicateTask (class in pyrosetta.rosetta.core.pack.task.operation) REPLONLY (pyrosetta.rosetta.core.chemical.VariantType attribute) REPLS_BB (pyrosetta.rosetta.core.chemical.VariantType attribute) Report (class in pyrosetta.rosetta.basic) (class in pyrosetta.rosetta.protocols.features) Report() (pyrosetta.rosetta.basic.gpu.Timer method) report() (pyrosetta.rosetta.core.energy_methods.AACompositionEnergy method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergy method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintHelper method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorExternal method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorMatrix method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorSVM method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup method) (pyrosetta.rosetta.protocols.buns.BuriedUnsatHbondFilter2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.ConservedPosMutationFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreCutoffFilter method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.constraint_filters.ShowConstraintsFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) (pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter method) (pyrosetta.rosetta.protocols.dna.RotamerDNAHBondFilter method) (pyrosetta.rosetta.protocols.dna_dock.DNAClashCheckFilter method) (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter method) (pyrosetta.rosetta.protocols.enzdes.LigBurialFilter method) (pyrosetta.rosetta.protocols.enzdes.LigDSasaFilter method) (pyrosetta.rosetta.protocols.enzdes.LigInterfaceEnergyFilter method) (pyrosetta.rosetta.protocols.enzdes.RemoveLigandFilter method) (pyrosetta.rosetta.protocols.enzdes.RepackWithoutLigandFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.filters.CalculatorFilter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.ContingentFilter method) (pyrosetta.rosetta.protocols.filters.FalseFilter method) (pyrosetta.rosetta.protocols.filters.Filter method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.filters.ReplicateFilter method) (pyrosetta.rosetta.protocols.filters.StochasticFilter method) (pyrosetta.rosetta.protocols.filters.TimeFilter method) (pyrosetta.rosetta.protocols.filters.TrueFalseFilter method) (pyrosetta.rosetta.protocols.filters.TrueFilter method) (pyrosetta.rosetta.protocols.filters.VectorPoseFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.CoreDunbrackFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.FragQualFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.InterlockingAromaFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.NcontactsFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.ParallelBetaPairingPreferenceFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureCountFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureHasResidueFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ConstraintFulfilmentFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ScorePoseSegmentFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.hbnet.HBNetScore method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilter method) (pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilter method) (pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilter method) (pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilter method) (pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilter method) (pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilter method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilter method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorer method) (pyrosetta.rosetta.protocols.pose_sewing.filters.HasDisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AtomicContactCountFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AverageDegreeFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.ClashWithTargetFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FNatFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.InterfaceHolesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.IRmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.LRmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdSimpleFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SpecificResiduesNearInterfaceFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SSamountFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreLoopsFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.Torsion method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) (pyrosetta.rosetta.protocols.recon_design.FitnessFilter method) (pyrosetta.rosetta.protocols.score_filters.GeometryFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreTypeFilter method) (pyrosetta.rosetta.protocols.simple_ddg.AlaScan method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScan method) (pyrosetta.rosetta.protocols.simple_ddg.InterfaceBindingEnergyDensityFilter method) (pyrosetta.rosetta.protocols.simple_ddg.SSElementBisectddGFilter method) (pyrosetta.rosetta.protocols.simple_filters.AbinitioBaseFilter method) (pyrosetta.rosetta.protocols.simple_filters.AngleToVector method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.AveragePathLengthFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.COFilter method) (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter method) (pyrosetta.rosetta.protocols.simple_filters.DisulfideEntropyFilter method) (pyrosetta.rosetta.protocols.simple_filters.DomainInterfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.EnergyPerResidueFilter method) (pyrosetta.rosetta.protocols.simple_filters.ExpiryFilter method) (pyrosetta.rosetta.protocols.simple_filters.FileExistFilter method) (pyrosetta.rosetta.protocols.simple_filters.FileRemoveFilter method) (pyrosetta.rosetta.protocols.simple_filters.HelixHelixAngleFilter method) (pyrosetta.rosetta.protocols.simple_filters.HolesFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHydrophobicResidueContactsFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceSasaFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterRepeatContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.IntraRepeatContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MembAccesResidueLipophilicityFilter method) (pyrosetta.rosetta.protocols.simple_filters.MotifScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.MPSpanAngleFilter method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilter method) (pyrosetta.rosetta.protocols.simple_filters.NeighborTypeFilter method) (pyrosetta.rosetta.protocols.simple_filters.NetChargeFilter method) (pyrosetta.rosetta.protocols.simple_filters.NMerPSSMEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.NMerSVMEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.NonSequentialNeighborsFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackStatFilter method) (pyrosetta.rosetta.protocols.simple_filters.PDDFScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.RangeFilter method) (pyrosetta.rosetta.protocols.simple_filters.ReadPoseExtraScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.RepeatParameterFilter method) (pyrosetta.rosetta.protocols.simple_filters.ReportFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueBurialFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueChiralityFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueIEFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueLipophilicityFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSelectionDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSetChainEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResiduesInInterfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.RGFilter method) (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter method) (pyrosetta.rosetta.protocols.simple_filters.SAXSScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) (pyrosetta.rosetta.protocols.simple_filters.SheetFilter method) (pyrosetta.rosetta.protocols.simple_filters.SidechainRmsdFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) (pyrosetta.rosetta.protocols.simple_filters.SpanTopologyMatchPoseFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSElementLengthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSElementMotifContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinder method) (pyrosetta.rosetta.protocols.simple_filters.StemFinder method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareSASAFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter method) (pyrosetta.rosetta.protocols.simple_filters.TerminusDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.TMsAACompFilter method) (pyrosetta.rosetta.protocols.simple_filters.TMsSpanMembraneFilter method) (pyrosetta.rosetta.protocols.simple_filters.TotalSasaFilter method) (pyrosetta.rosetta.protocols.simple_filters.Worst9merFilter method) report_aa_matrix() (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) report_ab_H3_kink_metrics_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) report_ab_metrics_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) report_adducts() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) report_after_apply() (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol.ParsedProtocolStep method) report_all() (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) report_all_ec() (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric method) report_all_es() (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric method) report_all_interface_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) report_aln_components() (pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator method) (pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator method) (pyrosetta.rosetta.protocols.evaluation.AlignEvaluator method) report_as_silent() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) report_at_end() (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol.ParsedProtocolStep method) report_atom_pairs() (pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures method) report_batch_inconsistency() (in module pyrosetta.rosetta.protocols.jd2.archive) report_binary_stats() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) report_CA_rmsd() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) report_call_order() (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) report_cdr_metrics_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) report_cdr_residue_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) report_cdr_residue_features_row() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) report_coordinate_constraints() (in module pyrosetta.rosetta.protocols.splice) report_crd() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) report_data() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) report_ddG() (pyrosetta.rosetta.protocols.simple_ddg.ddG method) report_des_pack_res() (in module pyrosetta.rosetta.protocols.splice) report_designable_packable_residues() (in module pyrosetta.rosetta.protocols.splice) report_dev() (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) report_diffs() (pyrosetta.rosetta.protocols.simple_ddg.DdGScan method) report_dist() (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) report_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeatures method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures method) (pyrosetta.rosetta.protocols.features.AtomTypesFeatures method) (pyrosetta.rosetta.protocols.features.BatchFeatures method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeatures method) (pyrosetta.rosetta.protocols.features.DdGFeatures method) (pyrosetta.rosetta.protocols.features.FeaturesReporter method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeatures method) (pyrosetta.rosetta.protocols.features.HBondFeatures method) (pyrosetta.rosetta.protocols.features.HBondParameterFeatures method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTest method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeatures method) (pyrosetta.rosetta.protocols.features.HelixCapFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.JobDataFeatures method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeatures method) (pyrosetta.rosetta.protocols.features.ModelFeatures method) (pyrosetta.rosetta.protocols.features.OrbitalsFeatures method) (pyrosetta.rosetta.protocols.features.PairFeatures method) (pyrosetta.rosetta.protocols.features.PdbDataFeatures method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeatures method) (pyrosetta.rosetta.protocols.features.PoseConformationFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures method) (pyrosetta.rosetta.protocols.features.ProtocolFeatures method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeatures method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeatures method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeatures method) (pyrosetta.rosetta.protocols.features.ResidueFeatures method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeatures method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeatures method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeatures method) (pyrosetta.rosetta.protocols.features.RotamerFeatures method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeatures method) (pyrosetta.rosetta.protocols.features.RuntimeFeatures method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeatures method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeatures method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeatures method) (pyrosetta.rosetta.protocols.features.ScreeningFeatures method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeatures method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeatures method) (pyrosetta.rosetta.protocols.features.SmotifFeatures method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeatures method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) (pyrosetta.rosetta.protocols.features.StructureFeatures method) (pyrosetta.rosetta.protocols.features.StructureScoresFeatures method) (pyrosetta.rosetta.protocols.features.TaskOperationFeatures method) (pyrosetta.rosetta.protocols.features.TotalScoreFeatures method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeatures method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeatures method) (pyrosetta.rosetta.protocols.features.WaterFeatures method) report_filter_name() (pyrosetta.rosetta.protocols.simple_filters.ReportFilter method) report_filters_to_pose() (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) report_final_score() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintHelper method) report_gdt_components() (pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluator method) report_haro_orbital_interactions() (pyrosetta.rosetta.protocols.features.OrbitalsFeatures method) report_heading_directions_of_all_AA_in_a_strand() (in module pyrosetta.rosetta.protocols.features.strand_assembly) report_hpol_orbital_interactions() (pyrosetta.rosetta.protocols.features.OrbitalsFeatures method) report_interface_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) report_interface_residue_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) report_interface_side_features() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) report_interres_angles() (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures method) report_interres_lengths() (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures method) report_intrares_angles() (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures method) report_intrares_lengths() (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures method) report_intrares_torsions() (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures method) report_parameter_features() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) report_parameter_features_schema_to_db() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) report_predicted_features() (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSQLite method) report_property() (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporter method) report_residue_pairs() (pyrosetta.rosetta.protocols.features.PairFeatures method) report_ressolv() (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) report_rms_and_scores() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) report_rot_prob() (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) report_rotamer_recovery() (pyrosetta.rosetta.protocols.rotamer_recovery.PerNativeRRReporterHuman method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSimple method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSQLite method) report_rotamer_recovery_features() (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSQLite method) report_rotamer_recovery_full() (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSQLite method) report_scorecomp() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) report_sequence() (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) report_silent() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) report_sm() (pyrosetta.rosetta.protocols.buns.BuriedUnsatHbondFilter2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.ConservedPosMutationFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreCutoffFilter method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.constraint_filters.ShowConstraintsFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter method) (pyrosetta.rosetta.protocols.dna_dock.DNAClashCheckFilter method) (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter method) (pyrosetta.rosetta.protocols.enzdes.LigBurialFilter method) (pyrosetta.rosetta.protocols.enzdes.LigDSasaFilter method) (pyrosetta.rosetta.protocols.enzdes.LigInterfaceEnergyFilter method) (pyrosetta.rosetta.protocols.enzdes.RemoveLigandFilter method) (pyrosetta.rosetta.protocols.enzdes.RepackWithoutLigandFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.filters.CalculatorFilter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.ContingentFilter method) (pyrosetta.rosetta.protocols.filters.FalseFilter method) (pyrosetta.rosetta.protocols.filters.Filter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.filters.ReplicateFilter method) (pyrosetta.rosetta.protocols.filters.StochasticFilter method) (pyrosetta.rosetta.protocols.filters.TimeFilter method) (pyrosetta.rosetta.protocols.filters.TrueFalseFilter method) (pyrosetta.rosetta.protocols.filters.TrueFilter method) (pyrosetta.rosetta.protocols.filters.VectorPoseFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.CoreDunbrackFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.FragQualFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.InterlockingAromaFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.NcontactsFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.ParallelBetaPairingPreferenceFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureCountFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureHasResidueFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ConstraintFulfilmentFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ScorePoseSegmentFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.hbnet.HBNetScore method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilter method) (pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilter method) (pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilter method) (pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilter method) (pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilter method) (pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilter method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilter method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorer method) (pyrosetta.rosetta.protocols.pose_sewing.filters.HasDisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AtomicContactCountFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AverageDegreeFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.ClashWithTargetFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FNatFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.InterfaceHolesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.IRmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.LRmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdSimpleFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SpecificResiduesNearInterfaceFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SSamountFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreLoopsFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.Torsion method) (pyrosetta.rosetta.protocols.recon_design.FitnessFilter method) (pyrosetta.rosetta.protocols.score_filters.GeometryFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreTypeFilter method) (pyrosetta.rosetta.protocols.simple_ddg.AlaScan method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScan method) (pyrosetta.rosetta.protocols.simple_ddg.InterfaceBindingEnergyDensityFilter method) (pyrosetta.rosetta.protocols.simple_ddg.SSElementBisectddGFilter method) (pyrosetta.rosetta.protocols.simple_filters.AbinitioBaseFilter method) (pyrosetta.rosetta.protocols.simple_filters.AngleToVector method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.AveragePathLengthFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.COFilter method) (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter method) (pyrosetta.rosetta.protocols.simple_filters.DisulfideEntropyFilter method) (pyrosetta.rosetta.protocols.simple_filters.DomainInterfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.EnergyPerResidueFilter method) (pyrosetta.rosetta.protocols.simple_filters.ExpiryFilter method) (pyrosetta.rosetta.protocols.simple_filters.FileExistFilter method) (pyrosetta.rosetta.protocols.simple_filters.FileRemoveFilter method) (pyrosetta.rosetta.protocols.simple_filters.HelixHelixAngleFilter method) (pyrosetta.rosetta.protocols.simple_filters.HolesFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHydrophobicResidueContactsFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceSasaFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterRepeatContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.IntraRepeatContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MembAccesResidueLipophilicityFilter method) (pyrosetta.rosetta.protocols.simple_filters.MotifScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.MPSpanAngleFilter method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilter method) (pyrosetta.rosetta.protocols.simple_filters.NeighborTypeFilter method) (pyrosetta.rosetta.protocols.simple_filters.NetChargeFilter method) (pyrosetta.rosetta.protocols.simple_filters.NMerPSSMEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.NMerSVMEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.NonSequentialNeighborsFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackStatFilter method) (pyrosetta.rosetta.protocols.simple_filters.PDDFScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.RangeFilter method) (pyrosetta.rosetta.protocols.simple_filters.ReadPoseExtraScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.RepeatParameterFilter method) (pyrosetta.rosetta.protocols.simple_filters.ReportFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueBurialFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueChiralityFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueIEFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueLipophilicityFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSelectionDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSetChainEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResiduesInInterfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.RGFilter method) (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter method) (pyrosetta.rosetta.protocols.simple_filters.SAXSScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) (pyrosetta.rosetta.protocols.simple_filters.SheetFilter method) (pyrosetta.rosetta.protocols.simple_filters.SidechainRmsdFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) (pyrosetta.rosetta.protocols.simple_filters.SpanTopologyMatchPoseFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSElementLengthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSElementMotifContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinder method) (pyrosetta.rosetta.protocols.simple_filters.StemFinder method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareSASAFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter method) (pyrosetta.rosetta.protocols.simple_filters.TerminusDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.TMsAACompFilter method) (pyrosetta.rosetta.protocols.simple_filters.TMsSpanMembraneFilter method) (pyrosetta.rosetta.protocols.simple_filters.TotalSasaFilter method) (pyrosetta.rosetta.protocols.simple_filters.Worst9merFilter method) report_string() (pyrosetta.rosetta.protocols.simple_filters.ReportFilter method) report_structure_features() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) report_subvalues() (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) report_symmetry() (pyrosetta.rosetta.protocols.simple_ddg.AlaScan method) report_test() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) report_unfolded() (in module pyrosetta.rosetta.protocols.fold_from_loops.utils) ReportEffectivePKA (class in pyrosetta.rosetta.protocols.simple_moves) ReportEffectivePKACreator (class in pyrosetta.rosetta.protocols.simple_moves) Reporter (class in pyrosetta.rosetta.basic) ReportFilter (class in pyrosetta.rosetta.protocols.simple_filters) ReportFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) ReportFSC (class in pyrosetta.rosetta.protocols.electron_density) ReportFSCCreator (class in pyrosetta.rosetta.protocols.electron_density) ReportGradientsMover (class in pyrosetta.rosetta.protocols.cryst) ReportGradientsMoverCreator (class in pyrosetta.rosetta.protocols.cryst) ReportPSSMDifferences (class in pyrosetta.rosetta.protocols.protein_interface_design) ReportSequenceDifferences (class in pyrosetta.rosetta.protocols.protein_interface_design) ReportToDB (class in pyrosetta.rosetta.protocols.features) ReportToDBCreator (class in pyrosetta.rosetta.protocols.features) ReportXYZ (class in pyrosetta.rosetta.protocols.simple_moves) ReportXYZCreator (class in pyrosetta.rosetta.protocols.simple_moves) represent_residue_selector() (in module pyrosetta.rosetta.core.select.residue_selector) representative_downstream_algorithm() (pyrosetta.rosetta.protocols.match.Matcher method) representative_group_matches() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) representative_seqpos() (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeSet method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) reprotonate_rdmol() (in module pyrosetta.rosetta.core.chemical.rdkit) REPULSIVE (pyrosetta.rosetta.core.chemical.AtomProperty attribute) repulsive (pyrosetta.rosetta.core.scoring.etable.AtomPairEnergy property) repulsive_ramp() (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) RepulsiveOnlyMover (class in pyrosetta.rosetta.protocols.simple_moves) request() (pyrosetta.rosetta.basic.mpi.DbMoverMessageListener method) (pyrosetta.rosetta.basic.mpi.MessageListener method) request_by_name() (pyrosetta.rosetta.basic.sampling.orientations.QuaternionGridManager method) request_by_radius() (pyrosetta.rosetta.basic.sampling.orientations.QuaternionGridManager method) request_by_size() (pyrosetta.rosetta.basic.sampling.orientations.QuaternionGridManager method) request_data_from_head_node() (in module pyrosetta.rosetta.basic.mpi) request_file() (pyrosetta.rosetta.utility.Inline_File_Provider_Hook method) request_fold_tree() (pyrosetta.rosetta.protocols.kinematic_closure.KicMover 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) REQUEST_MESSAGE_TAG (pyrosetta.rosetta.basic.mpi.mpi_tags attribute) REQUEST_SYMMETRIZE_BY_INTERSECTION (pyrosetta.rosetta.core.pack.task.PackerTaskSymmetryStatus attribute) request_symmetrize_by_intersection() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) REQUEST_SYMMETRIZE_BY_UNION (pyrosetta.rosetta.core.pack.task.PackerTaskSymmetryStatus attribute) request_symmetrize_by_union() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) require_all_target_residue_atom_coordinates() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.ScoringSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) require_atom_to_reside_in_active_site() (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) require_bcl() (in module pyrosetta.rosetta.core.chemical.bcl) require_candidate_residue_atoms_to_lie_near_target_atom() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.ScoringSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) require_context_graph() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) require_mm_bend() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) require_target_atom_coordinate() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.ScoringSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) required_attribute() (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute static method) required_name_attribute() (in module pyrosetta.rosetta.utility.tag) required_resnums() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyResidueRetentionRequirement method) required_separation_distance() (pyrosetta.rosetta.protocols.match.BumpGrid method) requires_a_setup_for_derivatives_for_residue_opportunity() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) requires_a_setup_for_derivatives_for_residue_pair_opportunity() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) requires_a_setup_for_minimizing_for_residue_pair_opportunity() (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) requires_a_setup_for_scoring_for_residue_opportunity_during_minimization() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring() (pyrosetta.rosetta.core.energy_methods.AACompositionEnergy method) (pyrosetta.rosetta.core.energy_methods.AARepeatEnergy method) (pyrosetta.rosetta.core.energy_methods.Abego method) (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.BranchEnergy method) (pyrosetta.rosetta.core.energy_methods.Burial_v2Energy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CCS_IMMSEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifDegreeEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.ChemicalShiftAnisotropyEnergy method) (pyrosetta.rosetta.core.energy_methods.ContactOrderEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.D2H_SA_Energy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.energy_methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FastSAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyDens method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HolesEnergy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.IntermolEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.LoopCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvPenalties method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneLipo method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergy method) (pyrosetta.rosetta.core.energy_methods.MissingEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.OtherPoseEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.PackStatEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.ProQ_Energy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy_Rohl method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_Fast method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_RNA method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergy method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RMS_Energy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalMappingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PartitionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SA_Energy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) (pyrosetta.rosetta.core.energy_methods.SecondaryStructureEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfVolEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.XtalMLEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomePackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.packing.HolesEnergyRes method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergy method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.EnsembleEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.ResidualDipolarCouplingEnergyRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergy method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy method) requires_a_setup_for_scoring_for_residue_pair_opportunity() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) requires_actcoord() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) requires_context_graph() (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) requires_h5py() (in module pyrosetta.protocols.h5_importer) requires_init() (in module pyrosetta.distributed) requires_pose() (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder 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.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy method) rerelax_type (pyrosetta.rosetta.protocols.mpi_refinement.MethodParams property) reroot() (in module pyrosetta.rosetta.core.pose) reroot_based_on_full_model_info() (in module pyrosetta.rosetta.protocols.stepwise.modeler) res (pyrosetta.bindings.pose.ResidueLabelAccessor attribute) (pyrosetta.rosetta.core.scoring.packstat.SimplePDB_Atom property) (pyrosetta.rosetta.protocols.cartesian.CartesianAtom property) res() (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) res1 (pyrosetta.rosetta.core.scoring.methods.ResidueAtomOverlaps property) (pyrosetta.rosetta.protocols.denovo_design.components.BondInfo property) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBInstruction property) res1() (pyrosetta.rosetta.core.pose.rna.BasePair method) (pyrosetta.rosetta.core.pose.rna.BaseStack method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBondsTrieVsTrieCachedDataContainer method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing method) res1_atom1_index() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) res1_atom1_int() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) res1_atom1_name() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) res1_atom2_index() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) res1_atom2_int() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) res1_atom2_name() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) res1_atom3_index() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) res1_atom3_int() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) res1_atom3_name() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) res1_nb() (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBondsTrieVsTrieCachedDataContainer method) res1_ovl1_overlaps (pyrosetta.rosetta.core.scoring.methods.ResidueAtomOverlaps property) res1_ovl2_overlaps (pyrosetta.rosetta.core.scoring.methods.ResidueAtomOverlaps property) res1_pointed_at_res2() (in module pyrosetta.rosetta.core.select.util) res2 (pyrosetta.rosetta.core.scoring.methods.ResidueAtomOverlaps property) (pyrosetta.rosetta.protocols.denovo_design.components.BondInfo property) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBInstruction property) res2() (pyrosetta.rosetta.core.pose.rna.BasePair method) (pyrosetta.rosetta.core.pose.rna.BaseStack method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBondsTrieVsTrieCachedDataContainer method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing method) res2_atom1_index() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) res2_atom1_int() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) res2_atom1_name() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) res2_atom2_index() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) res2_atom2_int() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) res2_atom2_name() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) res2_atom3_index() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) res2_atom3_int() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) res2_atom3_name() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) res2_nb() (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBondsTrieVsTrieCachedDataContainer method) res2_ovu1_overlaps (pyrosetta.rosetta.core.scoring.methods.ResidueAtomOverlaps property) res3() (pyrosetta.rosetta.core.scoring.CSA method) res_aa (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData property) res_anchor() (pyrosetta.rosetta.protocols.sic_dock.Rose method) res_filter_schema_w_attributes() (in module pyrosetta.rosetta.core.pack.task.operation) res_filter_xml_schema_group_name() (pyrosetta.rosetta.core.pack.task.operation.ResFilterFactory static method) res_for_rotamer() (pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.core.pack_basic.RotamerSetsBase method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) res_haslabel() (pyrosetta.rosetta.core.pose.PDBInfo method) res_ids() (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) res_in_chain() (in module pyrosetta.rosetta.core.pose) res_index_ (pyrosetta.rosetta.core.scoring.custom_pair_distance.resatom_and_func_struct property) res_interactions() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo method) res_is_boundary() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) res_is_core() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) res_is_mirrored() (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) res_labels() (pyrosetta.rosetta.core.scoring.packstat.SimplePDB method) res_labels_ (pyrosetta.rosetta.core.scoring.packstat.SimplePDB property) res_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) res_lvl_task_op_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.ResLvlTaskOperationLoader static method) res_lvl_task_op_schema_empty() (in module pyrosetta.rosetta.core.pack.task.operation) res_lvl_task_op_schema_w_attributes() (in module pyrosetta.rosetta.core.pack.task.operation) res_lvl_task_op_xml_schema_group_name() (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory static method) res_map() (pyrosetta.rosetta.core.import_pose.libraries.ChunkSet method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeSet method) res_min_data() (pyrosetta.rosetta.core.scoring.MinimizationNode method) res_move() (pyrosetta.rosetta.protocols.splice.Splice method) res_moved() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) res_name() (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) res_name1() (pyrosetta.rosetta.protocols.protein_interface_design.ReportPSSMDifferences method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) res_name2() (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) res_num() (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) (pyrosetta.rosetta.core.scoring.packing.PoseBallsLite method) res_pair_min_data() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) res_part_of_flexsegment() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) res_props() (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilter method) res_res_geometric_sol_one_way() (pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator method) res_res_min_distance() (in module pyrosetta.rosetta.protocols.simple_filters) res_res_weight() (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer method) res_rmsd() (in module pyrosetta.rosetta.protocols.protein_interface_design.filters) res_selector_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader static method) res_type_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) res_type_linking_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) res_type_linking_constraint_energy() (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) res_types() (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilter method) resA() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) resA_atom_index_ (pyrosetta.rosetta.core.scoring.custom_pair_distance.atoms_and_func_struct property) RESAMPLE (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.MoveType attribute) resample_full_model() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) RESAMPLE_INTERNAL_LOCAL (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.MoveType attribute) ResampleMover (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) ResampleMoverCreator (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) resatom_and_func_struct (class in pyrosetta.rosetta.core.scoring.custom_pair_distance) resB() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) resB_atom_index_ (pyrosetta.rosetta.core.scoring.custom_pair_distance.atoms_and_func_struct property) rescale() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) (pyrosetta.rosetta.protocols.md.Thermostat method) rescale_fastscoring_temp_bins() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) rescale_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) ResConnID (class in pyrosetta.rosetta.core.chemical) resconnid() (pyrosetta.rosetta.core.id.PartialAtomID method) rescore() (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) rescore_all_decoys() (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore method) rescore_fragment_crmsd() (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) rescoresolutionset() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) rescover (pyrosetta.rosetta.core.scoring.motif.MotifHits property) reserve() (pyrosetta.rosetta.core.fragment.FrameList method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.io.Remarks method) (pyrosetta.rosetta.core.scoring.motif.MotifHits method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotifs method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRanges method) (pyrosetta.rosetta.core.select.residue_selector.ResidueVector method) (pyrosetta.rosetta.numeric.Xforms method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultVector method) (pyrosetta.rosetta.protocols.denovo_design.components.BuildPhases method) (pyrosetta.rosetta.protocols.denovo_design.components.EnumeratedVectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.denovo_design.components.NamedSolution method) (pyrosetta.rosetta.protocols.denovo_design.components.NamedSolutions method) (pyrosetta.rosetta.protocols.denovo_design.components.VectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairings method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) (pyrosetta.rosetta.protocols.sewing.hashing.SegmentVector method) (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) (pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoints method) (pyrosetta.rosetta.RDKit.Conformer method) (pyrosetta.rosetta.std.unordered_map_basic_datacache_ResRotPair_float_basic_datacache_ResRotPairHasher_std_equal_to_basic_datacache_ResRotPair_std_allocator_std_pair_const_basic_datacache_ResRotPair_float_t method) (pyrosetta.rosetta.std.unordered_map_std_pair_char_char_int_core_sequence_CharPairHash_std_equal_to_std_pair_char_char_std_allocator_std_pair_const_std_pair_char_char_int_t method) (pyrosetta.rosetta.std.unordered_map_unsigned_long_numeric_MathMatrix_float_t method) (pyrosetta.rosetta.std.vector_core_io_AtomInformation method) (pyrosetta.rosetta.std.vector_core_io_RemarkInfo method) (pyrosetta.rosetta.std.vector_core_pose_Pose method) (pyrosetta.rosetta.std.vector_core_scoring_hbonds_graph_HBondInfo method) (pyrosetta.rosetta.std.vector_core_scoring_sc__DOT method) (pyrosetta.rosetta.std.vector_core_scoring_sc_Atom method) (pyrosetta.rosetta.std.vector_double method) (pyrosetta.rosetta.std.vector_float method) (pyrosetta.rosetta.std.vector_int method) (pyrosetta.rosetta.std.vector_numeric_xyzMatrix_double_t method) (pyrosetta.rosetta.std.vector_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.vector_protocols_cluster_Cluster method) (pyrosetta.rosetta.std.vector_protocols_motif_grafting_movers_MotifMatch method) (pyrosetta.rosetta.std.vector_RDGeom_Point3D method) (pyrosetta.rosetta.std.vector_RDKit_Dict_Pair method) (pyrosetta.rosetta.std.vector_std_list_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.vector_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t method) (pyrosetta.rosetta.std.vector_std_map_unsigned_long_unsigned_long_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_pair_std_shared_ptr_protocols_filters_Filter_protocols_filters_boolean_operations_t method) (pyrosetta.rosetta.std.vector_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_set_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_chemical_Orbital_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_fragment_FragSet_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_pose_Pose_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_cluster_calibur_Stru_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_hbnet_HBondNetStruct_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_std_list_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.vector_std_string method) (pyrosetta.rosetta.std.vector_std_vector_double_t method) (pyrosetta.rosetta.std.vector_std_vector_int_t method) (pyrosetta.rosetta.std.vector_std_vector_std_string_t method) (pyrosetta.rosetta.std.vector_std_vector_std_vector_double_t method) (pyrosetta.rosetta.std.vector_std_vector_unsigned_long_t method) (pyrosetta.rosetta.std.vector_unsigned_int method) (pyrosetta.rosetta.std.vector_unsigned_long method) (pyrosetta.rosetta.std.vector_utility_file_FileName method) (pyrosetta.rosetta.std.vector_utility_json_spirit_Pair_impl_utility_json_spirit_Config_vector_std_string_t method) (pyrosetta.rosetta.std.vector_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t method) (pyrosetta.rosetta.std.vector_utility_json_spirit_Value_impl_utility_json_spirit_Config_vector_std_string_t method) (pyrosetta.rosetta.std.vector_utility_signals_Link method) (pyrosetta.rosetta.std.vector_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.vector_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.std.vector_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.std.vector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.utility.deep_copy_vector1_std_shared_ptr_core_chemical_Orbital_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyOptionKey_utility_options_VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyVectorOptionKey_utility_options_VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanOptionKey_utility_options_BooleanOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanVectorOptionKey_utility_options_BooleanVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_FileOptionKey_utility_options_FileOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_FileVectorOptionKey_utility_options_FileVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerOptionKey_utility_options_IntegerOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerVectorOptionKey_utility_options_IntegerVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_OptionKey_utility_options_OptionTypes_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathOptionKey_utility_options_PathOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathVectorOptionKey_utility_options_PathVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealOptionKey_utility_options_RealOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealVectorOptionKey_utility_options_RealVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_ResidueChainVectorOptionKey_utility_options_ResidueChainVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringOptionKey_utility_options_StringOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringVectorOptionKey_utility_options_StringVectorOption_t method) (pyrosetta.rosetta.utility.vector0_core_conformation_ppo_torsion_bin method) (pyrosetta.rosetta.utility.vector0_core_id_AtomID_Map_bool_t method) (pyrosetta.rosetta.utility.vector0_core_io_AtomInformation method) (pyrosetta.rosetta.utility.vector0_double method) (pyrosetta.rosetta.utility.vector0_float method) (pyrosetta.rosetta.utility.vector0_int method) (pyrosetta.rosetta.utility.vector0_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector0_protocols_flexpack_interaction_graph_FlexbbSparseMatrixIndex method) (pyrosetta.rosetta.utility.vector0_std_list_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.utility.vector0_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector0_std_pair_float_float_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_moves_Mover_t method) (pyrosetta.rosetta.utility.vector0_std_string method) (pyrosetta.rosetta.utility.vector0_unsigned_char method) (pyrosetta.rosetta.utility.vector0_unsigned_long method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_double_3_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_double_5_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_utility_fixedsizearray0_double_3_3_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_utility_fixedsizearray0_double_5_5_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray1_double_16_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_core_io_AtomInformation_std_allocator_core_io_AtomInformation_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_int_std_allocator_int_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_std_list_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_list_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_std_allocator_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_std_pair_int_int_std_allocator_std_pair_int_int_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_basic_citation_manager_AuthorNames method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_Column method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_ForeignKey method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_Index method) (pyrosetta.rosetta.utility.vector1_basic_sampling_orientations_QuatDBMetadata method) (pyrosetta.rosetta.utility.vector1_bool method) (pyrosetta.rosetta.utility.vector1_char method) (pyrosetta.rosetta.utility.vector1_const_utility_vector1_int_std_allocator_int__star_t method) (pyrosetta.rosetta.utility.vector1_core_chemical_AA method) (pyrosetta.rosetta.utility.vector1_core_chemical_Adduct method) (pyrosetta.rosetta.utility.vector1_core_chemical_AtomICoor method) (pyrosetta.rosetta.utility.vector1_core_chemical_AtomType method) (pyrosetta.rosetta.utility.vector1_core_chemical_BondName method) (pyrosetta.rosetta.utility.vector1_core_chemical_io_merge_residue_behavior method) (pyrosetta.rosetta.utility.vector1_core_chemical_MutableResidueConnection method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResConnID method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResidueConnection method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty method) (pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingConformer method) (pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingSaturationType method) (pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter method) (pyrosetta.rosetta.utility.vector1_core_chemical_rna_PuckerState method) (pyrosetta.rosetta.utility.vector1_core_chemical_VariantType method) (pyrosetta.rosetta.utility.vector1_core_conformation_Atom method) (pyrosetta.rosetta.utility.vector1_core_conformation_PseudoBond method) (pyrosetta.rosetta.utility.vector1_core_conformation_signals_LengthEvent method) (pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue method) (pyrosetta.rosetta.utility.vector1_core_fragment_FragData method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_scores_VallFragmentScore method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection method) (pyrosetta.rosetta.utility.vector1_core_fragment_rna_SYN_ANTI_RESTRICTION method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_bool_t method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.utility.vector1_core_id_DOF_ID method) (pyrosetta.rosetta.utility.vector1_core_id_NamedAtomID method) (pyrosetta.rosetta.utility.vector1_core_id_TorsionID method) (pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range method) (pyrosetta.rosetta.utility.vector1_core_io_AtomInformation method) (pyrosetta.rosetta.utility.vector1_core_io_HELIXInformation method) (pyrosetta.rosetta.utility.vector1_core_io_LinkInformation method) (pyrosetta.rosetta.utility.vector1_core_io_ResidueInformation method) (pyrosetta.rosetta.utility.vector1_core_io_SHEETInformation method) (pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy method) (pyrosetta.rosetta.utility.vector1_core_io_SSBondInformation method) (pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Edge method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Jump method) (pyrosetta.rosetta.utility.vector1_core_kinematics_RT method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Stub method) (pyrosetta.rosetta.utility.vector1_core_optimization_DerivCheckDataPoint method) (pyrosetta.rosetta.utility.vector1_core_optimization_DOF_DataPoint method) (pyrosetta.rosetta.utility.vector1_core_pack_annealer_PointDwell method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbond method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_sap_BlockParam method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_DotSphere method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_exposed_hydrophobic_data method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_RotamerDots method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_SparseMatrixIndex method) (pyrosetta.rosetta.utility.vector1_core_pack_rotamer_set_ContinuousRotamerSet method) (pyrosetta.rosetta.utility.vector1_core_pack_scmin_ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.utility.vector1_core_pack_task_operation_ResiduePDBIndexIs_ChainPos method) (pyrosetta.rosetta.utility.vector1_core_pack_task_ResidueLevelTask_ method) (pyrosetta.rosetta.utility.vector1_core_pose_PDBInfo_AtomRecord method) (pyrosetta.rosetta.utility.vector1_core_pose_PDBInfo_ResidueRecord method) (pyrosetta.rosetta.utility.vector1_core_pose_Pose method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_Atom_Bin method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_BaseStack method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_Datum method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_Reactivity method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_SuiteInfo method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_VDW_RepScreenInfo method) (pyrosetta.rosetta.utility.vector1_core_pose_UnrecognizedAtomRecord method) (pyrosetta.rosetta.utility.vector1_core_scoring_bin_transitions_BT_PROPERTIES method) (pyrosetta.rosetta.utility.vector1_core_scoring_CSA method) (pyrosetta.rosetta.utility.vector1_core_scoring_DC method) (pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair method) (pyrosetta.rosetta.utility.vector1_core_scoring_disulfides_DisulfideDerivativeAtom method) (pyrosetta.rosetta.utility.vector1_core_scoring_dssp_Pairing method) (pyrosetta.rosetta.utility.vector1_core_scoring_dssp_StrandPairing method) (pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector method) (pyrosetta.rosetta.utility.vector1_core_scoring_epr_deer_EPRSpinLabel method) (pyrosetta.rosetta.utility.vector1_core_scoring_etable_EtableParamsOnePair method) (pyrosetta.rosetta.utility.vector1_core_scoring_etable_etrie_GenericResidueConnectionData method) (pyrosetta.rosetta.utility.vector1_core_scoring_fiber_diffraction_OneGaussianScattering method) (pyrosetta.rosetta.utility.vector1_core_scoring_GenTorsionParams method) (pyrosetta.rosetta.utility.vector1_core_scoring_Hairpin method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_HBondEdge method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_HBondNode method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_HBEvalTuple method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_HBondWeightType method) (pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_Loop method) (pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_LoopCycle method) (pyrosetta.rosetta.utility.vector1_core_scoring_mhc_epitope_energy_AlleleMatrix method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_MotifHit method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_ResPairMotif method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_Xfres method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_pcs_PCSSingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_pre_PRESingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_rdc_RDCSingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_packing_Ball method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBall method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBallCluster method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_LR_AtomData method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_LR_MP_AtomData method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_SimplePDB_Atom method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_Sphere method) (pyrosetta.rosetta.utility.vector1_core_scoring_power_diagram_SAnode method) (pyrosetta.rosetta.utility.vector1_core_scoring_RDC method) (pyrosetta.rosetta.utility.vector1_core_scoring_RDC_Rohl method) (pyrosetta.rosetta.utility.vector1_core_scoring_rna_RNA_Motif method) (pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType method) (pyrosetta.rosetta.utility.vector1_core_scoring_SmallAtNb method) (pyrosetta.rosetta.utility.vector1_core_scoring_SmoothScoreTermCoeffs method) (pyrosetta.rosetta.utility.vector1_core_scoring_SpringParams method) (pyrosetta.rosetta.utility.vector1_core_scoring_tableID method) (pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange method) (pyrosetta.rosetta.utility.vector1_core_sequence_Line method) (pyrosetta.rosetta.utility.vector1_core_sequence_SequenceAlignment method) (pyrosetta.rosetta.utility.vector1_double method) (pyrosetta.rosetta.utility.vector1_float method) (pyrosetta.rosetta.utility.vector1_int method) (pyrosetta.rosetta.utility.vector1_long method) (pyrosetta.rosetta.utility.vector1_numeric_CubicPolynomial method) (pyrosetta.rosetta.utility.vector1_numeric_geometry_hashing_Ball method) (pyrosetta.rosetta.utility.vector1_numeric_histograms_TwoDHistogram_unsigned_long_long_t method) (pyrosetta.rosetta.utility.vector1_numeric_HomogeneousTransform_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_BicubicSpline method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_CubicSpline method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_interp_range method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_Point method) (pyrosetta.rosetta.utility.vector1_numeric_MultiDimensionalHistogram method) (pyrosetta.rosetta.utility.vector1_numeric_random_WeightedSampler method) (pyrosetta.rosetta.utility.vector1_numeric_RocPoint method) (pyrosetta.rosetta.utility.vector1_numeric_urs_Quat method) (pyrosetta.rosetta.utility.vector1_numeric_xyzMatrix_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzTransform_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzVector_float_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray1D_double_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray2D_double_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_AlternativePairings method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_ClassicAbinitio_StageID method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_PairingStatEntry method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_StageID method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_AntibodyNumberingSchemeEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRDefinitionEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRNameEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_clusters_CDRClusterEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_clusters_ClusterData method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_design_PDBNumbering method) (pyrosetta.rosetta.utility.vector1_protocols_backbone_moves_local_backbone_mover_Residue method) (pyrosetta.rosetta.utility.vector1_protocols_backrub_BackrubSegment method) (pyrosetta.rosetta.utility.vector1_protocols_branch_angle_BranchCoef1 method) (pyrosetta.rosetta.utility.vector1_protocols_branch_angle_BranchCoef2 method) (pyrosetta.rosetta.utility.vector1_protocols_canonical_sampling_DbTrajectoryRecorder_Frame method) (pyrosetta.rosetta.utility.vector1_protocols_canonical_sampling_TorsionSpec method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_CartesianAtom method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_Angle method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_Bond method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_HarmonicDihedral method) (pyrosetta.rosetta.utility.vector1_protocols_cluster_DataPoint method) (pyrosetta.rosetta.utility.vector1_protocols_cluster_Exemplar method) (pyrosetta.rosetta.utility.vector1_protocols_constraints_additional_ConstraintEvaluator method) (pyrosetta.rosetta.utility.vector1_protocols_contact_map_Contact method) (pyrosetta.rosetta.utility.vector1_protocols_cyclic_peptide_PSM_StubMode method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_BondInfo method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_StructureSlice method) (pyrosetta.rosetta.utility.vector1_protocols_features_TaskOperationFeatures_Taskop_id_name_factory_ method) (pyrosetta.rosetta.utility.vector1_protocols_fold_from_loops_utils_NubSegment method) (pyrosetta.rosetta.utility.vector1_protocols_forge_build_Interval method) (pyrosetta.rosetta.utility.vector1_protocols_frag_picker_LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareTotalScore_t method) (pyrosetta.rosetta.utility.vector1_protocols_helical_bundle_BPC_Parameters method) (pyrosetta.rosetta.utility.vector1_protocols_hotspot_hashing_VectorPair method) (pyrosetta.rosetta.utility.vector1_protocols_hybridization_detailedControlsTagSetting method) (pyrosetta.rosetta.utility.vector1_protocols_indexed_structure_store_BackboneStub method) (pyrosetta.rosetta.utility.vector1_protocols_jd2_archive_Batch method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_chunk_library_ChunkLibraryPreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_dag_node_managers_ResultElements method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_full_model_FullModelPreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_standard_PreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_DisulfPairing method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_JumpSelector_JumpWeightDef method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_JumpSetup_JumpDef method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_ResiduePairJumpSetup_JumpDef method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewAtom method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewResidue method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_AtomProperties method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_GADockStageParams method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_Pharmacophore method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_ReweightableRepEnergy method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionDistrParams method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionType method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ligand_options_InterfaceInfo method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ProtLigPair_info method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolution method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolutionStore method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_ResTorsions method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_SheetPositions method) (pyrosetta.rosetta.utility.vector1_protocols_loops_Loop method) (pyrosetta.rosetta.utility.vector1_protocols_loops_LoopFromFileData method) (pyrosetta.rosetta.utility.vector1_protocols_loops_Loops method) (pyrosetta.rosetta.utility.vector1_protocols_loops_SerializedLoop method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_CentroidRotNum method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_RotData method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_TorsionRange method) (pyrosetta.rosetta.utility.vector1_protocols_match_Hit method) (pyrosetta.rosetta.utility.vector1_protocols_match_match_dspos1 method) (pyrosetta.rosetta.utility.vector1_protocols_match_ProbeRadius method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_BuildSet method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_hit method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_SampleStrategyData method) (pyrosetta.rosetta.utility.vector1_protocols_md_Constraint method) (pyrosetta.rosetta.utility.vector1_protocols_md_MDscheduleData method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_AAMatrix method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_RotMatrix method) (pyrosetta.rosetta.utility.vector1_protocols_membrane_SpanInfo method) (pyrosetta.rosetta.utility.vector1_protocols_monte_carlo_AcceptedScores method) (pyrosetta.rosetta.utility.vector1_protocols_motif_grafting_movers_motif2scaffold_indexes method) (pyrosetta.rosetta.utility.vector1_protocols_moves_TrialCounter method) (pyrosetta.rosetta.utility.vector1_protocols_mpi_refinement_MethodParams method) (pyrosetta.rosetta.utility.vector1_protocols_multistate_design_SingleStateEntityData method) (pyrosetta.rosetta.utility.vector1_protocols_nonlocal_Chunk method) (pyrosetta.rosetta.utility.vector1_protocols_optimize_weights_WeightRangeConstraint method) (pyrosetta.rosetta.utility.vector1_protocols_pack_daemon_StructureFileNames method) (pyrosetta.rosetta.utility.vector1_protocols_pdbinfo_manipulations_SequenceSpecification method) (pyrosetta.rosetta.utility.vector1_protocols_pmut_scan_Mutant method) (pyrosetta.rosetta.utility.vector1_protocols_pmut_scan_MutationData method) (pyrosetta.rosetta.utility.vector1_protocols_pose_creation_MergePDBMover_Overlap method) (pyrosetta.rosetta.utility.vector1_protocols_pose_creation_SliceToMiniProteinMover_Chunk method) (pyrosetta.rosetta.utility.vector1_protocols_pose_metric_calculators_EnergiesData method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_mutt method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_tm_region method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_VLBInstruction method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_Transformation method) (pyrosetta.rosetta.utility.vector1_protocols_qsar_ColorGradient method) (pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBResidueRange method) (pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment method) (pyrosetta.rosetta.utility.vector1_protocols_recces_Histogram method) (pyrosetta.rosetta.utility.vector1_protocols_relax_DatabaseRelaxScript method) (pyrosetta.rosetta.utility.vector1_protocols_rigid_Partner method) (pyrosetta.rosetta.utility.vector1_protocols_rosetta_scripts_ParsedProtocol_ParsedProtocolStep method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataCenter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataLanthanide method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsEnergyParameter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsGridSearchParameter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsInputLine method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs_PCS_data_per_lanthanides method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs_PCS_line_data method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs1_PCS_data_per_lanthanides_Ts1 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs1_PCS_line_data_Ts1 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_data_per_lanthanides_Ts2 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_line_data_Ts2 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs3_PCS_data_per_lanthanides_Ts3 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs3_PCS_line_data_Ts3 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs4_PCS_data_per_lanthanides_Ts4 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs4_PCS_line_data_Ts4 method) (pyrosetta.rosetta.utility.vector1_protocols_seeded_abinitio_SegmentSpec method) (pyrosetta.rosetta.utility.vector1_protocols_sewing_data_storage_ContactDescription method) (pyrosetta.rosetta.utility.vector1_protocols_sewing_data_storage_LigandDescription method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_Quat method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_RegionalConnections method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_ResidueDepthFrag method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_IonizableResidue method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_LoggedFragmentMover_Item method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_TorsionPerturbType method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_WaterRot method) (pyrosetta.rosetta.utility.vector1_protocols_splice_BBDofs method) (pyrosetta.rosetta.utility.vector1_protocols_splice_ResidueBBDofs method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_protein_MainChainTorsionSet method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_rna_Combine_Tags_Info method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_rna_phosphate_PhosphateMove method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_monte_carlo_mover_Attachment method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_monte_carlo_mover_StepWiseMove method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_sampler_copy_dofs_ResidueAlternativeSet method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_CstResInteractions method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ExternalGeomSampler method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ResInteractions method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_SingleConstraint method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint method) (pyrosetta.rosetta.utility.vector1_protocols_trajectory_DbTrajectoryWriter_Frame method) (pyrosetta.rosetta.utility.vector1_short method) (pyrosetta.rosetta.utility.vector1_signed_char method) (pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_downstream_hit_t method) (pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_upstream_hit_t method) (pyrosetta.rosetta.utility.vector1_std_array_int_3_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_std_shared_ptr_const_protocols_match_downstream_SecMatchResiduePairEvaluator_unsigned_long_t method) 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(pyrosetta.rosetta.utility.vector1_std_map_core_chemical_AA_utility_vector1_double_std_allocator_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_protocols_jumping_cstType_unsigned_long_std_less_protocols_jumping_cstType_std_allocator_std_pair_const_protocols_jumping_cstType_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_protocols_jumping_dofType_unsigned_long_std_less_protocols_jumping_dofType_std_allocator_std_pair_const_protocols_jumping_dofType_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_shared_ptr_const_core_conformation_Residue_double_std_less_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_pair_const_std_shared_ptr_const_core_conformation_Residue_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_core_id_NamedAtomID_std_less_std_string_std_allocator_std_pair_const_std_string_core_id_NamedAtomID_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_numeric_xyzVector_double_std_less_std_string_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_unsigned_long_std_less_std_string_std_allocator_std_pair_const_std_string_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_core_chemical_AA_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_core_chemical_AA_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_shared_ptr_protocols_frag_picker_CandidatesCollector_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_frag_picker_CandidatesCollector_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_unsigned_long_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_utility_keys_Key2Tuple_unsigned_long_unsigned_long_unsigned_long_std_less_utility_keys_Key2Tuple_unsigned_long_unsigned_long_std_allocator_std_pair_const_utility_keys_Key2Tuple_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_unsigned_long_std_less_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_std_allocator_std_pair_const_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_bool_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_core_id_AtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_core_kinematics_Jump_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_std_pair_core_id_AtomID_core_id_AtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_DOF_ID_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_NamedAtomID_core_id_NamedAtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_TorsionID_core_id_TorsionID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_TorsionID_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_io_HeaderInformation_CompoundToken_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_io_raw_data_DisulfideFile_ResNum_core_io_raw_data_DisulfideFile_ResNum_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_aa_composition_energy_TailFunction_core_scoring_aa_composition_energy_TailFunction_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_disulfides_CentroidDisulfideEnergyComponents_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_disulfides_DisulfideMatchingEnergyComponents_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_disulfides_FullatomDisulfideEnergyComponents_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_int_int_t method) 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(pyrosetta.rosetta.utility.vector1_std_pair_std_list_std_shared_ptr_const_core_conformation_Residue_utility_vector1_std_shared_ptr_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_std_allocator_std_shared_ptr_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_pair_unsigned_long_unsigned_long_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_set_unsigned_long_std_set_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_const_core_pose_ResidueIndexDescription_std_shared_ptr_const_core_pose_ResidueIndexDescription_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_const_numeric_expression_parser_Expression_std_shared_ptr_protocols_pack_daemon_SurrogateVariableExpression_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_core_io_silent_SilentStruct_utility_file_FileName_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_calc_taskop_movers_DesignRepackMover_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_calc_taskop_movers_DesignRepackMover_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_filters_Filter_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_genetic_algorithm_Entity_std_pair_utility_vector1_double_std_allocator_double_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_hotspot_hashing_HotspotStubSet_std_pair_std_shared_ptr_protocols_hotspot_hashing_HotspotStub_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_jd3_InnerLarvalJob_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_jd3_JobSummary_std_shared_ptr_protocols_jd3_JobResult_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_string_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_string_core_kinematics_Jump_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_string_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_string_protocols_ligand_docking_Translate_info_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_string_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_string_std_shared_ptr_const_protocols_qsar_scoring_grid_GridSet_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_string_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_vector_unsigned_long_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_protocols_ligand_docking_ga_ligand_dock_Pharmacophore_t method) (pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_protocols_sic_dock_Vec3_t method) (pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_std_pair_core_chemical_AA_core_chemical_AA_t method) (pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_std_shared_ptr_const_numeric_expression_parser_Expression_t method) 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(pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_AtomPairConstraintsData_std_allocator_std_shared_ptr_protocols_frag_picker_scores_AtomPairConstraintsData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_FourAtomsConstraintData_std_allocator_std_shared_ptr_protocols_frag_picker_scores_FourAtomsConstraintData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_Entity_std_allocator_std_shared_ptr_protocols_genetic_algorithm_Entity_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_std_allocator_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_jd3_JGJobNode_std_allocator_std_shared_ptr_protocols_jd3_JGJobNode_t method) 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(pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_void__star__std_allocator_void__star__t method) reserve_buffers() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) reserve_destination_size() (pyrosetta.rosetta.utility.subset_mapping method) reserve_edge_space() (pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) reserve_threads() (pyrosetta.rosetta.basic.thread_manager.RosettaThreadManager method) reserved_tag (pyrosetta.rosetta.RDKit.RDValue 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(pyrosetta.rosetta.core.pack.rotamer_set.BumpSelector method) (pyrosetta.rosetta.core.pose.rna.VDW_Grid method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTraceFactory method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup method) (pyrosetta.rosetta.core.scoring.packstat.AreaAccumulator method) Reset() (pyrosetta.rosetta.core.scoring.sc.ContactMolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ElectrostaticComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ElectrostaticSimilarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeSimilarityCalculator method) reset() (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.cppdb.backend.statement method) (pyrosetta.rosetta.cppdb.ref_ptr_cppdb_backend_connection_t method) (pyrosetta.rosetta.cppdb.ref_ptr_cppdb_backend_loadable_driver_t method) (pyrosetta.rosetta.cppdb.ref_ptr_cppdb_backend_statement_t method) (pyrosetta.rosetta.cppdb.ref_ptr_cppdb_pool_t method) (pyrosetta.rosetta.cppdb.statement method) (pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.checkpoint.Timer static method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.denovo_design.components.EnumeratedVectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.evaluation.TimeEvaluator method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.hybridization.HybridizeFoldtreeDynamic method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy method) (pyrosetta.rosetta.protocols.match.output.LimitHitsPerRotamerFilter method) (pyrosetta.rosetta.protocols.match.output.MatchGrouper method) (pyrosetta.rosetta.protocols.match.output.SameChiBinComboGrouper method) (pyrosetta.rosetta.protocols.match.output.SameRotamerComboGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) (pyrosetta.rosetta.protocols.match.output.StateAccumulatingMatchFilter method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MixedMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) (pyrosetta.rosetta.protocols.moves.TrialCounter method) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters static method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.GridSearchIterator method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.GridSearchIteratorCA method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.GridSearchIterator_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.GridSearchIterator_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.GridSearchIterator_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.GridSearchIterator_Ts4 method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.ProteinAtrRepScreener method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.RNA_AtrRepScreener method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.SimplePoseSelection method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.SimpleRMSD_Screener method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWiseMasterPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.stepwise.screener.AlignRMSD_Screener method) (pyrosetta.rosetta.protocols.stepwise.screener.AnchorSugarScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.BaseBinMapUpdater method) (pyrosetta.rosetta.protocols.stepwise.screener.BaseCentroidScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.BulgeApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.CentroidDistanceScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.FastForwardToNextResidueAlternative method) (pyrosetta.rosetta.protocols.stepwise.screener.FastForwardToNextRigidBody method) (pyrosetta.rosetta.protocols.stepwise.screener.IntegrationTestBreaker method) (pyrosetta.rosetta.protocols.stepwise.screener.O2PrimeScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PackScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PartitionContactScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PhosphateScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PoseSelectionScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.ProteinCCD_ClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.ResidueContactScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryResidueBasedScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryStubBasedScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.SampleApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.Scorer method) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseResiduePairScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.StubApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.StubDistanceScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.SugarInstantiator method) (pyrosetta.rosetta.protocols.stepwise.screener.TagDefinition method) (pyrosetta.rosetta.protocols.stepwise.screener.VDW_BinScreener method) (pyrosetta.rosetta.protocols.stepwise.StepWiseSampleAndScreen method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.RDKit.Dict method) (pyrosetta.rosetta.RDKit.RingInfo method) reset_3d_projection() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) reset_accept_counter() (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) reset_accessed_options() (pyrosetta.rosetta.utility.tag.Tag method) reset_accounting() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) reset_all_flags() (pyrosetta.rosetta.numeric.ClusteringTreeNode method) reset_all_properies() (pyrosetta.rosetta.core.chemical.Atom method) reset_allowed_scoring() (pyrosetta.rosetta.core.scoring.MembraneTopology method) reset_alternate_states_for_uncommited_substitution() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) reset_and_get_clusters() (pyrosetta.rosetta.protocols.simple_moves.AtomHash method) reset_and_initialize_data() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) reset_arrays_danger_expert_only() (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase method) reset_base_type_cop() (pyrosetta.rosetta.core.chemical.MutableResidueType method) reset_baseline() (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) reset_baselines() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) reset_bond_distance_to_atom() (pyrosetta.rosetta.core.chemical.MutableResidueType method) reset_boundaries() (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) reset_calibration_constants() (pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator method) reset_chain_endings() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) reset_chimaera_contacts() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) reset_copying_settings() (pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.Parameter method) (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) reset_count() (pyrosetta.rosetta.protocols.contact_map.Contact method) reset_counters() (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) reset_counts() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) reset_coval() (pyrosetta.rosetta.utility.heap method) reset_cycle_index() (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.moves.CycleMover method) reset_delta_filter_baselines() (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) reset_edge_list_iterator_for_node() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) reset_energy_methods() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) reset_ensemble_trial_counters() (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) reset_eval_count() (pyrosetta.rosetta.core.optimization.func_1d method) reset_filters() (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.match.output.MatchConsolidator method) (pyrosetta.rosetta.protocols.match.output.MatchOutputter method) (pyrosetta.rosetta.protocols.match.output.MatchProcessor method) reset_from_interface() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) reset_from_ref() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor method) reset_grouper() (pyrosetta.rosetta.protocols.match.output.MatchConsolidator method) reset_hbs() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) reset_helices() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) reset_jump_rb_deltas() (pyrosetta.rosetta.core.optimization.MinimizerMap method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) reset_mainchain_torsion_potential_names() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) reset_mode() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) reset_move_data() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) reset_mover_data() (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) reset_nblist() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) reset_num_connections() (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) reset_octahedral_metal_positions() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) reset_option_input() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) reset_order() (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) reset_pose() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) reset_rb_trial_counters() (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) reset_recovery() (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecovery method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSimple method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSQLite method) reset_relaxed() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) reset_relaxed_for_neighbors() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) reset_res_moved() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) reset_residue_list() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) reset_residue_type_set_for_conf() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) reset_rpe_calculations_count() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) reset_sample_index() (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) reset_sampling_and_perturbation_settings() (pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.Parameter method) (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) reset_sampling_and_perturbing_info() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) reset_score_multiply_to_reasonable_default() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) reset_scorefxn() (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) reset_specific() (pyrosetta.rosetta.cppdb.session method) (pyrosetta.rosetta.utility.sql_database.session method) reset_square_planar_metal_positions() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) reset_square_pyramidal_metal_positions() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) reset_state() (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_streambuf_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) reset_state_energies() (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) reset_statistics() (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator method) reset_status() (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop 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.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler 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.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder 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.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover 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.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover 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.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize 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.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.forge.components.BDR 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.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) (pyrosetta.rosetta.protocols.hydrate.Hydrate method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler 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.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover 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.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM 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_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover 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.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover 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.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DsspMover method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.Mover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover 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.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot 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.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop 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.PrepackMover 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.SecretionOptimizationMover 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.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover 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.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover 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.IdealizeHelicesMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax 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.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover 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.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover 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_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover 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.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover 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.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover 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.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.star.StarAbinitio 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.SideChainCopier method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler 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.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover 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.monte_carlo.StepWiseMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) reset_structure_moved() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) reset_surf() (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) reset_surface_residue_information() (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) reset_task_factory() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) reset_tensor() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_tensor method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_tensor_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_tensor_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_tensor_Ts4 method) reset_tetrahedral_metal_positions() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) reset_timer() (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) reset_tmh_insert() (pyrosetta.rosetta.core.scoring.MembraneTopology method) reset_to_original_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) reset_trigonal_planar_metal_positions() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) reset_trigonal_pyramidal_metal_positions() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) reset_unique_id() (pyrosetta.rosetta.protocols.motifs.IRCollection method) reset_value_settings() (pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.Parameter method) (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) reset_x() (in module pyrosetta.rosetta.protocols.toolbox) ResetBaselineMover (class in pyrosetta.rosetta.protocols.monte_carlo) ResetBaselineMoverCreator (class in pyrosetta.rosetta.protocols.monte_carlo) ResetBondLength (class in pyrosetta.rosetta.core.chemical) ResetFoldTree (class in pyrosetta.rosetta.protocols.simple_moves) ResetFoldTreeCreator (class in pyrosetta.rosetta.protocols.simple_moves) ResetFullModelInfoMover (class in pyrosetta.rosetta.protocols.simple_moves) ResetFullModelInfoMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) resfile() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.forge.components.BDR method) resfile_at() (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) resfile_commands() (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) resfile_general_property() (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter method) resfile_name() (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter method) resfile_name_ (pyrosetta.rosetta.protocols.pack_daemon.StructureFileNames property) resfile_prefix() (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter method) resfile_suffix() (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter method) ResfileCommand (class in pyrosetta.rosetta.core.pack.task) ResfileCommandOperation (class in pyrosetta.rosetta.protocols.task_operations) ResfileCommandOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) ResfileContents (class in pyrosetta.rosetta.core.pack.task) ResfileReaderException (class in pyrosetta.rosetta.core.pack.task) resfiles() (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) ResFilter (class in pyrosetta.rosetta.core.pack.task.operation) ResFilterComposition (class in pyrosetta.rosetta.core.pack.task.operation) ResFilterCreator (class in pyrosetta.rosetta.core.pack.task.operation) ResFilterFactory (class in pyrosetta.rosetta.core.pack.task.operation) ResHasher (class in pyrosetta.rosetta.protocols.mean_field) ResHashMap (class in pyrosetta.rosetta.protocols.mean_field)

resi (pyrosetta.rosetta.protocols.toolbox.Node property) resi() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.numeric.geometry.hashing.Ball method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) resi1() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) resi2() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) ResId (class in pyrosetta.rosetta.protocols.moves) resid (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.PlaceableRotamer property) resID (pyrosetta.rosetta.protocols.sparta.RingData property) resid() (pyrosetta.rosetta.core.chemical.ResConnID method) (pyrosetta.rosetta.core.conformation.RotamerSetBase method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.splice.BBDofs method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) resID1 (pyrosetta.rosetta.core.io.LinkInformation property) (pyrosetta.rosetta.core.io.SSBondInformation property) resID2 (pyrosetta.rosetta.core.io.LinkInformation property) (pyrosetta.rosetta.core.io.SSBondInformation property) resid_ (pyrosetta.rosetta.numeric.geometry.hashing.Ball property) resid_2_moltenres() (pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.core.pack_basic.RotamerSetsBase method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) resid_2_moltenres_vector() (pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) resid_2_moltenresid() (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets method) resid_for_entry() (pyrosetta.rosetta.core.scoring.trie.CPDataCorrespondence method) residList (pyrosetta.rosetta.protocols.sparta.GDB property) (pyrosetta.rosetta.protocols.sparta.PDB property) (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) residListOne (pyrosetta.rosetta.protocols.sparta.PDB property) resids() (in module pyrosetta.rosetta.core.select) RESIDUAL_DIPOLAR_COUPLING_DATA (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) RESIDUAL_DIPOLAR_COUPLING_DATA_ROHL (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) RESIDUAL_DIPOLAR_COUPLING_SEGMENTS_DATA (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) residual_squared_of_points_to_plane() (in module pyrosetta.rosetta.numeric.geometry) ResidualDipolarCoupling (class in pyrosetta.rosetta.core.scoring) ResidualDipolarCoupling_Rohl (class in pyrosetta.rosetta.core.scoring) ResidualDipolarCouplingEnergy (class in pyrosetta.rosetta.core.energy_methods) ResidualDipolarCouplingEnergy_Rohl (class in pyrosetta.rosetta.core.energy_methods) ResidualDipolarCouplingEnergy_RohlCreator (class in pyrosetta.rosetta.core.energy_methods) ResidualDipolarCouplingEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) ResidualDipolarCouplingEnergyRigidSegments (class in pyrosetta.rosetta.protocols.scoring.methods) ResidualDipolarCouplingEnergyRigidSegmentsCreator (class in pyrosetta.rosetta.protocols.scoring.methods) ResidualDipolarCouplingRigidSegments (class in pyrosetta.rosetta.protocols.scoring) Residue (class in pyrosetta.rosetta.core.conformation) (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover) RESIDUE (pyrosetta.rosetta.core.conformation.signals.IdentityEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag attribute) residue() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.conformation.UltraLightResidue method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.func.ConformationXYZ method) (pyrosetta.rosetta.core.scoring.func.FourPointsFunc method) (pyrosetta.rosetta.core.scoring.func.ResiduePairXYZ method) (pyrosetta.rosetta.core.scoring.func.ResidueXYZ method) (pyrosetta.rosetta.core.scoring.func.XYZ_Func method) (pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint_AA method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStub method) (pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint method) (pyrosetta.rosetta.protocols.simple_filters.ResidueBurialFilter method) residue1 (pyrosetta.rosetta.core.scoring.motif.MotifHit property) residue2 (pyrosetta.rosetta.core.scoring.motif.MotifHit property) residue_action() (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AROMATIC method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.CHARGED method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PROPERTY method) (pyrosetta.rosetta.core.pack.task.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) RESIDUE_ALTERNATIVE (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) RESIDUE_ALTERNATIVE_COMB (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) residue_alternative_set() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) residue_alternatives_rotamer() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) RESIDUE_APPEND (pyrosetta.rosetta.core.conformation.signals.LengthEvent attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag attribute) RESIDUE_APPLIER (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) residue_atom (pyrosetta.rosetta.protocols.sewing.data_storage.LigandContact property) residue_atom_pair_energy() (pyrosetta.rosetta.core.scoring.elec.CountPairRepresentative method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairAll method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover3 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover34 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover3full method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover4 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairGeneric method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairNone method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) residue_atom_pair_energy_backbone_backbone() (pyrosetta.rosetta.core.scoring.elec.CountPairRepresentative method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairAll method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover3 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover34 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover3full method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover4 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairGeneric method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairNone method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) residue_atom_pair_energy_sidechain_backbone() (pyrosetta.rosetta.core.scoring.elec.CountPairRepresentative method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairAll method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover3 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover34 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover3full method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover4 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairGeneric method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairNone method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) residue_atom_pair_energy_sidechain_sidechain() (pyrosetta.rosetta.core.scoring.elec.CountPairRepresentative method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairAll method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover3 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover34 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover3full method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover4 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairGeneric method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairNone method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) residue_atom_pair_energy_sidechain_whole() (pyrosetta.rosetta.core.scoring.elec.CountPairRepresentative method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairAll method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover3 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover34 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover3full method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover4 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairGeneric method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairNone method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) residue_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) residue_atomtree_collection() (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection method) residue_atomtree_collection_op() (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection method) residue_base2_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) residue_base_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) residue_base_name() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) residue_begin (pyrosetta.rosetta.protocols.features.SecondaryStructureSegment property) residue_center_of_mass() (in module pyrosetta.rosetta.core.conformation.symmetry) (in module pyrosetta.rosetta.core.pose) RESIDUE_CHAIN_VECTOR_OPTION (pyrosetta.rosetta.utility.options.OptionTypes attribute) RESIDUE_COLOR (pyrosetta.rosetta.protocols.viewer.graphics_states_param.ColorMode attribute) residue_conformations_redundant() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) residue_connect_atom() (pyrosetta.rosetta.core.chemical.MutableResidueType method) residue_connect_atom_index() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) residue_connection() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) residue_connection_conn_id() (pyrosetta.rosetta.core.conformation.Residue method) residue_connection_id_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) residue_connection_is_polymeric() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) residue_connection_partner() (pyrosetta.rosetta.core.conformation.Residue method) residue_connections_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) RESIDUE_CONTACT (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) residue_cop() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) RESIDUE_CPK_COLOR (pyrosetta.rosetta.protocols.viewer.graphics_states_param.ColorMode attribute) residue_data() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) residue_decomposition_calculator() (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) RESIDUE_DELETE (pyrosetta.rosetta.core.conformation.signals.LengthEvent attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag attribute) residue_derivatives() (pyrosetta.rosetta.core.scoring.GenericBondedPotential method) residue_diff() (pyrosetta.rosetta.protocols.splice.SpliceManager method) residue_end (pyrosetta.rosetta.protocols.features.SecondaryStructureSegment property) residue_energy() (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.GenericBondedPotential method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) residue_energy_ext() (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) residue_entries_to_pose() (in module pyrosetta.rosetta.protocols.indexed_structure_store) residue_env_score() (pyrosetta.rosetta.core.scoring.dna.DNA_EnvPairPotential method) residue_fast_pair_energy_attached_H() (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) residue_forms_disulfide() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) residue_fraction_buried() (pyrosetta.rosetta.protocols.simple_filters.ResidueBurialFilter method) residue_gws_string() (in module pyrosetta.rosetta.core.io.carbohydrates) residue_hbonds() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) residue_id (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueEntry property) residue_id() (pyrosetta.rosetta.core.conformation.AtomGraphVertexData method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) residue_in_chains() (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) residue_index() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) residue_indices() (pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues method) Residue_info (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna) residue_info() (pyrosetta.rosetta.core.scoring.facts.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.facts.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) residue_info_ (pyrosetta.rosetta.core.scoring.facts.FACTSPoseInfo property) residue_is_floppy() (in module pyrosetta.rosetta.protocols.sic_dock) residue_is_in_fold_tree() (pyrosetta.rosetta.core.kinematics.FoldTree method) residue_is_surface() (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) residue_is_vital() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) residue_iterated_on() (pyrosetta.rosetta.core.scoring.constraints.CstResNeighbConstIterator method) (pyrosetta.rosetta.core.scoring.constraints.CstResNeighbIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.ResidueNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.ResidueNeighborIterator method) residue_lDDT() (pyrosetta.rosetta.core.scoring.lDDT_Calculator method) RESIDUE_LIST (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) residue_list() (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) residue_name() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) residue_near_water() (in module pyrosetta.rosetta.core.scoring.hbonds) (in module pyrosetta.rosetta.protocols.hydrate) residue_neighbors() (pyrosetta.rosetta.protocols.simple_filters.NonSequentialNeighborsFilter method) residue_neighbors_updated() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) residue_num() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) residue_number (pyrosetta.rosetta.protocols.sewing.data_storage.LigandContact property) residue_number_string() (in module pyrosetta.rosetta.utility.tag) residue_numbers_ (pyrosetta.rosetta.protocols.pdbinfo_manipulations.SequenceSpecification property) residue_numbers_into_pose() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) residue_onebody_energies_array() (in module pyrosetta.bindings.energies) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) residue_packed() (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) residue_packer_states() (in module pyrosetta.rosetta.protocols.rosetta_scripts) residue_pair() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing method) residue_pair_constraint_exists() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) residue_pair_constraints_exists() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) residue_pair_derivatives() (pyrosetta.rosetta.core.scoring.GenericBondedPotential method) residue_pair_energies_array() (in module pyrosetta.bindings.energies) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) residue_pair_energy() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.Constraints method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.GenericBondedPotential method) (pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.rna.RNA_TorsionPotential method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) residue_pair_energy_aro_aro() (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) residue_pair_energy_ext() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) residue_pair_score() (pyrosetta.rosetta.core.scoring.dna.DNA_EnvPairPotential method) residue_pairs() (in module pyrosetta.bindings.pose) (pyrosetta.rosetta.core.pose.Pose method) residue_point_graph_from_conformation() (in module pyrosetta.rosetta.core.conformation) residue_position() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) RESIDUE_PREPEND (pyrosetta.rosetta.core.conformation.signals.LengthEvent attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag attribute) residue_range_gws_string() (in module pyrosetta.rosetta.core.io.carbohydrates) residue_range_is_protein() (pyrosetta.rosetta.protocols.features.BetaTurnDetection method) residue_rmsd_nosuper() (in module pyrosetta.rosetta.core.scoring) residue_rmsd_super() (in module pyrosetta.rosetta.core.scoring) residue_rotamer_recovery() (in module pyrosetta.rosetta.core.pack) residue_sc_rmsd_no_super() (in module pyrosetta.rosetta.core.scoring) (in module pyrosetta.rosetta.protocols.hotspot_hashing) residue_score() (pyrosetta.rosetta.core.scoring.electron_density_atomwise.ElectronDensityAtomwise method) residue_selector() (pyrosetta.rosetta.core.pack.task.operation.ReadResfile method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ScorePoseSegmentFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilter method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB method) residue_selector1() (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric method) residue_selector2() (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric method) residue_selector_single_from_line() (in module pyrosetta.rosetta.core.chemical) residue_selector_xml_schema_group_name() (pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorFactory static method) residue_selectors_to_indices() (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover static method) residue_subset() (in module pyrosetta.rosetta.protocols.pose_metric_calculators) residue_subset_fragment_store (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore property) residue_task() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) residue_total_energies() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) residue_total_energies_array() (in module pyrosetta.bindings.energies) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) residue_total_energy() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) residue_type() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) residue_type_ (pyrosetta.rosetta.protocols.legacy_sewing.SewResidue property) residue_type_all_patches_name() (in module pyrosetta.rosetta.core.chemical) residue_type_base_name() (in module pyrosetta.rosetta.core.chemical) residue_type_base_names() (pyrosetta.rosetta.core.io.StructFileRep method) residue_type_param_set() (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) residue_type_ptr() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) residue_type_set() (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) residue_type_set_for_conf() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) residue_type_set_for_pose() (pyrosetta.rosetta.core.pose.Pose method) residue_type_set_mode() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) residue_types_from_saccharide_sequence() (in module pyrosetta.rosetta.core.pose) residue_types_from_sequence() (in module pyrosetta.rosetta.core.pose) residue_types_identical() (in module pyrosetta.rosetta.core.chemical) residue_typeset_mode() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) residue_z_position() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) ResidueAlternativeSet (class in pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs) ResidueAlternativeStepWiseSampler (class in pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs) ResidueAlternativeStepWiseSamplerComb (class in pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs) ResidueArrayAnnealableEnergy (class in pyrosetta.rosetta.core.scoring.annealing) ResidueArrayAnnealingEvaluator (class in pyrosetta.rosetta.core.pack.interaction_graph) ResidueAtomOverlaps (class in pyrosetta.rosetta.core.scoring.methods) ResidueAtomTreeCollection (class in pyrosetta.rosetta.core.pack.scmin) ResidueAtomTreeCollectionMomento (class in pyrosetta.rosetta.core.pack.scmin) ResidueBackboneEntry (class in pyrosetta.rosetta.protocols.indexed_structure_store) ResidueBBDofs (class in pyrosetta.rosetta.protocols.splice) ResidueBurialFeatures (class in pyrosetta.rosetta.protocols.features) ResidueBurialFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueBurialFilter (class in pyrosetta.rosetta.protocols.simple_filters) ResidueBurialFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) ResidueCartBondedParameters (class in pyrosetta.rosetta.core.energy_methods) ResidueChainVectorOption (class in pyrosetta.rosetta.utility.options) ResidueChainVectorOptionKey (class in pyrosetta.rosetta.utility.options) ResidueChiralityFilter (class in pyrosetta.rosetta.protocols.simple_filters) ResidueChiralityFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) ResidueConformationFeatures (class in pyrosetta.rosetta.protocols.features) ResidueConformationFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueConformerFilter (class in pyrosetta.rosetta.protocols.enzdes) ResidueConformerFilterCreator (class in pyrosetta.rosetta.protocols.enzdes) ResidueConnection (class in pyrosetta.rosetta.core.chemical) ResidueConstraints (class in pyrosetta.rosetta.core.scoring.constraints) ResidueContactScreener (class in pyrosetta.rosetta.protocols.stepwise.screener) ResidueCoordinateChangeList (class in pyrosetta.rosetta.core.kinematics) ResidueCountFilter (class in pyrosetta.rosetta.protocols.simple_filters) ResidueCountFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) ResidueCouplingConstraint (class in pyrosetta.rosetta.core.scoring.constraints) ResidueDatabaseIO (class in pyrosetta.rosetta.core.chemical) ResidueDataCacheIndex (class in pyrosetta.rosetta.core.conformation.residue_datacache) ResidueDecompositionByChainCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) ResidueDecompositionCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) ResidueDepthCalculator (class in pyrosetta.rosetta.protocols.simple_filters) ResidueDepthData (class in pyrosetta.rosetta.protocols.simple_filters) ResidueDepthFilter (class in pyrosetta.rosetta.protocols.simple_filters) ResidueDepthFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) ResidueDepthFrag (class in pyrosetta.rosetta.protocols.simple_filters) ResidueDihedrals (class in pyrosetta.rosetta.protocols.denovo_design.components) ResidueDistanceFilter (class in pyrosetta.rosetta.protocols.simple_filters) ResidueDistanceFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) ResidueDOFReporter (class in pyrosetta.rosetta.core.pack.dunbrack) ResidueElement (class in pyrosetta.rosetta.protocols.environment.claims) ResidueEntry (class in pyrosetta.rosetta.protocols.indexed_structure_store) ResidueExclParams (class in pyrosetta.rosetta.core.scoring) ResidueFactory (class in pyrosetta.rosetta.core.conformation) ResidueFeature (class in pyrosetta.rosetta.protocols.comparative_modeling.features) ResidueFeatureFactory (class in pyrosetta.rosetta.protocols.comparative_modeling.features) ResidueFeatures (class in pyrosetta.rosetta.protocols.features) ResidueFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueGridScoresFeatures (class in pyrosetta.rosetta.protocols.features) ResidueGridScoresFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueGroupIGEdgeUpweighter (class in pyrosetta.rosetta.protocols.toolbox) ResidueHasProperty (class in pyrosetta.rosetta.core.pack.task.operation) ResidueHasPropertyCreator (class in pyrosetta.rosetta.core.pack.task.operation) ResidueIdentifier (class in pyrosetta.rosetta.protocols.loops) ResidueIEFilter (class in pyrosetta.rosetta.protocols.simple_filters) ResidueIEFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) ResidueIndexDescription (class in pyrosetta.rosetta.core.pose) ResidueIndexDescriptionChainEnd (class in pyrosetta.rosetta.core.pose) ResidueIndexDescriptionLastResidue (class in pyrosetta.rosetta.core.pose) ResidueIndexDescriptionPDB (class in pyrosetta.rosetta.core.pose) ResidueIndexDescriptionPoseNum (class in pyrosetta.rosetta.core.pose) ResidueIndexDescriptionRefPose (class in pyrosetta.rosetta.core.pose) ResidueIndexIs (class in pyrosetta.rosetta.core.pack.task.operation) ResidueIndexIsCreator (class in pyrosetta.rosetta.core.pack.task.operation) ResidueIndexIsnt (class in pyrosetta.rosetta.core.pack.task.operation) ResidueIndexIsntCreator (class in pyrosetta.rosetta.core.pack.task.operation) ResidueIndexSelector (class in pyrosetta.rosetta.core.select.residue_selector) ResidueIndexSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) ResidueInformation (class in pyrosetta.rosetta.core.io) ResidueInMembraneSelector (class in pyrosetta.rosetta.core.select.residue_selector) ResidueInMembraneSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) ResidueInSequenceMotifSelector (class in pyrosetta.rosetta.core.select.residue_selector) ResidueInSequenceMotifSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) ResidueKinemageWriter (class in pyrosetta.rosetta.protocols.match.output) ResidueKinWriter (class in pyrosetta.rosetta.core.conformation) ResidueLabelAccessor (class in pyrosetta.bindings.pose) ResidueLabelsToPymolSelectionMover (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) ResidueLabelsToPymolSelectionMoverCreator (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) ResidueLacksProperty (class in pyrosetta.rosetta.core.pack.task.operation) ResidueLacksPropertyCreator (class in pyrosetta.rosetta.core.pack.task.operation) ResidueLevelTask (class in pyrosetta.rosetta.core.pack.task) ResidueLevelTask_ (class in pyrosetta.rosetta.core.pack.task) ResidueLipophilicityFilter (class in pyrosetta.rosetta.protocols.simple_filters) ResidueLipophilicityFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) ResidueListStepWiseSampler (class in pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs) ResidueMask (class in pyrosetta.rosetta.protocols.constel) ResidueMatcher (class in pyrosetta.rosetta.core.conformation) ResidueName3Is (class in pyrosetta.rosetta.core.pack.task.operation) ResidueName3IsCreator (class in pyrosetta.rosetta.core.pack.task.operation) ResidueName3Isnt (class in pyrosetta.rosetta.core.pack.task.operation) ResidueName3IsntCreator (class in pyrosetta.rosetta.core.pack.task.operation) ResidueNameSelector (class in pyrosetta.rosetta.core.select.residue_selector) ResidueNameSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) ResidueNblistData (class in pyrosetta.rosetta.core.scoring) ResidueNeighborConstIterator (class in pyrosetta.rosetta.core.scoring) ResidueNeighborIterator (class in pyrosetta.rosetta.core.scoring) ResidueNetwork (class in pyrosetta.rosetta.protocols.toolbox) ResidueOrientEntry (class in pyrosetta.rosetta.protocols.indexed_structure_store) ResiduePair (class in pyrosetta.rosetta.protocols.fldsgn) ResiduePairEvalType (class in pyrosetta.rosetta.core.pack.interaction_graph) ResiduePairJump (class in pyrosetta.rosetta.protocols.jumping) ResiduePairJumpSetup (class in pyrosetta.rosetta.protocols.jumping) ResiduePairJumpSetup.JumpDef (class in pyrosetta.rosetta.protocols.jumping) ResiduePairJumpSingle (class in pyrosetta.rosetta.protocols.jumping) ResiduePairNeighborList (class in pyrosetta.rosetta.core.scoring) ResiduePairXYZ (class in pyrosetta.rosetta.core.scoring.func) ResiduePDBIndexIs (class in pyrosetta.rosetta.core.pack.task.operation) ResiduePDBIndexIs.ChainPos (class in pyrosetta.rosetta.core.pack.task.operation) ResiduePDBIndexIsCreator (class in pyrosetta.rosetta.core.pack.task.operation) ResiduePDBIndexIsnt (class in pyrosetta.rosetta.core.pack.task.operation) ResiduePDBIndexIsnt.ChainPos (class in pyrosetta.rosetta.core.pack.task.operation) ResiduePDBIndexIsntCreator (class in pyrosetta.rosetta.core.pack.task.operation) ResiduePDBInfoHasLabel (class in pyrosetta.rosetta.core.pack.task.operation) ResiduePDBInfoHasLabelCreator (class in pyrosetta.rosetta.core.pack.task.operation) ResiduePDBInfoHasLabelSelector (class in pyrosetta.rosetta.core.select.residue_selector) ResiduePDBInfoHasLabelSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) ResiduePDBInfoLacksLabel (class in pyrosetta.rosetta.core.pack.task.operation) ResiduePDBInfoLacksLabelCreator (class in pyrosetta.rosetta.core.pack.task.operation) ResidueProbDesignOperation (class in pyrosetta.rosetta.protocols.task_operations) ResidueProbDesignOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) ResidueProperties (class in pyrosetta.rosetta.core.chemical) ResidueProperty (class in pyrosetta.rosetta.core.chemical) ResiduePropertySelector (class in pyrosetta.rosetta.core.select.residue_selector) ResiduePropertySelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) ResidueRange (class in pyrosetta.rosetta.core.select.residue_selector) ResidueRanges (class in pyrosetta.rosetta.core.select.residue_selector) ResidueReplacementRebuildMover (class in pyrosetta.rosetta.protocols.ncbb) ResidueReplacementRebuildMoverCreator (class in pyrosetta.rosetta.protocols.ncbb) residues (pyrosetta.rosetta.core.pose.Pose property) (pyrosetta.rosetta.protocols.forge.remodel.Segment property) (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) (pyrosetta.rosetta.protocols.ligand_docking.Ligand_info property) residues() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomToAxisConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraint method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedDihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueCouplingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.RTConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERChiSqMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERData method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDecayData method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceBounds method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceDistribution method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJaccardMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJSMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERMiscMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEEROverlapMethod method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.core.scoring.packing.HolesParamsRes method) (pyrosetta.rosetta.core.scoring.rna.RNA_Motif method) (pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) residues1() (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) residues2() (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) residues_ (pyrosetta.rosetta.protocols.legacy_sewing.SewSegment property) (pyrosetta.rosetta.protocols.loop_grower.SheetPositions property) residues_adjacent_for_subunit_pair() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) residues_are_different() (pyrosetta.rosetta.protocols.dna.PDBOutput method) residues_are_interface_pairs() (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) residues_compatible() (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) residues_contact_screen (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) residues_downstream_of_jump() (in module pyrosetta.rosetta.core.kinematics) residues_for_atom_name_remapping() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) residues_interact() (in module pyrosetta.rosetta.core.scoring.methods) residues_per_repeat() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) residues_per_turn() (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix method) residues_to_align_on_pose() (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) residues_to_align_on_template() (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) residues_to_ignore_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) residues_to_mutate() (pyrosetta.rosetta.protocols.ddg.ddGMover method) residues_upstream_of_jump() (in module pyrosetta.rosetta.core.kinematics) ResidueScoresFeatures (class in pyrosetta.rosetta.protocols.features) ResidueScoresFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueSecondaryStructureFeatures (class in pyrosetta.rosetta.protocols.features) ResidueSecondaryStructureFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueSelectionDistanceFilter (class in pyrosetta.rosetta.protocols.simple_filters) ResidueSelectionDistanceFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) ResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) (pyrosetta.rosetta.basic.citation_manager.CitedModuleType attribute) ResidueSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) ResidueSelectorFactory (class in pyrosetta.rosetta.core.select.residue_selector) ResidueSelectorLoader (class in pyrosetta.rosetta.protocols.parser) ResidueSelectorLoaderCreator (class in pyrosetta.rosetta.protocols.parser) ResidueSetChainEnergyFilter (class in pyrosetta.rosetta.protocols.simple_filters) ResidueSetChainEnergyFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) ResidueSidechainEntry (class in pyrosetta.rosetta.protocols.indexed_structure_store) ResiduesInInterfaceFilter (class in pyrosetta.rosetta.protocols.simple_filters) ResiduesInInterfaceFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) ResidueSpanSelector (class in pyrosetta.rosetta.core.select.residue_selector) ResidueSpanSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) residueStubCentroid() (pyrosetta.rosetta.protocols.hotspot_hashing.StubGenerator static method) residueStubCentroidFrame() (pyrosetta.rosetta.protocols.hotspot_hashing.StubGenerator static method) residueStubOrientFrame() (pyrosetta.rosetta.protocols.hotspot_hashing.StubGenerator static method) ResidueSummaryMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) ResidueSummaryMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.metrics) ResidueTorsionRestraints (class in pyrosetta.rosetta.protocols.ligand_docking) ResidueTotalScoresFeatures (class in pyrosetta.rosetta.protocols.features) ResidueTotalScoresFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueType (class in pyrosetta.rosetta.core.chemical) residueType() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) ResidueTypeBase (class in pyrosetta.rosetta.core.chemical) ResidueTypeConstraint (class in pyrosetta.rosetta.core.scoring.constraints) ResidueTypeConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) ResidueTypeConstraintGeneratorCreator (class in pyrosetta.rosetta.protocols.constraint_generator) ResidueTypeConstraintMover (class in pyrosetta.rosetta.protocols.constraint_movers) ResidueTypeConstraintMoverCreator (class in pyrosetta.rosetta.protocols.constraint_movers) ResidueTypeFilter (class in pyrosetta.rosetta.core.pack.task.operation) ResidueTypeFilterCreator (class in pyrosetta.rosetta.core.pack.task.operation) ResidueTypeFinder (class in pyrosetta.rosetta.core.chemical) ResidueTypeKinWriter (class in pyrosetta.rosetta.core.chemical) ResidueTypeLinkingConstraint (class in pyrosetta.rosetta.core.scoring.constraints) ResidueTypeSelector (class in pyrosetta.rosetta.core.chemical) ResidueTypeSelectorSingle (class in pyrosetta.rosetta.core.chemical) ResidueTypeSet (class in pyrosetta.rosetta.core.chemical) ResidueTypeSetCache (class in pyrosetta.rosetta.core.chemical) ResidueTypesFeatures (class in pyrosetta.rosetta.protocols.features) ResidueTypesFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ResidueVector (class in pyrosetta.rosetta.core.select.residue_selector) ResidueVicinityCstGeneratorCreator (class in pyrosetta.rosetta.protocols.forge.remodel) ResidueVicinityInfo (class in pyrosetta.rosetta.protocols.forge.remodel) ResidueVicinityRCG (class in pyrosetta.rosetta.protocols.forge.remodel) ResidueXYZ (class in pyrosetta.rosetta.core.scoring.func) residx (pyrosetta.rosetta.protocols.simple_moves.AtomHashNode property) resindex() (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPDB method) ResInteractions (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) resize() (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.DataCache_basic_datacache_CacheableData_t method) (pyrosetta.rosetta.basic.datacache.DataCache_CacheableData method) (pyrosetta.rosetta.basic.datacache.DataCache_core_pose_datacache_CacheableObserver_t method) (pyrosetta.rosetta.core.fragment.FrameList method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.id.AtomID_Map_AtomID method) (pyrosetta.rosetta.core.id.AtomID_Map_bool method) (pyrosetta.rosetta.core.id.AtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_MP_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_Real method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_NamedAtomID method) (pyrosetta.rosetta.core.id.SequenceMapping method) (pyrosetta.rosetta.core.io.raw_data.DecoyStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerCouplings method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerLinks method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) (pyrosetta.rosetta.core.scoring.Helices method) (pyrosetta.rosetta.core.scoring.motif.MotifHits method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotifs method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.Strands method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRanges method) (pyrosetta.rosetta.core.select.residue_selector.ResidueVector method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fft_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) (pyrosetta.rosetta.numeric.random.WeightedSampler method) (pyrosetta.rosetta.numeric.Xforms method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultVector method) (pyrosetta.rosetta.protocols.denovo_design.components.BuildPhases method) (pyrosetta.rosetta.protocols.denovo_design.components.EnumeratedVectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.denovo_design.components.NamedSolution method) (pyrosetta.rosetta.protocols.denovo_design.components.VectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairings method) (pyrosetta.rosetta.protocols.frag_picker.LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareByScoreCombination_t method) (pyrosetta.rosetta.protocols.frag_picker.LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareTotalScore_t method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore method) (pyrosetta.rosetta.protocols.jumping.JumpSample method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.loops.LoopsFileData method) (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) (pyrosetta.rosetta.protocols.sewing.hashing.SegmentVector method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.RDKit.Conformer method) (pyrosetta.rosetta.std.list_const_protocols_match_Hit__star__t method) (pyrosetta.rosetta.std.list_core_id_AtomID_t method) (pyrosetta.rosetta.std.list_core_io_rcsb_ExperimentalTechnique_t method) (pyrosetta.rosetta.std.list_core_scoring_custom_pair_distance_atoms_and_func_struct_t method) (pyrosetta.rosetta.std.list_core_scoring_power_diagram_PDvertex__star__t method) (pyrosetta.rosetta.std.list_double_t method) (pyrosetta.rosetta.std.list_int_t method) (pyrosetta.rosetta.std.list_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.list_protocols_match_Hit_t method) (pyrosetta.rosetta.std.list_protocols_multistage_rosetta_scripts_mover_or_filter_t method) (pyrosetta.rosetta.std.list_protocols_pockets_spherical_coor_triplet_t method) (pyrosetta.rosetta.std.list_RDKit_Atom__star__t method) (pyrosetta.rosetta.std.list_RDKit_Bond__star__t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BasePair_t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BaseStack_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_double_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.list_std_set_std_string_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_operation_ResLvlTaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_chunk_library_inputters_ChunkLibraryInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_full_model_inputters_FullModelInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_inputters_PoseInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_PoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_SecondaryPoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_XMLSchemaParticle_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_interaction_graph_AnnealableGraphBase_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_rotamer_set_RotamerOperation_t method) 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(pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerVectorOptionKey_utility_options_IntegerVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_OptionKey_utility_options_OptionTypes_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathOptionKey_utility_options_PathOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathVectorOptionKey_utility_options_PathVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealOptionKey_utility_options_RealOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealVectorOptionKey_utility_options_RealVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_ResidueChainVectorOptionKey_utility_options_ResidueChainVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringOptionKey_utility_options_StringOption_t method) 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(pyrosetta.rosetta.utility.vector1_core_chemical_ResConnID method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResidueConnection method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty method) (pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingConformer method) (pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingSaturationType method) (pyrosetta.rosetta.utility.vector1_core_chemical_rna_PuckerState method) (pyrosetta.rosetta.utility.vector1_core_chemical_VariantType method) (pyrosetta.rosetta.utility.vector1_core_conformation_Atom method) (pyrosetta.rosetta.utility.vector1_core_conformation_PseudoBond method) (pyrosetta.rosetta.utility.vector1_core_conformation_signals_LengthEvent method) (pyrosetta.rosetta.utility.vector1_core_fragment_FragData method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_scores_VallFragmentScore method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection method) (pyrosetta.rosetta.utility.vector1_core_fragment_rna_SYN_ANTI_RESTRICTION method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_bool_t method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.utility.vector1_core_id_DOF_ID method) (pyrosetta.rosetta.utility.vector1_core_id_NamedAtomID method) (pyrosetta.rosetta.utility.vector1_core_id_TorsionID method) (pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range method) (pyrosetta.rosetta.utility.vector1_core_io_AtomInformation method) (pyrosetta.rosetta.utility.vector1_core_io_HELIXInformation method) (pyrosetta.rosetta.utility.vector1_core_io_LinkInformation method) (pyrosetta.rosetta.utility.vector1_core_io_ResidueInformation method) (pyrosetta.rosetta.utility.vector1_core_io_SHEETInformation method) (pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy method) (pyrosetta.rosetta.utility.vector1_core_io_SSBondInformation method) (pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Edge method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Jump method) (pyrosetta.rosetta.utility.vector1_core_kinematics_RT method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Stub method) (pyrosetta.rosetta.utility.vector1_core_optimization_DerivCheckDataPoint method) (pyrosetta.rosetta.utility.vector1_core_optimization_DOF_DataPoint method) (pyrosetta.rosetta.utility.vector1_core_pack_annealer_PointDwell method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbond method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_sap_BlockParam method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_DotSphere method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_RotamerDots method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_SparseMatrixIndex method) (pyrosetta.rosetta.utility.vector1_core_pack_rotamer_set_ContinuousRotamerSet method) (pyrosetta.rosetta.utility.vector1_core_pack_scmin_ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.utility.vector1_core_pack_task_ResidueLevelTask_ method) (pyrosetta.rosetta.utility.vector1_core_pose_PDBInfo_AtomRecord method) (pyrosetta.rosetta.utility.vector1_core_pose_PDBInfo_ResidueRecord method) (pyrosetta.rosetta.utility.vector1_core_pose_Pose method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_Atom_Bin method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_BaseStack method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_SuiteInfo method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_VDW_RepScreenInfo method) (pyrosetta.rosetta.utility.vector1_core_pose_UnrecognizedAtomRecord method) (pyrosetta.rosetta.utility.vector1_core_scoring_bin_transitions_BT_PROPERTIES method) (pyrosetta.rosetta.utility.vector1_core_scoring_CSA method) (pyrosetta.rosetta.utility.vector1_core_scoring_DC method) (pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair method) (pyrosetta.rosetta.utility.vector1_core_scoring_disulfides_DisulfideDerivativeAtom method) (pyrosetta.rosetta.utility.vector1_core_scoring_dssp_Pairing method) (pyrosetta.rosetta.utility.vector1_core_scoring_dssp_StrandPairing method) (pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector method) (pyrosetta.rosetta.utility.vector1_core_scoring_epr_deer_EPRSpinLabel method) (pyrosetta.rosetta.utility.vector1_core_scoring_etable_EtableParamsOnePair method) (pyrosetta.rosetta.utility.vector1_core_scoring_etable_etrie_GenericResidueConnectionData method) (pyrosetta.rosetta.utility.vector1_core_scoring_fiber_diffraction_OneGaussianScattering method) (pyrosetta.rosetta.utility.vector1_core_scoring_GenTorsionParams method) (pyrosetta.rosetta.utility.vector1_core_scoring_Hairpin method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_HBondNode method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_HBEvalTuple method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_HBondWeightType method) (pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_Loop method) (pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_LoopCycle method) (pyrosetta.rosetta.utility.vector1_core_scoring_mhc_epitope_energy_AlleleMatrix method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_MotifHit method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_ResPairMotif method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_Xfres method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_pcs_PCSSingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_pre_PRESingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_rdc_RDCSingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBallCluster method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_LR_AtomData method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_LR_MP_AtomData method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_SimplePDB_Atom method) (pyrosetta.rosetta.utility.vector1_core_scoring_RDC method) (pyrosetta.rosetta.utility.vector1_core_scoring_RDC_Rohl method) (pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType method) (pyrosetta.rosetta.utility.vector1_core_scoring_SmoothScoreTermCoeffs method) (pyrosetta.rosetta.utility.vector1_core_scoring_SpringParams method) (pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange method) (pyrosetta.rosetta.utility.vector1_core_sequence_Line method) (pyrosetta.rosetta.utility.vector1_core_sequence_SequenceAlignment method) (pyrosetta.rosetta.utility.vector1_double method) (pyrosetta.rosetta.utility.vector1_float method) (pyrosetta.rosetta.utility.vector1_int method) (pyrosetta.rosetta.utility.vector1_long method) (pyrosetta.rosetta.utility.vector1_numeric_CubicPolynomial method) (pyrosetta.rosetta.utility.vector1_numeric_geometry_hashing_Ball method) (pyrosetta.rosetta.utility.vector1_numeric_histograms_TwoDHistogram_unsigned_long_long_t method) (pyrosetta.rosetta.utility.vector1_numeric_HomogeneousTransform_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_BicubicSpline method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_CubicSpline method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_interp_range method) (pyrosetta.rosetta.utility.vector1_numeric_MultiDimensionalHistogram method) (pyrosetta.rosetta.utility.vector1_numeric_random_WeightedSampler method) (pyrosetta.rosetta.utility.vector1_numeric_urs_Quat method) (pyrosetta.rosetta.utility.vector1_numeric_xyzMatrix_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzTransform_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzVector_float_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray1D_double_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray2D_double_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_AlternativePairings method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_ClassicAbinitio_StageID method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_PairingStatEntry method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_StageID method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_AntibodyNumberingSchemeEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRDefinitionEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRNameEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_clusters_CDRClusterEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_clusters_ClusterData method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_design_PDBNumbering method) (pyrosetta.rosetta.utility.vector1_protocols_canonical_sampling_DbTrajectoryRecorder_Frame method) (pyrosetta.rosetta.utility.vector1_protocols_canonical_sampling_TorsionSpec method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_CartesianAtom method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_Angle method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_Bond method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_HarmonicDihedral method) (pyrosetta.rosetta.utility.vector1_protocols_contact_map_Contact method) (pyrosetta.rosetta.utility.vector1_protocols_cyclic_peptide_PSM_StubMode method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_BondInfo method) (pyrosetta.rosetta.utility.vector1_protocols_fold_from_loops_utils_NubSegment method) (pyrosetta.rosetta.utility.vector1_protocols_forge_build_Interval method) (pyrosetta.rosetta.utility.vector1_protocols_helical_bundle_BPC_Parameters method) (pyrosetta.rosetta.utility.vector1_protocols_hotspot_hashing_VectorPair method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_chunk_library_ChunkLibraryPreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_dag_node_managers_ResultElements method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_full_model_FullModelPreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_standard_PreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_DisulfPairing method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewAtom method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewResidue method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_AtomProperties method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_GADockStageParams method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_Pharmacophore method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_ReweightableRepEnergy method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionDistrParams method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionType method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ligand_options_InterfaceInfo method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ProtLigPair_info method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolution method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolutionStore method) (pyrosetta.rosetta.utility.vector1_protocols_loops_Loop method) (pyrosetta.rosetta.utility.vector1_protocols_loops_LoopFromFileData method) (pyrosetta.rosetta.utility.vector1_protocols_loops_Loops method) (pyrosetta.rosetta.utility.vector1_protocols_loops_SerializedLoop method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_CentroidRotNum method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_TorsionRange method) (pyrosetta.rosetta.utility.vector1_protocols_match_Hit method) (pyrosetta.rosetta.utility.vector1_protocols_match_match_dspos1 method) (pyrosetta.rosetta.utility.vector1_protocols_match_ProbeRadius method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_BuildSet method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_hit method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_SampleStrategyData method) (pyrosetta.rosetta.utility.vector1_protocols_md_Constraint method) (pyrosetta.rosetta.utility.vector1_protocols_md_MDscheduleData method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_AAMatrix method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_RotMatrix method) (pyrosetta.rosetta.utility.vector1_protocols_membrane_SpanInfo method) (pyrosetta.rosetta.utility.vector1_protocols_motif_grafting_movers_motif2scaffold_indexes method) (pyrosetta.rosetta.utility.vector1_protocols_moves_TrialCounter method) (pyrosetta.rosetta.utility.vector1_protocols_mpi_refinement_MethodParams method) (pyrosetta.rosetta.utility.vector1_protocols_multistate_design_SingleStateEntityData method) (pyrosetta.rosetta.utility.vector1_protocols_optimize_weights_WeightRangeConstraint method) (pyrosetta.rosetta.utility.vector1_protocols_pack_daemon_StructureFileNames method) (pyrosetta.rosetta.utility.vector1_protocols_pdbinfo_manipulations_SequenceSpecification method) (pyrosetta.rosetta.utility.vector1_protocols_pmut_scan_Mutant method) (pyrosetta.rosetta.utility.vector1_protocols_pose_metric_calculators_EnergiesData method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_mutt method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_tm_region method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_VLBInstruction method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_Transformation method) (pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBResidueRange method) (pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment method) (pyrosetta.rosetta.utility.vector1_protocols_rigid_Partner method) (pyrosetta.rosetta.utility.vector1_protocols_rosetta_scripts_ParsedProtocol_ParsedProtocolStep method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataCenter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsEnergyParameter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsGridSearchParameter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsInputLine method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs_PCS_line_data method) (pyrosetta.rosetta.utility.vector1_protocols_seeded_abinitio_SegmentSpec method) (pyrosetta.rosetta.utility.vector1_protocols_sewing_data_storage_ContactDescription method) (pyrosetta.rosetta.utility.vector1_protocols_sewing_data_storage_LigandDescription method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_Quat method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_ResidueDepthFrag method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_TorsionPerturbType method) (pyrosetta.rosetta.utility.vector1_protocols_splice_BBDofs method) (pyrosetta.rosetta.utility.vector1_protocols_splice_ResidueBBDofs method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_rna_Combine_Tags_Info method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_monte_carlo_mover_Attachment method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_monte_carlo_mover_StepWiseMove method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_CstResInteractions method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ExternalGeomSampler method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ResInteractions method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_SingleConstraint method) (pyrosetta.rosetta.utility.vector1_protocols_trajectory_DbTrajectoryWriter_Frame method) (pyrosetta.rosetta.utility.vector1_short method) (pyrosetta.rosetta.utility.vector1_signed_char method) (pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_downstream_hit_t method) (pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_upstream_hit_t method) (pyrosetta.rosetta.utility.vector1_std_array_int_3_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_std_shared_ptr_const_protocols_match_downstream_SecMatchResiduePairEvaluator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_shared_ptr_const_numeric_expression_parser_Expression_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_shared_ptr_protocols_pack_daemon_NPDPropCalculator_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_list_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_core_chemical_AA_utility_vector1_double_std_allocator_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_protocols_jumping_cstType_unsigned_long_std_less_protocols_jumping_cstType_std_allocator_std_pair_const_protocols_jumping_cstType_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_protocols_jumping_dofType_unsigned_long_std_less_protocols_jumping_dofType_std_allocator_std_pair_const_protocols_jumping_dofType_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_shared_ptr_const_core_conformation_Residue_double_std_less_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_pair_const_std_shared_ptr_const_core_conformation_Residue_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_core_id_NamedAtomID_std_less_std_string_std_allocator_std_pair_const_std_string_core_id_NamedAtomID_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_numeric_xyzVector_double_std_less_std_string_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_unsigned_long_std_less_std_string_std_allocator_std_pair_const_std_string_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_core_chemical_AA_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_core_chemical_AA_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_shared_ptr_protocols_frag_picker_CandidatesCollector_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_frag_picker_CandidatesCollector_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_unsigned_long_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_utility_keys_Key2Tuple_unsigned_long_unsigned_long_unsigned_long_std_less_utility_keys_Key2Tuple_unsigned_long_unsigned_long_std_allocator_std_pair_const_utility_keys_Key2Tuple_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_unsigned_long_std_less_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_std_allocator_std_pair_const_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_bool_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_core_id_AtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_core_kinematics_Jump_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_std_pair_core_id_AtomID_core_id_AtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_DOF_ID_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_NamedAtomID_core_id_NamedAtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_TorsionID_core_id_TorsionID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_TorsionID_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_io_HeaderInformation_CompoundToken_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_io_raw_data_DisulfideFile_ResNum_core_io_raw_data_DisulfideFile_ResNum_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_aa_composition_energy_TailFunction_core_scoring_aa_composition_energy_TailFunction_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_disulfides_CentroidDisulfideEnergyComponents_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_disulfides_DisulfideMatchingEnergyComponents_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_disulfides_FullatomDisulfideEnergyComponents_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_int_int_t method) (pyrosetta.rosetta.utility.vector1_std_pair_int_std_shared_ptr_const_core_conformation_ResidueMatcher_t method) (pyrosetta.rosetta.utility.vector1_std_pair_int_unsigned_long_t 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(pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_kinematics_tree_Atom_std_allocator_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_optimization_DOF_Node_std_allocator_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_pack_interaction_graph_NPDHBond_std_allocator_std_shared_ptr_core_pack_interaction_graph_NPDHBond_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_pack_task_ResfileCommand_std_allocator_std_shared_ptr_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_scoring_saxs_DistanceHistogram_std_allocator_std_shared_ptr_core_scoring_saxs_DistanceHistogram_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_sequence_Cell_std_allocator_std_shared_ptr_core_sequence_Cell_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_antibody_PDBLandmark_std_allocator_std_shared_ptr_protocols_antibody_PDBLandmark_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_fldsgn_topology_HelixPairing_std_allocator_std_shared_ptr_protocols_fldsgn_topology_HelixPairing_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_std_allocator_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_flexpack_rotamer_set_FlexbbRotamerSet_std_allocator_std_shared_ptr_protocols_flexpack_rotamer_set_FlexbbRotamerSet_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_quota_QuotaPool_std_allocator_std_shared_ptr_protocols_frag_picker_quota_QuotaPool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_AdaptiveScoreHistogram_std_allocator_std_shared_ptr_protocols_frag_picker_scores_AdaptiveScoreHistogram_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_AtomPairConstraintsData_std_allocator_std_shared_ptr_protocols_frag_picker_scores_AtomPairConstraintsData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_FourAtomsConstraintData_std_allocator_std_shared_ptr_protocols_frag_picker_scores_FourAtomsConstraintData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_Entity_std_allocator_std_shared_ptr_protocols_genetic_algorithm_Entity_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_std_allocator_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_jd3_JGJobNode_std_allocator_std_shared_ptr_protocols_jd3_JGJobNode_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_minimization_packing_MinimalRotamer_std_allocator_std_shared_ptr_protocols_minimization_packing_MinimalRotamer_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_pose_sewing_data_storage_SegmentEnvelope_std_allocator_std_shared_ptr_protocols_pose_sewing_data_storage_SegmentEnvelope_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_keys_Key2Tuple_unsigned_long_unsigned_long_std_allocator_utility_keys_Key2Tuple_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_keys_Key3Tuple_unsigned_long_unsigned_long_unsigned_long_std_allocator_utility_keys_Key3Tuple_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_std_allocator_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_std_allocator_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_std_allocator_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_std_allocator_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_void__star__std_allocator_void__star__t method) resize_asu() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) resize_atom_records() (pyrosetta.rosetta.core.pose.PDBInfo method) resize_bb_donor_acceptor_arrays() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) resize_bb_ids() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) resize_bbs() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) resize_espGrid_to_match_pocketGrid() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) resize_for_xyz_matrix() (pyrosetta.rosetta.protocols.hybridization.TMalign method) resize_natm_variables() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) resize_residue_records() (pyrosetta.rosetta.core.pose.PDBInfo method) resize_semi_vectors() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) resl_score (pyrosetta.rosetta.core.scoring.packing.HolesResult property) reslabels (pyrosetta.rosetta.core.pose.Pose property) ResLvlTaskOperation (class in pyrosetta.rosetta.core.pack.task.operation) ResLvlTaskOperationCreator (class in pyrosetta.rosetta.core.pack.task.operation) ResLvlTaskOperationFactory (class in pyrosetta.rosetta.core.pack.task.operation) ResLvlTaskOperationLoader (class in pyrosetta.rosetta.protocols.parser) ResLvlTaskOperationLoaderCreator (class in pyrosetta.rosetta.protocols.parser) resmap1_ (pyrosetta.rosetta.core.scoring.motif.MotifHits property) resmap2_ (pyrosetta.rosetta.core.scoring.motif.MotifHits property) ResMut (class in pyrosetta.rosetta.protocols.constel) resn() (pyrosetta.rosetta.protocols.splice.BBDofs method) resName (pyrosetta.rosetta.core.io.AtomInformation property) (pyrosetta.rosetta.core.io.ModifiedResidueInformation property) resname (pyrosetta.rosetta.protocols.forge.remodel.LineObject property) resName (pyrosetta.rosetta.protocols.sparta.PDB_Entry property) (pyrosetta.rosetta.protocols.sparta.RingData property) resName() (pyrosetta.rosetta.core.io.ResidueInformation method) resname() (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) resName1 (pyrosetta.rosetta.core.io.LinkInformation property) (pyrosetta.rosetta.core.io.SSBondInformation property) resName2 (pyrosetta.rosetta.core.io.LinkInformation property) (pyrosetta.rosetta.core.io.SSBondInformation property) resnum (pyrosetta.rosetta.core.scoring.packstat.SimplePDB_Atom property) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering property) (pyrosetta.rosetta.protocols.hbnet.HBondResStruct property) (pyrosetta.rosetta.protocols.legacy_sewing.Basis property) (pyrosetta.rosetta.protocols.legacy_sewing.HashValue property) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover.mutt property) (pyrosetta.rosetta.protocols.sewing.hashing.HashValue property) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter.mutt property) resNum (pyrosetta.rosetta.protocols.sparta.PDB_Entry property) resnum() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.Sequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.protocols.comparative_modeling.features.ResidueFeature method) (pyrosetta.rosetta.protocols.comparative_modeling.features.SSFeature method) (pyrosetta.rosetta.protocols.comparative_modeling.features.TorsionFeature method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.parser.BluePrint method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.Torsion method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.sewing.data_storage.Basis method) (pyrosetta.rosetta.protocols.simple_filters.EnergyPerResidueFilter method) (pyrosetta.rosetta.protocols.simple_filters.NonSequentialNeighborsFilter method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) resnum_ (pyrosetta.rosetta.protocols.legacy_sewing.SewResidue property) resnum_and_chain() (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) resnum_exists_in_set() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) resnum_map() (pyrosetta.rosetta.protocols.parser.BluePrint method) ResnumFromStringsWithRangesSelector (class in pyrosetta.rosetta.protocols.antibody.design) resnums() (pyrosetta.rosetta.protocols.simple_filters.ResidueIEFilter method) resnums_allow_design() (pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation method) resnums_from_bool_mask() (in module pyrosetta.rosetta.core.pack.task.residue_selector) resnums_from_task() (in module pyrosetta.rosetta.core.pack.task.residue_selector) resolution (pyrosetta.rosetta.protocols.antibody.CDRDBPose property) (pyrosetta.rosetta.protocols.antibody.CDRDBSequence property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult property) resolution() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) ResolutionSwitcher (class in pyrosetta.rosetta.protocols.abinitio) resolve_as_serialized_loop_from_pose() (pyrosetta.rosetta.protocols.loops.LoopFromFileData method) resolve_as_serialized_loops() (pyrosetta.rosetta.protocols.loops.LoopsFileData method) resolve_db_partition() (in module pyrosetta.rosetta.basic.database) resolve_index() (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionChainEnd method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionLastResidue method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPDB method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPoseNum method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionRefPose method) resolve_jump() (pyrosetta.rosetta.core.environment.SequenceAnnotation method) resolve_loop_indices() (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) resolve_loop_indices_once() (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) resolve_loopfile_indices() (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) resolve_loops() (pyrosetta.rosetta.protocols.loops.LoopsFileData method) resolve_partial_atom_id() (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) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) resolve_seq() (pyrosetta.rosetta.core.environment.SequenceAnnotation method) resolve_sequence_label() (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) resolve_store_path() (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager method) resolve_trie_vs_path() (pyrosetta.rosetta.core.scoring.trie.RotamerTrieBase method) resolve_trie_vs_trie() (pyrosetta.rosetta.core.scoring.trie.RotamerTrieBase method) resolve_uncommitted_substitution() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) resolver() (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) Resonance (class in pyrosetta.rosetta.protocols.noesy_assign) resonance() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) resonance_id() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) ResonanceList (class in pyrosetta.rosetta.protocols.noesy_assign) resonances() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) resonances_at_residue() (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) resource_deallocation_msg (pyrosetta.rosetta.protocols.jd3.deallocation.deallocation_msg_type attribute) resource_definition_xsd() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobQueen method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen method) (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) resource_loader_xsd_type_definition_w_attributes() (in module pyrosetta.rosetta.basic.resource_manager) resource_loader_xsd_type_definition_w_attributes_and_repeatable_subelements() (in module pyrosetta.rosetta.basic.resource_manager) RESOURCE_MANAGED_JOB (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum attribute) resource_manager() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) resource_name() (pyrosetta.rosetta.protocols.jd3.deallocation.ResourceDeallocationMessage method) ResourceDeallocationMessage (class in pyrosetta.rosetta.protocols.jd3.deallocation) ResourceLoader (class in pyrosetta.rosetta.basic.resource_manager) ResourceLoaderCreator (class in pyrosetta.rosetta.basic.resource_manager) ResourceLoaderFactory (class in pyrosetta.rosetta.basic.resource_manager) ResourceLocator (class in pyrosetta.rosetta.basic.resource_manager) ResourceLocatorCreator (class in pyrosetta.rosetta.basic.resource_manager) ResourceLocatorFactory (class in pyrosetta.rosetta.basic.resource_manager) ResourceManager (class in pyrosetta.rosetta.basic.resource_manager) ResourceManagerCreator (class in pyrosetta.rosetta.basic.resource_manager) ResourceManagerFactory (class in pyrosetta.rosetta.basic.resource_manager) resources_that_have_been_declared() (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) ResourceStream (class in pyrosetta.rosetta.basic.resource_manager) ResPairMinimizationData (class in pyrosetta.rosetta.core.scoring) ResPairMotif (class in pyrosetta.rosetta.core.scoring.motif) ResPairMotifMetaBinner (class in pyrosetta.rosetta.core.scoring.motif) ResPairMotifQuery (class in pyrosetta.rosetta.core.scoring.motif) ResPairMotifs (class in pyrosetta.rosetta.core.scoring.motif) respect_this_movemap() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) respond_to_peripheral_hitlist_change() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) respond_to_primary_hitlist_change() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) ResPred (class in pyrosetta.rosetta.protocols.mean_field) ResRangePredicate (class in pyrosetta.rosetta.core.scoring) ResRotPair (class in pyrosetta.rosetta.basic.datacache) ResRotPairHasher (class in pyrosetta.rosetta.basic.datacache) resSeq (pyrosetta.rosetta.core.io.AtomInformation property) (pyrosetta.rosetta.core.pose.PDBInfo.ResidueRecord property) (pyrosetta.rosetta.protocols.loops.LoopConfiguration attribute) resSeq() (pyrosetta.rosetta.core.io.ResidueInformation method) resSeq1 (pyrosetta.rosetta.core.io.LinkInformation property) (pyrosetta.rosetta.core.io.SSBondInformation property) resSeq2 (pyrosetta.rosetta.core.io.LinkInformation property) (pyrosetta.rosetta.core.io.SSBondInformation property) ResSingleMinimizationData (class in pyrosetta.rosetta.core.scoring) ResSurfaceFullList (pyrosetta.rosetta.protocols.sparta.PDB property) ResSurfacePartList (pyrosetta.rosetta.protocols.sparta.PDB property) rest_and_clause_token() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestAndClause method) rest_expression_token() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestExpression method) rest_or_clause_token() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestOrClause method) rest_term_token() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestTerm method) restart() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.BOINCJobDistributor method) (pyrosetta.rosetta.protocols.jd2.FileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.JobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.ShuffleFileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.VectorPoseJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor method) restart_mode() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) restart_simulation() (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder 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.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy method) restore() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem.Memento method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) restore_archive() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) restore_cter() (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) restore_from_file() (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) restore_lazaridis_IMM1_behavior() (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover method) restore_original_cst() (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) restore_original_foldtree() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) restore_pose_from_rbsegs() (in module pyrosetta.rosetta.protocols.rbsegment_relax) restore_residues() (in module pyrosetta.rosetta.protocols.forge.methods) restore_status() (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) restoreState() (pyrosetta.rosetta.numeric.random.mt19937_RG method) (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) ResTorsions (class in pyrosetta.rosetta.protocols.loop_grower) restrain_ligand_nbr_atom() (in module pyrosetta.rosetta.protocols.ligand_docking) restrain_protein_Calphas() (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) restrict_aas() (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation static method) restrict_aatypes_for_selection() (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) restrict_absent_canonical_aas() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) restrict_absent_nas() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) restrict_access() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) restrict_dna_rotamers() (in module pyrosetta.rosetta.protocols.dna) restrict_identities() (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) restrict_non_nbrs_from_repacking() (in module pyrosetta.toolbox.mutants) restrict_nonnative_canonical_aas() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) restrict_only_design_to_loops() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoops method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) restrict_prec() (in module pyrosetta.rosetta.core.io.pose_to_sfr) restrict_restypes() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) restrict_sequence_profile() (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) restrict_to_aligned_segments() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation method) restrict_to_canonical_aas() (in module pyrosetta.rosetta.protocols.multistate_design) restrict_to_interfacial_loop_packing() (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) restrict_to_nbrs() (pyrosetta.rosetta.protocols.ddg.ddGMover method) restrict_to_protein_residues() (in module pyrosetta.rosetta.protocols.ligand_docking) restrict_to_repacking() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover 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.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop 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.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) restrict_to_repacking_chain1() (pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation method) restrict_to_repacking_chain2() (pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation method) (pyrosetta.rosetta.protocols.splice.Splice method) restrict_to_residue() (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) restrict_to_residues() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) restrict_to_restypes_with_all_properties() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) restrict_to_restypes_with_at_least_one_property() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) restrict_to_single_sequence() (in module pyrosetta.rosetta.protocols.dna) RestrictAAsFromProbabilities (class in pyrosetta.rosetta.protocols.task_operations) RestrictAAsFromProbabilitiesCreator (class in pyrosetta.rosetta.protocols.task_operations) RestrictAbsentCanonicalAAS (class in pyrosetta.rosetta.core.pack.task.operation) RestrictAbsentCanonicalAASCreator (class in pyrosetta.rosetta.core.pack.task.operation) RestrictAbsentCanonicalAASExceptNativeRLT (class in pyrosetta.rosetta.core.pack.task.operation) RestrictAbsentCanonicalAASExceptNativeRLTCreator (class in pyrosetta.rosetta.core.pack.task.operation) RestrictAbsentCanonicalAASRLT (class in pyrosetta.rosetta.core.pack.task.operation) RestrictAbsentCanonicalAASRLTCreator (class in pyrosetta.rosetta.core.pack.task.operation) RestrictByCalculatorsOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictByCalculatorsOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) RestrictChainToRepackingOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictChainToRepackingOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) RestrictConservedLowDdgOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictConservedLowDdgOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) RestrictDesignToProteinDNAInterface (class in pyrosetta.rosetta.protocols.dna) RestrictDesignToProteinDNAInterfaceCreator (class in pyrosetta.rosetta.protocols.dna) RestrictIdentitiesAtAlignedPositionsOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictIdentitiesAtAlignedPositionsOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) RestrictIdentitiesOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictIdentitiesOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) RestrictInteractionGraphThreadsOperation (class in pyrosetta.rosetta.core.pack.task.operation) RestrictInteractionGraphThreadsOperationCreator (class in pyrosetta.rosetta.core.pack.task.operation) RestrictInterGroupVectorOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictInterGroupVectorOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) restriction_type_name() (in module pyrosetta.rosetta.utility.tag) RestrictNativeResiduesOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictNativeResiduesOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) RestrictNonSurfaceToRepackingOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictNonSurfaceToRepackingOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) RestrictOperationsBase (class in pyrosetta.rosetta.protocols.task_operations) RestrictResiduesToRepackingOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictResiduesToRepackingOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) RestrictResidueToRepacking (class in pyrosetta.rosetta.core.pack.task.operation) RestrictResidueToRepackingCreator (class in pyrosetta.rosetta.core.pack.task.operation) RestrictToAlignedSegmentsOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictToAlignedSegmentsOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) RestrictToCDRH3Loop (class in pyrosetta.rosetta.protocols.task_operations) RestrictToCDRH3LoopCreator (class in pyrosetta.rosetta.protocols.task_operations) RestrictToCDRsAndNeighbors (class in pyrosetta.rosetta.protocols.antibody.task_operations) RestrictToCDRsAndNeighborsCreator (class in pyrosetta.rosetta.protocols.antibody.task_operations) RestrictToInterface (class in pyrosetta.rosetta.protocols.simple_task_operations) RestrictToInterfaceCreator (class in pyrosetta.rosetta.protocols.simple_task_operations) RestrictToInterfaceOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictToInterfaceOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) RestrictToInterfaceVectorOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictToInterfaceVectorOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) RestrictToLoops (class in pyrosetta.rosetta.protocols.simple_task_operations) RestrictToLoopsAndNeighbors (class in pyrosetta.rosetta.protocols.simple_task_operations) RestrictToLoopsAndNeighborsCreator (class in pyrosetta.rosetta.protocols.simple_task_operations) RestrictToLoopsCreator (class in pyrosetta.rosetta.protocols.simple_task_operations) RestrictToMoveMapChiOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictToNeighborhoodOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictToNeighborhoodOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) RestrictToRepacking (class in pyrosetta.rosetta.core.pack.task.operation) RestrictToRepackingCreator (class in pyrosetta.rosetta.core.pack.task.operation) RestrictToRepackingRLT (class in pyrosetta.rosetta.core.pack.task.operation) RestrictToRepackingRLTCreator (class in pyrosetta.rosetta.core.pack.task.operation) RestrictToResidueProperties (class in pyrosetta.rosetta.core.pack.task.operation) RestrictToResiduePropertiesCreator (class in pyrosetta.rosetta.core.pack.task.operation) RestrictToSpecifiedBaseResidueTypes (class in pyrosetta.rosetta.core.pack.task.operation) RestrictToSpecifiedBaseResidueTypesCreator (class in pyrosetta.rosetta.core.pack.task.operation) RestrictToTerminiOperation (class in pyrosetta.rosetta.protocols.task_operations) RestrictToTerminiOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) RestrictYSDesign (class in pyrosetta.rosetta.core.pack.task.operation) RestrictYSDesignCreator (class in pyrosetta.rosetta.core.pack.task.operation) restype (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.PlaceableRotamer property) restype() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) (pyrosetta.rosetta.protocols.match.upstream.ProteinUpstreamBuilder method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamBuilder method) restype_ (pyrosetta.rosetta.protocols.match.upstream.BuildSet property) restype_atomno() (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) restype_char() (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) restype_destruction_observer() (pyrosetta.rosetta.core.energy_methods.IdealParametersDatabase method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.PairFuncMap method) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap method) (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeMap method) restype_for_rotblock() (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet method) restype_geom_ (pyrosetta.rosetta.protocols.match.upstream.BuildSet property) restype_geometry() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) restype_id_2_collision_check_id() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) restype_index() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) restype_name1() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) restype_name2() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) restype_set() (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) restype_to_rdmol_options (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAlignerOptions property) RestypeDestructionEvent (class in pyrosetta.rosetta.core.chemical) ResTypeFragmentMover (class in pyrosetta.rosetta.protocols.simple_moves) restypeinfo() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) ResTypeSequence_lt (class in pyrosetta.rosetta.protocols.dna) RestypeToRDMol (class in pyrosetta.rosetta.core.chemical.rdkit) RestypeToRDMolOptions (class in pyrosetta.rosetta.core.chemical.rdkit) result (class in pyrosetta.rosetta.cppdb) (class in pyrosetta.rosetta.cppdb.backend) (pyrosetta.rosetta.basic.ExecutionResult property) result() (pyrosetta.rosetta.protocols.environment.EnvClaimBroker method) result.next_row (class in pyrosetta.rosetta.cppdb.backend) result_id() (pyrosetta.rosetta.protocols.jd3.JGResultNode method) (pyrosetta.rosetta.protocols.jd3.output.MultipleOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.output.OutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification method) result_outputter() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobQueen method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen method) (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) result_query_string() (pyrosetta.rosetta.protocols.wum.DatabaseEntryWorkUnit method) result_residues (pyrosetta.rosetta.protocols.indexed_structure_store.DirectSegmentLookupResult property) result_sizes() (in module pyrosetta.rosetta.protocols.antibody.grafting) ResultElements (class in pyrosetta.rosetta.protocols.jd3.dag_node_managers) ResultOutputter (class in pyrosetta.rosetta.protocols.jd3.output) results_to_keep() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.EvenlyPartitionedNodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) retain_top() (in module pyrosetta.rosetta.core.fragment) retraction_prob() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix method) retrieve() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) retrieve_all_types_with_variants_aa() (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) retrieve_all_types_with_variants_residuetypecops() (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) retrieve_and_reset_node_recently_completed() (pyrosetta.rosetta.protocols.jd3.job_distributors.JobExtractor method) retrieve_base_partner_from_pose() (in module pyrosetta.rosetta.core.scoring.dna) retrieve_bulges() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) retrieve_bulges_s() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect static method) retrieve_calculator() (pyrosetta.rosetta.core.pose.metrics.CalculatorFactory method) retrieve_centroid_scatter_from_pose() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) retrieve_connection_architect() (in module pyrosetta.rosetta.protocols.denovo_design.connection) retrieve_constraints() (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) retrieve_CSA_from_pose() (in module pyrosetta.rosetta.core.scoring) retrieve_DC_from_pose() (in module pyrosetta.rosetta.core.scoring) retrieve_denovo_architect() (in module pyrosetta.rosetta.protocols.denovo_design.architects) retrieve_energy() (pyrosetta.rosetta.core.scoring.constraints.CstResNeighbConstIterator method) (pyrosetta.rosetta.core.scoring.constraints.CstResNeighbIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbIterator method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.ResidueNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.ResidueNeighborIterator method) retrieve_fa_scatter_from_pose() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) retrieve_lengths() (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) retrieve_loop_abegos() (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator method) retrieve_next_message() (pyrosetta.rosetta.utility.SimulateMPIData method) retrieve_observer() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) retrieve_RDC_from_pose() (in module pyrosetta.rosetta.core.scoring) retrieve_RDC_ROHL_from_pose() (in module pyrosetta.rosetta.core.scoring) retrieve_RDC_segments_from_pose() (in module pyrosetta.rosetta.protocols.scoring) retrieve_register_shifts() (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) retrieve_remarks() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) retrieve_residue_num_of_rkde() (in module pyrosetta.rosetta.protocols.features.strand_assembly) retrieve_tensor_from_svd() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide method) RetrieveStoredTaskOperation (class in pyrosetta.rosetta.protocols.task_operations) RetrieveStoredTaskOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) retry_limit() (pyrosetta.rosetta.protocols.jd3.LarvalJob method) return_centroid() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) return_combine_history() (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) return_complex_type_for_MatcherConstraint() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo static method) return_file_callback() (pyrosetta.rosetta.utility.Inline_File_Provider_Hook method) return_hbond_to_queue() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) return_key() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) return_lowest_poses_in_clusters() (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) return_nearest_residue() (in module pyrosetta.rosetta.core.conformation.symmetry) (in module pyrosetta.rosetta.core.pose) return_pseudo_hits() (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) return_region() (in module pyrosetta.rosetta.protocols.grafting) return_results_breadth_first() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManagerStorageMatrix method) return_results_depth_first() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManagerStorageMatrix method) return_silent() (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) return_top_poses_in_clusters() (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) ReturnResidueSubsetSelector (class in pyrosetta.rosetta.core.select.residue_selector) ReturnSidechainMover (class in pyrosetta.rosetta.protocols.simple_moves) revamp_weight_by_burial() (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) REVDAT (pyrosetta.rosetta.core.io.pdb.RecordType attribute) reverse() (pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t method) (pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t method) (pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t method) (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.id.SequenceMapping method) (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.RT method) (pyrosetta.rosetta.core.scoring.dssp.Pairing method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERChiSqMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceDistribution method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJaccardMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJSMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERMiscMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEEROverlapMethod method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.std.list_const_protocols_match_Hit__star__t method) (pyrosetta.rosetta.std.list_core_id_AtomID_t method) (pyrosetta.rosetta.std.list_core_io_rcsb_ExperimentalTechnique_t method) (pyrosetta.rosetta.std.list_core_scoring_custom_pair_distance_atoms_and_func_struct_t method) (pyrosetta.rosetta.std.list_core_scoring_power_diagram_PDvertex__star__t method) (pyrosetta.rosetta.std.list_double_t method) (pyrosetta.rosetta.std.list_int_t method) (pyrosetta.rosetta.std.list_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.list_protocols_match_Hit_t method) (pyrosetta.rosetta.std.list_protocols_multistage_rosetta_scripts_mover_or_filter_t method) (pyrosetta.rosetta.std.list_protocols_pockets_spherical_coor_triplet_t method) (pyrosetta.rosetta.std.list_RDKit_Atom__star__t method) (pyrosetta.rosetta.std.list_RDKit_Bond__star__t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BasePair_t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BaseStack_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_double_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.list_std_set_std_string_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_operation_ResLvlTaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_chunk_library_inputters_ChunkLibraryInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_full_model_inputters_FullModelInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_inputters_PoseInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_PoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_SecondaryPoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_XMLSchemaParticle_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_interaction_graph_AnnealableGraphBase_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_rotamer_set_RotamerOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_task_operation_TaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_power_diagram_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_deallocation_DeallocationMessage_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_LarvalJob_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_output_OutputSpecification_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_pose_outputters_SecondaryPoseOutputter_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_CrossPeak_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.std.list_std_string_t method) (pyrosetta.rosetta.std.list_unsigned_long_t method) (pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t method) (pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t method) (pyrosetta.rosetta.std.list_utility_tag_XMLSchemaSimpleSubelementList_ElementSummary_t method) (pyrosetta.rosetta.std.list_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.list_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) reverse_chains() (in module pyrosetta.rosetta.protocols.denovo_design.components) reverse_connections() (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) reverse_in_place() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) reverse_in_place_unsafe() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) reverse_index_ (pyrosetta.rosetta.protocols.cluster.calibur.AdjacentList property) reverse_lengths() (in module pyrosetta.rosetta.protocols.denovo_design.components) reverse_lookup() (pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t method) (pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t method) (pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t method) reverse_move() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) reverse_orientations() (in module pyrosetta.rosetta.protocols.denovo_design.components) reverse_score_filter() (pyrosetta.rosetta.core.io.silent.SilentFileData method) reversed() (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelicalFragment method) reversion_scan() (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) Revert (class in pyrosetta.rosetta.protocols.protein_interface_design) revert() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) revert_last_added_contact() (pyrosetta.rosetta.protocols.sewing.hashing.LigandBindingResPlacer method) revert_score() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) revert_to_pre_talaris_2013_defaults() (in module pyrosetta.rosetta.core.init) revise_root_and_moving_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) revise_root_and_moving_res_list() (in module pyrosetta.rosetta.protocols.stepwise.modeler) revision() (pyrosetta.rosetta.utility.Version static method) revision_id() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) revoke_all_access() (pyrosetta.rosetta.core.environment.DofPassport method) RevRefinementResultComparitor (class in pyrosetta.rosetta.protocols.electron_density) ReweightableRepEnergy (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) ReweightData (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty) rewind_column() (pyrosetta.rosetta.cppdb.result method) Rf (pyrosetta.rosetta.core.chemical.element.Elements attribute) RFd_like (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) RG (pyrosetta.rosetta.basic.ProfTag attribute) Rg (pyrosetta.rosetta.core.chemical.element.Elements attribute) rg (pyrosetta.rosetta.core.energy_methods.RG_Local_MinData property) (pyrosetta.rosetta.core.energy_methods.RG_MinData property) (pyrosetta.rosetta.core.scoring.ScoreType attribute) rg() (in module pyrosetta.rosetta.numeric.random) (pyrosetta.rosetta.protocols.symmetry.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SymmetrySlider method) RG_Energy_Fast (class in pyrosetta.rosetta.core.energy_methods) RG_Energy_FastCreator (class in pyrosetta.rosetta.core.energy_methods) RG_Energy_RNA (class in pyrosetta.rosetta.core.energy_methods) RG_Energy_RNACreator (class in pyrosetta.rosetta.core.energy_methods) RG_LOCAL (pyrosetta.rosetta.basic.ProfTag attribute) rg_local (pyrosetta.rosetta.core.scoring.ScoreType attribute) RG_Local_MinData (class in pyrosetta.rosetta.core.energy_methods) RG_LOCAL_MINDATA (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) RG_LocalEnergy (class in pyrosetta.rosetta.core.energy_methods) RG_LocalEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) RG_MinData (class in pyrosetta.rosetta.core.energy_methods) RG_MINDATA (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) rgb_to_hsv() (in module pyrosetta.rosetta.numeric) RGFilter (class in pyrosetta.rosetta.protocols.simple_filters) rgsigma() (pyrosetta.rosetta.core.optimization.CMAES_Minimizer method) rgstr_shift() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing method) Rh (pyrosetta.rosetta.core.chemical.element.Elements attribute) RHIJU_COLOR (pyrosetta.rosetta.protocols.viewer.graphics_states_param.ColorMode attribute) rho (pyrosetta.rosetta.protocols.pockets.spherical_coor_triplet property) (pyrosetta.rosetta.protocols.pockets.triplet_and_originnum property) rho() (pyrosetta.rosetta.core.scoring.packing.HolesParamsRes method) (pyrosetta.rosetta.core.scoring.packstat.PackingScore method) RID_FileSource (class in pyrosetta.rosetta.core.pose) RID_Source (class in pyrosetta.rosetta.core.pose) right (pyrosetta.rosetta.protocols.forge.build.Interval property) right() (pyrosetta.rosetta.numeric.ClusteringTreeNode method) (pyrosetta.rosetta.protocols.topology_broker.claims.BBClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.CutClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.LegacyRootClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.SequenceClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.SymmetryClaim method) right_ (pyrosetta.rosetta.core.pack.dunbrack.BBIndNRChiSample_float_t property) right_cdf() (pyrosetta.rosetta.core.scoring.Ramachandran2B method) right_cdf_for_torsion_bin() (pyrosetta.rosetta.core.scoring.Ramachandran2B method) right_child() (pyrosetta.rosetta.numeric.kdtree.KDNode method) right_justified() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) right_justify() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) right_multiply_by() (pyrosetta.rosetta.numeric.Quaternion_double_t method) right_multiply_by_inverse_of() (pyrosetta.rosetta.numeric.Quaternion_double_t method) RIGHT_PAREN (pyrosetta.rosetta.numeric.expression_parser.TokenType attribute) right_stub_atoms() (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) RIGID_BODY (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) rigid_body_move() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) rigid_body_rotamer() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) rigid_body_trial() (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) RIGID_BODY_WITH_RESIDUE_ALTERNATIVES (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) RIGID_BODY_WITH_RESIDUE_LIST (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) RIGID_CORE_RESAMPLING (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax.IterationStage attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeBase attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeBase.IterationStage attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid.IterationStage attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom.IterationStage attribute) rigid_transform_3D() (in module pyrosetta.toolbox.numpy_utils) RigidBodyDeterministicSpinMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyDofPerturbMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyDofRandomizeMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyDofRandomTransMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyDofSeqPerturbMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyDofSeqRandomizeMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyDofSeqTransMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyDofTransMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyInfo (class in pyrosetta.rosetta.protocols.docking) RigidBodyMotionMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyMoveBaseRSO (class in pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations) RigidBodyMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyMoveRSO (class in pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations) RigidBodyPerturbMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyPerturbNoCenterMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyPerturbNoCenterMoverCreator (class in pyrosetta.rosetta.protocols.rigid) RigidBodyPerturbRandomJumpMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyRandomizeMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyRandomTMHMover (class in pyrosetta.rosetta.protocols.topology_broker) RigidBodySilentStruct (class in pyrosetta.rosetta.core.io.silent) RigidBodySilentStructCreator (class in pyrosetta.rosetta.core.io.silent) RigidBodySpinMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyStepWiseSampler (class in pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body) RigidBodyStepWiseSamplerValueRange (class in pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body) RigidBodyStepWiseSamplerWithResidueAlternatives (class in pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body) RigidBodyStepWiseSamplerWithResidueList (class in pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body) RigidBodyTiltMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyTiltMoverCreator (class in pyrosetta.rosetta.protocols.rigid) RigidBodyTransMover (class in pyrosetta.rosetta.protocols.rigid) RigidBodyTransMoverCreator (class in pyrosetta.rosetta.protocols.rigid) RigidChunkClaimer (class in pyrosetta.rosetta.protocols.topology_broker) RigidChunkClaimer.CM_SuggestFixResidue (class in pyrosetta.rosetta.protocols.topology_broker) RigidChunkCM (class in pyrosetta.rosetta.protocols.abinitio.abscript) RigidChunkCMCreator (class in pyrosetta.rosetta.protocols.abinitio.abscript) RigidLigandBuilder (class in pyrosetta.rosetta.protocols.match.downstream) RigidScore (class in pyrosetta.rosetta.protocols.sic_dock) RigidSearchMover (class in pyrosetta.rosetta.protocols.ligand_docking) ring_affix_from_ring_size() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager static method) ring_atoms() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) ring_close (pyrosetta.rosetta.core.scoring.ScoreType attribute) ring_conformer() (pyrosetta.rosetta.core.conformation.Residue method) ring_conformer_set() (pyrosetta.rosetta.core.chemical.ResidueType method) RING_CONFORMERS (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) ring_current_coeff() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) ring_current_effect() (in module pyrosetta.rosetta.core.scoring.rna.chemical_shift) ring_height() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) RING_HYBRID (pyrosetta.rosetta.core.chemical.Hybridization attribute) ring_intensity() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) ring_pos() (in module pyrosetta.rosetta.core.scoring.rna.chemical_shift) ring_radius() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) ring_saturation_type() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) ring_saturation_types() (pyrosetta.rosetta.core.chemical.ResidueType method) ring_size() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) (pyrosetta.rosetta.core.chemical.rings.RingConformerSet method) ring_size_to_morphemes_map_file() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager static method) RingClosureEnergy (class in pyrosetta.rosetta.core.energy_methods) RingClosureEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) RingConformationMover (class in pyrosetta.rosetta.protocols.simple_moves) RingConformationMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) RingConformer (class in pyrosetta.rosetta.core.chemical.rings) RingConformerManager (class in pyrosetta.rosetta.core.chemical.rings) RingConformerSet (class in pyrosetta.rosetta.core.chemical.rings) RingData (class in pyrosetta.rosetta.protocols.sparta) ringFact (pyrosetta.rosetta.protocols.sparta.RingData property) RingInfo (class in pyrosetta.rosetta.RDKit) ringness() (pyrosetta.rosetta.core.chemical.Bond method) RingNo (pyrosetta.rosetta.protocols.sparta.PDB property) RingPlaneFlipMover (class in pyrosetta.rosetta.protocols.carbohydrates) RingPlaneFlipMoverCreator (class in pyrosetta.rosetta.protocols.carbohydrates) RingSaturationType (class in pyrosetta.rosetta.core.chemical.rings) rise() (pyrosetta.rosetta.protocols.dna.DNABasestep method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) rjust() (in module pyrosetta.rosetta.ObjexxFCL) rKirkwood() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) rlto_datamap_category() (in module pyrosetta.rosetta.core.pack.task.operation) RM_BB (pyrosetta.rosetta.core.scoring.motif.RM_Type attribute) rm_jump_neighbor() (pyrosetta.rosetta.core.environment.FoldTreeSketch.Node method) rm_peptide_neighbor() (pyrosetta.rosetta.core.environment.FoldTreeSketch.Node method) RM_PH (pyrosetta.rosetta.core.scoring.motif.RM_Type attribute) RM_PO (pyrosetta.rosetta.core.scoring.motif.RM_Type attribute) RM_SC (pyrosetta.rosetta.core.scoring.motif.RM_Type attribute) rm_seq_label() (pyrosetta.rosetta.core.environment.SequenceAnnotation method) RM_Type (class in pyrosetta.rosetta.core.scoring.motif) RM_Type_NONE (pyrosetta.rosetta.core.scoring.motif.RM_Type attribute) rm_virt_phosphate() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) RMOT_end_of_list (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType attribute) RMOT_general_string (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType attribute) RMOT_integer (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType attribute) RMOT_invalid (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType attribute) RMOT_nonnegative_integer (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType attribute) RMOT_real (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType attribute) RMOT_residue_selector (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType attribute) RMOT_residue_selector_list (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType attribute) RMOT_rosetta_bool (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType attribute) RMOT_task_operation (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType attribute) RMOT_task_operation_list (pyrosetta.rosetta.utility.xsd_util.RosettaModuleOptionType attribute) rms (pyrosetta.rosetta.core.scoring.motif.MotifHit property) (pyrosetta.rosetta.core.scoring.ScoreType attribute) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfo property) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfo property) rms() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) (pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData method) (pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoint method) rms_at_all_corresponding_atoms() (in module pyrosetta.rosetta.core.scoring) rms_at_corresponding_atoms() (in module pyrosetta.rosetta.core.scoring) rms_at_corresponding_atoms_no_super() (in module pyrosetta.rosetta.core.scoring) rms_at_corresponding_heavy_atoms() (in module pyrosetta.rosetta.core.scoring) rms_cutoff() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) rms_cutoff_ (pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions property) rms_cutoff_loop() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) RMS_Energy (class in pyrosetta.rosetta.core.energy_methods) RMS_EnergyCreator (class in pyrosetta.rosetta.core.energy_methods) rms_error_with_noise() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) rms_fit() (in module pyrosetta.rosetta.numeric.model_quality) rms_pose_list() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) rms_wrapper() (in module pyrosetta.rosetta.numeric.model_quality) rms_wrapper_slow_and_correct() (in module pyrosetta.rosetta.numeric.model_quality) RMSComparator (class in pyrosetta.rosetta.protocols.loop_grower) rmsd (pyrosetta.rosetta.protocols.ligand_docking.Transform_info property) RMSD (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data property) rmsd (pyrosetta.rosetta.protocols.pose_length_moves.Chain property) RMSD (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member property) rmsd (pyrosetta.rosetta.protocols.stepwise.modeler.rna.output_data_struct property) RMSD() (in module pyrosetta.rosetta.protocols.cluster.calibur) rmsd() (pyrosetta.rosetta.core.fragment.FragmentRmsd method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary method) (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinder method) (pyrosetta.rosetta.protocols.simple_filters.StemFinder method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner method) (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) rmsd_all (pyrosetta.rosetta.core.scoring.rmsd_atoms attribute) rmsd_all_heavy (pyrosetta.rosetta.core.scoring.rmsd_atoms attribute) rmsd_atom_total (pyrosetta.rosetta.core.scoring.rmsd_atoms attribute) rmsd_atoms (class in pyrosetta.rosetta.core.scoring) rmsd_between_coordinates() (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) rmsd_count (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) rmsd_cutoff() (pyrosetta.rosetta.protocols.pose_metric_calculators.FragQualCalculator method) rmsd_cutoff_1() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) rmsd_cutoff_2() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) rmsd_include_motif() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) rmsd_include_unconstrained() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) rmsd_match (pyrosetta.rosetta.protocols.indexed_structure_store.BackboneStub property) rmsd_over_alignment_atoms() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner method) rmsd_over_residue_list() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) rmsd_protein_bb_ca (pyrosetta.rosetta.core.scoring.rmsd_atoms attribute) rmsd_protein_bb_heavy (pyrosetta.rosetta.core.scoring.rmsd_atoms attribute) rmsd_protein_bb_heavy_including_O (pyrosetta.rosetta.core.scoring.rmsd_atoms attribute) rmsd_res_in_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner method) rmsd_residues_to_ignore_native() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) rmsd_residues_to_ignore_prediction() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) rmsd_sc (pyrosetta.rosetta.core.scoring.rmsd_atoms attribute) rmsd_sc_heavy (pyrosetta.rosetta.core.scoring.rmsd_atoms attribute) rmsd_screen() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) rmsd_threshold() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) rmsd_to_best() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_RMSDToBestSummary method) rmsd_tolerance (pyrosetta.rosetta.protocols.indexed_structure_store.DirectSegmentLookupConfig property) (pyrosetta.rosetta.protocols.indexed_structure_store.SegmentSequenceProfileConfig property) rmsd_wrt_correct_minimized (pyrosetta.rosetta.protocols.stepwise.modeler.rna.output_data_struct property) rmsd_wrt_minimized (pyrosetta.rosetta.protocols.stepwise.modeler.rna.output_data_struct property) RmsData (class in pyrosetta.rosetta.numeric.model_quality) RmsdEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) RmsdEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) RmsdFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) RmsdFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) RmsdFromResidueSelectorFilter (class in pyrosetta.rosetta.protocols.fold_from_loops.filters) RmsdFromResidueSelectorFilterCreator (class in pyrosetta.rosetta.protocols.fold_from_loops.filters) RMSDMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) RMSDMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.metrics) RMSDReporter (class in pyrosetta.rosetta.protocols.pose_reporters) RMSDReporterCreator (class in pyrosetta.rosetta.protocols.pose_reporters) RmsdSimpleFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) RmsdSimpleFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) RmsdTargetEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) rmsf() (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) rmsfitca3() (in module pyrosetta.rosetta.numeric.model_quality) rmsthreshold (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GADockStageParams property) RMStonative() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) RMSVallData (class in pyrosetta.rosetta.protocols.frags) RMSwrapper() (in module pyrosetta.rosetta.protocols.simple_filters) RMT_end_of_list (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType attribute) RMT_filter (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType attribute) RMT_invalid (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType attribute) RMT_mover (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType attribute) RMT_res_lvl_task_operation (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType attribute) RMT_residue_selector (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType attribute) RMT_sub_element (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType attribute) RMT_task_operation (pyrosetta.rosetta.utility.xsd_util.RosettaModuleType attribute) Rn (pyrosetta.rosetta.core.chemical.element.Elements attribute) rN (pyrosetta.rosetta.protocols.sparta.PDB property) (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) RNA (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) RNA_AddDeleteMonteCarlo (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna) RNA_AnalyticLoopCloser (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) RNA_ANTI_CHI (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) rna_anti_chi_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) RNA_AtomVDW (class in pyrosetta.rosetta.core.scoring.rna) RNA_AtrRepChecker (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker) RNA_AtrRepScreener (class in pyrosetta.rosetta.protocols.stepwise.legacy.screener) rna_backbone_backbone (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_backbone_backbone_pair_energy() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) RNA_base_atoms() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) rna_base_axis (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_base_axis_pairwise (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_base_backbone (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_base_backbone_pair_energy() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) rna_base_pair (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_base_pair_handler() (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) rna_base_pair_pairwise (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_base_pair_xy_filename() (pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions method) rna_base_stack (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_base_stack_axis (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_base_stack_axis_pairwise (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_base_stack_pairwise (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_base_stagger (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_base_stagger_pairwise (pyrosetta.rosetta.core.scoring.ScoreType attribute) RNA_BaseCentroidChecker (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker) RNA_BasePairHandler (class in pyrosetta.rosetta.core.import_pose) RNA_BasicOptions (class in pyrosetta.rosetta.core.import_pose.options) RNA_BLOCK_STACK_ABOVE (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) rna_block_stack_above_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) RNA_BLOCK_STACK_BELOW (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) rna_block_stack_below_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) rna_bond_geometry (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_bond_geometry_energy() (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) RNA_BULGE (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) rna_bulge (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_bulge_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) RNA_BulgeEnergy (class in pyrosetta.rosetta.core.energy_methods) RNA_BulgeEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) rna_centroid_info() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) RNA_CentroidInfo (class in pyrosetta.rosetta.core.scoring.rna) RNA_CHAIN_CLOSABLE_GEOMETRY (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) RNA_CHAIN_CLOSABLE_GEOMETRY_RESIDUE_BASED (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) RNA_CHAIN_CLOSABLE_GEOMETRY_STUB_BASED (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) RNA_CHAIN_CLOSURE (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) RNA_ChainClosableGeometryChecker (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker) RNA_ChainClosableGeometryResidueBasedScreener (class in pyrosetta.rosetta.protocols.stepwise.screener) RNA_ChainClosableGeometryScreener (class in pyrosetta.rosetta.protocols.stepwise.screener) RNA_ChainClosableGeometryStubBasedScreener (class in pyrosetta.rosetta.protocols.stepwise.screener) RNA_ChainClosureChecker (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker) RNA_ChainClosureScreener (class in pyrosetta.rosetta.protocols.stepwise.screener) rna_chem_map (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_chem_map_lores (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_chem_shift (pyrosetta.rosetta.core.scoring.ScoreType attribute) RNA_ChemicalMappingEnergy (class in pyrosetta.rosetta.core.energy_methods) RNA_ChemicalMappingEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) RNA_ChemicalShiftEnergy (class in pyrosetta.rosetta.core.energy_methods) RNA_ChemicalShiftEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) RNA_ChemicalShiftPotential (class in pyrosetta.rosetta.core.scoring.rna.chemical_shift) RNA_CHI (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) RNA_ChiStepWiseSampler (class in pyrosetta.rosetta.protocols.stepwise.sampler.rna) rna_chunk_library() (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) RNA_ChunkLibrary (class in pyrosetta.rosetta.core.import_pose.libraries) rna_coarse_dist (pyrosetta.rosetta.core.scoring.ScoreType attribute) RNA_CoarseDistEnergy (class in pyrosetta.rosetta.core.energy_methods) RNA_CoarseDistEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) RNA_Coarsify (class in pyrosetta.rosetta.protocols.rna.movers) RNA_CoarsifyCreator (class in pyrosetta.rosetta.protocols.rna.movers) RNA_CS_parameters (class in pyrosetta.rosetta.core.scoring.rna.chemical_shift) RNA_CS_residue_parameters (class in pyrosetta.rosetta.core.scoring.rna.chemical_shift) RNA_CSA_JobDistributor (class in pyrosetta.rosetta.protocols.rna.setup) rna_data() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) rna_data_backbone (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_data_base (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_data_info() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) RNA_DataBackboneEnergy (class in pyrosetta.rosetta.core.energy_methods) RNA_DataBackboneEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) RNA_DataInfo (class in pyrosetta.rosetta.core.pose.rna) RNA_DataReader (class in pyrosetta.rosetta.core.io.rna) RNA_Datum (class in pyrosetta.rosetta.core.pose.rna) RNA_Decoarsify (class in pyrosetta.rosetta.protocols.rna.movers) RNA_DecoarsifyCreator (class in pyrosetta.rosetta.protocols.rna.movers) RNA_DeNovoJobOutputter (class in pyrosetta.rosetta.protocols.jd2) RNA_DeNovoJobOutputterCreator (class in pyrosetta.rosetta.protocols.jd2) RNA_DeNovoMasterMover (class in pyrosetta.rosetta.protocols.rna.denovo.movers) RNA_DeNovoOptimizer (class in pyrosetta.rosetta.protocols.rna.movers) RNA_DeNovoParameters (class in pyrosetta.rosetta.core.import_pose) RNA_DeNovoPoseInitializer (class in pyrosetta.rosetta.protocols.rna.denovo) RNA_DeNovoProtocol (class in pyrosetta.rosetta.protocols.rna.denovo) RNA_DeNovoProtocolCreator (class in pyrosetta.rosetta.protocols.rna.denovo) RNA_DeNovoProtocolMover (class in pyrosetta.rosetta.protocols.rna.denovo.movers) RNA_DeNovoProtocolMoverCreator (class in pyrosetta.rosetta.protocols.rna.denovo.movers) RNA_DeNovoProtocolOptions (class in pyrosetta.rosetta.core.import_pose.options) RNA_DeNovoSetup (class in pyrosetta.rosetta.core.import_pose) RNA_DMS_LowResolutionPotential (class in pyrosetta.rosetta.core.scoring.rna.data) RNA_DMS_Potential (class in pyrosetta.rosetta.core.scoring.rna.data) rna_dna_match() (in module pyrosetta.rosetta.core.chemical.rna) RNA_ELEC_NBLIST (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) rna_elec_pair_nblist (pyrosetta.rosetta.core.scoring.min_pair_data attribute) RNA_EnergyMethodOptions (class in pyrosetta.rosetta.core.scoring.rna) rna_fa_atr_base (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_fa_elec_one_way() (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) RNA_FA_ElecEnergy (class in pyrosetta.rosetta.core.energy_methods) RNA_FA_ElecEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) rna_fa_rep_base (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_filtered_base_base_info() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) RNA_FilteredBaseBaseInfo (class in pyrosetta.rosetta.core.pose.rna) RNA_FittedTorsionInfo (class in pyrosetta.rosetta.core.chemical.rna) rna_fragment_library() (pyrosetta.rosetta.core.import_pose.libraries.RNA_LibraryManager method) rna_fragment_monte_carlo() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) rna_fragment_mover() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) RNA_FragmentHomologyExclusion (class in pyrosetta.rosetta.core.fragment.rna) RNA_FragmentMonteCarlo (class in pyrosetta.rosetta.protocols.rna.denovo) RNA_FragmentMonteCarloOptions (class in pyrosetta.rosetta.core.import_pose.options) RNA_FragmentMonteCarloOutputter (class in pyrosetta.rosetta.protocols.rna.denovo.output) RNA_FragmentMover (class in pyrosetta.rosetta.protocols.rna.denovo.movers) RNA_Fragments (class in pyrosetta.rosetta.core.fragment.rna) RNA_FullAtomStackingEnergy (class in pyrosetta.rosetta.core.energy_methods) RNA_FullAtomStackingEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) RNA_FullAtomVDW_BasePhosphate (class in pyrosetta.rosetta.core.energy_methods) RNA_FullAtomVDW_BasePhosphateCreator (class in pyrosetta.rosetta.core.energy_methods) rna_helix_mover() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) RNA_HelixAssembler (class in pyrosetta.rosetta.core.import_pose) RNA_HelixMover (class in pyrosetta.rosetta.protocols.rna.denovo.movers) RNA_IdealCoord (class in pyrosetta.rosetta.core.pose.rna) RNA_Info (class in pyrosetta.rosetta.core.chemical.rna) RNA_info() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) RNA_JobDistributor (class in pyrosetta.rosetta.protocols.rna.setup) rna_jr_suite (pyrosetta.rosetta.core.scoring.ScoreType attribute) RNA_JR_SuiteEnergy (class in pyrosetta.rosetta.core.energy_methods) RNA_JR_SuiteEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) rna_jump_library() (pyrosetta.rosetta.core.import_pose.libraries.RNA_LibraryManager method) rna_jump_library_cop() (pyrosetta.rosetta.core.import_pose.libraries.RNA_LibraryManager method) rna_jump_mover() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) RNA_JumpLibrary (class in pyrosetta.rosetta.core.import_pose.libraries) RNA_JumpMover (class in pyrosetta.rosetta.core.import_pose) RNA_KIC (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) RNA_KIC_Sampler (class in pyrosetta.rosetta.protocols.stepwise.sampler.rna) RNA_KINEMATIC_CLOSER (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) RNA_KinematicCloser (class in pyrosetta.rosetta.protocols.stepwise.sampler.rna) rna_legacy_output_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) RNA_LibraryManager (class in pyrosetta.rosetta.core.import_pose.libraries) RNA_LJ_BaseEnergy (class in pyrosetta.rosetta.core.energy_methods) RNA_LJ_BaseEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) rna_loop_closer() (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) RNA_LoopCloser (class in pyrosetta.rosetta.protocols.rna.movers) RNA_LowResolutionPotential (class in pyrosetta.rosetta.core.scoring.rna) RNA_LowResolutionPotentialCreator (class in pyrosetta.rosetta.core.scoring.rna) rna_mg_point (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_mg_point_indirect (pyrosetta.rosetta.core.scoring.ScoreType attribute) RNA_MgPointEnergy (class in pyrosetta.rosetta.core.energy_methods) RNA_MgPointEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) RNA_Minimizer (class in pyrosetta.rosetta.protocols.rna.denovo.movers) RNA_MinimizerOptions (class in pyrosetta.rosetta.core.import_pose.options) RNA_MonteCarloJobDistributor (class in pyrosetta.rosetta.protocols.rna.setup) RNA_Motif (class in pyrosetta.rosetta.core.scoring.rna) rna_motif (pyrosetta.rosetta.core.scoring.ScoreType attribute) RNA_Motifs (class in pyrosetta.rosetta.core.scoring.rna) RNA_MotifType (class in pyrosetta.rosetta.core.scoring.rna) RNA_NORTH_SUGAR (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) RNA_NUCLEOSIDE (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) RNA_NucleosideStepWiseSampler (class in pyrosetta.rosetta.protocols.stepwise.sampler.rna) RNA_O2PrimeMover (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna) rna_options() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) rna_pairing_list() (pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler method) (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) (pyrosetta.rosetta.core.import_pose.RNA_JumpMover method) RNA_PairingTemplate (class in pyrosetta.rosetta.core.import_pose.libraries) RNA_PairwiseLowResolutionEnergy (class in pyrosetta.rosetta.core.energy_methods) RNA_PairwiseLowResolutionEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) rna_params() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) rna_partition (pyrosetta.rosetta.core.scoring.ScoreType attribute) RNA_PartitionEnergy (class in pyrosetta.rosetta.core.energy_methods) RNA_PartitionEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) rna_protein_docking() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) rna_protein_docking_freq() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) rna_protein_docking_legacy() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) rna_raw_base_base_info() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) RNA_RawBaseBaseInfo (class in pyrosetta.rosetta.core.pose.rna) rna_reactivities() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) RNA_Reactivity (class in pyrosetta.rosetta.core.pose.rna) RNA_ReactivityType (class in pyrosetta.rosetta.core.pose.rna) RNA_Relaxer (class in pyrosetta.rosetta.protocols.rna.denovo.movers) rna_repulsive (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_repulsive_pair_energy() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) rna_residue_name_to_num() (in module pyrosetta.rosetta.core.scoring.rna) RNA_ResidueLevelTask (class in pyrosetta.rosetta.core.pack.task.rna) rna_rg (pyrosetta.rosetta.core.scoring.ScoreType attribute) RNA_SAMPLE_SUGAR (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) rna_sample_sugar_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) RNA_SCORING_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) rna_scoring_info_from_pose() (in module pyrosetta.rosetta.core.scoring.rna) RNA_ScoringInfo (class in pyrosetta.rosetta.core.scoring.rna) RNA_SecStruct (class in pyrosetta.rosetta.core.pose.rna) rna_secstruct() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) RNA_SECSTRUCT_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) rna_secstruct_legacy() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) RNA_SecStructLegacyInfo (class in pyrosetta.rosetta.core.pose.rna.secstruct_legacy) RNA_SilentStruct (class in pyrosetta.rosetta.core.io.silent) RNA_SilentStructCreator (class in pyrosetta.rosetta.core.io.silent) RNA_SOUTH_SUGAR (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) rna_stub_coord_hack (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_stub_coord_lr (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) RNA_StubCoordinateEnergy (class in pyrosetta.rosetta.core.energy_methods) RNA_StubCoordinateEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) RNA_SUGAR (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) rna_sugar_close (pyrosetta.rosetta.core.scoring.ScoreType attribute) RNA_SugarCloseEnergy (class in pyrosetta.rosetta.core.energy_methods) RNA_SugarCloseEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) RNA_SugarStepWiseSampler (class in pyrosetta.rosetta.protocols.stepwise.sampler.rna) rna_suite (pyrosetta.rosetta.core.scoring.ScoreType attribute) RNA_SUITE (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) rna_suite_lr (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) RNA_SuiteAssignment (class in pyrosetta.rosetta.core.pose.rna) RNA_SuiteEnergy (class in pyrosetta.rosetta.core.energy_methods) RNA_SuiteEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) RNA_SuiteInfo (class in pyrosetta.rosetta.core.pose.rna) RNA_SuiteName (class in pyrosetta.rosetta.core.pose.rna) RNA_SuitePotential (class in pyrosetta.rosetta.core.scoring.rna) RNA_SuiteStepWiseSampler (class in pyrosetta.rosetta.protocols.stepwise.sampler.rna) RNA_SYN_CHI (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) rna_syn_chi_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) rna_task() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) RNA_TERMINAL (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) rna_terminal_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) RNA_Torsion (class in pyrosetta.rosetta.core.chemical.rna) rna_torsion (pyrosetta.rosetta.core.scoring.ScoreType attribute) rna_torsion_sc (pyrosetta.rosetta.core.scoring.ScoreType attribute) RNA_TorsionEnergy (class in pyrosetta.rosetta.core.energy_methods) RNA_TorsionEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) RNA_TorsionMover (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna) RNA_TorsionPotential (class in pyrosetta.rosetta.core.scoring.rna) RNA_TorsionScreener (class in pyrosetta.rosetta.protocols.stepwise.sampler.screener) rna_update_last_controlling_chi() (pyrosetta.rosetta.core.chemical.rna.RNA_Info static method) rna_vdw (pyrosetta.rosetta.core.scoring.ScoreType attribute) RNA_VDW_BinChecker (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker) RNA_VDW_Energy (class in pyrosetta.rosetta.core.energy_methods) RNA_VDW_EnergyCreator (class in pyrosetta.rosetta.core.energy_methods) RNAAtomType (class in pyrosetta.rosetta) RNAIdealizeMover (class in pyrosetta.rosetta.protocols.rna.movers) RNAIdealizeMoverCreator (class in pyrosetta.rosetta.protocols.rna.movers) RNAseH (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) RNAThreadAndMinimizeMover (class in pyrosetta.rosetta.protocols.rna.movers) RNAThreadAndMinimizeMoverCreator (class in pyrosetta.rosetta.protocols.rna.movers) rng_type() (pyrosetta.rosetta.basic.random.RandomGeneratorSettings method) rnl_pose() (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) rnp_aa_to_rna_backbone (pyrosetta.rosetta.core.scoring.ScoreType attribute) rnp_base_pair (pyrosetta.rosetta.core.scoring.ScoreType attribute) rnp_env (pyrosetta.rosetta.core.scoring.ScoreType attribute) rnp_high_res_cycles() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) rnp_high_res_relax() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) RNP_HighResMover (class in pyrosetta.rosetta.protocols.rna.denovo.movers) RNP_LowResEnergy (class in pyrosetta.rosetta.core.energy_methods) RNP_LowResEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) RNP_LowResPairDistEnergy (class in pyrosetta.rosetta.core.energy_methods) RNP_LowResPairDistEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) RNP_LowResPairDistPotential (class in pyrosetta.rosetta.core.scoring.rna) RNP_LowResPotential (class in pyrosetta.rosetta.core.scoring.rna) RNP_LowResStackData (class in pyrosetta.rosetta.core.scoring.rna) RNP_LowResStackEnergy (class in pyrosetta.rosetta.core.energy_methods) RNP_LowResStackEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) rnp_min_first() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) rnp_pack_first() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) rnp_pair (pyrosetta.rosetta.core.scoring.ScoreType attribute) rnp_pair_dist (pyrosetta.rosetta.core.scoring.ScoreType attribute) rnp_ramp_rep() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) rnp_stack (pyrosetta.rosetta.core.scoring.ScoreType attribute) rnp_stack_xy (pyrosetta.rosetta.core.scoring.ScoreType attribute) rnp_vdw (pyrosetta.rosetta.core.scoring.ScoreType attribute) roc_curve() (pyrosetta.rosetta.numeric.RocCurve method) RocCurve (class in pyrosetta.rosetta.numeric) RocPoint (class in pyrosetta.rosetta.numeric) RocStatus (class in pyrosetta.rosetta.numeric) roll() (pyrosetta.rosetta.protocols.dna.DNABasestep method) rollback() (pyrosetta.rosetta.cppdb.backend.connection method) (pyrosetta.rosetta.cppdb.session method) (pyrosetta.rosetta.cppdb.transaction method) (pyrosetta.rosetta.utility.sql_database.session method) (pyrosetta.rosetta.utility.sql_database.transaction method) rollbackBatchEdit() (pyrosetta.rosetta.RDKit.RWMol method) rolling_score() (in module pyrosetta.rosetta.protocols.frag_picker.scores) RollMover (class in pyrosetta.rosetta.protocols.rigid) RollMoverCreator (class in pyrosetta.rosetta.protocols.rigid) ROMol (class in pyrosetta.rosetta.RDKit) root (pyrosetta.rosetta.core.chemical.carbohydrates.RootData property) root() (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.numeric.kdtree.KDTree method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) root1() (pyrosetta.rosetta.core.scoring.hbonds.Polynomial_1d method) (pyrosetta.rosetta.numeric.Polynomial_1d method) root2() (pyrosetta.rosetta.core.scoring.hbonds.Polynomial_1d method) (pyrosetta.rosetta.numeric.Polynomial_1d method) root_at_first_rigid_body() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) root_atom() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) root_expression() (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) root_from_code() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager static method) root_node_for_greedy_opt() (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover static method) RootData (class in pyrosetta.rosetta.core.chemical.carbohydrates) rootj() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) Rose (class in pyrosetta.rosetta.protocols.sic_dock) ROSETTA (pyrosetta.rosetta.protocols.cluster.calibur.EST_THRESHOLD_MODE attribute) rosetta2methyl() (pyrosetta.rosetta.protocols.noesy_assign.MethylNames method) rosetta2nmr() (pyrosetta.rosetta.protocols.noesy_assign.MethylNames method) rosetta_names_from_pdb_code() (pyrosetta.rosetta.core.io.NomenclatureManager static method) rosetta_num (pyrosetta.rosetta.core.io.raw_data.DisulfideFile attribute) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile.NumberingSystem attribute) rosetta_recharge_fullatom() (in module pyrosetta.rosetta.core.chemical) rosetta_res_type() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) rosetta_resName() (pyrosetta.rosetta.core.io.ResidueInformation method) rosetta_retype_fullatom() (in module pyrosetta.rosetta.core.chemical) rosetta_scripts_complex_type_naming_func() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser static method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsSchemaValidator static method) rosetta_scripts_element_name() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser static method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsSchemaValidator static method) RosettaModuleOptionType (class in pyrosetta.rosetta.utility.xsd_util) RosettaModuleType (class in pyrosetta.rosetta.utility.xsd_util) RosettaScriptsJobQueen (class in pyrosetta.rosetta.protocols.rosetta_scripts) RosettaScriptsOptionError (class in pyrosetta.rosetta.utility.excn) RosettaScriptsParser (class in pyrosetta.rosetta.protocols.rosetta_scripts) RosettaScriptsSchemaValidator (class in pyrosetta.rosetta.protocols.rosetta_scripts) RosettaTensorflowManager (class in pyrosetta.rosetta.basic.tensorflow_manager) RosettaTensorflowProtocolBase (class in pyrosetta.rosetta.basic.tensorflow_manager) RosettaThreadAllocation (class in pyrosetta.rosetta.basic.thread_manager) RosettaThreadAssignmentInfo (class in pyrosetta.rosetta.basic.thread_manager) RosettaThreadManager (class in pyrosetta.rosetta.basic.thread_manager) RosettaThreadManagerAdvancedAPIKey (class in pyrosetta.rosetta.basic.thread_manager) RosettaThreadManagerInitializationTracker (class in pyrosetta.rosetta.basic.thread_manager) RosettaThreadRequestOriginatingLevel (class in pyrosetta.rosetta.basic.thread_manager) RosI (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) RosO (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) ROT (class in pyrosetta.rosetta.protocols.splice) rot (pyrosetta.rosetta.core.pack.dunbrack.ChiSet property) (pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy property) rot() (pyrosetta.rosetta.numeric.Py_xyzTransform_double static method) (pyrosetta.rosetta.numeric.xyzTransform_double_t static method) (pyrosetta.rosetta.numeric.xyzTransform_float_t static method) rot1 (pyrosetta.rosetta.protocols.jumping.dofType attribute) rot2 (pyrosetta.rosetta.protocols.jumping.dofType attribute) ROT2res() (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation method) rot_center() (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover 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.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover 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.topology_broker.RigidBodyRandomTMHMover method) rot_deg() (pyrosetta.rosetta.numeric.Py_xyzTransform_double static method) (pyrosetta.rosetta.numeric.xyzTransform_double_t static method) (pyrosetta.rosetta.numeric.xyzTransform_float_t static method) rot_ind() (pyrosetta.rosetta.protocols.mean_field.RotProb method) rot_index (pyrosetta.rosetta.protocols.hbnet.HBondResStruct property) rot_level() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) rot_magnitude() (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) rot_matrices() (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) rot_matrix() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) rot_num (pyrosetta.rosetta.protocols.make_rot_lib.CentroidRotNum property) rot_number() (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptERotamerData method) rot_pose() (in module pyrosetta.rosetta.protocols.sic_dock) rot_prob_accumulation_limit_ (pyrosetta.rosetta.protocols.match.upstream.BuildSet property) rot_sample_from_name() (in module pyrosetta.rosetta.core.pack.task) rot_sets() (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) rot_well() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) ROT_X (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetric attribute) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetric.DOF attribute) ROT_Y (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetric attribute) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetric.DOF attribute) ROT_Z (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetric attribute) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetric.DOF attribute) rotamer() (pyrosetta.rosetta.core.conformation.RotamerSetBase method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_5_t method) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.core.pack_basic.RotamerSetsBase method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) rotamer_bb_torsion_indices() (pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification method) rotamer_bonds() (pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo method) rotamer_couplings() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) rotamer_couplings_exist() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) rotamer_data_cache() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) Rotamer_db_file() (pyrosetta.rosetta.protocols.splice.RotLibOut method) rotamer_energy() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) rotamer_energy_deriv() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) rotamer_for_moltenres() (pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.core.pack_basic.RotamerSetsBase method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) rotamer_for_residue() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) rotamer_from_chi() (in module pyrosetta.rosetta.core.pack.dunbrack) rotamer_from_chi_02() (in module pyrosetta.rosetta.core.pack.dunbrack) rotamer_id (pyrosetta.rosetta.protocols.loophash.BBExtraData property) rotamer_index() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptERotamerData method) rotamer_information_from_PDB_stream() (in module pyrosetta.rosetta.core.pack.rotamers) rotamer_is_glycine() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) rotamer_is_proline() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) rotamer_library() (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) rotamer_library_specification() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) rotamer_library_specification_nonconst() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) rotamer_links() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) rotamer_links_exist() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) rotamer_operations() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) rotamer_prob_buried() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) rotamer_prob_buried_semi() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) rotamer_prob_nonburied() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) rotamer_prob_nonburied_semi() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) rotamer_probability() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_float_t method) rotamer_recovery() (in module pyrosetta.rosetta.core.pack) rotamer_ref() (pyrosetta.rosetta.core.conformation.RotamerSetBase method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) rotamer_sampling_data_xml_schema_attributes() (in module pyrosetta.rosetta.core.pack.task.operation) rotamer_seq_sep() (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBondsTrieVsTrieCachedDataContainer method) rotamer_set_contains_rotamer() (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) rotamer_set_for_moltenres() (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets method) rotamer_set_for_moltenresidue() (pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) rotamer_set_for_res() (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets method) rotamer_set_for_residue() (pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) rotamer_sets() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) rotamer_sets_from_pose() (in module pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) ROTAMER_TRIALS (pyrosetta.rosetta.basic.ProfTag attribute) rotamer_trials() (in module pyrosetta.rosetta.core.pack) RotamerAssigningAnnealer (class in pyrosetta.rosetta.core.pack.annealer) RotamerBoltzCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) RotamerBoltzmannWeight (class in pyrosetta.rosetta.protocols.calc_taskop_filters) RotamerBoltzmannWeight2 (class in pyrosetta.rosetta.protocols.calc_taskop_filters) RotamerBoltzmannWeight2.ScoreType (class in pyrosetta.rosetta.protocols.calc_taskop_filters) RotamerBoltzmannWeight2Creator (class in pyrosetta.rosetta.protocols.calc_taskop_filters) RotamerBoltzmannWeightEvaluator (class in pyrosetta.rosetta.protocols.toolbox) RotamerBoltzmannWeightFeatures (class in pyrosetta.rosetta.protocols.features) RotamerBoltzmannWeightFeaturesCreator (class in pyrosetta.rosetta.protocols.features) RotamerBoltzmannWeightFilterCreator (class in pyrosetta.rosetta.protocols.calc_taskop_filters) RotamerBuildingData (class in pyrosetta.rosetta.core.pack.dunbrack) RotamerConstraint (class in pyrosetta.rosetta.core.pack.dunbrack) RotamerCouplings (class in pyrosetta.rosetta.core.pack.rotamer_set) RotamerDNAHBondFilter (class in pyrosetta.rosetta.protocols.dna) RotamerDots (class in pyrosetta.rosetta.core.pack.interaction_graph) RotamerDotsCache (class in pyrosetta.rosetta.core.pack.interaction_graph) RotamerDotsRadiusData (class in pyrosetta.rosetta.core.pack.interaction_graph) RotamerDumpMover (class in pyrosetta.rosetta.protocols.RotamerDump) RotamerExplosion (class in pyrosetta.rosetta.core.pack.task.operation) RotamerExplosionCreator (class in pyrosetta.rosetta.core.pack.task.operation) RotamerFeatures (class in pyrosetta.rosetta.protocols.features) RotamerFeaturesCreator (class in pyrosetta.rosetta.protocols.features) rotameric_amino_acids (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet property) rotameric_chi_mimic_EX_flags (pyrosetta.rosetta.protocols.match.upstream.ChiStrategy attribute) rotameric_chi_partition_sd_range (pyrosetta.rosetta.protocols.match.upstream.ChiStrategy attribute) rotameric_chi_step_by_value (pyrosetta.rosetta.protocols.match.upstream.ChiStrategy attribute) rotameric_chi_step_wi_sd_range (pyrosetta.rosetta.protocols.match.upstream.ChiStrategy attribute) rotameric_n_bb (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet property) rotameric_n_chi (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet property) RotamericData_1_1_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_1_2_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_1_3_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_1_4_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_1_5_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_2_1_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_2_2_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_2_3_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_2_4_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_2_5_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_3_1_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_3_2_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_3_3_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_3_4_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_3_5_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_4_1_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_4_2_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_4_3_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_4_4_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_4_5_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_5_1_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_5_2_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_5_3_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_5_4_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericData_5_5_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_1_1_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_1_2_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_1_3_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_1_4_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_1_5_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_2_1_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_2_2_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_2_3_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_2_4_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_2_5_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_3_1_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_3_2_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_3_3_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_3_4_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_3_5_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_4_1_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_4_2_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_4_3_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_4_4_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_4_5_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_5_1_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_5_2_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_5_3_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_5_4_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibrary_5_5_t (class in pyrosetta.rosetta.core.pack.dunbrack) RotamericSingleResidueDunbrackLibraryParser (class in pyrosetta.rosetta.core.pack.dunbrack) rotamerid (pyrosetta.rosetta.core.pack.annealer.RotSub property) RotamerizeMover (class in pyrosetta.rosetta.protocols.minimization_packing) RotamerLibrary (class in pyrosetta.rosetta.core.pack.dunbrack) RotamerLibraryInterpolationScratch (class in pyrosetta.rosetta.core.pack.dunbrack) RotamerLibraryScratchSpace (class in pyrosetta.rosetta.core.pack.dunbrack) RotamerLibrarySpecification (class in pyrosetta.rosetta.core.chemical.rotamers) RotamerLibrarySpecificationCreator (class in pyrosetta.rosetta.core.chemical.rotamers) RotamerLibrarySpecificationFactory (class in pyrosetta.rosetta.core.chemical.rotamers) RotamerLinks (class in pyrosetta.rosetta.core.pack.rotamer_set) RotamerOperation (class in pyrosetta.rosetta.core.pack.rotamer_set) RotamerPairEnergies (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) RotamerRecovery (class in pyrosetta.rosetta.protocols.pose_metric_calculators) (class in pyrosetta.rosetta.protocols.rotamer_recovery) RotamerRecoveryFactory (class in pyrosetta.rosetta.protocols.rotamer_recovery) RotamerRecoveryFeatures (class in pyrosetta.rosetta.protocols.features) RotamerRecoveryFeaturesCreator (class in pyrosetta.rosetta.protocols.features) RotamerRecoveryMover (class in pyrosetta.rosetta.protocols.rotamer_recovery) RotamerRecoveryMoverCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RotamerRotamerHasher (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) rotamers (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) rotamers_for_trials() (in module pyrosetta.rosetta.protocols.ligand_docking) rotamers_on_same_bbconf() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) RotamerSet (class in pyrosetta.rosetta.core.pack.rotamer_set) RotamerSet_ (class in pyrosetta.rosetta.core.pack.rotamer_set) RotamerSetBase (class in pyrosetta.rosetta.core.conformation) RotamerSetFactory (class in pyrosetta.rosetta.core.pack.rotamer_set) RotamerSetOperation (class in pyrosetta.rosetta.core.pack.rotamer_set) RotamerSets (class in pyrosetta.rosetta.core.pack.rotamer_set) rotamersets() (pyrosetta.rosetta.protocols.multistate_design.PackingState method) RotamerSetsBase (class in pyrosetta.rosetta.core.pack_basic) RotamerSetsFactory (class in pyrosetta.rosetta.core.pack.rotamer_set) RotamerSetsOperation (class in pyrosetta.rosetta.core.pack.rotamer_set) RotamerSubset (class in pyrosetta.rosetta.core.pack.rotamer_set) RotamerSubsetRepacker (class in pyrosetta.rosetta.protocols.pack_daemon) RotamerSubsets (class in pyrosetta.rosetta.core.pack.rotamer_set) RotamerTrialsMinMover (class in pyrosetta.rosetta.protocols.minimization_packing) RotamerTrialsMinMoverCreator (class in pyrosetta.rosetta.protocols.minimization_packing) RotamerTrialsMover (class in pyrosetta.rosetta.protocols.minimization_packing) RotamerTrialsMoverCreator (class in pyrosetta.rosetta.protocols.minimization_packing) RotamerTrialsRefiner (class in pyrosetta.rosetta.protocols.loop_modeling.refiners) RotamerTrialsRefinerCreator (class in pyrosetta.rosetta.protocols.loop_modeling.refiners) RotamerTrieBase (class in pyrosetta.rosetta.core.scoring.trie) Rotate (class in pyrosetta.rosetta.protocols.ligand_docking) rotate() (in module pyrosetta.bindings.pose) (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) rotate_anchor_to_x_axis() (in module pyrosetta.rosetta.core.pose.symmetry) rotate_around_atom() (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) rotate_around_downstream_centroid() (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) Rotate_info (class in pyrosetta.rosetta.protocols.ligand_docking) rotate_into_nucleobase_frame() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) rotate_into_phosphate_frame() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) rotate_segment() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) RotateCreator (class in pyrosetta.rosetta.protocols.ligand_docking) RotateJumpAxisMover (class in pyrosetta.rosetta.protocols.rigid) Rotates (class in pyrosetta.rosetta.protocols.ligand_docking) RotatesCreator (class in pyrosetta.rosetta.protocols.ligand_docking) RotateSegmentMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) RotateSegmentMoverCreator (class in pyrosetta.rosetta.protocols.denovo_design.movers) rotation() (pyrosetta.rosetta.core.kinematics.Stub method) (pyrosetta.rosetta.numeric.linear_algebra.EllipseParameters method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) rotation_ (pyrosetta.rosetta.protocols.electron_density.RBfitResult property) (pyrosetta.rosetta.protocols.loop_grower.SheetPositions property) rotation_angle() (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.xyzTransform_double_t method) (pyrosetta.rosetta.numeric.xyzTransform_float_t method) rotation_angle_degrees() (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.xyzTransform_double_t method) (pyrosetta.rosetta.numeric.xyzTransform_float_t method) rotation_axis() (in module pyrosetta.rosetta.numeric) (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.xyzTransform_double_t method) (pyrosetta.rosetta.numeric.xyzTransform_float_t method) rotation_axis_angle() (in module pyrosetta.rosetta.numeric) rotation_by_axis() (pyrosetta.rosetta.core.kinematics.Jump method) rotation_by_matrix() (pyrosetta.rosetta.core.kinematics.Jump method) rotation_cosine() (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.xyzTransform_double_t method) (pyrosetta.rosetta.numeric.xyzTransform_float_t method) rotation_matrix() (in module pyrosetta.rosetta.numeric) (pyrosetta.rosetta.basic.sampling.orientations.Quaternion method) (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) rotation_matrix_from_euler_angles() (in module pyrosetta.rosetta.core.scoring.nmr) rotation_sine() (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.xyzTransform_double_t method) (pyrosetta.rosetta.numeric.xyzTransform_float_t method) RotationMover (class in pyrosetta.rosetta.protocols.membrane) RotationMoverCreator (class in pyrosetta.rosetta.protocols.membrane) RotationRange (class in pyrosetta.rosetta.protocols.denovo_design.movers) RotationSearchPattern (class in pyrosetta.rosetta.protocols.hotspot_hashing) RotData (class in pyrosetta.rosetta.protocols.make_rot_lib) rotid_on_moltenresidue() (pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.core.pack_basic.RotamerSetsBase method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) RotLibdb (class in pyrosetta.rosetta.protocols.splice) RotLibOut (class in pyrosetta.rosetta.protocols.splice) RotLibOutCreator (class in pyrosetta.rosetta.protocols.splice) RotM (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data property) RotMatrix (class in pyrosetta.rosetta.protocols.mean_field) rotno (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.PlaceableRotamer property) rotno_2_packed_rotno() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) rotno_2_rotwell() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) RotProb (class in pyrosetta.rosetta.protocols.mean_field) rotprob() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) rots_from_pose() (pyrosetta.rosetta.protocols.pose_metric_calculators.RotamerRecovery method) rotset_for_moltenres() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) rotset_for_residue() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) RotSub (class in pyrosetta.rosetta.core.pack.annealer) rotwell() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_float_t method) rotwell_2_packed_rotno() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) rotwell_2_rotno() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) rotx (pyrosetta.rosetta.protocols.loophash.LegacyLeapIndex property) roty (pyrosetta.rosetta.protocols.loophash.LegacyLeapIndex property) rotz (pyrosetta.rosetta.protocols.loophash.LegacyLeapIndex property) round() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) round_expired() (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) round_to_float() (in module pyrosetta.rosetta.protocols.features.strand_assembly) round_to_Real() (in module pyrosetta.rosetta.protocols.features.strand_assembly) (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilter method) round_to_Size() (in module pyrosetta.rosetta.protocols.features.strand_assembly) rounds() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) roundtype (pyrosetta.rosetta.protocols.mpi_refinement.MethodParams property) roundtype() (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) row() (pyrosetta.rosetta.cppdb.statement method) (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) row_x() (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) row_y() (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) row_z() (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) RowDataBase (class in pyrosetta.rosetta.basic.database.insert_statement_generator) rows() (pyrosetta.rosetta.core.sequence.DP_Matrix method) (pyrosetta.rosetta.numeric.xyzMatrix_double_t static method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t static method) rp0 (pyrosetta.rosetta.core.scoring.fiber_diffraction.Hankel property) rpad() (in module pyrosetta.rosetta.ObjexxFCL) rpadded() (in module pyrosetta.rosetta.ObjexxFCL) RPM_FilterStats (class in pyrosetta.rosetta.core.scoring.motif) RPM_Type (class in pyrosetta.rosetta.core.scoring.motif) rpm_type1() (in module pyrosetta.rosetta.core.scoring.motif) rpm_type2() (in module pyrosetta.rosetta.core.scoring.motif) RPM_Type_NONE (pyrosetta.rosetta.core.scoring.motif.RPM_Type attribute) RPT_end_of_list (pyrosetta.rosetta.core.conformation.parametric.RealPerturbationType attribute) RPT_gaussian (pyrosetta.rosetta.core.conformation.parametric.RealPerturbationType attribute) RPT_uniform (pyrosetta.rosetta.core.conformation.parametric.RealPerturbationType attribute) RPT_unknown_type (pyrosetta.rosetta.core.conformation.parametric.RealPerturbationType attribute) RRComparer (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRComparerAutomorphicRMSD (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRComparerAutomorphicRMSDCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRComparerChiDiff (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRComparerChiDiffCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRComparerCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRComparerElecDensDiff (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRComparerElecDensDiffCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRComparerRotBins (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRComparerRotBinsCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRProtocol (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRProtocolCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRProtocolMinPack (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRProtocolMinPackCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRProtocolMover (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRProtocolMoverCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRProtocolPackRotamers (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRProtocolPackRotamersCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRProtocolReferenceStructure (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRProtocolReferenceStructureCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRProtocolRelax (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRProtocolRelaxCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRProtocolRotamerTrials (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRProtocolRotamerTrialsCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRProtocolRTMin (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRProtocolRTMinCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRReporter (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRReporterCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRReporterHuman (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRReporterHumanCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRReporterSimple (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRReporterSimpleCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRReporterSQLite (class in pyrosetta.rosetta.protocols.rotamer_recovery) RRReporterSQLiteCreator (class in pyrosetta.rosetta.protocols.rotamer_recovery) rsd (pyrosetta.rosetta.protocols.canonical_sampling.TorsionSpec property) rsd() (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.id.PartialAtomID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.optimization.DOF_Node method) (pyrosetta.rosetta.core.scoring.AtomNeighbor method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMove method) rsd1() (pyrosetta.rosetta.core.id.JumpID method) rsd1type() (pyrosetta.rosetta.core.scoring.ResidueExclParams method) rsd2() (pyrosetta.rosetta.core.id.JumpID method) rsd2type() (pyrosetta.rosetta.core.scoring.ResidueExclParams method) rsd_closest_to_chain_com() (in module pyrosetta.rosetta.protocols.membrane) rsd_closest_to_chain_tm_com() (in module pyrosetta.rosetta.protocols.membrane) rsd_closest_to_pose_tm_com() (in module pyrosetta.rosetta.protocols.membrane) rsd_id() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) rsd_neighbor_denominator() (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) rsd_rsd_energy() (pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential method) rsd_sasa() (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) rsd_set_from_cmd_line() (in module pyrosetta.rosetta.core.chemical) rsds() (pyrosetta.rosetta.protocols.nmr.pre.PREDistanceRecord method) rsigma (pyrosetta.rosetta.core.scoring.ScoreType attribute) rsigma_dot_initializer() (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential static method) Rsmn2x2 (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) Rsmn3x3 (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) Rsmn3x3_Half (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) rsrfilename() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) rstrip() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) rstrip_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) rstripped() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) rstripped_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) rswitch() (pyrosetta.rosetta.core.scoring.constraints.BoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) RT (class in pyrosetta.rosetta.core.kinematics) rt() (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) rt6() (pyrosetta.rosetta.core.scoring.motif.Xfrag method) (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.xyzTransform_double_t method) (pyrosetta.rosetta.numeric.xyzTransform_float_t method) rt_ (pyrosetta.rosetta.protocols.jumping.DisulfTemplate property) (pyrosetta.rosetta.protocols.jumping.PairingTemplate property) RT_from_epos() (pyrosetta.rosetta.core.scoring.disulfides.RT_helper static method) RT_helper (class in pyrosetta.rosetta.core.scoring.disulfides) rt_min() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) rt_templates() (pyrosetta.rosetta.protocols.jumping.MembraneJump method) RTConstraint (class in pyrosetta.rosetta.core.scoring.constraints) RTMin (class in pyrosetta.rosetta.core.pack) rtmin() (pyrosetta.rosetta.core.pack.RTMin method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) rtrim() (in module pyrosetta.rosetta.utility) Ru (pyrosetta.rosetta.core.chemical.element.Elements attribute) run() (in module pyrosetta.rosetta.protocols.ddg.CartesianddG) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.CartesianMinimizer method) (pyrosetta.rosetta.core.optimization.CMAES_Minimizer method) (pyrosetta.rosetta.core.optimization.GA_Minimizer method) (pyrosetta.rosetta.core.optimization.JJH_Minimizer method) (pyrosetta.rosetta.core.optimization.Minimizer method) (pyrosetta.rosetta.core.optimization.NelderMeadSimplex method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) (pyrosetta.rosetta.core.pack.annealer.DebuggingAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FASTERAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbCoupledRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbLinkingRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbPwatSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.MultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.annealer.RotamerAssigningAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SequenceSymmetricAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SimAnnealerBase method) (pyrosetta.rosetta.core.pack.annealer.SmartFixbbSimAnnealer method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.flexpack.annealer.FlexbbSimAnnealer method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.jd2.DebugOut_MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd2.MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd2.WriteOut_MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd3.chunk_library.MoverAndChunkLibraryJob method) (pyrosetta.rosetta.protocols.jd3.Job method) (pyrosetta.rosetta.protocols.jd3.jobs.MoverJob method) (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotential method) (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Sampler method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecovery method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolMinPack method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolPackRotamers method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolReferenceStructure method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRelax method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRotamerTrials method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRTMin method) (pyrosetta.rosetta.protocols.rpc.JSON_RPC method) (pyrosetta.rosetta.protocols.stepwise.StepWiseSampleAndScreen method) (pyrosetta.rosetta.protocols.wum.DatabaseEntryWorkUnit method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.WorkUnit_Wait method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.tests.bindings.core.test_pose.TestPoseIO method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent method) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs method) run_A_ANN_Prediction() (pyrosetta.rosetta.protocols.sparta.Sparta method) run_aio() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) run_blast() (in module pyrosetta.rosetta.protocols.tcr) run_boinc_debug() (in module pyrosetta.rosetta.protocols.abinitio) run_cluster() (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) run_command() (in module pyrosetta.rosetta.protocols.frag_picker) run_decomp_svd() (pyrosetta.rosetta.basic.svd.SVD_Solver method) run_function_in_threads() (pyrosetta.rosetta.basic.thread_manager.RosettaThreadManager method) run_mc() (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) run_metrics() (in module pyrosetta.rosetta.core.simple_metrics) run_pack() (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) run_packer() (pyrosetta.rosetta.protocols.multistate_design.PackingState method) run_psipred() (pyrosetta.rosetta.core.io.external.PsiPredInterface method) run_psipred_prob() (pyrosetta.rosetta.core.io.external.PsiPredInterface method) run_rattle1() (pyrosetta.rosetta.protocols.md.Rattle method) run_rattle2() (pyrosetta.rosetta.protocols.md.Rattle method) run_score_svd_on_matrix() (pyrosetta.rosetta.basic.svd.SVD_Solver method) run_score_svd_without_solving() (pyrosetta.rosetta.basic.svd.SVD_Solver method) run_shear_min_pack() (in module pyrosetta.rosetta.protocols.carbohydrates) run_solve_svd() (pyrosetta.rosetta.basic.svd.SVD_Solver method) RunAll (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover attribute) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover.ExecutionMode attribute) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe attribute) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe.ExecutionMode attribute) running_job() (pyrosetta.rosetta.protocols.jd3.job_distributors.JobExtractor method) RunSimpleMetricsMover (class in pyrosetta.rosetta.protocols.analysis.simple_metrics) RunSimpleMetricsMoverCreator (class in pyrosetta.rosetta.protocols.analysis.simple_metrics) runSpartaANN() (pyrosetta.rosetta.protocols.sparta.ANN method) runtime() (pyrosetta.rosetta.protocols.rpc.JSON_RPC method) RuntimeFeatures (class in pyrosetta.rosetta.protocols.features) RuntimeFeaturesCreator (class in pyrosetta.rosetta.protocols.features) rvjump_pose (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) RWMol (class in pyrosetta.rosetta.RDKit)