Index – S

S (pyrosetta.rosetta.core.chemical.element.Elements attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.AtomicOrbitalTypes attribute) s (pyrosetta.rosetta.core.optimization.lbfgs_iteration_data property) s() (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering method) (pyrosetta.rosetta.utility.py.Value method) s1() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing method) s1_ (pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2A_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3A_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t property) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t property) s1_end() (pyrosetta.rosetta.core.scoring.Hairpin method) s1_start() (pyrosetta.rosetta.core.scoring.Hairpin method) S2() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) s2() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing method) (pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO method) s2_ (pyrosetta.rosetta.ObjexxFCL.FArray3A_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t property) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t property) s2_end() (pyrosetta.rosetta.core.scoring.Hairpin method) s2_start() (pyrosetta.rosetta.core.scoring.Hairpin method) s2d() (pyrosetta.rosetta.utility.subset_mapping method) s3_ (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t property) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t property) s4_ (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t property) s_ik (pyrosetta.rosetta.protocols.cluster.Exemplar property) s_kk (pyrosetta.rosetta.protocols.cluster.DataPoint property) S_NITROSYLATION (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes attribute) S_p_sp3 (pyrosetta.rosetta.core.chemical.orbitals.orbital_type_enum attribute) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics attribute) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics.orbital_type_name attribute) S_PEPTOID (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) s_vectors (pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1.screw_construct_struct property) sa (pyrosetta.rosetta.core.scoring.ScoreType attribute) sa() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) SA_Energy (class in pyrosetta.rosetta.core.energy_methods) SA_EnergyCreator (class in pyrosetta.rosetta.core.energy_methods) sa_faraggi_max() (in module pyrosetta.rosetta.protocols.frag_picker) sa_norm() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) sa_weight() (pyrosetta.rosetta.core.scoring.packing.HolesParams method) saa (pyrosetta.rosetta.protocols.constel.ResMut property) SACCHARIDE (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType attribute) safe() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) safe_read() (in module pyrosetta.rosetta.core.chemical.gasteiger) safe_root_ (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) safe_secstruct() (in module pyrosetta.rosetta.protocols.jumping) (pyrosetta.rosetta.protocols.jumping.JumpSample method) safe_segment() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) safe_set_extended_torsions_and_idealize_loops() (in module pyrosetta.rosetta.protocols.loops) safe_write() (in module pyrosetta.rosetta.core.chemical.gasteiger) safely_append_polymer_residue_after_seqpos() (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) safely_prepare_statement() (in module pyrosetta.rosetta.basic.database) safely_prepend_polymer_residue_before_seqpos() (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) safely_read_from_database() (in module pyrosetta.rosetta.basic.database) safely_write_to_database() (in module pyrosetta.rosetta.basic.database) SaltBridgeCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) SaltBridgeFeatures (class in pyrosetta.rosetta.protocols.features) SaltBridgeFeaturesCreator (class in pyrosetta.rosetta.protocols.features) same() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.InnerMultiThreadingJob method) (pyrosetta.rosetta.protocols.minimization_packing.MinimalRotamer method) same_chain() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) same_dimensions() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) same_edge() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.TenANeighborEdge method) (pyrosetta.rosetta.core.scoring.TwelveANeighborEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) (pyrosetta.rosetta.protocols.jd3.JobDirectedEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) (pyrosetta.rosetta.utility.graph.DirectedEdge method) (pyrosetta.rosetta.utility.graph.Edge method) (pyrosetta.rosetta.utility.graph.LowMemEdge method) same_helix() (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) same_ignoring_spaces() (in module pyrosetta.rosetta.utility) same_link() (in module pyrosetta.rosetta.core.io) same_peak() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) same_pose() (in module pyrosetta.rosetta.protocols.denovo_design) same_residue_type() (pyrosetta.rosetta.protocols.minimization_packing.MinimalRotamer method) same_rsdpairs() (pyrosetta.rosetta.core.scoring.ResidueExclParams method) same_type() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.standard.StandardInnerLarvalJob method) same_type_as_me() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.id.SequenceMapping 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.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.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.Energies 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.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.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.numeric.interpolation.spline.CompoundInterpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.Interpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.SimpleInterpolator 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.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.jumping.ChainbreakDistFunc method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) SameChiBinComboGrouper (class in pyrosetta.rosetta.protocols.match.output) SameRotamerComboGrouper (class in pyrosetta.rosetta.protocols.match.output) SameSequenceAndDSPositionGrouper (class in pyrosetta.rosetta.protocols.match.output) SameSequenceGrouper (class in pyrosetta.rosetta.protocols.match.output) SameSign (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign attribute) SameStrand (class in pyrosetta.rosetta.protocols.jumping) sampind (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet property) SAMPLE (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) sample() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionSampler method) sample_abinitio_ (pyrosetta.rosetta.protocols.hybridization.detailedControlsTagSetting property) sample_all_chi() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) sample_all_conformers() (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) sample_all_rotations_at_jump() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) SAMPLE_APPLIER (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) SAMPLE_APPLIER_WITH_RESIDUE_LIST (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) sample_beta() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) sample_both_sugar_base_rotamer() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) sample_cis_peptide_bond (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) sample_conformation() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) sample_farnesyl() (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) sample_first() (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) sample_five_prime_phosphate() (pyrosetta.rosetta.core.pack.task.rna.RNA_ResidueLevelTask method) sample_fragments() (in module pyrosetta.rosetta.protocols.ddg.CartesianddG) sample_jump() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) sample_level() (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) sample_ligand() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) sample_loops() (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) sample_mode() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams method) sample_near_nucleoside_torsion() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) sample_near_suite_torsion() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) sample_o2prime_hydrogen() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) sample_ONLY_multiple_virtual_sugar() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) sample_pc (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) sample_pH() (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) sample_phosphates() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) sample_proton_chi() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) sample_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) sample_residues() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) sample_ring_conformers() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) sample_rna_chi() (pyrosetta.rosetta.core.pack.task.rna.RNA_ResidueLevelTask method) sample_second() (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) sample_strategy_for_chi() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) sample_strategy_for_chi_ (pyrosetta.rosetta.protocols.match.upstream.BuildSet property) sample_sugar (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarModeling property) sample_template_ (pyrosetta.rosetta.protocols.hybridization.detailedControlsTagSetting property) sample_third() (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) sample_three_prime_phosphate() (pyrosetta.rosetta.core.pack.task.rna.RNA_ResidueLevelTask method) sample_types() (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) sample_zero_probs_at() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) SampleApplier (class in pyrosetta.rosetta.protocols.stepwise.screener) SampleAtAlignedpositions() (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB method) SAMPLED_ROSETTA (pyrosetta.rosetta.protocols.cluster.calibur.EST_THRESHOLD_MODE attribute) sampleEnum (class in pyrosetta.rosetta.protocols.hybridization) SampleFarnesylMover (class in pyrosetta.rosetta.protocols.farnesyl) SampleFarnesylMoverCreator (class in pyrosetta.rosetta.protocols.farnesyl) SampleGrid (class in pyrosetta.rosetta.protocols.magnesium) sampler_ (pyrosetta.rosetta.protocols.stepwise.StepWiseSampleAndScreen property) sampler_assert_no_virt_sugar_sampling() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) sampler_extra_beta_rotamer() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) sampler_extra_epsilon_rotamer() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) sampler_include_torsion_value_in_tag() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) sampler_max_centroid_distance() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) sampler_num_pose_kept() (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) sampler_perform_phosphate_pack() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) sampler_silent_file() (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) sampler_try_sugar_instantiation() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) SampleRotamersFromPDB (class in pyrosetta.rosetta.protocols.splice) SampleRotamersFromPDB_RotamerSetOperation (class in pyrosetta.rosetta.protocols.splice) SampleRotamersFromPDBCreator (class in pyrosetta.rosetta.protocols.splice) SamplerPlusPlus (class in pyrosetta.rosetta.protocols.toolbox) SamplerPlusPlusType (class in pyrosetta.rosetta.protocols.toolbox) samples() (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler method) (pyrosetta.rosetta.protocols.match.upstream.ProteinSCSampler method) SampleSequenceFromProbabilities (class in pyrosetta.rosetta.protocols.simple_moves) SampleSequenceFromProbabilitiesCreator (class in pyrosetta.rosetta.protocols.simple_moves) SampleStrategyData (class in pyrosetta.rosetta.protocols.match.upstream) SampleTiltAngles (class in pyrosetta.rosetta.protocols.membrane.benchmark) SampleTiltAnglesCreator (class in pyrosetta.rosetta.protocols.membrane.benchmark) sampling_data() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT method) sampling_data_setup() (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction method) sampling_fold_tree() (pyrosetta.rosetta.protocols.abinitio.CoordinateConstraintKC method) (pyrosetta.rosetta.protocols.abinitio.KinematicControl method) sampling_id_for_current_rotamer() (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet method) sampling_protocol() (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) sampling_set() (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) sampling_temperature() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) sampLoc() (pyrosetta.rosetta.numeric.fourier.SO3coeffs method) SandwichFeatures (class in pyrosetta.rosetta.protocols.features.strand_assembly) SandwichFeaturesCreator (class in pyrosetta.rosetta.protocols.features.strand_assembly) SandwichFragment (class in pyrosetta.rosetta.protocols.features.strand_assembly) SaneDockingProtocol (class in pyrosetta.rosetta.protocols.docking.stateless) SaneMinMover (class in pyrosetta.rosetta.protocols.minimization_packing) SaneMinMoverCreator (class in pyrosetta.rosetta.protocols.minimization_packing) sanitize (pyrosetta.rosetta.core.chemical.rdkit.RestypeToRDMolOptions property) sanity_check() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.core.scoring.motif.MotifHash method) (pyrosetta.rosetta.core.scoring.motif.XformScore method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_double_t method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_float method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_float_t method) (pyrosetta.rosetta.protocols.sic_dock.xyzStripeHashPoseWithMeta method) SAnode (class in pyrosetta.rosetta.core.scoring) (class in pyrosetta.rosetta.core.scoring.power_diagram) sap_atom_sasa() (in module pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) sap_calculate_selector() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions method) sap_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) sap_goal() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions method) sap_lb_goal() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions method) sap_parameter_options() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric method) SapConstraint (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) SapConstraintEnergy (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) SapConstraintEnergyCreator (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) SapConstraintHelper (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) SapConstraintOptions (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) SapDatabase (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) SapMathConstraint (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) SapParameterOptions (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) SapScoreMetric (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) SapScoreMetricCreator (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) sasa (pyrosetta.rosetta.core.scoring.packstat.SimplePDB_Atom property) (pyrosetta.rosetta.core.scoring.packstat.Sphere property) SASA (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData property) sasa() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelicalFragment method) sasa_ (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo property) sasa_core() (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) sasa_lr (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) sasa_method_hp_mode() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) sasa_metric_mode() (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) sasa_metric_mode_from_name() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa static method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod static method) sasa_metric_name_from_mode() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa static method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod static method) sasa_selector() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions method) sasa_surface() (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) SasaCalc (class in pyrosetta.rosetta.core.scoring.sasa) SasaCalculator2 (class in pyrosetta.rosetta.core.pose.metrics.simple_calculators) SasaCalculatorLegacy (class in pyrosetta.rosetta.core.pose.metrics.simple_calculators) SASAEnergy (class in pyrosetta.rosetta.core.energy_methods) SASAEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) sasaF2() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) sasaF2_ (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo property) SasaMethod (class in pyrosetta.rosetta.core.scoring.sasa) SasaMethodEnum (class in pyrosetta.rosetta.core.scoring.sasa) SasaMethodHPMode (class in pyrosetta.rosetta.core.scoring.sasa) SasaMethodType_total (pyrosetta.rosetta.core.scoring.sasa.SasaMethodEnum attribute) SasaMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) SasaMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.metrics) SasaOptions (class in pyrosetta.rosetta.core.scoring.packstat) SASAPotential (class in pyrosetta.rosetta.core.scoring) SasaRadii (class in pyrosetta.rosetta.core.scoring.sasa) SasaRadii_total (pyrosetta.rosetta.core.scoring.sasa.SasaRadii attribute) SasaResult (class in pyrosetta.rosetta.core.scoring.packstat) satisfies() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalLengthRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyIntraSegmentRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementSet method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyResidueRetentionRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentDsspRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentLengthRequirement method) saturation (pyrosetta.rosetta.protocols.hbnet.DecoratedNetworkState property) save_aa_probabilities_to_file() (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover static method) save_all_in_one() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) SAVE_ARCHIVE (pyrosetta.rosetta.basic.ProfTag attribute) save_archive() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) save_binary() (pyrosetta.rosetta.protocols.cluster.APCluster method) save_candidates() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) save_checkpoint_file() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) save_cluster_tree() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) save_crash_report() (in module pyrosetta.rosetta.utility) save_crash_report_to_console() (in module pyrosetta.rosetta.utility) save_crash_report_to_file() (in module pyrosetta.rosetta.utility) save_db() (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) save_decoys() (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) save_energy() (pyrosetta.rosetta.core.scoring.constraints.CstResNeighbIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbIterator method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.ResidueNeighborIterator method) save_fragments() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) save_into_pose() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) save_jump_histogram() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) save_momento() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) save_MSAcst_file() (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) save_remarks() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) save_schema() (in module pyrosetta.rosetta.protocols.rosetta_scripts) save_scores() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) save_seq_name() (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) save_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.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) save_times() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) save_to_checkpoint() (pyrosetta.rosetta.protocols.splice.Splice method) save_to_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) save_trial_number_to_checkpoint() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) SaveAndRetrieveSidechains (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) SaveAndRetrieveSidechainsCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) saved_accept_file_name() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) saved_native_pose() (in module pyrosetta.rosetta.core.pose) saved_reference_pose() (in module pyrosetta.rosetta.core.pose) (in module pyrosetta.rosetta.protocols.rosetta_scripts) saved_trial_number_file() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) saveGDB() (pyrosetta.rosetta.protocols.sparta.GDB method) SavePDBInfoMover (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) SavePDBInfoMoverCreator (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) SavePoseConstraintToFileFilter (class in pyrosetta.rosetta.protocols.constraint_filters) SavePoseConstraintToFileFilterCreator (class in pyrosetta.rosetta.protocols.constraint_filters) SavePoseMover (class in pyrosetta.rosetta.protocols.rosetta_scripts) SavePoseMoverCreator (class in pyrosetta.rosetta.protocols.rosetta_scripts) SaveProbabilitiesMetricMover (class in pyrosetta.rosetta.protocols.simple_moves) SaveProbabilitiesMetricMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) SaveResfileToDiskFilter (class in pyrosetta.rosetta.protocols.simple_filters) SaveResfileToDiskFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) SaveSequenceToCommentsMover (class in pyrosetta.rosetta.protocols.simple_moves) SaveSequenceToCommentsMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) saveState() (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) SAXS (pyrosetta.rosetta.basic.ProfTag attribute) saxs_cen_score (pyrosetta.rosetta.core.scoring.ScoreType attribute) saxs_fa_score (pyrosetta.rosetta.core.scoring.ScoreType attribute) saxs_score (pyrosetta.rosetta.core.scoring.ScoreType attribute) SAXSEnergy (class in pyrosetta.rosetta.core.energy_methods) SAXSEnergyCEN (class in pyrosetta.rosetta.core.energy_methods) SAXSEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) SAXSEnergyCreatorCEN (class in pyrosetta.rosetta.core.energy_methods) SAXSEnergyCreatorFA (class in pyrosetta.rosetta.core.energy_methods) SAXSEnergyFA (class in pyrosetta.rosetta.core.energy_methods) SAXSScoreFilter (class in pyrosetta.rosetta.protocols.simple_filters) Sb (pyrosetta.rosetta.core.chemical.element.Elements attribute) sbisect() (in module pyrosetta.rosetta.numeric.kinematic_closure) sbumpc() (pyrosetta.rosetta.std.filebuf method) (pyrosetta.rosetta.std.streambuf method) (pyrosetta.rosetta.std.stringbuf method) (pyrosetta.rosetta.std.wstreambuf method) (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) Sc (pyrosetta.rosetta.core.chemical.element.Elements attribute) sc (pyrosetta.rosetta.core.scoring.sc._RESULTS property) (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueEntry property) SC_BB (pyrosetta.rosetta.core.scoring.motif.RPM_Type attribute) sc_bounding_sphere() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) SC_BRANCH_POINT (pyrosetta.rosetta.core.chemical.VariantType attribute) SC_FRAGMENT (pyrosetta.rosetta.core.chemical.VariantType attribute) sc_H_orbital() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics method) sc_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) SC_ONLY (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph attribute) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph.Subsitution attribute) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph attribute) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph.Subsitution attribute) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph attribute) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph.Subsitution attribute) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph attribute) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph.Subsitution attribute) sc_only() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareSASAFilter method) SC_ORBITALS (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) SC_PH (pyrosetta.rosetta.core.scoring.motif.RPM_Type attribute) SC_PO (pyrosetta.rosetta.core.scoring.motif.RPM_Type attribute) sc_sc (pyrosetta.rosetta.core.pack.interaction_graph.ResiduePairEvalType attribute) SC_SC (pyrosetta.rosetta.core.scoring.motif.RPM_Type attribute) SC_TIP_ONLY (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover.AtomSelector attribute) sc_tip_only() (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) sc_value (pyrosetta.rosetta.protocols.analysis.InterfaceData property) sc_whole (pyrosetta.rosetta.core.pack.interaction_graph.ResiduePairEvalType attribute) scaf_name() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) scaffold_build_id() (pyrosetta.rosetta.protocols.match.Hit method) (pyrosetta.rosetta.protocols.match.upstream_hit method) ScaffoldBuildPoint (class in pyrosetta.rosetta.protocols.match.upstream) scaffoldHigh (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes property) scaffoldLow (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes property) scalar() (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) scalar_weighted() (in module pyrosetta.rosetta.protocols.constraint_generator) ScalarOption (class in pyrosetta.rosetta.utility.options) ScalarOption_T_utility_options_BooleanOptionKey_bool_t (class in pyrosetta.rosetta.utility.options) ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t (class in pyrosetta.rosetta.utility.options) ScalarOption_T_utility_options_IntegerOptionKey_int_t (class in pyrosetta.rosetta.utility.options) ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t (class in pyrosetta.rosetta.utility.options) ScalarOption_T_utility_options_RealOptionKey_double_t (class in pyrosetta.rosetta.utility.options) ScalarOption_T_utility_options_StringOptionKey_std_string_t (class in pyrosetta.rosetta.utility.options) ScalarOptionKey (class in pyrosetta.rosetta.utility.options) ScalarWeightedFunc (class in pyrosetta.rosetta.core.scoring.func) scale() (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t method) SCALE1 (pyrosetta.rosetta.core.io.pdb.RecordType attribute) SCALE2 (pyrosetta.rosetta.core.io.pdb.RecordType attribute) SCALE3 (pyrosetta.rosetta.core.io.pdb.RecordType attribute) scale_ (pyrosetta.rosetta.core.scoring.hbonds.AssignmentScaleAndDerivVectID property) scale_axis_stagger() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) scale_diag (pyrosetta.rosetta.numeric.nls.lm_control_struct property) scale_factor() (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff method) scale_inneriterations() (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.flexpack.annealer.FlexbbSimAnnealer method) scale_outeriterations() (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.flexpack.annealer.FlexbbSimAnnealer method) scale_target_proximity_to_other_conformations() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) scale_target_proximity_to_starting_conformation() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) scale_temperatures() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) scale_twobody_energy() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) scaleIntensities() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) ScaleMapIntensities (class in pyrosetta.rosetta.protocols.electron_density) ScaleMapIntensitiesCreator (class in pyrosetta.rosetta.protocols.electron_density) scaling() (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) SCAN (class in pyrosetta.rosetta.core.pack.task) scan() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticScanner method) (pyrosetta.rosetta.numeric.expression_parser.BooleanExpressionScanner method) SCdisplay_state (pyrosetta.rosetta.protocols.viewer.GraphicsState property) SCdisplayState (class in pyrosetta.rosetta.protocols.viewer.graphics_states_param) scfxn_rules_for_energy() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) scfxn_rules_for_weight() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) scheduled() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) Scheduler (class in pyrosetta.rosetta.protocols.mpi_refinement) Schema (class in pyrosetta.rosetta.basic.database.schema_generator) schema() (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.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.RadiusOfGyrationFeatures 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.UnrecognizedAtomFeatures method) (pyrosetta.rosetta.protocols.features.WaterFeatures method) schema_ct_naming_function() (pyrosetta.rosetta.protocols.chemistries.ChemistryLoaderCreator method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoaderCreator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoaderCreator method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoaderCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoaderCreator method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DatabaseSessionLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator method) (pyrosetta.rosetta.protocols.parser.FragSetLoaderCreator method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoaderCreator method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoaderCreator method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoaderCreator method) (pyrosetta.rosetta.protocols.parser.PackerPaletteLoaderCreator method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoaderCreator method) (pyrosetta.rosetta.protocols.parser.ResLvlTaskOperationLoaderCreator method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoaderCreator method) (pyrosetta.rosetta.protocols.parser.SimpleMetricLoaderCreator method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoaderCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoaderCreator method) schema_for_resource_definition_file() (pyrosetta.rosetta.basic.resource_manager.ResourceManager static method) schema_has_been_set() (pyrosetta.rosetta.utility.tag.XMLValidator method) scheme_types_ (pyrosetta.rosetta.core.sequence.ScoringSchemeFactory property) SchemePlaceMotifsMover (class in pyrosetta.rosetta.protocols.matdes) SchemePlaceMotifsMoverCreator (class in pyrosetta.rosetta.protocols.matdes) scind (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet property) scmin_numerical_derivative_check() (pyrosetta.rosetta.core.pack.scmin.SCMinMultifunc method) SCMinMinimizerMap (class in pyrosetta.rosetta.core.pack.scmin) SCMinMultifunc (class in pyrosetta.rosetta.core.pack.scmin) SCORE (pyrosetta.rosetta.basic.ProfTag attribute) score (pyrosetta.rosetta.core.fragment.picking_old.vall.scores.VallFragmentScore property) (pyrosetta.rosetta.core.scoring.packing.HolesResult property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult property) (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.ResultElements property) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.PlaceableRotamer property) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover.tm_region property) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter.tm_region property) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member property) score() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.FragData method) (pyrosetta.rosetta.core.optimization.Particle 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.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.DockingScoreFunction 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.hbonds.graph.HBondEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint 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.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleScore method) (pyrosetta.rosetta.core.scoring.mm.MMBondLengthScore method) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.core.scoring.packstat.PackingScore method) (pyrosetta.rosetta.core.scoring.ProQPotential method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.core.sequence.Cell method) (pyrosetta.rosetta.core.sequence.ChemicalShiftScoringScheme method) (pyrosetta.rosetta.core.sequence.CompassScoringScheme method) (pyrosetta.rosetta.core.sequence.CompositeScoringScheme 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.SequenceAlignment method) (pyrosetta.rosetta.core.sequence.SimpleScoringScheme method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric static method) (pyrosetta.rosetta.numeric.RocPoint 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.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.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.fldsgn.potentials.sspot.HSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction 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.frag_picker.scores.ABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) (pyrosetta.rosetta.protocols.hbnet.HBNetScore method) (pyrosetta.rosetta.protocols.hbnet.NetworkState method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilter method) (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyAssemblyScoreFunction method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyAssemblyScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyBlosumScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyCalciumMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyClashScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyInterModelMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyPartnerMotifScorer method) (pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilter method) (pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilter method) (pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilter method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy 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.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.MatchEvaluator 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.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint 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.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) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.recon_design.FitnessFilter method) (pyrosetta.rosetta.protocols.residue_optimization.MetapatchEnumeration 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.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandAssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorer method) (pyrosetta.rosetta.protocols.sic_dock.BuriedPolarScore method) (pyrosetta.rosetta.protocols.sic_dock.CBScore method) (pyrosetta.rosetta.protocols.sic_dock.ConstraintSetScore method) (pyrosetta.rosetta.protocols.sic_dock.EdgeStandScore method) (pyrosetta.rosetta.protocols.sic_dock.HelixScore method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.sic_dock.LinkerScore method) (pyrosetta.rosetta.protocols.sic_dock.RigidScore method) (pyrosetta.rosetta.protocols.sic_dock.scores.MotifHashRigidScore method) (pyrosetta.rosetta.protocols.sic_dock.scores.TrisBpyScore method) (pyrosetta.rosetta.protocols.sic_dock.XfoxmScore 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) (pyrosetta.rosetta.protocols.simple_moves.FragmentCost method) (pyrosetta.rosetta.protocols.simple_moves.GunnCost method) (pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoint method) score1 (pyrosetta.rosetta.core.scoring.motif.MotifHit property) score2 (pyrosetta.rosetta.core.scoring.motif.MotifHit property) score_ (pyrosetta.rosetta.protocols.electron_density.RBfitResult property) (pyrosetta.rosetta.protocols.electron_density.RefinementResult property) score_alignment() (in module pyrosetta.rosetta.protocols.tcr) score_and_add_energies_to_map() (pyrosetta.rosetta.core.io.raw_data.ScoreMap static method) score_and_dump_natives() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) score_and_output() (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) score_atom_pair() (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) score_basis() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) score_basis_125() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) score_basis_pair() (pyrosetta.rosetta.protocols.sewing.hashing.Hasher method) SCORE_BEGIN_NOTIFY (pyrosetta.rosetta.basic.ProfTag attribute) score_by_scoretype() (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) score_constraints() (pyrosetta.rosetta.protocols.ligand_docking.Transform method) score_cut() (pyrosetta.rosetta.protocols.magnesium.MgScanner method) score_cut_count (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Filterer_Count property) score_cut_PDB() (pyrosetta.rosetta.protocols.magnesium.MgScanner method) score_cutoff_ (pyrosetta.rosetta.protocols.pose_sewing.filters.CSSettings property) score_d2() (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilter method) score_delta() (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) score_diff_after_minimization() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) score_disulfide() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential method) SCORE_DOT (pyrosetta.rosetta.basic.ProfTag attribute) SCORE_END_NOTIFY (pyrosetta.rosetta.basic.ProfTag attribute) score_extra() (pyrosetta.rosetta.protocols.sic_dock.scores.TrisBpyScore method) score_file() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) score_filter (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) score_filter() (pyrosetta.rosetta.core.io.silent.SilentFileData method) SCORE_FINALIZE (pyrosetta.rosetta.basic.ProfTag attribute) score_for_aa_pair() (pyrosetta.rosetta.core.sequence.Blosum62Map method) score_fragment() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) score_fragment_from_cache() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) score_full() (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) score_fun8() (pyrosetta.rosetta.protocols.hybridization.TMalign method) score_function() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.ddg.ddGMover 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.PDBOutput method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover 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.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.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.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) (pyrosetta.rosetta.protocols.moves.SimulatedTempering method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) score_function_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader static method) score_fxn() (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) score_hybrid() (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) score_id_name() (pyrosetta.rosetta.protocols.fold_from_loops.filters.ScorePoseSegmentFromResidueSelectorFilter method) score_init() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) score_ligand() (pyrosetta.rosetta.protocols.ligand_docking.Transform method) score_ligands() (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) SCORE_LINE_STRINGS (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) score_log_file() (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) SCORE_LONG_RANGE_ENERGIES (pyrosetta.rosetta.basic.ProfTag attribute) SCORE_MAP (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) score_map (pyrosetta.rosetta.protocols.qsar.qsarOptData property) score_map() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) score_matrix_rmsd() (pyrosetta.rosetta.protocols.hybridization.TMalign method) score_matrix_rmsd_sec() (pyrosetta.rosetta.protocols.hybridization.TMalign method) score_meta() (pyrosetta.rosetta.protocols.sic_dock.scores.MotifHashRigidScore method) score_multiply() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) score_multiply_factor() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) SCORE_NEIGHBOR_ENERGIES (pyrosetta.rosetta.basic.ProfTag attribute) score_of_bin() (pyrosetta.rosetta.core.scoring.motif.XformScore method) score_of_bin_normalized() (pyrosetta.rosetta.core.scoring.motif.XformScore method) score_one() (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) SCORE_ONEBODY_ENERGIES (pyrosetta.rosetta.basic.ProfTag attribute) score_only (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) score_only() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) score_output_file_name() (pyrosetta.rosetta.protocols.match.MatcherTask method) score_pairmatrix() (pyrosetta.rosetta.protocols.fldsgn.filters.ParallelBetaPairingPreferenceFilter method) score_pose() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.sparta.Sparta method) score_pose_per_residue() (pyrosetta.rosetta.protocols.sparta.Sparta method) score_res_z() (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) score_selector() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions method) SCORE_SETUP (pyrosetta.rosetta.basic.ProfTag attribute) score_table_filename() (pyrosetta.rosetta.core.io.StructFileRep method) score_table_labels() (pyrosetta.rosetta.core.io.StructFileRep method) score_table_lines() (pyrosetta.rosetta.core.io.StructFileRep method) score_table_weights() (pyrosetta.rosetta.core.io.StructFileRep method) score_term_ (pyrosetta.rosetta.protocols.features.TopCountOfAllInputs property) (pyrosetta.rosetta.protocols.features.TopCountOfEachInput property) score_this_disulfide() (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfidePotential method) score_this_disulfide_old() (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfidePotential method) score_threshold() (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) score_tuple() (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCost method) (pyrosetta.rosetta.protocols.simple_moves.GunnCost method) score_type (pyrosetta.rosetta.protocols.mpi_refinement.MethodParams property) score_type() (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.DOF_Constraint 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.helical_bundle.BundleReporterFilter method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.simple_filters.EnergyPerResidueFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueIEFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter method) (pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation method) score_type_2_active() (pyrosetta.rosetta.core.scoring.EnergyGraph method) score_type_from_name() (in module pyrosetta.rosetta.core.scoring) (pyrosetta.rosetta.core.scoring.ScoreTypeManager static method) score_type_name() (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter method) (pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation method) score_type_threshold() (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) score_types() (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.PolymerBondedEnergyContainer 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) score_types_by_method_type() (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) score_types_for_method() (pyrosetta.rosetta.core.energy_methods.AACompositionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.AARepeatEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.AbegoEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.BranchEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.Burial_v2EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.BurialEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CCS_IMMSEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifDegreeEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ChainbreakEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ChemicalShiftAnisotropyEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ContactOrderEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.D2H_SA_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DEEREnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DipolarCouplingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DirectReadoutEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DistanceChainbreakEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DNA_EnvPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.EnvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAllCreator method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAroCreator method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FastSAXSEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyDensCreator method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.GoapEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.HolesEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.IntermolEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.LinearBranchEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.LinearChainbreakEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.LK_hackCreator method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.LoopCloseEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvPenaltiesCreator method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MembraneLipoCreator method) (pyrosetta.rosetta.core.energy_methods.MgEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MissingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebodyCreator method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.OtherPoseEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.P_AA_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.PackStatEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.PairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.pHEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ProQ_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2BCreator method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonicalCreator method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy_RohlCreator method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_FastCreator method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_RNACreator method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RMS_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalMappingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalShiftEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphateCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_PartitionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SA_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SASAEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCreatorCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCreatorFA method) (pyrosetta.rosetta.core.energy_methods.SecondaryStructureEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SurfEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SurfVolEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.XtalMLEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergyCreator method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergyCreator method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergyCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenaltyCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenaltyCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergyCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomePackEnergyCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergyCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergyCreator method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergyCreator method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergyCreator method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergyCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergyCreator method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergyCreator method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergyCreator method) (pyrosetta.rosetta.core.scoring.etable.EtableClassicIntraEnergyCreator method) (pyrosetta.rosetta.core.scoring.etable.EtableEnergyCreator method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergyCreator method) (pyrosetta.rosetta.core.scoring.interface_.DDPscoreCreator method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergyCreator method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergyCreator method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergyCreator method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInterCreator method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntraCreator method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergyCreator method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergyCreator method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergyCreator method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergyCreator method) (pyrosetta.rosetta.core.scoring.nv.NVscoreCreator method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScoreCreator method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotentialCreator method) (pyrosetta.rosetta.core.scoring.sym_e.symECreator method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_EnergyCreator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergyCreator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergyCreator method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergyCreator method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergyCreator method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergyCreator method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergyCreator method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.EnsembleEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PseudocontactShiftEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PseudocontactShiftEnergyCreator_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PseudocontactShiftEnergyCreator_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PseudocontactShiftEnergyCreator_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PseudocontactShiftEnergyCreator_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.ResidualDipolarCouplingEnergyRigidSegmentsCreator method) (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergyCreator method) score_variation() (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) score_variations() (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) score_zero_scores() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) ScoreCache (class in pyrosetta.rosetta.core.energy_methods) ScoreCutoffFilter (class in pyrosetta.rosetta.protocols.score_filters) ScoreCutoffFilterCreator (class in pyrosetta.rosetta.protocols.score_filters) scored (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) scored_base_pair_list() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) scored_base_stack_list() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) scored_frag_close() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) scored_frag_cycle_ratio() (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) ScoredBridgingWater (class in pyrosetta.rosetta.core.scoring.lkball) ScoreEValuator (class in pyrosetta.rosetta.protocols.frag_picker.scores) ScoreEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) scorefile_name() (pyrosetta.rosetta.protocols.dna.PDBOutput method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmtfJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) ScoreFileData (class in pyrosetta.rosetta.core.io.raw_data) ScoreFileData.const_iterator (class in pyrosetta.rosetta.core.io.raw_data) ScoreFileData.iterator (class in pyrosetta.rosetta.core.io.raw_data) ScoreFileOutputSpecification (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) ScoreFileOutputter (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) ScoreFileOutputterCreator (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) ScoreFileSilentStruct (class in pyrosetta.rosetta.core.io.silent) ScoreFileSilentStructCreator (class in pyrosetta.rosetta.core.io.silent) ScoreFunction (class in pyrosetta.rosetta.core.scoring) (pyrosetta.rosetta.basic.citation_manager.CitedModuleType attribute) scorefunction() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) scorefunction_ptr() (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) ScoreFunctionFactory (class in pyrosetta.rosetta.core.scoring) ScoreFunctionFeatures (class in pyrosetta.rosetta.protocols.features) ScoreFunctionFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ScoreFunctionInfo (class in pyrosetta.rosetta.core.scoring) ScoreFunctionKey (class in pyrosetta.rosetta.core.scoring) ScoreFunctionLoader (class in pyrosetta.rosetta.protocols.parser) ScoreFunctionLoaderCreator (class in pyrosetta.rosetta.protocols.parser) scorefxn() (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover 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.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator 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) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.TotalScoreFeatures method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ScorePoseSegmentFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelector method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ShortLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover 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.MgScanner method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.multistate_design.MultiStateFitnessFunction method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.simple_ddg.AlaScan method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScan method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter method) (pyrosetta.rosetta.protocols.simple_filters.EnergyPerResidueFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueIEFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover 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.SpliceManager method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWiseMasterPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) (pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation method) scorefxn_cen_cst() (pyrosetta.rosetta.protocols.loophash.LocalInserter_SimpleMin method) scorefxn_dens (pyrosetta.rosetta.protocols.electron_density.MinimizePoseIntoDensityOptions property) scorefxn_docking() (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) scorefxn_low() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) scorefxn_minimize() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize 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) scorefxn_obj() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) scorefxn_pack() (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) scorefxn_packing() (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) scorefxn_rama_cst() (pyrosetta.rosetta.protocols.loophash.LocalInserter_SimpleMin method) scorefxn_refine (pyrosetta.rosetta.protocols.electron_density.MinimizePoseIntoDensityOptions property) scorefxn_refine_rb (pyrosetta.rosetta.protocols.electron_density.MinimizePoseIntoDensityOptions property) scorefxn_repack() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize 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) scorefxn_update_from_options() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) scorefxn_weight_ (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.HBondBonusOptions property) scorefxns() (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) ScoreJumpFileSilentStruct (class in pyrosetta.rosetta.core.io.silent) ScoreJumpFileSilentStructCreator (class in pyrosetta.rosetta.core.io.silent) scoreline_prefix() (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) ScoreMap (class in pyrosetta.rosetta.core.io.raw_data) ScoreMover (class in pyrosetta.rosetta.protocols.simple_moves) ScoreMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) ScoreNormalization (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) ScoreOnlyJobOutputter (class in pyrosetta.rosetta.protocols.jd2) ScoreOnlyJobOutputterCreator (class in pyrosetta.rosetta.protocols.jd2) ScorePoseSegmentFromResidueSelectorFilter (class in pyrosetta.rosetta.protocols.fold_from_loops.filters) ScorePoseSegmentFromResidueSelectorFilterCreator (class in pyrosetta.rosetta.protocols.fold_from_loops.filters) Scorer (class in pyrosetta.rosetta.protocols.stepwise.screener) SCORER (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) ScoreRmsPoint (class in pyrosetta.rosetta.protocols.toolbox) ScoreRmsPoints (class in pyrosetta.rosetta.protocols.toolbox) scores (pyrosetta.distributed.packed_pose.core.PackedPose attribute) (pyrosetta.rosetta.core.pose.Pose property) scores() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.core.sequence.SequenceAlignment method) scores_ (pyrosetta.rosetta.core.energy_methods.ScoreCache property) (pyrosetta.rosetta.core.scoring.motif.XformScore property) scores_present() (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) ScoreStructJSON (class in pyrosetta.rosetta.core.io.raw_data) ScoreStructText (class in pyrosetta.rosetta.core.io.raw_data) ScoreTerm (pyrosetta.rosetta.basic.citation_manager.CitedModuleType attribute) ScoreTermValueBasedSelector (class in pyrosetta.rosetta.core.select.residue_selector) ScoreTermValueBasedSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) ScoreType (class in pyrosetta.rosetta.core.scoring) ScoreTypeFeatures (class in pyrosetta.rosetta.protocols.features) ScoreTypeFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ScoreTypeFilter (class in pyrosetta.rosetta.protocols.score_filters) ScoreTypeFilterCreator (class in pyrosetta.rosetta.protocols.score_filters) ScoreTypeManager (class in pyrosetta.rosetta.core.scoring) scoring() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) scoring_begin() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) scoring_end() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) scoring_grid_loader_ct_namer() (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader static method) scoring_grid_xml_schema_group_name() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridFactory static method) scoring_matrix() (pyrosetta.rosetta.core.sequence.MatrixScoringScheme method) scoring_schemes() (pyrosetta.rosetta.core.sequence.CompositeScoringScheme method) scoringEval_counter (pyrosetta.rosetta.protocols.match.downstream.ScoringSecMatchRPE property) ScoringGridLoader (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) ScoringGridLoaderCreator (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) ScoringManager (class in pyrosetta.rosetta.core.scoring) ScoringScheme (class in pyrosetta.rosetta.core.sequence) ScoringSchemeFactory (class in pyrosetta.rosetta.core.sequence) ScoringSecMatchRPE (class in pyrosetta.rosetta.protocols.match.downstream) SCPA_cterm_isopeptide_lariat (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type attribute) SCPA_cyclization_type (class in pyrosetta.rosetta.protocols.cyclic_peptide_predict) SCPA_invalid_type (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type attribute) SCPA_n_to_c_amide_bond (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type attribute) SCPA_nterm_isopeptide_lariat (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type attribute) SCPA_number_of_types (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type attribute) SCPA_sidechain_isopeptide (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type attribute) SCPA_terminal_disulfide (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type attribute) SCPA_thioether_lariat (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SCPA_cyclization_type attribute) scratch_dir() (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.ExternalEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluator method) scratch_pose() (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepLibrary method) screen() (pyrosetta.rosetta.protocols.stepwise.sampler.screener.RNA_TorsionScreener method) screen_all() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) screen_phosphate() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) screeners_ (pyrosetta.rosetta.protocols.stepwise.StepWiseSampleAndScreen property) SCREENING_FILE (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum attribute) ScreeningFeatures (class in pyrosetta.rosetta.protocols.features) ScreeningFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ScreeningJobInputter (class in pyrosetta.rosetta.protocols.jd2) ScreeningJobInputterCreator (class in pyrosetta.rosetta.protocols.jd2) ScriptCM (class in pyrosetta.rosetta.protocols.environment) scriptcm_group_name() (pyrosetta.rosetta.protocols.environment.ScriptCM static method) scriptcm_subelement_ct_namer() (pyrosetta.rosetta.protocols.environment.ScriptCM static method) ScriptCMCreator (class in pyrosetta.rosetta.protocols.environment) SCS_Antibody_Database_Result (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_Base (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_BlastComparator (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_BlastComparator_BitScore_Resolution (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_BlastFilter_by_alignment_length (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_BlastFilter_by_OCD (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_BlastFilter_by_outlier (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_BlastFilter_by_pdbid (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_BlastFilter_by_sequence_identity (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_BlastFilter_by_sequence_length (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_BlastFilter_by_template_bfactor (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_BlastFilter_by_template_resolution (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_BlastFilter_nonmatching_prolines (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_BlastPlus (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_BlastResult (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_Comparator (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_Functor (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_Helper (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_LoopOverSCs (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_MultiTemplate (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_Result (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_Results (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_ResultSet (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_ResultVector (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_SubstitutionMatrix (class in pyrosetta.rosetta.protocols.antibody.grafting) SCS_SubstitutionMatrixResult (class in pyrosetta.rosetta.protocols.antibody.grafting) sd (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.ConstraintConditions property) sd() (pyrosetta.rosetta.core.scoring.constraints.BoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.HarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.MinMultiHarmonicFunc method) (pyrosetta.rosetta.protocols.denovo_design.components.FoldGraph method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) sd_ang() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) sd_dih() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) sd_dis() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) sd_index (class in pyrosetta.rosetta.core.io.mmtf) sd_range() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) sdens (pyrosetta.rosetta.core.scoring.APBSConfig.R_PARAM property) sdev() (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) sdf_type() (pyrosetta.rosetta.core.chemical.sdf.MolFileIOBond method) SDFParser (class in pyrosetta.rosetta.core.chemical.sdf) Se (pyrosetta.rosetta.core.chemical.element.Elements attribute) se_choice_opt (pyrosetta.rosetta.utility.tag.CTGenSubelementBehavior attribute) se_choice_req (pyrosetta.rosetta.utility.tag.CTGenSubelementBehavior attribute) se_none (pyrosetta.rosetta.utility.tag.CTGenSubelementBehavior attribute) se_ordered_sets (pyrosetta.rosetta.utility.tag.CTGenSubelementBehavior attribute) se_repeatable (pyrosetta.rosetta.utility.tag.CTGenSubelementBehavior attribute) se_single_opt (pyrosetta.rosetta.utility.tag.CTGenSubelementBehavior attribute) se_single_req (pyrosetta.rosetta.utility.tag.CTGenSubelementBehavior attribute) se_single_req_ordered (pyrosetta.rosetta.utility.tag.CTGenSubelementBehavior attribute) seal_jumps() (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) sealed_symmetric_fold_tree() (in module pyrosetta.rosetta.core.pose.symmetry) SealFoldTreeMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) SealFoldTreeMoverCreator (class in pyrosetta.rosetta.protocols.denovo_design.movers) search_IG_for_networks() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) search_random_poses() (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) search_results_to_pdb() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) search_rigid_body_orientation() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) search_x() (in module pyrosetta.rosetta.core.scoring.packstat) SearchPattern (class in pyrosetta.rosetta.protocols.hotspot_hashing) SearchPatternExpansion (class in pyrosetta.rosetta.protocols.hotspot_hashing) SearchPatternRotSetOp (class in pyrosetta.rosetta.protocols.hotspot_hashing) SearchPatternTransform (class in pyrosetta.rosetta.protocols.hotspot_hashing) Searchpoints() (pyrosetta.rosetta.protocols.hotspot_hashing.CartesianSearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.ComposeSearchPatterns method) (pyrosetta.rosetta.protocols.hotspot_hashing.ConstPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.LSMSearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.PartitionedSearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.RotationSearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.SearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.SearchPatternExpansion method) (pyrosetta.rosetta.protocols.hotspot_hashing.SearchPatternTransform method) (pyrosetta.rosetta.protocols.hotspot_hashing.SICPatternAtTransform method) (pyrosetta.rosetta.protocols.hotspot_hashing.SphericalRotationSearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.SurfaceSearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.TestPattern method) searchpoints_ (pyrosetta.rosetta.protocols.hotspot_hashing.CartesianSearchPattern property) (pyrosetta.rosetta.protocols.hotspot_hashing.RotationSearchPattern property) (pyrosetta.rosetta.protocols.hotspot_hashing.SphericalRotationSearchPattern property) sec_str() (pyrosetta.rosetta.protocols.hybridization.TMalign method) secant() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) secant_interpolation() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) SecMatchEvaluatorFactory (class in pyrosetta.rosetta.protocols.match.downstream) SecMatchResiduePairEvaluator (class in pyrosetta.rosetta.protocols.match.downstream) second (pyrosetta.rosetta.core.fragment.FragID property) second() (pyrosetta.rosetta.protocols.match.downstream_hit method) (pyrosetta.rosetta.protocols.match.Hit method) second_res (pyrosetta.rosetta.basic.datacache.ResRotPair property) second_rot (pyrosetta.rosetta.basic.datacache.ResRotPair property) second_substrates_or_byproducts (pyrosetta.rosetta.core.enzymes.EnzymeData property) secondary_output_index (pyrosetta.rosetta.protocols.jd3.JobOutputIndex property) secondary_pose_outputter_creators() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory method) secondary_pose_outputter_xml_schema_group_name() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory static method) secondary_pose_outputters_from_command_line() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory method) secondary_shifts() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) SECONDARY_STRUCTURE_ENERGY (pyrosetta.rosetta.basic.ProfTag attribute) SECONDARY_STRUCTURE_HSPAIR_ENERGY (pyrosetta.rosetta.basic.ProfTag attribute) SECONDARY_STRUCTURE_SHEETS_FROM_DIMERS_ENERGY (pyrosetta.rosetta.basic.ProfTag attribute) SECONDARY_STRUCTURE_SSPAIR_ENERGY (pyrosetta.rosetta.basic.ProfTag attribute) secondary_structure_weights() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) SecondaryIdentity (class in pyrosetta.rosetta.protocols.frag_picker.scores) SecondaryMatcherToDownstreamResidue (class in pyrosetta.rosetta.protocols.match.downstream) SecondaryMatcherToUpstreamResidue (class in pyrosetta.rosetta.protocols.match.downstream) SecondaryMatchProtocol (class in pyrosetta.rosetta.protocols.enzdes) SecondaryMatchUpstreamResProcessor (class in pyrosetta.rosetta.protocols.match.downstream) SecondaryPoseOutputter (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) SecondaryPoseOutputterCreator (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) SecondarySimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) SecondaryStructure (class in pyrosetta.rosetta.core.fragment) SecondaryStructureCountFilter (class in pyrosetta.rosetta.protocols.fldsgn.filters) SecondaryStructureCountFilterCreator (class in pyrosetta.rosetta.protocols.fldsgn.filters) SecondaryStructureEnergy (class in pyrosetta.rosetta.core.energy_methods) SecondaryStructureEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) SecondaryStructureFilter (class in pyrosetta.rosetta.protocols.fldsgn.filters) SecondaryStructureFilterCreator (class in pyrosetta.rosetta.protocols.fldsgn.filters) SecondaryStructureHasResidueFilter (class in pyrosetta.rosetta.protocols.fldsgn.filters) SecondaryStructureHasResidueFilterCreator (class in pyrosetta.rosetta.protocols.fldsgn.filters) SecondaryStructureMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) SecondaryStructureMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.metrics) SecondaryStructureMPM (class in pyrosetta.rosetta.protocols.match) SecondaryStructurePool (class in pyrosetta.rosetta.protocols.frag_picker.quota) SecondaryStructurePotential (class in pyrosetta.rosetta.core.scoring) SecondaryStructureSegment (class in pyrosetta.rosetta.protocols.features) SecondaryStructureSegmentFeatures (class in pyrosetta.rosetta.protocols.features) SecondaryStructureSegmentFeaturesCreator (class in pyrosetta.rosetta.protocols.features) SecondaryStructureSelector (class in pyrosetta.rosetta.core.select.residue_selector) SecondaryStructureSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) SecondaryStructureType (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) SecondaryStructureWeights (class in pyrosetta.rosetta.core.scoring) seconds() (pyrosetta.rosetta.protocols.simple_filters.ExpiryFilter method) SecretionOptimizationMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) SecretionOptimizationMover.mutt (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) SecretionOptimizationMover.tm_region (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) SecretionOptimizationMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) SecretionPredictionFilter (class in pyrosetta.rosetta.protocols.simple_filters) SecretionPredictionFilter.mutt (class in pyrosetta.rosetta.protocols.simple_filters) SecretionPredictionFilter.tm_region (class in pyrosetta.rosetta.protocols.simple_filters) SecretionPredictionFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) secstruct (pyrosetta.rosetta.core.fragment.rna.TorsionSet property) (pyrosetta.rosetta.protocols.jumping.DisulfTemplate property) (pyrosetta.rosetta.protocols.jumping.PairingTemplate property) secstruct() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.fragment.BBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.DownJumpSRFD method) (pyrosetta.rosetta.core.fragment.FragData method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.fragment.SecstructSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.UpJumpSRFD 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.pose.Pose method) (pyrosetta.rosetta.core.pose.rna.RNA_SecStruct method) (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.frags.RMSVallData method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.parser.BluePrint method) secstruct_defined() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) SecStructFinder (class in pyrosetta.rosetta.protocols.ncbb) SecStructFinderCreator (class in pyrosetta.rosetta.protocols.ncbb) SecStructGen (class in pyrosetta.rosetta.core.fragment.picking_old.vall.gen) SecStructInfo (class in pyrosetta.rosetta.protocols.denovo_design.architects) SecStructMinimizeMover (class in pyrosetta.rosetta.protocols.ncbb) SecStructMinimizeMoverCreator (class in pyrosetta.rosetta.protocols.ncbb) SecStructMinimizeMultiFunc (class in pyrosetta.rosetta.protocols.ncbb) SecstructSRFD (class in pyrosetta.rosetta.core.fragment) section() (in module pyrosetta.rosetta.protocols.sparta) section_index() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) see_edge_or_core_or_loop_or_short_edge() (in module pyrosetta.rosetta.protocols.features.strand_assembly) see_whether_model_is_H_bonded_by_terminal_strands() (in module pyrosetta.rosetta.protocols.legacy_sewing) see_whether_sheet_is_antiparallel() (in module pyrosetta.rosetta.protocols.features.strand_assembly) see_whether_sheets_can_be_combined() (in module pyrosetta.rosetta.protocols.features.strand_assembly) see_whether_this_sw_has_SS_bond() (in module pyrosetta.rosetta.protocols.features.strand_assembly) seed() (pyrosetta.rosetta.basic.random.RandomGeneratorSettings method) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) seed_centroids() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) seed_offset() (pyrosetta.rosetta.basic.random.RandomGeneratorSettings method) SeedFoldTree (class in pyrosetta.rosetta.protocols.seeded_abinitio) SeedFoldTreeCreator (class in pyrosetta.rosetta.protocols.seeded_abinitio) SeedSettings (class in pyrosetta.rosetta.protocols.pose_sewing.movers) SeedSetupMover (class in pyrosetta.rosetta.protocols.seeded_abinitio) SeedSetupMoverCreator (class in pyrosetta.rosetta.protocols.seeded_abinitio) seek_beg() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) seekg() (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) seekp() (pyrosetta.logging_support.PythonLoggingSink method) (pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t method) (pyrosetta.rosetta.basic.ComparingTracer method) (pyrosetta.rosetta.basic.MemTracerImpl method) (pyrosetta.rosetta.basic.MemTracerImpl.TracerProxyImpl method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.TracerImpl method) (pyrosetta.rosetta.basic.TracerImpl.TracerProxyImpl method) (pyrosetta.rosetta.basic.TracerToFile method) (pyrosetta.rosetta.protocols.frag_picker.QuotaDebug method) (pyrosetta.rosetta.std.iostream method) (pyrosetta.rosetta.std.ofstream method) (pyrosetta.rosetta.std.ostream method) (pyrosetta.rosetta.std.ostringstream method) (pyrosetta.rosetta.std.stringstream method) (pyrosetta.rosetta.std.wostream 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) seg1 (pyrosetta.rosetta.protocols.denovo_design.components.BondInfo property) seg2 (pyrosetta.rosetta.protocols.denovo_design.components.BondInfo property) Segment (class in pyrosetta.rosetta.protocols.denovo_design.components) (class in pyrosetta.rosetta.protocols.features) (class in pyrosetta.rosetta.protocols.forge.remodel) segment() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.denovo_design.components.FoldGraph method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) segment1_ids() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) segment2_ids() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) segment_cluster_tolerance (pyrosetta.rosetta.protocols.indexed_structure_store.DirectSegmentLookupConfig property) segment_group() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) segment_id (pyrosetta.rosetta.protocols.features.SecondaryStructureSegment property) (pyrosetta.rosetta.protocols.legacy_sewing.HashValue property) (pyrosetta.rosetta.protocols.sewing.data_storage.LigandContact property) (pyrosetta.rosetta.protocols.sewing.hashing.HashValue property) segment_id() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.sewing.data_storage.Basis method) segment_id_ (pyrosetta.rosetta.protocols.legacy_sewing.SewSegment property) segment_ids() (pyrosetta.rosetta.protocols.legacy_sewing.Model method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) segment_length() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) segment_match_counts (pyrosetta.rosetta.protocols.legacy_sewing.HashResult property) segment_matches (pyrosetta.rosetta.protocols.legacy_sewing.HashResult property) segment_name() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) segment_name_set() (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairSet method) segment_names_ordered() (pyrosetta.rosetta.protocols.splice.SpliceManager method) segment_object_name() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub static method) segment_profile() (pyrosetta.rosetta.protocols.indexed_structure_store.SegmentSequenceProfile method) segment_to_local() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) segment_to_pose() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) segment_type() (pyrosetta.rosetta.protocols.splice.SpliceManager method) segment_vector() (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentGenerator method) (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) (pyrosetta.rosetta.protocols.sewing.hashing.EdgeMapGenerator method) (pyrosetta.rosetta.protocols.sewing.hashing.Hasher method) segment_vector_dssp() (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) SegmentContactOrderScorer (class in pyrosetta.rosetta.protocols.sewing.scoring) SegmentContactOrderScorerCreator (class in pyrosetta.rosetta.protocols.sewing.scoring) SegmentCounts (class in pyrosetta.rosetta.protocols.denovo_design.components) SegmentCounts.SegmentType (class in pyrosetta.rosetta.protocols.denovo_design.components) SegmentedAtomPairConstraintGenerator (class in pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator) SegmentedAtomPairConstraintGeneratorCreator (class in pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator) SegmentEnvelope (class in pyrosetta.rosetta.protocols.pose_sewing.data_storage) SegmentGraph (class in pyrosetta.rosetta.protocols.legacy_sewing) SegmentHybridizer (class in pyrosetta.rosetta.protocols.seeded_abinitio) SegmentHybridizerCreator (class in pyrosetta.rosetta.protocols.seeded_abinitio) segmentID (pyrosetta.rosetta.core.io.AtomInformation property) (pyrosetta.rosetta.core.pose.PDBInfo.ResidueRecord property) segmentID() (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.pose.PDBInfo method) segmentIDs_ (pyrosetta.rosetta.protocols.pdbinfo_manipulations.SequenceSpecification property) SegmentInsert (class in pyrosetta.rosetta.protocols.forge.build) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBInstructionType attribute) SegmentPairing (class in pyrosetta.rosetta.protocols.denovo_design.components) SegmentPairing.PairingType (class in pyrosetta.rosetta.protocols.denovo_design.components) SegmentPairSet (class in pyrosetta.rosetta.protocols.denovo_design.components) SegmentRebuild (class in pyrosetta.rosetta.protocols.forge.build) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBInstructionType attribute) segments() (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing method) (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) segments_ (pyrosetta.rosetta.protocols.legacy_sewing.Model property) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentSettings property) segments_in_movable_group() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) SegmentSequenceProfile (class in pyrosetta.rosetta.protocols.indexed_structure_store) SegmentSequenceProfileConfig (class in pyrosetta.rosetta.protocols.indexed_structure_store) SegmentSequenceProfileMover (class in pyrosetta.rosetta.protocols.indexed_structure_store.movers) SegmentSequenceProfileMoverCreator (class in pyrosetta.rosetta.protocols.indexed_structure_store.movers) SegmentSequenceProfileResult (class in pyrosetta.rosetta.protocols.indexed_structure_store) SegmentSpec (class in pyrosetta.rosetta.protocols.seeded_abinitio) SegmentSwap (class in pyrosetta.rosetta.protocols.forge.build) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBInstructionType attribute) SegmentVector (class in pyrosetta.rosetta.protocols.sewing.hashing) segs_can_chimerize() (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) 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) (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.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) select_best_networks() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) select_best_poses() (in module pyrosetta.rosetta.protocols.ligand_docking) select_cav_balls() (in module pyrosetta.rosetta.core.scoring.packstat) select_density_points() (in module pyrosetta.rosetta.protocols.electron_density) select_entry_by_name() (pyrosetta.rosetta.protocols.splice.RBInMover method) select_epitope_residues() (in module pyrosetta.rosetta.protocols.antibody) select_final_loop() (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) select_fragments() (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector method) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector method) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector method) select_interface_residues() (in module pyrosetta.rosetta.protocols.interface) select_jump() (pyrosetta.rosetta.protocols.symmetry.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SymmetrySlider method) select_loop_frags() (in module pyrosetta.rosetta.protocols.loops) select_loop_residues() (in module pyrosetta.rosetta.protocols.loops) select_only_alpha_aas() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) select_only_FAMILYVW() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) select_orient_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) select_orient_atoms_standard_logic() (pyrosetta.rosetta.core.chemical.ResidueType method) select_parts() (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) select_phore_match() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo method) select_points() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner method) select_poses() (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelector method) select_positive_phi() (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) select_random() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) select_random_move() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) select_random_set() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) select_range_len() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) select_range_mul() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) select_range_start() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) select_RBsegments() (in module pyrosetta.rosetta.protocols.rbsegment_relax) select_relevant_states() (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction method) (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunctionDriver method) (pyrosetta.rosetta.protocols.pack_daemon.MultistateAggregateFunction method) select_residues() (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter method) select_rotamer() (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) select_rotamer_subset() (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) select_score() (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) SelectByDeltaScoreOperation (class in pyrosetta.rosetta.protocols.task_operations) SelectByDeltaScoreOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) SelectByDensityFitOperation (class in pyrosetta.rosetta.protocols.task_operations) SelectByDensityFitOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) SelectBySASAOperation (class in pyrosetta.rosetta.protocols.task_operations) SelectBySASAOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) SelectDensityPointsOptions (class in pyrosetta.rosetta.protocols.electron_density) selected() (pyrosetta.rosetta.protocols.moves.SwitchMover method) selected_boundary_residues() (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) selected_core_residues() (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) selected_resis() (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter method) selected_resis_property() (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter method) selected_surface_residues() (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) SelectedResidueCountMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) SelectedResidueCountMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.metrics) SelectedResiduesMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) SelectedResiduesMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.metrics) SelectedResiduesPyMOLMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) SelectedResiduesPyMOLMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.metrics) SelectedResPredicate (class in pyrosetta.rosetta.core.scoring) SelectGdtEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) selection_is_symmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper method) selection_jumps() (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.ExclusivelySharedJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpForResidue method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) selection_low() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) selection_positions() (in module pyrosetta.rosetta.core.select.residue_selector) (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelector method) (pyrosetta.rosetta.core.select.residue_selector.BFactorSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BlockSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ChainSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ConfluentSelector method) (pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.FractionSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelector method) (pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector method) (pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelector method) (pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelector method) (pyrosetta.rosetta.protocols.antibody.design.ResnumFromStringsWithRangesSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.environment.claims.EnvLabelSelector method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ConstraintResidueSelector method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.CutpointResidueSelector method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ProteinResidueSelector method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelector method) (pyrosetta.rosetta.protocols.residue_selectors.HBondSelector method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.NativeSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) selection_tag() (pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB method) SelectMaxsubEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) selectmode() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) selector() (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShell method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToResidueProperties method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToSpecifiedBaseResidueTypes method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.environment.claims.TorsionClaim method) (pyrosetta.rosetta.protocols.environment.claims.XYZClaim method) (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) selector1() (pyrosetta.rosetta.core.scoring.sc.ElectrostaticSimilarityCalculator method) (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) selector2() (pyrosetta.rosetta.core.scoring.sc.ElectrostaticSimilarityCalculator method) (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) selector_ (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker property) Selector_AA (class in pyrosetta.rosetta.core.chemical) Selector_BASENAME (class in pyrosetta.rosetta.core.chemical) Selector_CMDFLAG (class in pyrosetta.rosetta.core.chemical) Selector_HAS_ATOMS (class in pyrosetta.rosetta.core.chemical) Selector_MATCH_VARIANTS (class in pyrosetta.rosetta.core.chemical) Selector_NAME1 (class in pyrosetta.rosetta.core.chemical) Selector_NAME3 (class in pyrosetta.rosetta.core.chemical) Selector_NO_VARIANTS (class in pyrosetta.rosetta.core.chemical) Selector_PROPERTY (class in pyrosetta.rosetta.core.chemical) selector_type (class in pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector) Selector_UPPER_ATOM (class in pyrosetta.rosetta.core.chemical) Selector_VARIANT_TYPE (class in pyrosetta.rosetta.core.chemical) SelectorLogicParser (class in pyrosetta.rosetta.core.select.residue_selector) selectors() (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilter method) SelectRDC_Evaluator (class in pyrosetta.rosetta.protocols.simple_filters) SelectResiduesByLayer (class in pyrosetta.rosetta.core.select.util) SelectResiduesWithinChainOperation (class in pyrosetta.rosetta.protocols.task_operations) SelectResiduesWithinChainOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) SelectRmsdEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) self_pure_test_virtual_p() (pyrosetta.rosetta.utility.py.OverloadTest method) self_pure_test_virtual_ref() (pyrosetta.rosetta.utility.py.OverloadTest method) self_test_virtual_p() (pyrosetta.rosetta.utility.py.OverloadTest method) self_test_virtual_ref() (pyrosetta.rosetta.utility.py.OverloadTest method) semi (pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy property) semiexpl_water_hbgeom_score() (pyrosetta.rosetta.protocols.pose_metric_calculators.SemiExplicitWaterUnsatisfiedPolarsCalculator method) SemiExplicitWaterUnsatisfiedPolarsCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) semirotameric_ncaa_rotlib() (pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification method) SemiRotamericSingleResidueDunbrackLibrary_1_1_t (class in pyrosetta.rosetta.core.pack.dunbrack) SemiRotamericSingleResidueDunbrackLibrary_1_2_t (class in pyrosetta.rosetta.core.pack.dunbrack) SemiRotamericSingleResidueDunbrackLibrary_1_3_t (class in pyrosetta.rosetta.core.pack.dunbrack) SemiRotamericSingleResidueDunbrackLibrary_1_4_t (class in pyrosetta.rosetta.core.pack.dunbrack) SemiRotamericSingleResidueDunbrackLibrary_1_5_t (class in pyrosetta.rosetta.core.pack.dunbrack) SemiRotamericSingleResidueDunbrackLibrary_2_1_t (class in pyrosetta.rosetta.core.pack.dunbrack) SemiRotamericSingleResidueDunbrackLibrary_2_2_t (class in pyrosetta.rosetta.core.pack.dunbrack) SemiRotamericSingleResidueDunbrackLibrary_2_3_t (class in pyrosetta.rosetta.core.pack.dunbrack) SemiRotamericSingleResidueDunbrackLibrary_2_4_t (class in pyrosetta.rosetta.core.pack.dunbrack) SemiRotamericSingleResidueDunbrackLibrary_2_5_t (class in pyrosetta.rosetta.core.pack.dunbrack) send_any() (pyrosetta.rosetta.protocols.moves.PyMOLMover method) send_char_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI static method) send_colors() (pyrosetta.rosetta.protocols.moves.PyMOLMover method) send_data_to_head_node() (in module pyrosetta.rosetta.basic.mpi) send_double_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI static method) send_doubles_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI static method) send_energy() (pyrosetta.rosetta.protocols.moves.PyMOLMover method) send_foldtree() (pyrosetta.rosetta.protocols.moves.PyMOLMover method) send_hbonds() (pyrosetta.rosetta.protocols.moves.PyMOLMover method) send_integer_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI static method) send_integers_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI static method) send_membrane_planes() (pyrosetta.rosetta.protocols.moves.PyMOLMover method) send_movemap() (pyrosetta.rosetta.protocols.moves.PyMOLMover method) send_polars() (pyrosetta.rosetta.protocols.moves.PyMOLMover method) send_RAW_Energies() (pyrosetta.rosetta.protocols.moves.PyMOLMover method) send_size_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI static method) send_sizes_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI static method) send_spin_down_signal() (pyrosetta.rosetta.protocols.pack_daemon.MPIMultistateFitnessFunction method) send_ss() (pyrosetta.rosetta.protocols.moves.PyMOLMover method) send_string_to_node() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI static method) send_to_stdout() (pyrosetta.rosetta.core.optimization.NumericalDerivCheckResult method) sendMessage() (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) senior_authors() (pyrosetta.rosetta.basic.citation_manager.Citation method) sep_aa1_ (pyrosetta.rosetta.core.scoring.motif.ResPairMotifMetaBinner property) sep_aa2_ (pyrosetta.rosetta.core.scoring.motif.ResPairMotifMetaBinner property) sep_aa_ (pyrosetta.rosetta.core.scoring.motif.ResPairMotifMetaBinner property) sep_bfac_ (pyrosetta.rosetta.core.scoring.motif.ResPairMotifMetaBinner property) sep_dist_ (pyrosetta.rosetta.core.scoring.motif.ResPairMotifMetaBinner property) sep_dssp_ (pyrosetta.rosetta.core.scoring.motif.ResPairMotifMetaBinner property) sep_hb_ (pyrosetta.rosetta.core.scoring.motif.ResPairMotifMetaBinner property) sep_lj_ (pyrosetta.rosetta.core.scoring.motif.ResPairMotifMetaBinner property) sep_nbrs_ (pyrosetta.rosetta.core.scoring.motif.ResPairMotifMetaBinner property) sep_ss() (pyrosetta.rosetta.core.scoring.packing.HolesParams method) sep_ss_ (pyrosetta.rosetta.core.scoring.motif.ResPairMotifMetaBinner property) separated_energy (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData property) separated_interface_score (pyrosetta.rosetta.protocols.analysis.InterfaceData property) separated_SASA (pyrosetta.rosetta.protocols.analysis.InterfaceData property) separated_sasa (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData property) separated_total_energy (pyrosetta.rosetta.protocols.analysis.InterfaceData property) SeparateDnaFromNonDna (class in pyrosetta.rosetta.protocols.dna) SeparateDnaFromNonDnaCreator (class in pyrosetta.rosetta.protocols.dna) SEPTANOSE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) seq() (pyrosetta.rosetta.core.sequence.CompositeSequence method) seq1() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) seq2() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) seq_aln_file() (pyrosetta.rosetta.protocols.splice.RotLibOut method) seq_design_basic (pyrosetta.rosetta.protocols.antibody.design.SeqDesignStrategyEnum attribute) seq_design_conservative (pyrosetta.rosetta.protocols.antibody.design.SeqDesignStrategyEnum attribute) seq_design_none (pyrosetta.rosetta.protocols.antibody.design.SeqDesignStrategyEnum attribute) seq_design_profile_sets (pyrosetta.rosetta.protocols.antibody.design.SeqDesignStrategyEnum attribute) seq_design_profile_sets_combined (pyrosetta.rosetta.protocols.antibody.design.SeqDesignStrategyEnum attribute) seq_design_profiles (pyrosetta.rosetta.protocols.antibody.design.SeqDesignStrategyEnum attribute) seq_design_strategy_enum_to_string() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignEnumManager method) seq_design_strategy_is_present() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignEnumManager method) seq_design_strategy_string_to_enum() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignEnumManager method) seq_design_strategy_to_enum() (in module pyrosetta.rosetta.protocols.antibody.design) seq_design_strategy_to_string() (in module pyrosetta.rosetta.protocols.antibody.design) seq_end() (pyrosetta.rosetta.protocols.features.helixAssembly.HelicalFragment method) seq_from_file() (pyrosetta.rosetta.core.sequence.SequenceFactory method) seq_num (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData property) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Residue_info property) seq_pdb_str() (in module pyrosetta.rosetta.protocols.dna) seq_sep (pyrosetta.rosetta.protocols.jumping.DisulfPairing property) seq_sep_intercept() (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) seq_sep_M2 (pyrosetta.rosetta.core.scoring.hbonds.HBSeqSep attribute) seq_sep_M3 (pyrosetta.rosetta.core.scoring.hbonds.HBSeqSep attribute) seq_sep_M4 (pyrosetta.rosetta.core.scoring.hbonds.HBSeqSep attribute) seq_sep_MAX (pyrosetta.rosetta.core.scoring.hbonds.HBSeqSep attribute) seq_sep_other (pyrosetta.rosetta.core.scoring.hbonds.HBSeqSep attribute) seq_sep_P2 (pyrosetta.rosetta.core.scoring.hbonds.HBSeqSep attribute) seq_sep_P3 (pyrosetta.rosetta.core.scoring.hbonds.HBSeqSep attribute) seq_sep_P4 (pyrosetta.rosetta.core.scoring.hbonds.HBSeqSep attribute) seq_sep_PM1 (pyrosetta.rosetta.core.scoring.hbonds.HBSeqSep attribute) seq_sep_type_from_name() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) seq_start() (pyrosetta.rosetta.protocols.features.helixAssembly.HelicalFragment method) seq_to_str() (in module pyrosetta.rosetta.protocols.dna) SEQADV (pyrosetta.rosetta.core.io.pdb.RecordType attribute) seqdep_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) SeqDesignStrategyEnum (class in pyrosetta.rosetta.protocols.antibody.design) SeqDesignStrategyEnum_total (pyrosetta.rosetta.protocols.antibody.design.SeqDesignStrategyEnum attribute) seqid() (pyrosetta.rosetta.core.environment.FoldTreeSketch.Node method) seqmap() (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) seqNum (pyrosetta.rosetta.core.io.ModifiedResidueInformation property) seqNum1 (pyrosetta.rosetta.core.io.CisPeptideInformation property) (pyrosetta.rosetta.core.io.HELIXInformation property) (pyrosetta.rosetta.core.io.SHEETInformation property) seqNum2 (pyrosetta.rosetta.core.io.CisPeptideInformation property) (pyrosetta.rosetta.core.io.HELIXInformation property) (pyrosetta.rosetta.core.io.SHEETInformation property) seqpos() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) (pyrosetta.rosetta.core.io.rna.RDAT method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint method) (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) (pyrosetta.rosetta.protocols.motifs.BuildPosition method) seqpos1() (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint method) seqpos2() (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint method) seqpos_for_geomcst() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) seqpos_map_size() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache method) seqposes_no_mutate_str() (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) seqprof() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation method) seqprof_wt_aa() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) SeqprofConsensusOperation (class in pyrosetta.rosetta.protocols.task_operations) SeqprofConsensusOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) SEQRES (pyrosetta.rosetta.core.io.pdb.RecordType attribute) seqs() (pyrosetta.rosetta.core.sequence.CompositeSequence method) seqs_from_cmd_lines() (in module pyrosetta.rosetta.core.sequence) seqsep() (pyrosetta.rosetta.core.scoring.lDDT_Calculator method) SeqSymmAnnealerSetup (class in pyrosetta.rosetta.core.pack.annealer) Sequence (class in pyrosetta.rosetta.core.sequence) sequence (pyrosetta.rosetta.protocols.antibody.CDRDBSequence property) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain property) (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) (pyrosetta.rosetta.protocols.loophash.BBExtraData property) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover.tm_region property) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter.tm_region property) (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) sequence() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.fragment.BBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.DownJumpSRFD method) (pyrosetta.rosetta.core.fragment.FragData 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.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.raw_data.DecoyFileData method) (pyrosetta.rosetta.core.io.raw_data.DecoyStruct method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreFileData method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructJSON method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.rna.RDAT 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) (pyrosetta.rosetta.core.io.silent.SimpleSequenceData method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.CompositeSequence 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.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frags.RMSVallData method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.SequenceMetric method) (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist method) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) (pyrosetta.rosetta.protocols.parser.BluePrint method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) sequence_ (pyrosetta.rosetta.protocols.pdbinfo_manipulations.SequenceSpecification property) sequence_comment_id() (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) SEQUENCE_COMPARISON (pyrosetta.rosetta.basic.ProfTag attribute) sequence_constraint() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) sequence_coupling() (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint method) sequence_file_contents() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) sequence_indices() (pyrosetta.rosetta.core.sequence.SequenceAlignment method) sequence_last() (pyrosetta.rosetta.cppdb.backend.statement method) (pyrosetta.rosetta.cppdb.statement method) sequence_map_from_pdbinfo() (in module pyrosetta.rosetta.core.pose) sequence_mapping() (pyrosetta.rosetta.core.sequence.SequenceAlignment method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) sequence_matches() (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) sequence_mode() (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) sequence_mutated() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) sequence_number_resolver() (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) sequence_profile() (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint method) (pyrosetta.rosetta.protocols.splice.SpliceSegment method) sequence_recovery() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesSeqRecoveryCache method) sequence_sep() (pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple method) sequence_separation() (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.FindEndpointsOperation method) sequence_space() (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) sequence_symmetric_uid_prefix() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) SequenceAlignment (class in pyrosetta.rosetta.core.sequence) SequenceAlignmentHasher (class in pyrosetta.rosetta.core.sequence) SequenceAnnotation (class in pyrosetta.rosetta.core.environment) SequenceClaim (class in pyrosetta.rosetta.protocols.topology_broker.claims) SequenceClaim.ClaimRight (class in pyrosetta.rosetta.protocols.topology_broker.claims) SequenceClaimer (class in pyrosetta.rosetta.protocols.topology_broker) SequenceComparison (class in pyrosetta.rosetta.protocols.pose_metric_calculators) SequenceConstraint (class in pyrosetta.rosetta.core.scoring.aa_composition_energy) SequenceCoupling (class in pyrosetta.rosetta.core.sequence) SequenceCoupling1BDConstraint (class in pyrosetta.rosetta.protocols.constraints_additional) SequenceCoupling1BDConstraintCreator (class in pyrosetta.rosetta.protocols.constraints_additional) SequenceCouplingConstraint (class in pyrosetta.rosetta.protocols.constraints_additional) SequenceCouplingConstraintCreator (class in pyrosetta.rosetta.protocols.constraints_additional) SequenceCouplingCreator (class in pyrosetta.rosetta.core.sequence) SequenceCreator (class in pyrosetta.rosetta.core.sequence) SequenceDependentRefEnergy (class in pyrosetta.rosetta.core.energy_methods) SequenceDependentRefEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) SequenceDistance (class in pyrosetta.rosetta.protocols.simple_filters) SequenceDistanceFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) SequenceFactory (class in pyrosetta.rosetta.core.sequence) SequenceIdentity (class in pyrosetta.rosetta.protocols.frag_picker.scores) SequenceMapping (class in pyrosetta.rosetta.core.id) SequenceMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics) SequenceMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.metrics) (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics) SequenceMetricMode (class in pyrosetta.rosetta.core.simple_metrics.metrics) SequenceMotifTaskOperation (class in pyrosetta.rosetta.protocols.task_operations) SequenceMotifTaskOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) SequenceMover (class in pyrosetta.rosetta.protocols.moves) SequenceMoverCreator (class in pyrosetta.rosetta.protocols.moves) SequenceNumberResolver (class in pyrosetta.rosetta.protocols.topology_broker) SequenceProfile (class in pyrosetta.rosetta.core.sequence) SequenceProfileConstraint (class in pyrosetta.rosetta.core.scoring.constraints) SequenceProfileConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) SequenceProfileCreator (class in pyrosetta.rosetta.core.sequence) SequenceProfileMover (class in pyrosetta.rosetta.protocols.simple_moves) SequenceProfileMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) SequenceRecoveryFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) SequenceRecoveryFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) SequenceRecoveryMetric (class in pyrosetta.rosetta.protocols.analysis.simple_metrics) SequenceRecoveryMetricCreator (class in pyrosetta.rosetta.protocols.analysis.simple_metrics) sequences() (pyrosetta.rosetta.core.io.rna.RDAT method) sequences_are_in_frame() (pyrosetta.rosetta.core.sequence.SequenceAlignment method) SequenceShiftMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) SequenceSimilarityMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) SequenceSimilarityMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.metrics) SequenceSpecification (class in pyrosetta.rosetta.protocols.pdbinfo_manipulations) SequenceSymmetricAnnealer (class in pyrosetta.rosetta.core.pack.annealer) SEQUENTIAL (pyrosetta.rosetta.core.conformation.symmetry.SlideType attribute) sequential_order() (pyrosetta.rosetta.protocols.loops.Loops method) SequentialSymmetrySlider (class in pyrosetta.rosetta.protocols.symmetry) ser_to_helix_bb() (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.HBondBonusOptions method) ser_to_helix_bb_ (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.HBondBonusOptions property) serial (pyrosetta.rosetta.core.io.AtomInformation property) Serial_Refine (class in pyrosetta.rosetta.protocols.mpi_refinement) serialize() (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.PartialAtomID method) (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingle method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingle method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingle method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) (pyrosetta.rosetta.numeric.interpolation.spline.CompoundInterpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.Interpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.SimpleInterpolator method) (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash 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.qsar.scoring_grid.AtrGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom 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.GridSet 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) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore method) (pyrosetta.rosetta.protocols.wum.SilentStructStore method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) serialize_graph_json() (in module pyrosetta.rosetta.protocols.legacy_sewing) serialize_ids() (in module pyrosetta.rosetta.protocols.features) serialize_residue_xyz_coords() (in module pyrosetta.rosetta.protocols.features) serialize_to_file() (pyrosetta.rosetta.protocols.wum.SilentStructStore method) serialize_weights() (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) serialized_loops_from_string() (in module pyrosetta.rosetta.protocols.loops) SERIALIZED_POSE_FILE (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum attribute) SerializedLoop (class in pyrosetta.rosetta.protocols.loops) SerializedPoseJobInputter (class in pyrosetta.rosetta.protocols.jd2) SerializedPoseJobInputterCreator (class in pyrosetta.rosetta.protocols.jd2) SerializedPoseJobOutputter (class in pyrosetta.rosetta.protocols.jd2) SerializedPoseJobOutputterCreator (class in pyrosetta.rosetta.protocols.jd2) SeriesJacobians (class in pyrosetta.rosetta.core.kinematics.jacobian) SeriesJacobianTypeEnum (class in pyrosetta.rosetta.core.kinematics.jacobian) session (class in pyrosetta.rosetta.cppdb) (class in pyrosetta.rosetta.utility.sql_database) set (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GenKICPerturberEffect attribute) Set() (in module pyrosetta) set() (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.id.AtomID 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.kinematics.inverse.AlignmentAtom method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.numeric.IntervalSet_Double method) (pyrosetta.rosetta.numeric.IntervalSet_double_t 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_predict.HierarchicalHybridJD_SASASummary method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.utility.DenseBoolMap_5_0_t method) set3D() (pyrosetta.rosetta.RDKit.Conformer method) set_1_to_1_format() (pyrosetta.rosetta.protocols.pdbinfo_manipulations.SequenceSpecification method) set_2D_torsion_to_pose() (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler2D method) set_3D_torsion_to_pose() (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler3D method) set_a_form_range() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) set_A_index() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_per_lanthanides method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_per_lanthanides_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_per_lanthanides_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_per_lanthanides_Ts4 method) Set_AA (class in pyrosetta.rosetta.core.chemical) set_aa() (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) set_aa_composition_setup_files() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_AA_name3() (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) set_aa_probabilities() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_aa_probabilities_from_file() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_aa_probability_set() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_aa_temp() (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) set_aa_type() (pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex method) set_aas_allowed() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) set_ab_fold_tree() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) set_ab_has_light_chain() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) set_ab_info() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) set_abba_bins_binfile() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_abego() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) set_abort_on_failed_loop() (pyrosetta.rosetta.protocols.LoopRebuild method) set_absolute_stereochemistry() (pyrosetta.rosetta.core.chemical.Atom method) set_absolute_threshold() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerChiDiff method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerElecDensDiff method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerRotBins method) set_abstract() (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) set_acc() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_accept_aborted_loops_() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover 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) set_accept_blocks_missing_header() (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) set_accept_no_op_moves() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_acceptor_selector() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) set_accessed() (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) set_accurate_sasa_and_recalc() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintHelper method) set_action() (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric method) (pyrosetta.rosetta.protocols.filters.TrueFalseFilter method) set_action_value() (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric method) set_active_pose_constraints() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache method) set_active_restype_index() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) set_active_site_grid() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) set_add_alanine_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) set_add_c_terminal_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) set_add_constraints() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_add_delete_frequency() (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_add_hetatm() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) set_add_hydrophobic_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) set_add_jump_on_rechain() (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) set_add_lead_zero_to_tag() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_add_ligand_to_pose() (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) set_add_n_terminal_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) set_add_non_init_chunks() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_add_overall_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) set_add_padding() (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) set_add_peptide_plane_variants() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_add_probability() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_add_proposal_density_factor() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_add_target_to_pose() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) set_add_target_types() (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) set_add_terminal_types_on_rechain() (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) set_add_virt_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_add_virt_res_as_root() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_additional_task_operarations() (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.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockTaskFactory method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) set_additional_type_to_add() (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) set_additional_type_to_remove() (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) set_adduct_flag() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) set_adp_strategy() (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) set_aggregate_function() (pyrosetta.rosetta.protocols.multistate_design.MultiStateFitnessFunction method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) set_AHD_cutoff() (pyrosetta.rosetta.protocols.buns.BuriedUnsatisfiedPolarsCalculator2 method) set_akash_dyepos() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_ala_pose() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_alias() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) set_alias_name() (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) set_align_file() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_align_only_over_base_atoms() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_align_output() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) set_align_pdb() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) set_align_pose() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) set_align_reference_atom_ids() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GAOptimizer method) set_align_to_native() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) set_aligned_chunk() (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) set_alignment_anchor_res() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) set_alignment_atoms() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) set_alignment_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_alignment_settings() (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) set_all_chi() (pyrosetta.rosetta.core.conformation.Residue method) set_all_current_jobs_as_deletable() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) set_all_data() (pyrosetta.rosetta.core.simple_metrics.SimpleMetricData method) set_all_energies() (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) set_all_extra_parameters() (pyrosetta.rosetta.core.chemical.AtomType method) set_all_flags() (pyrosetta.rosetta.numeric.ClusteringTreeNode method) set_all_jumps_minimizable() (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) set_all_lores_score_final() (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) set_all_nu() (pyrosetta.rosetta.core.conformation.Residue method) set_all_residues() (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) set_all_ring_nu() (pyrosetta.rosetta.core.conformation.Residue method) set_all_rna_fragments_file() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_allocated() (pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t method) set_allow_anchor_repack() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_allow_base_pair_only_centroid_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_allow_base_pair_only_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker method) set_allow_bulge() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_allow_bulge_at_chainbreak() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_allow_chain_boundary_jump_partner_right_at_fixed_BP() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_allow_consecutive_bulges() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_allow_delete() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) set_allow_design_cdr() (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) set_allow_design_neighbor_antigen() (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) set_allow_design_neighbor_framework() (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) set_allow_dof() (pyrosetta.rosetta.core.conformation.symmetry.SymDof method) set_allow_fixed_res_at_moving_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_allow_fragment_moves_in_bps() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_allow_glycan_torsion_moves() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_allow_insert_res() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) set_allow_internal_hinge_moves() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_allow_internal_local_moves() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_allow_multiple_results() (pyrosetta.rosetta.core.select.jump_selector.JumpForResidue method) set_allow_phosphate_virtualization() (pyrosetta.rosetta.core.pack.task.rna.RNA_ResidueLevelTask method) set_allow_rebuild_bulge_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_allow_repacking() (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) set_allow_scoring() (pyrosetta.rosetta.core.scoring.MembraneTopology method) set_allow_split_off() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_allow_submotif_split() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_allow_syn_pyrimidine() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_allow_tmh_scoring() (pyrosetta.rosetta.core.scoring.MembraneTopology method) set_allow_virtual_o2prime_hydrogens() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_allow_virtual_side_chains() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_allowed_bulge_res() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_allowed_failure_before_extend() (pyrosetta.rosetta.protocols.LoopRebuild method) set_allowed_failure_before_stop() (pyrosetta.rosetta.protocols.LoopRebuild method) set_allowed_residues_by_position() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_alpha() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.EulerAngles method) set_alpha_beta_pattern() (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) set_alphabet() (pyrosetta.rosetta.core.scoring.constraints.ResidueCouplingConstraint method) set_already_completed_job_count() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_already_defined_element() (pyrosetta.rosetta.utility.tag.XMLSchemaRepeatableCTNode method) set_already_defined_element_w_alt_name() (pyrosetta.rosetta.utility.tag.XMLSchemaRepeatableCTNode method) set_alt_state() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) set_alter_foldtree() (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) set_alternate() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) set_alternate_no_E_update() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) set_alternative_search_paths() (pyrosetta.rosetta.utility.io.izstream static method) set_always_rotamer_one() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) set_ambiguous_hnq() (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) set_amide_mm() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) set_amino_acid_type() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSewingResidue method) set_amino_acid_types() (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) set_anchor_noise_constraints_mode() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_anchor_offset() (pyrosetta.rosetta.protocols.multistate_design.PartitionAggregateFunction method) set_anchor_repacking() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_anchor_res() (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree 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) set_anchor_residue() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_anchor_via_constraints() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_ang_D1D2D3() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_ang_U1D2_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_ang_U2D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_angle() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) set_angle1_func() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_angle2_func() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_angle_atom() (pyrosetta.rosetta.core.energy_methods.GoapRsdType method) set_angle_exponent() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) set_angle_length_relax_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_angle_max() (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) set_angle_params_helices_on_sheet() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) set_angle_params_helix_sheet() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) set_angle_range() (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) set_angle_range_bb() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_angle_range_chi() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_angle_range_free_bb() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_angle_range_free_chi() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_angle_range_from_init() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) set_angle_range_from_init_torsions() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) set_angle_ranges() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) set_angle_relax_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_angle_sd() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_angle_shift_factor() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) set_angle_sigma2() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential method) set_angle_threshold() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) set_angle_tolerance() (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) set_angle_wts() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential method) set_angles() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) set_annealer_observer() (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.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.flexpack.annealer.FlexbbSimAnnealer method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) set_annotations() (pyrosetta.rosetta.core.io.rna.RDAT method) set_antibody_info() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) set_antiparallel_weight() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_application_name() (in module pyrosetta.rosetta.utility) set_apply_residue_alternative_sampler_() (pyrosetta.rosetta.protocols.stepwise.legacy.screener.ProteinAtrRepScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.O2PrimeScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PackScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PhosphateScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.ProteinCCD_ClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.SampleApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.SugarInstantiator method) set_apply_selector_to_native() (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric method) set_apply_vdw_cut() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_apply_virtual_res_variant_at_dinucleotide() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) set_approved() (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) set_aqueous_pore_parameters() (pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo method) (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) set_architect() (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) set_archive() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) set_array() (pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t method) set_array_size() (pyrosetta.rosetta.utility.graph.ArrayPool_double_t method) set_assembly_scorers() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_assert_jump_point_in_fixed_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_assign_incomplete() (pyrosetta.rosetta.protocols.loop_grower.LoopComparator method) set_assign_state_to_all_nodes_immediately() (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.SmartFixbbSimAnnealer method) set_assume_atom_ids_invariant() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer method) set_asu_only() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.protocols.moves.DsspMover method) set_asymm_unit_fold_tree() (in module pyrosetta.rosetta.core.conformation.symmetry) (in module pyrosetta.rosetta.core.pose.symmetry) set_asymmdump() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_atmid() (pyrosetta.rosetta.core.energy_methods.GoapRsdType method) set_atom() (pyrosetta.rosetta.core.io.nmr.AtomSelection method) (pyrosetta.rosetta.core.kinematics.MoveMap method) set_atom1() (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) set_atom2() (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) set_atom_bin_size() (pyrosetta.rosetta.core.pose.rna.VDW_Grid method) set_atom_derivatives() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingle method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingle method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingle method) set_atom_id() (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) set_atom_IDs() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) set_atom_level_domain_map() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_atom_mode() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) set_atom_names_for_distance_measure() (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) set_atom_pair_func() (pyrosetta.rosetta.core.scoring.custom_pair_distance.PairFuncMap method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_atom_pair_sd() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_atom_selector() (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) set_atom_type() (pyrosetta.rosetta.core.chemical.MutableResidueType method) set_atom_type_radii() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDistSasaCalculator method) set_atom_vector() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSewingResidue method) set_atomic_depth_apo_surface() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_atomic_depth_deeper_than() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_atomic_depth_poly_leu() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_atomic_depth_probe_radius() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_atomic_depth_resolution() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_atomic_depth_selection() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_atoms() (pyrosetta.rosetta.protocols.environment.claims.JumpClaim method) set_atoms1() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_atoms2() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_atr_rep_screen() (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) set_atr_rep_screen_for_docking() (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) set_atrdist_params_helix_strands() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) set_attach_boinc_ghost_observer() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) set_attached_res() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) set_attachment_type() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) set_attachments() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) set_auto_detect_glycan_connections() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_auto_detect_symmetry() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) set_auto_frag_insertion_weight() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_auto_h3_constraint() (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) set_auto_stop() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_auto_tune() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_auto_update() (pyrosetta.rosetta.core.scoring.NeighborList method) set_autofilter() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_autofilter_score_quantile() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_autofoldtree() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) set_autoinitialize() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) set_autotemp() (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) set_averaging_type() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) set_ax() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) set_babmotifs() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) set_backbone() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_backbone_backbone_acceptor() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) set_backbone_backbone_donor() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) set_backbone_bin (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) set_backbone_burial() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) set_backbone_exposed() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) set_backbone_heavyatom() (pyrosetta.rosetta.core.chemical.MutableResidueType method) set_backbone_mover() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_backbone_moves() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_backbone_moves_substrate() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_backbone_only() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) set_backrub_mover() (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) set_bad() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.InnerMultiThreadingJob method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.standard.StandardInnerLarvalJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) set_ball_radius() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_base_and_pucker_state() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarModeling method) set_base_atom_name() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_base_base_atom_name() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_base_only() (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterface method) set_base_pair_rmsd_cutoff() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_base_pair_rotation_mag() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_base_pair_translation_mag() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_base_partner() (in module pyrosetta.rosetta.core.scoring.dna) set_base_segment_chainbreak_constraints() (in module pyrosetta.rosetta.protocols.dna) set_base_state() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) set_base_type_cop() (pyrosetta.rosetta.core.chemical.MutableResidueType method) set_base_types() (pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToSpecifiedBaseResidueTypes method) set_basis_map_generator() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_basis_pair() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) set_batch_description() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) set_batch_name() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) set_batch_relax() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) set_bb() (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex method) (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) set_bb_bb() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_bb_dihedral_tolerance() (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) set_BB_dofs() (pyrosetta.rosetta.protocols.splice.SpliceManager method) set_bb_grid() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) (pyrosetta.rosetta.protocols.match.upstream.ProteinUpstreamBuilder method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamBuilder method) set_bb_id() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_bb_movemap() (in module pyrosetta.rosetta.protocols.hydrate) set_bb_stdev() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_bb_torsion() (in module pyrosetta.rosetta.core.pose) set_bb_true_range() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_bb_xyz_aligned() (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) set_bbmove() (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) set_bbox_padding() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) set_beamscorecutoff() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_beamwidth() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_behaviour() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_BenchMark() (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) set_benchmark() (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) set_bend_angle() (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) set_bendangle() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential method) set_best_geometry_score() (pyrosetta.rosetta.protocols.sewing.hashing.LigandBindingResPlacer method) set_best_grid_point() (pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch method) set_best_score() (pyrosetta.rosetta.protocols.multistate_design.PackingState method) (pyrosetta.rosetta.protocols.multistate_design.SingleState method) set_beta() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.EulerAngles method) set_bfactor() (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) set_bfactors_from_atom_id_map() (in module pyrosetta.rosetta.core.pose) set_bias_sampling() (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_bicelle_edge_steepness() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) set_bIdealLoopClosing() (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) set_big_frag_insertion_weight() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_big_fragments() (pyrosetta.rosetta.protocols.hybridization.MRMover method) set_bin() (pyrosetta.rosetta.core.pose.rna.VDW_Grid method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) set_bin_max() (pyrosetta.rosetta.core.pose.rna.VDW_Grid method) set_bin_name() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) set_bin_offset() (pyrosetta.rosetta.core.pose.rna.VDW_Grid method) set_bin_params_file_name() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) set_bin_size() (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_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) set_bin_width() (pyrosetta.rosetta.protocols.match.Bool3DGrid method) (pyrosetta.rosetta.protocols.match.downstream.ActiveSiteGrid method) set_binary_output() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) set_binary_rna_output() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) set_binding_cycles() (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_binfile_and_load() (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) set_bInitDofs() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer 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.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) set_binname() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) set_binname_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) set_binname_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) set_binrange_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) set_binrange_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) set_blank_score_terms() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_blastp_executable() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastPlus method) set_block_number() (pyrosetta.rosetta.core.select.residue_selector.BlockSelector method) set_block_size() (pyrosetta.rosetta.utility.graph.ArrayPool_double_t method) set_block_stack() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_block_stack_above_res() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_block_stack_below_res() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_blueprint() (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilter method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) set_blueprint_file() (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter method) set_boltz_rank() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_boltzmann_choice_post_enumerated_minimize() (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) set_boltzmann_factor() (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel method) set_boltzmann_rotamer_mover() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_boltzmann_temp() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) set_bond() (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) set_bond_angle() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) set_bond_length() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) set_bondangle (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) set_bonded_orbitals() (pyrosetta.rosetta.core.chemical.Atom method) set_bondlength (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) set_bonus_map() (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) set_bonus_score() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) set_boolean_option() (in module pyrosetta.rosetta.basic.options) set_boolean_vector_option() (in module pyrosetta.rosetta.basic.options) set_bootstrap() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) set_boundary() (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) set_boundary_residues() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_bounded() (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_bounded_width() (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) set_bounding_box() (pyrosetta.rosetta.protocols.match.Bool3DGrid method) (pyrosetta.rosetta.protocols.match.BumpGrid method) (pyrosetta.rosetta.protocols.match.downstream.ActiveSiteGrid method) (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) set_bp_res() (pyrosetta.rosetta.protocols.recces.params.RECCES_Parameters method) set_bps_moves() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_branch_atom() (pyrosetta.rosetta.core.energy_methods.GoapRsdType method) set_branches() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_branches_true_range() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_break_disulfide_bonds() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) set_breaking_selector() (pyrosetta.rosetta.core.select.residue_selector.ConfluentSelector method) set_bridge() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) set_bridge_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) set_broker() (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) set_buffer_length() (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) set_build_all_loops_() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover 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) set_build_attempts_() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover 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) set_build_ideal_geometry() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) set_build_overlap() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) set_build_round1_hits_twice() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) set_build_site_only() (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_builder() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) set_bulge_res() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) set_bulges() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) set_bump_check() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_bump_overlap_factor() (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_bump_tolerance() (pyrosetta.rosetta.protocols.match.Matcher method) set_bundle_symmetry() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) set_bundle_symmetry_copies() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) set_bundleparametersset_index() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) set_burial_cutoff() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_burial_cutoff_apo() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_c_cyd_seqpos() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_C_term_DSSP() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) set_C_term_length() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) set_c_terminal_neighbor() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) set_c_terminal_parent() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) set_c_terminal_segment() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) set_ca_only() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) set_cacb_dihedral_tolerance() (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) set_cache_limit() (pyrosetta.rosetta.protocols.trajectory.DbTrajectoryWriter method) set_cache_options() (pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector method) set_cache_selection() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_cache_size() (in module pyrosetta.rosetta.basic.database) (pyrosetta.rosetta.protocols.match.output.UpstreamHitCacher method) set_cacheable_cluster_data_to_pose() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) set_cached_resfile() (pyrosetta.rosetta.core.pack.task.operation.ReadResfile method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) set_calc_dSASA() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_calc_hbond_sasaE() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_calc_helices() (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter method) set_calc_in_hours() (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) set_calc_loops() (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter method) set_calc_rms_res() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder 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.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_calculate_jacobians() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) set_calculate_silent_Es() (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) set_calculated() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) set_calculation_method() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_calculator() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters method) set_calculator_by_name() (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) set_camelid() (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) set_camelid_constraints() (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) set_can_be_deleted() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) set_can_be_set_sampled_perturbed_copied() (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) set_candidates_collector() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_cap_ends() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) set_careful_base_pair_classifier() (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential method) set_cart_min() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) set_cartesian() (pyrosetta.rosetta.core.pack.RTMin method) (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRelax method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRTMin method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) set_cartesian_bonded_linear() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_cartesian_bonded_parameters() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_cartesian_bonded_skip_cutpoints() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_cartesian_minimize() (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) set_cartesian_relax_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_cartfrag_overlap() (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) set_catalytic_atoms() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) set_ccd_close() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) set_ccd_close_res() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) set_CCD_torsions_to_zero() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) set_cdr() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.CDRSeqDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) set_CDR_cluster() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) set_cdr_design_options() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) set_CDR_loops() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) set_cdr_only() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) set_cdr_range() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) set_cdr_set_options() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_cdrs() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) set_cdrs_to_use() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeatures method) set_cen_cst_weight() (pyrosetta.rosetta.protocols.hybridization.MRMover method) set_cen_dist() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_cen_scorefunction() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_cen_scorefxn() (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) set_cenrot() (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) set_cenrot_scorefunction() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_censcale() (pyrosetta.rosetta.protocols.hybridization.MRMover method) set_center() (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) (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.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid 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.VdwGrid method) set_center_jumps_in_single_stranded() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_centerofmass() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) set_centroid() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) set_centroid_bin_max() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) set_centroid_bin_min() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) set_centroid_bin_size() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) set_centroid_density_weight() (pyrosetta.rosetta.protocols.hybridization.MRMover method) set_centroid_loop_building() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) set_centroid_output() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) set_centroid_score_diff_cut() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_centroid_scorefunction() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_centroid_scorefxn() (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) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_centroid_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_centroid_weights() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) set_cereal_pickleable() (in module pyrosetta.distributed.utility.pickle) set_chain() (pyrosetta.rosetta.core.io.nmr.AtomSelection method) (pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilter method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (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) (pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation method) set_chain_boundaries() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_chain_connections() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) (pyrosetta.rosetta.core.import_pose.RNA_JumpMover method) set_chain_id() (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate_info method) (pyrosetta.rosetta.protocols.ligand_docking.Translate_info method) set_chain_letter() (pyrosetta.rosetta.protocols.ligand_docking.Rotate_info method) (pyrosetta.rosetta.protocols.ligand_docking.Translate_info method) set_chain_strings() (pyrosetta.rosetta.core.select.residue_selector.ChainSelector method) set_chain_to_degrease() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) set_chain_to_design() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) set_chain_to_modify() (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) set_chainbreak() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_chainbreak_bias() (pyrosetta.rosetta.protocols.rigid.RigidBodyMotionMover method) set_chainbreak_max() (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) set_chainbreak_ramping() (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) set_chainbreak_weight() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_chains() (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) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) set_chains_whose_residues_are_separate_chemical_entities() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_change_chi_without_replacing_residue() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) set_changed() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) set_char_msg() (pyrosetta.rosetta.utility.SimulateMPIMessage method) set_charge() (pyrosetta.rosetta.core.io.nmr.ParaIon method) set_charged_residues_map() (pyrosetta.rosetta.core.energy_methods.PBLifetimeCache method) set_check_if_residues_are_Ctermini() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_check_if_residues_are_Ntermini() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_check_ss() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) set_checkpoint() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_checkpoint_gzip() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) set_checkpoint_prefix() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) set_checkpoint_rename() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) set_checkpoint_write_interval() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) set_checkpointing_frequency() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_checksymm() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_chemical_bond_from_upstream_to_downstream() (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_chi() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) set_chi_according_to_coordinates() (in module pyrosetta.rosetta.core.conformation) set_chi_mean() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) set_chi_rotamers() (pyrosetta.rosetta.core.chemical.MutableChiRecord method) set_chi_sd() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) set_chi_stdev() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_chi_step() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner method) set_chi_torsions() (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) set_chi_true_range() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_chimaeric_status() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) set_chis() (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSewingResidue method) set_chiwidth() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) set_choices() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) set_choose_random() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) set_chunk_initialization_pdb_files() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_chunk_insertion_weight() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_chunk_pdb_files() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_chunk_silent_files() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_chunk_size() (pyrosetta.rosetta.utility.sql_database.session method) set_ciBR_only() (pyrosetta.rosetta.core.pack.annealer.FASTERAnnealer method) (pyrosetta.rosetta.protocols.pack_daemon.FASTER_IG_Repacker method) set_cif_files() (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) set_cis_peptide_bonds() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary method) set_cl_value() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.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) set_clash_check_types() (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) set_clash_checking() (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) set_clash_radius() (pyrosetta.rosetta.protocols.sewing.requirements.ClashRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandClashRequirement method) set_clash_score() (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer method) set_clear_designable_residues() (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) set_close_loops() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) set_close_loops_after_each_move() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_closest_states_on_other_bbs() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) set_closure_attempts() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) set_clust_cutoff() (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) set_clust_radius() (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) set_cluster() (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) set_cluster_by_all_atom() (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) set_cluster_by_all_atom_rmsd() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) set_cluster_by_protein_backbone() (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) set_cluster_csts_data_cutoff() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_cluster_csts_use_mean_cst_data() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_cluster_csts_use_outlier_data() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_cluster_data() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) set_cluster_metric() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobSummary method) set_cluster_metric_tag() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob method) set_cluster_num() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_cluster_radius() (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.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_cluster_rmsd() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection 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) set_clustercheck() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_clusters() (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) set_cmd() (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter method) set_combine_long_loop_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_combine_ratio() (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluator method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) set_command() (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.ExternalEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluator method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation method) set_comments() (pyrosetta.rosetta.core.io.rna.RDAT method) set_common_data_tags() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.TagManager method) set_comp_constraint_aa() (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) set_comparer_info() (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) set_comparison_pose() (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric method) set_comparison_type() (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_complete() (pyrosetta.rosetta.core.id.PartialAtomID method) set_completed() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) set_component_file() (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) set_composite_action() (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_computation_type() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) set_compute_interface_delta_hbond_unsat() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_compute_interface_energy() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_compute_interface_sc() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_compute_packstat() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) set_compute_separated_sasa() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_computed() (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) set_cone_parameters() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) set_conf_clash_resolution() (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) set_conf_clash_tolerance() (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) set_conf_cluster() (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) set_conf_comparer() (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) set_conf_generate_3d() (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) set_conf_sample_bond_angles() (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) set_conf_sample_dihed() (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) set_conf_sample_rings() (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) set_conf_tolerance() (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) set_conformational_data() (pyrosetta.rosetta.core.energy_methods.PBLifetimeCache method) set_conformer_switch_probability() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_connect_info_cutoff() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_cons_design_data_source() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_conserved() (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) set_consider_already_bonded() (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) set_consider_mainchain_only() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelector method) set_const_data() (pyrosetta.rosetta.core.pose.Pose method) set_const_reference_segment() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) set_constrain() (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) set_constrain_bb_angle() (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) set_constrain_bb_cacb_dihedral() (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) set_constrain_bb_dihedral() (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) set_constrain_ca_ca_dist() (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) set_constrain_to_closest() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_constrain_vlvh_qq() (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) set_constraint() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_constraint_file() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_constraint_func() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) set_constraint_weight() (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_constraints() (in module pyrosetta.rosetta.protocols.rbsegment_relax) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.CstMinimizationData method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreCutoffFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreLoopsFilter method) set_constraints_file() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_constraints_from_link_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_constraints_NtoC() (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) set_constraints_only() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_contact_distance_cutoff() (pyrosetta.rosetta.protocols.sewing.requirements.KeepLigandContactsRequirement method) set_contact_resnum_string() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_contact_resnums_string() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_contact_selector() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_contacts() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) set_contents() (pyrosetta.rosetta.protocols.checkpoint.FileBuffer method) set_context_pose() (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) set_context_update_step() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_continue_until_none_missing() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_continuous_sheets() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_continuous_weight() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_conventional_chains() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) set_conventional_numbering() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) set_conventional_segids() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) set_convert_protein_centroid() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_coord_cst_weight_array() (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) set_coord_frame_ref() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) set_coord_selector_rs() (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) set_coordfile() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_coordinate_cacher() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter method) set_coordinate_constraints_during_minimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_coordinates() (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.fragment.BBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) (pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint method) set_coordinates_for_rotamer() (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) set_coords() (pyrosetta.rosetta.core.conformation.UltraLightResidue method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) set_coords_for_clash_check() (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) set_copies_pitch() (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) set_copy_DOF() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) set_copy_dofs_info() (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) set_copy_from_parameters_index() (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) set_copy_identity() (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) set_copy_suffix() (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) set_copy_torsions() (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) set_core_chemical_gasteiger_GasteigerAtomTypeData_AtomicOrbitalTypes_t (class in pyrosetta.rosetta.std) set_core_id_DOF_ID_t (class in pyrosetta.rosetta.std) set_core_id_PartialAtomID_t (class in pyrosetta.rosetta.std) set_core_residues() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_correct_polymer_dependent_atoms() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) set_corresponding_atoms_robust() (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) set_cos_theta() (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) (pyrosetta.rosetta.core.scoring.SAnode method) set_count_data() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection method) set_count_gly_as_polar() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) set_counted() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) set_couplings() (pyrosetta.rosetta.core.pack.task.operation.SetRotamerCouplings method) set_create_db() (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) set_crick_params_file_for_helix() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) set_crick_params_filename() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix method) set_cross_chain_boundaries() (pyrosetta.rosetta.core.select.residue_selector.BFactorSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) set_crossover() (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairGeneric method) set_crystinfo() (pyrosetta.rosetta.core.pose.PDBInfo method) set_cst_action() (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) set_cst_block() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) set_cst_cache() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver method) set_cst_fa_file() (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) set_cst_file() (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) set_cst_file_name() (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) set_cst_gap() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) set_cst_map_file() (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) set_cst_map_file_contents() (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) set_cst_sdev() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) set_cst_source() (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluator method) set_cst_string() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) set_cst_term_ramping() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_cst_weight() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) set_cst_width() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) set_cstAtoms() (pyrosetta.rosetta.protocols.jumping.ResiduePairJump method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) set_cstfile() (pyrosetta.rosetta.protocols.denovo_design.constraints.FileConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) set_cstid_list() (pyrosetta.rosetta.protocols.enzdes.RepackWithoutLigandFilter method) set_cstInfo() (pyrosetta.rosetta.protocols.jumping.ResiduePairJump method) set_cstio() (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) set_cstweight() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) set_cterm_included() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_cummulative_time() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_cumul_hbonds() (pyrosetta.rosetta.protocols.simple_pose_metric_calculators.NumberHBondsCalculator method) set_cumulative_peak_volume() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) set_current() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) set_current_confnum() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) set_current_cycle() (pyrosetta.rosetta.protocols.features.TrajectoryMapFeatures method) set_current_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) set_current_jump() (pyrosetta.rosetta.protocols.symmetry.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SymmetrySlider method) set_current_no_E_update() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) set_current_pose_landing_atom() (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.GaussianChainFuncPotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.LoopClosePotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.SixDTransRotPotentialEvaluator method) set_current_pose_landing_xyz() (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.GaussianChainFuncPotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.LoopClosePotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.SixDTransRotPotentialEvaluator method) set_current_pose_takeoff_atom() (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.GaussianChainFuncPotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.LoopClosePotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.SixDTransRotPotentialEvaluator method) set_current_pose_takeoff_xyz() (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.GaussianChainFuncPotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.LoopClosePotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.SixDTransRotPotentialEvaluator method) set_current_round() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_FinalFullatomRefinementMoveGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_HelixCoilMoveGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_SigmoidalTemperatureScheduleGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator method) set_current_tag() (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) set_custom_angle() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_custom_data() (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) set_custom_dihedral() (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) set_custom_rama_table() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) set_custom_type() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric method) (pyrosetta.rosetta.protocols.filters.FilterValueMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric method) set_cut() (pyrosetta.rosetta.protocols.loops.Loop method) set_cut_res() (pyrosetta.rosetta.protocols.splice.Splice method) set_cutoff() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreCutoffFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreLoopsFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_cutoff_angle() (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorer method) set_cutoff_buried_surface_area() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) set_cutoff_distance() (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorer method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) set_cutoff_lr() (pyrosetta.rosetta.core.scoring.CenHBPotential method) set_cutoff_sr() (pyrosetta.rosetta.core.scoring.CenHBPotential method) set_cutoffs() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric method) set_cutpoint() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) set_cutpoint_closed() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) set_cutpoint_closed_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_cutpoint_open_in_full_model() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) set_cutpoint_open_list() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_cutpoints_closed() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) set_cutpoints_cyclize() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) set_cutpoints_open() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) set_cycle() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters static method) set_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler 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.MembraneAbinitio method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ShortLoopClosure method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_cycles_adjust() (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) set_cycles_inner() (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) set_cycles_outer() (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) set_cyclic_residue_mappings() (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) set_cyclization_type() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_cyclize_res() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) set_cys_types() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) set_d() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) set_D_alpha_compfile_contents() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_D_beta_compfile_contents() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_dalphaball_sasa() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_dangling_res() (pyrosetta.rosetta.protocols.recces.params.RECCES_Parameters method) set_data() (pyrosetta.rosetta.core.scoring.ResPairMinimizationData method) (pyrosetta.rosetta.core.scoring.ResSingleMinimizationData method) set_data_annotations() (pyrosetta.rosetta.core.io.rna.RDAT method) set_data_int() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) set_data_real() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) set_data_source() (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) set_data_str() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) set_database_name() (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) set_database_path() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastPlus method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_LoopOverSCs method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrix method) set_database_pq_schema() (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) set_db_mode() (pyrosetta.rosetta.utility.sql_database.session method) set_db_name() (pyrosetta.rosetta.utility.sql_database.session method) set_db_partition() (pyrosetta.rosetta.utility.sql_database.session method) set_db_path() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) set_db_reporter() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) set_dcut() (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) set_dcut1() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) set_dcut2() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) set_ddG_cutoff() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver method) set_ddG_filter() (pyrosetta.rosetta.protocols.simple_ddg.InterfaceBindingEnergyDensityFilter method) set_debug() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower 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.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) set_debug_pdbs() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_decoy_compatibility() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) set_decoy_tag() (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) set_decoys_returned() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) set_deep_optimization() (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) set_default() (pyrosetta.rosetta.core.scoring.facts.FACTSPotential method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy 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.cyclic_peptide.PeptideCyclizeMover 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.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockTaskFactory method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover 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.ub_e2c.ubi_e2c_modeler method) set_default_assembly_scorers() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_default_bonus() (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) set_default_bridge_type() (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilter method) set_default_coordinate_settings() (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) set_default_crick_params_file() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) set_default_final_stream() (pyrosetta.rosetta.basic.MemTracerImpl static method) (pyrosetta.rosetta.basic.TracerImpl static method) set_default_helix_length() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) set_default_mc() (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) set_default_minimization_settings() (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) set_default_minimizer() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_default_move_map() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) set_default_movemap() (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) set_default_moveset_phase1() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_default_moveset_phase2() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_default_moveset_phase3() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_default_options() (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) set_default_protocol() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) set_default_requirements() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_default_residue_name() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) set_default_score_functions() (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) set_default_scores() (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) set_default_settings() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.LoopRebuild 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) set_default_value() (pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter 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) set_defaults() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions 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.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.CDRSeqDesignOptions method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.dna.PDBOutput method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.esm_perplexity.EsmPerplexityTensorflowProtocol method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmtfJobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) (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.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover 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.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mpi_refinement.Clusterer 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.mpi_refinement.Serial_Refine 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) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilter method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController 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) set_defaults_from_cmdline() (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) set_degree_vicinity() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) set_delete_interface_native_sidechains() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) set_delete_probability() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_delta() (pyrosetta.rosetta.core.pose.Pose method) set_delta_omega1_guesses() (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) set_delta_omega1_max() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters method) set_delta_omega1_min() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters method) set_delta_prob_cutoff() (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities method) set_delta_z1_guesses() (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) set_den_fit_metric() (pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector method) set_denovo_scorefxn() (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) set_density_sc_scale_byres() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_density_sf() (pyrosetta.rosetta.protocols.loop_grower.LoopComparator method) set_depth() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) set_deriv_check() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) set_deriv_check_result() (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) set_deriv_cutoff() (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) set_derivative_graph() (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) set_design() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) set_design_chains() (pyrosetta.rosetta.protocols.docking.DockTaskFactory method) set_design_framework_conservative() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) set_design_framework_conserved_res() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) set_design_H3_stem() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) set_design_layer() (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) set_design_layers() (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) set_design_loop() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoops method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) set_design_neighbors() (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) set_design_options() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_design_protocol() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_design_selector_rs() (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) set_design_shell() (pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator method) (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) set_design_target_res() (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) set_design_taskset() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_design_x_positions() (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) set_designable_residues() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesSeqRecoveryCache method) set_designing_with_noncanonicals() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_desymmeterize() (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler method) set_desymmetrize_residue_selector() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) set_detect_bonds() (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) set_detect_disulfide_in_separated_pose() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_detect_interface() (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) set_detect_pseudobonds() (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) set_deterministic_flag() (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) set_dew_waters_not_to_be_included() (in module pyrosetta.rosetta.protocols.hydrate) set_dG_ins_threshold() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) set_dG_tolerance() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) set_dG_weight() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) set_diagonal() (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_float_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) set_dihedral (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) set_dihedral() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) set_dihedral_angle() (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) set_dihedral_constraint_weight() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_dihedral_mask() (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) set_dihedral_pattern() (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) set_dihedrals() (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) set_dihedrals_from_linkage_conformer_data() (in module pyrosetta.rosetta.core.pose.carbohydrates) set_dimension() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) set_dimension_sizes() (pyrosetta.rosetta.utility.LexicographicalIterator method) set_dimensions() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) set_direction() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_dis() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_dis_D1D2() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_dis_D2D3() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_dis_U1D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_disable_packing_and_design() (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) set_disable_sampling_of_loop_takeoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) set_disabled() (pyrosetta.rosetta.protocols.checkpoint.CheckPointer method) set_disabled_except_during_packing() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) set_disallow_bps_at_extra_min_res() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_disallow_deletion_of_last_residue() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) set_disallow_pack_polar_hydrogens() (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) set_disallow_quench() (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.flexpack.annealer.FlexbbSimAnnealer method) set_disallow_realign() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_dist() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential method) (pyrosetta.rosetta.protocols.nmr.pre.PREDistanceRecord method) set_dist_cutoff() (pyrosetta.rosetta.protocols.buns.BuriedUnsatisfiedPolarsCalculator2 method) set_dist_cutoff_multiplier() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) set_dist_exponent() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) set_dist_midpoint() (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) set_dist_sigma2() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential method) set_dist_to_connect_point() (pyrosetta.rosetta.core.scoring.etable.etrie.CountPairData_1_1 method) (pyrosetta.rosetta.core.scoring.etable.etrie.CountPairData_1_2 method) (pyrosetta.rosetta.core.scoring.etable.etrie.CountPairData_1_3 method) (pyrosetta.rosetta.core.scoring.etable.etrie.CountPairDataGeneric method) (pyrosetta.rosetta.core.scoring.etable.etrie.GenericResidueConnectionData method) set_dist_wts() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential method) set_distance() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) set_distance_center_to_atom1() (pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch method) set_distance_cutoff() (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorer method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_distance_matrix() (pyrosetta.rosetta.protocols.contact_map.ContactMap method) set_distance_mode() (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorer method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric method) set_distance_sphere_for_atom() (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.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid 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.VdwGrid method) set_distance_tolerance() (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) set_distinguish_pucker() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_disulf() (pyrosetta.rosetta.protocols.hybridization.MRMover method) set_disulf_file() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) set_disulfide_atom_name() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) set_disulfide_file() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_dlig_nmeg_limit() (pyrosetta.rosetta.protocols.pack_daemon.DaemonSet method) (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) set_Dmax() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) set_dna_a_path() (pyrosetta.rosetta.protocols.dna_dock.DNAClashCheckFilter method) set_dna_b_path() (pyrosetta.rosetta.protocols.dna_dock.DNAClashCheckFilter method) set_do_add_delete() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) set_do_checks() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer method) set_do_inner() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_do_minimization() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) set_do_minimize() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) set_do_no_op_random() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) set_do_not_autoassign_SS() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_do_not_sample_multiple_virtual_sugar() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_do_outer() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_do_screen() (pyrosetta.rosetta.protocols.stepwise.screener.AlignRMSD_Screener method) set_do_screens() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) set_do_sfxn_eval_every_iteration() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_dock_chunks() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) set_dock_chunks_res() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_dock_each_chunk() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_dock_each_chunk_per_chain() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_dock_first_cycles() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_dock_high_res_scorefunction() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) set_dock_into_density() (pyrosetta.rosetta.core.import_pose.options.RNA_BasicOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) set_dock_into_density_legacy() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_dock_jump() (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) set_dock_low_res_scorefunction() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) set_dock_mcm_protocol() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) set_dock_min() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) set_dock_min_protocol() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) set_dock_pert() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_dock_post_graft() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_dock_ppk() (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_dock_ppk_protocol() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) set_dock_rounds() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_dock_rtmin() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_dock_score_func() (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) set_dock_second_cycles() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_docking() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_docking_foldtree() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) set_docking_frequency() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_docking_highres_mover() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) set_docking_local_refine() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) set_docking_move_size() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_docking_pose() (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) set_dof() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) set_DOF() (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) set_DOF_id() (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) set_dofs() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) set_DOFs() (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) set_dofs_pdb_name() (pyrosetta.rosetta.protocols.splice.Splice method) set_domain() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) set_donor_selector() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) set_donor_structure() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_dont_fail_if_no_solution_found() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) set_double_msg() (pyrosetta.rosetta.utility.SimulateMPIMessage method) set_double_t (class in pyrosetta.rosetta.std) set_doubles_msg() (pyrosetta.rosetta.utility.SimulateMPIMessage method) set_downstream_algorithm() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) set_downstream_builder() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.PDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_downstream_chain() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_downstream_master() (pyrosetta.rosetta.protocols.match.output.DownstreamCoordinateKinemageWriter method) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) set_downstream_orientation_atoms() (pyrosetta.rosetta.protocols.match.MatcherTask method) set_downstream_pose() (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.MatcherTask method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_downstream_restype() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) set_downstream_writer() (pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) set_drift() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_driver() (pyrosetta.rosetta.cppdb.backend.connection method) set_drop_best() (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric method) set_dry_run() (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover method) set_ds_atom_ids_needed() (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) set_dSASA_cutoff() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) set_dsbuilder() (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) set_dssp_code() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) (pyrosetta.rosetta.protocols.sewing.requirements.DsspSpecificLengthRequirement method) set_dswriter() (pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage method) set_dt() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_dump() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_dump_dir() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) set_dump_freq() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_dump_multis() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) set_dump_pdb() (pyrosetta.rosetta.core.import_pose.options.RNA_BasicOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_dump_pdbs() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) set_dump_silent() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_dump_singles() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) set_dump_stems() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) set_dump_weights_file() (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) set_dumpbeam() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_dumperrors() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_dumpfinalbeam() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_dumping_app() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_dumprms() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_dwell_cutoff() (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) set_e2g2_diubi_fold_tree() (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) set_edge() (pyrosetta.rosetta.core.pose.rna.RNA_Datum method) set_edge1() (pyrosetta.rosetta.core.pose.rna.BasePair method) set_edge2() (pyrosetta.rosetta.core.pose.rna.BasePair method) set_edge_data() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) set_edge_file() (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) set_edge_file_name() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_edge_file_reader() (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) set_edge_index() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) set_edge_map_generator() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_edge_weight() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) set_effective_sequence_separation() (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraint method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) (pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint method) set_efficiency() (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) set_Eig_xx() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) set_Eig_yy() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) set_Eig_zz() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) set_elec_scale() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) set_elec_sigmoidal_die_params() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_element_radii() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDistSasaCalculator method) set_element_w_attributes() (pyrosetta.rosetta.utility.tag.XMLSchemaRepeatableCTNode method) set_eliminated_due_to_dist_violations() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) set_elimination_candidate() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) set_elimination_comment() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) set_eliminator() (pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminatorTaskOperation method) set_eliminator_function() (pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminator method) set_else() (pyrosetta.rosetta.protocols.filters.IfThenFilter method) set_Emin_obj() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_empty_voxel_color() (pyrosetta.rosetta.protocols.match.Bool3DGridKinemageWriter method) set_enable_design() (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.relax.FastRelax method) set_end() (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) set_end_bias() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) set_end_graft() (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) set_end_position() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix method) set_end_temperature() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_ending_residue() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseSegment method) set_energy() (pyrosetta.rosetta.core.chemical.mainchain_potential.MainchainScoreTable method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.protocols.jd3.job_summaries.StandardPoseJobSummary method) (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_energy_cutoff() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_energy_landscape_evaluator() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.pose_metric_calculators.RotamerBoltzCalculator method) set_energy_method_options() (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) set_energy_state() (pyrosetta.rosetta.core.energy_methods.PBLifetimeCache method) set_energy_terms() (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor method) set_energy_to_beat() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) set_enforce_continuity_at_pi() (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.SixDTransRotPotential method) set_enrichment_threshold() (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation method) set_ensemble1() (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) set_ensemble2() (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) set_ensemble_diversity() (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) set_ensured_sites() (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) set_entity_correspondence() (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) set_entity_element() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.multistate_design.MultiStateEntity method) set_entity_resfile() (pyrosetta.rosetta.protocols.pack_daemon.DaemonSet method) set_entity_template() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) (pyrosetta.rosetta.protocols.genetic_algorithm.Mutate1Randomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) set_enumerate() (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_enumerate_ligand_rotamers() (pyrosetta.rosetta.protocols.match.MatcherTask method) set_enumeration_shell() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) set_enz_input_data() (pyrosetta.rosetta.protocols.match.MatcherTask method) set_enzdes_loops_file() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver method) set_enzio_param() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) set_enzyme() (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) set_enzyme_chain() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_epitope_residues() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_eps() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_epsilon() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_equiv() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerLinks method) (pyrosetta.rosetta.protocols.symmetry.NCSResMapping method) set_erraser() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_error_norms() (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) set_error_on_missing_segment() (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) set_error_on_out_of_bounds_index() (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) set_error_out_on_complex_cycles() (pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph method) set_errorfull_deltaE_threshold() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase 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.MultiplexedAnnealableGraph 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.ResidueArrayAnnealingEvaluator 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) set_etable() (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) set_euler_alpha_values() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) set_euler_angle_bin_max() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) set_euler_angle_bin_min() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) set_euler_angle_bin_size() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) set_euler_bin_widths() (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) set_euler_gamma_values() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) set_euler_z_bin_max() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) set_euler_z_bin_min() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) set_euler_z_bin_size() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) set_euler_z_values() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) set_eval_base_pairs() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_evaluate_local() (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) set_evaluation() (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) (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) set_evaluator() (pyrosetta.rosetta.protocols.match.output.MatchConsolidator method) (pyrosetta.rosetta.protocols.match.output.MatchOutputter method) (pyrosetta.rosetta.protocols.match.output.MatchProcessor method) set_evaluators() (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.dna.PDBOutput method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmtfJobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) set_exact() (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) set_excise_mini_pose() (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) set_exclude_bb_atoms() (pyrosetta.rosetta.protocols.simple_filters.HolesFilter method) set_exclude_chain_termini() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) set_exclude_consecutive() (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) set_exclude_polar_atoms_by_charge() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_exclude_submotifs() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_excluded_positions() (pyrosetta.rosetta.protocols.helix_capper.HelixNCapperMover method) (pyrosetta.rosetta.protocols.vip.VIP_Mover method) set_excluded_residues() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HPool_RMSD method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.Pool_RMSD method) set_excluded_sites() (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) set_exclusion_distance() (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) set_exhaustive_fragment_insertion() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_existing_residue() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) set_exit_if_missing_heavy_atoms() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_exit_on_fail() (pyrosetta.rosetta.protocols.stepwise.legacy.screener.RNA_AtrRepScreener method) set_expand_loop_takeoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_expecting_n_ligands() (pyrosetta.rosetta.protocols.metal_interface.ZincSiteFinder method) set_experimental_ddg() (pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData method) set_experimental_ddg_bind() (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData method) set_explicit_hydrogen_included_radii_set() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_explicit_rotamers() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) set_exponent() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_SigmoidalTemperatureScheduleGenerator method) set_expression() (pyrosetta.rosetta.numeric.expression_parser.AbsoluteValueExpression method) (pyrosetta.rosetta.numeric.expression_parser.NotExpression method) (pyrosetta.rosetta.numeric.expression_parser.SquarerootExpression method) (pyrosetta.rosetta.numeric.expression_parser.UnaryExpression method) (pyrosetta.rosetta.protocols.pack_daemon.ExpExpression method) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) (pyrosetta.rosetta.protocols.pack_daemon.LnExpression method) (pyrosetta.rosetta.protocols.pack_daemon.Mean method) (pyrosetta.rosetta.protocols.pack_daemon.VectorFunction method) (pyrosetta.rosetta.protocols.pack_daemon.VMax method) (pyrosetta.rosetta.protocols.pack_daemon.VMin method) set_extend_existing_networks() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_extend_h3_before_modeling() (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) set_extend_mode() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_extend_ss() (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator method) set_extended() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) set_extended_loop() (pyrosetta.rosetta.protocols.LoopRebuild method) set_extended_torsions() (in module pyrosetta.rosetta.protocols.loops) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover 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) set_extended_torsions_and_idealize_loops() (in module pyrosetta.rosetta.protocols.loops) set_extension_prob() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix method) set_external_position() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) set_external_position_for_resA() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) set_external_position_for_resA_in_parameter_block() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) set_external_position_for_resB() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) set_external_position_for_resB_in_parameter_block() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) set_externally_generated_packer_solution() (in module pyrosetta.rosetta.core.pack.interaction_graph) set_extra_beta() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) set_extra_bodies() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) set_extra_bodies_chains() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) set_extra_chi() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions 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_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) set_extra_data_1() (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash 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.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore 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) set_extra_data_2() (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash 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.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore 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) set_extra_data_3() (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash 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.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore 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) set_extra_epsilon() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) set_extra_loose_rep_cutoff() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker method) set_extra_minimize_chi_res() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) set_extra_minimize_jump_res() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) set_extra_minimize_res() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_extra_parameter() (pyrosetta.rosetta.core.chemical.AtomType method) set_extra_penalty() (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) set_extra_samples() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) set_extrapolate_scale() (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) set_fa_cst_weight() (pyrosetta.rosetta.protocols.hybridization.MRMover method) set_fa_dun_cutoff() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) set_fa_dun_cutoff_for_constraint() (pyrosetta.rosetta.protocols.match.Matcher method) set_fa_rep_thresh() (pyrosetta.rosetta.protocols.dna_dock.DNAClashCheckFilter method) (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilter method) set_fa_score_function() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) set_fa_scorefunction() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) set_fa_scorefxn() (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) set_facet_alpha() (pyrosetta.rosetta.protocols.match.Bool3DGridKinemageWriter method) set_facet_color() (pyrosetta.rosetta.protocols.match.Bool3DGridKinemageWriter method) set_facet_master() (pyrosetta.rosetta.protocols.match.Bool3DGridKinemageWriter method) set_fafilter() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_fail_on_missing_cache() (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeatures method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities method) set_fallback_strategy() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_famin() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_farray_from_sso() (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver static method) set_fast() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) set_fast_restyping() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_fasta_file() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) set_fasta_file_contents() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) set_fasta_files() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) set_fastas() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) set_favor_bonus() (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) set_favor_native() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GAOptimizer method) set_favor_native_bonus() (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) set_fcen10() (pyrosetta.rosetta.core.scoring.CenListInfo method) set_fcen12() (pyrosetta.rosetta.core.scoring.CenListInfo method) set_fcen6() (pyrosetta.rosetta.core.scoring.CenListInfo method) set_field_strength() (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingleSet method) set_figure_out_prepack_res() (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) set_file_contents() (pyrosetta.rosetta.utility.io.FileContentsMap method) (pyrosetta.rosetta.utility.tag.XMLErrorHandler method) set_file_option() (in module pyrosetta.rosetta.basic.options) set_file_reading_token() (pyrosetta.rosetta.protocols.loops.Loops method) set_file_vector_option() (in module pyrosetta.rosetta.basic.options) set_filename() (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (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) (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) set_filename_root() (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) set_filenames() (pyrosetta.rosetta.core.import_pose.pose_stream.PDBPoseInputStream method) set_filetype() (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) set_filter() (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.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStub method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) set_filter_attach_boinc_ghost_observer() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) set_filter_behaviour() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) set_filter_bin() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) set_filter_by_lj() (pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_filter_by_phipsi() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_filter_chain_closure() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_filter_chain_closure_distance() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_filter_chain_closure_halfway() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_filter_complex_cycles() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_filter_during_design() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_filter_for_previous_clash() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer method) set_filter_for_previous_contact() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer method) set_filter_lores_base_pairs() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_filter_lores_base_pairs_early() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_filter_native_big_bins() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_filter_omega() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) set_filter_out_high() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) set_filter_out_low() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) set_filter_rama_cutoff_energy() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) set_filter_resnum() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) set_filter_SASA() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) set_filter_score() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) set_filter_structs() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) set_filter_templates() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_filter_type() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) set_filter_user_alignment_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_filter_vdw() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_filter_virtual_res_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_filter_weight() (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) set_filterbeams() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_filtered_area() (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric method) set_filtered_d_median() (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric method) set_filtered_sc() (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric method) set_filterprevious() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) set_filters() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_final_fold_tree() (pyrosetta.rosetta.protocols.abinitio.CoordinateConstraintKC method) (pyrosetta.rosetta.protocols.abinitio.KinematicControl method) set_final_frlx_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_final_min_pack_min() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) set_final_optimization_n_iter() (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) set_find_native() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_find_only_native() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_finer_sampling_at_chain_closure() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_finish_scorefxn() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) set_finish_stage() (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) set_finite() (pyrosetta.rosetta.core.scoring.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) set_first() (pyrosetta.rosetta.core.scoring.packstat.trace method) (pyrosetta.rosetta.core.select.residue_selector.FractionSelector method) set_first_cycle() (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) set_first_expression() (pyrosetta.rosetta.numeric.expression_parser.AddExpression method) (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.BinaryExpression method) (pyrosetta.rosetta.numeric.expression_parser.DivideExpression method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.MaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MinExpression method) (pyrosetta.rosetta.numeric.expression_parser.MultiplyExpression method) (pyrosetta.rosetta.numeric.expression_parser.OrExpression method) (pyrosetta.rosetta.numeric.expression_parser.SubtractExpression method) (pyrosetta.rosetta.protocols.pack_daemon.PowExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VectorFunction2 method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) set_first_selector() (pyrosetta.rosetta.protocols.pose_sewing.filters.HasDisulfideFilter method) set_fitness() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.multistate_design.MultiStateEntity method) set_five_prime_chain_break_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_five_prime_phosphate_res() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) set_fiveprime_cap() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) set_fiveprime_res() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) set_fix_angles() (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_fix_backbone() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_fix_cataa() (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) set_fix_catalytic_aa() (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) set_fix_lengths() (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_fix_ligands() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) set_fix_torsions() (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_fixed_energies() (pyrosetta.rosetta.core.scoring.MinimizationGraph method) set_fixed_if_moving() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) set_fixed_res() (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.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_fixed_residues() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_fixed_stems() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_fixed_stub() (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraint method) set_flags() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics method) set_flank_residue_min() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) set_flank_size() (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) set_flat_bottom_constraints() (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) set_flat_score_multiply() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) set_flip_rate() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) set_floating_base() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_floating_base_anchor_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_focus() (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) set_focus_selector() (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) set_focused_geomcst_id() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) set_fold_tree() (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_fold_tree_and_chainbreaks() (pyrosetta.rosetta.protocols.jumping.JumpSample method) set_fold_tree_and_cutpoints() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) set_fold_tree_from_loops() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) set_fold_tree_from_silent_file() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) set_fold_tree_from_symm_data() (in module pyrosetta.rosetta.core.conformation.symmetry) set_fold_tree_in_pose() (pyrosetta.rosetta.protocols.jumping.JumpSample method) set_fold_tree_io() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_fold_tree_nodes() (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover 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) set_fold_tree_root() (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) set_fold_tree_type() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_folder() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) set_folding_window() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) set_foldtree() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) set_force_align() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_force_anti_chi_res_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_force_bitflip() (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) set_force_centroid_interaction() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_force_cluster() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_force_combined_gaussian_approximation() (pyrosetta.rosetta.core.scoring.func.GaussianChainFunc method) set_force_exact_min() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) set_force_internal() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_force_job_purging() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) set_force_moving_res_for_erraser() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_force_nonideal() (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.relax.FastRelax method) set_force_north_paper_db() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_force_north_sugar_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_force_phosphate_instantiation() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_force_repack() (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) set_force_south_sugar_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_force_submotif_without_intervening_bulge() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_force_syn_chi_res_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_force_unique_moves() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) set_force_user_defined_jumps() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_force_virts_for_refinement() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) set_forced_silent_struct_type() (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) set_forget_chains_and_interface() (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterface method) set_format_from_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) set_frac_by_recomb() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) set_fraction() (pyrosetta.rosetta.core.select.residue_selector.FractionSelector method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) set_fractions() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) set_frag3() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_frag_1mer_insertion_weight() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_frag_files() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) set_frag_size() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) set_frag_sizes() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) set_frag_weight_aligned() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_frag_weight_file() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) set_fragmelt() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_fragment_probs() (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) set_fragments() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) set_frags() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_fragset() (pyrosetta.rosetta.protocols.pose_metric_calculators.FragQualCalculator method) set_fragtrials() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_frames() (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) set_free_peptide() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) set_free_residues() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_free_rsd() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_freq() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D.Spin method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D.Spin method) set_frequency() (pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequencies method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDatabase method) (pyrosetta.rosetta.protocols.trajectory.DbTrajectoryWriter method) set_from() (pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector method) set_from_cdr() (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) set_from_other_chains() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_from_same_chain() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_from_scheme() (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) set_from_scratch_frequency() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_ft_close_chains() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_ft_mover() (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) set_full_accuracy_when_scoring() (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) set_full_length_loop_rmsd_clustering() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) set_full_model_parameters() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) (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) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) set_full_packing_frequency() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) set_full_repack() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_full_sequence() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_full_to_sub() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_full_type_name() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSewingResidue method) set_fullatom() (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) set_fullatom_density_weight() (pyrosetta.rosetta.protocols.hybridization.MRMover method) set_fullatom_loop_building() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) set_fullatom_pose() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) set_fullatom_scorefunction() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) set_fullatom_scorefxn() (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) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) set_func() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorer method) set_func_for_weight() (pyrosetta.rosetta.protocols.moves.RampingMover method) set_function() (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) set_Fv() (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) set_gamma() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) set_Gamma() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_gamma() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.EulerAngles method) set_gap_size() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_gasteiger_atom_type() (pyrosetta.rosetta.core.chemical.MutableResidueType method) set_gasteiger_atom_typeset() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) set_gaussian() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) set_gaussian_stdev() (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion 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_Suite method) set_gaussian_stdevs_recces_turner() (in module pyrosetta.rosetta.protocols.recces) set_gaussian_stdevs_thermal_sampler() (in module pyrosetta.rosetta.protocols.recces) set_gdt() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) set_gen_fixed() (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) set_general_overlap_tolerance() (pyrosetta.rosetta.protocols.match.BumpGrid method) set_general_phi_sd() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_general_psi_sd() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_generation_tag() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) set_generator() (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) set_genericRBMoveStepsize() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) set_generous() (pyrosetta.rosetta.protocols.simple_pose_metric_calculators.NumberHBondsCalculator method) set_generous_hbonds() (pyrosetta.rosetta.protocols.buns.BuriedUnsatisfiedPolarsCalculator2 method) set_generous_hbonds_() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_geomcst_for_superposition_from_enz_io() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) set_geometry_score_weight() (pyrosetta.rosetta.protocols.sewing.hashing.LigandBindingResPlacer method) set_ghost_loops() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_gJ() (pyrosetta.rosetta.core.io.nmr.ParaIon method) set_global() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) set_global_for_parameters_set() (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) set_global_optimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) set_global_sample_res_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_global_seq_file() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) set_glycam_pdb_format() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) set_glycan_iupac_bb_torsions() (in module pyrosetta.rosetta.core.pose.carbohydrates) set_glycan_iupac_chi_torsions() (in module pyrosetta.rosetta.core.pose.carbohydrates) set_glycan_sampler_kt() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) set_glycan_sampler_rounds() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) set_glycan_sequon_type() (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) set_GlyCorrection_values() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) set_GlyCorrection_values_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) set_glycosidic_torsion() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) set_glycosylation() (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) set_glycosylation_position() (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) set_glycosylation_refinement() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_glycosylation_residue() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_glycosylation_weights() (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) set_glycosylations() (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) set_gradual_constraints() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_graft_design_cdrs() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_graft_design_options() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_graft_h1() (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) set_graft_h2() (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) set_graft_h3() (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) set_graft_l1() (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) set_graft_l2() (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) set_graft_l3() (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) set_greedy() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_grid_atom1() (pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch method) set_grid_atom2() (pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch method) set_grid_dim_with_maxRad() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) set_grid_max_radius() (pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch method) set_grid_min_radius() (pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch method) set_grid_param() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter 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) set_grid_search_center() (pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch method) set_grid_vdw_weight() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_gridsearch_iterator() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) set_gridsearch_range() (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) set_group_discriminator() (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) set_group_ids() (pyrosetta.rosetta.protocols.minimization_packing.UserDefinedGroupDiscriminator method) set_group_subelement() (pyrosetta.rosetta.utility.tag.XMLSchemaRepeatableCTNode method) set_grouper() (pyrosetta.rosetta.protocols.match.output.MatchConsolidator method) set_grow_attempts_() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover 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) set_GTPase_lys() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) set_guarantee_no_DNA() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_guarded_loops_not_in_charge() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover 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) set_h3_loop_csts_hr() (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) set_h3_loop_csts_lr() (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) set_h3_stem_graft() (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) set_half_width() (pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction method) set_handedness_score_flag() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_hardsphere_bump_check() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_harmonic_constants() (pyrosetta.rosetta.protocols.normalmode.NormalMode method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) set_has_density_map() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) set_has_silent_in() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) set_hash_euclidean_bin_width() (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.MatcherTask method) set_hash_euclidean_bin_widths() (pyrosetta.rosetta.protocols.match.Matcher method) set_hash_euler_bin_width() (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.MatcherTask method) set_hash_euler_bin_widths() (pyrosetta.rosetta.protocols.match.Matcher method) set_hash_gridding() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) set_hash_subgridding() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) set_hashed() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_hb_e_cutoff() (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) set_hbnet_energy_ramping() (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) set_hbond_cutoff() (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter method) set_hbond_energy_cutoff() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelector method) (pyrosetta.rosetta.protocols.residue_selectors.HBondSelector method) set_hbond_options() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) set_hbond_types() (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) set_hbonds() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary method) set_hbonds_energy_cutoff() (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilter method) set_hbonds_num_threshold() (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilter method) set_heat_after_cycles() (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) set_helical_substruct_res() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_helical_substructs() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) set_helicalMoveStepsize() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) set_helix_assignment_file() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) set_helix_assignment_file_contents() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) set_helix_length() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) set_helix_length_for_helix() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) set_helix_mover_magnitude() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) set_helix_range() (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) set_hh_angle() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) set_hh_angle_sigma2() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) set_hh_angle_wts() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) set_hh_rules_2021() (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator method) set_highres_conformer_filter_type() (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel method) set_highres_score_func() (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) set_highres_scorefxn() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_hightemp() (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.flexpack.annealer.FlexbbSimAnnealer method) set_hires_scorefxn() (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) set_histogram_max() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_histogram_min() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_histogram_spacing() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_history() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) set_history_size() (pyrosetta.rosetta.protocols.pack_daemon.MPIMultistateFitnessFunction method) (pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction method) set_hit_cacher() (pyrosetta.rosetta.protocols.match.output.SameChiBinComboGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) set_hpairset() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential method) set_hs_angle() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) set_hs_angle_sigma2() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) set_hs_angle_wts() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) set_hs_atr_dist() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) set_hs_atr_dist_sigma2() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) set_hs_atr_dist_wts() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) set_hsheet_repl_dist() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) set_hxl_dist_cutoff() (pyrosetta.rosetta.protocols.buns.BuriedUnsatisfiedPolarsCalculator2 method) set_hybrid_protocol() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) set_hydrate() (pyrosetta.rosetta.protocols.magnesium.MgScanner method) set_hydrate_magnesiums() (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) set_hydration() (pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams method) set_IAM() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) set_icoor() (pyrosetta.rosetta.core.chemical.MutableResidueType method) set_id() (pyrosetta.rosetta.core.optimization.DOF_Node method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.MotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.constraints.FileConstraintGenerator 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.FoldArchitectMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator 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) (pyrosetta.rosetta.protocols.frag_picker.scores.ABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) (pyrosetta.rosetta.protocols.optimize_weights.OptEVariableExpression 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.rna.RNA_ChiStepWiseSampler 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.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.trRosetta_protocols.constraint_generators.trRosettaConstraintGenerator method) set_ideal_abego() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) set_ideal_angle_about_contact() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ideal_angle_about_metal() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ideal_dihedral_3() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ideal_dihedral_about_contact() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ideal_dihedral_about_metal() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ideal_distance() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ideal_sheets() (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) set_ideal_xyz() (pyrosetta.rosetta.core.chemical.MutableResidueType method) set_idealize() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) set_idealize_conformers() (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) set_idealize_coord() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler 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) set_idealize_insert() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_idealize_loop_first() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_idealize_torsions() (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) set_identity() (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) set_identity_rotation() (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) set_identity_transform() (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) set_ids() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) set_IGEdgeReweights() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) set_ignore_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) set_ignore_bb_heavy_unsats() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_ignore_cmdline_for_build_points() (pyrosetta.rosetta.protocols.match.MatcherTask method) set_ignore_default_docking_task() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) set_ignore_default_task() (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) set_ignore_FARFAR_no_auto_bulge_parent_tag() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_ignore_FARFAR_no_auto_bulge_tag() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_ignore_light_chain() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_ignore_negative_intensity() (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) set_ignore_pikaa_natro() (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) set_ignore_pose_datacache() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_ignore_pose_profile_length_mismatch() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation method) set_ignore_register_shift() (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilter method) set_ignore_scoretypes() (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric method) set_ignore_secstruct() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_ignore_segments() (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) set_ignore_sugars() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_ignore_surface_res() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_ignore_unconnected_upper() (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) set_ignore_unmatched_virtual_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_ignore_unrecognized_res() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecovery method) set_ignore_waters() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_ignore_zero_occupancy() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_iha_cut() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) set_iha_penalty_mode() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) set_iha_penalty_slope() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) set_implicit_hydrogen_included_radii_set() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_important_residues() (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) set_in_pose() (pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals method) set_include_adjacent_residues() (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation method) set_include_backbone_atoms() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD method) set_include_background_energies() (pyrosetta.rosetta.protocols.pack_daemon.DaemonSet method) (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) set_include_bb_bb() (pyrosetta.rosetta.protocols.residue_selectors.HBondSelector method) set_include_carbon_sulfer_only_in_hydrophobic_calc() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_include_cdr4_in_optimization() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_include_current_ds() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) set_include_default_linear_chainbreak() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) set_include_focus() (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector method) set_include_focus_in_subset() (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) set_include_His_chain_terminus() (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilter method) set_include_hydrogens_explicitly() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_include_native_restype() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_include_native_type() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_include_neighbors() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) set_include_only_scoretypes() (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric method) set_include_only_set_depth() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) set_include_probe_radius_in_atom_radii() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_include_probe_radius_in_calc() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) set_include_protein_omega() (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric method) set_include_rama_prepro_and_proclose() (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric method) set_include_root() (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) set_include_self() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) set_include_terminal_loops() (pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector method) set_include_virt_waters() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) set_increase_cycles() (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) set_indent() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) set_index() (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.utility.libsvm.Svm_node_rosetta method) (pyrosetta.rosetta.utility.SimulateMPIMessage method) set_index_range() (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) set_indices() (pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector method) set_infile() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_info() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) set_inherit_scorefxn_temperature() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) set_init() (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) set_init_from_pose() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) set_init_pose() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) set_init_states() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) set_initial_decoy_stddev() (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData method) set_initial_guesses() (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) set_initial_pose() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) set_initial_structures_provided() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_initial_values() (pyrosetta.rosetta.protocols.qsar.qsarOptFunc method) set_inner_bb_cycles() (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) set_inner_ca_only() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_inner_cycles() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) set_inner_loop_cycles() (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) set_inner_min_seq_sep() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_inner_radius() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) set_inner_sd() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_inner_unweighted_function() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_inner_use_harmonic_function() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_inner_weight() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_inp_chi() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_input_code() (pyrosetta.rosetta.protocols.sparta.ANN method) set_input_initialization_pdbs() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) set_input_is_angle_in_degrees() (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) set_input_pdbs() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) set_input_pose() (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) set_input_pose_is_fa() (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) set_input_poses() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) set_input_res() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_input_res_initialize() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_input_res_vectors() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_input_resnum_and_chain_and_segid() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) set_input_scan_res() (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.SampleGrid method) set_input_set() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) set_input_set_selector() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.protocols.residue_selectors.HBondSelector method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) set_input_set_str() (pyrosetta.rosetta.protocols.residue_selectors.HBondSelector method) set_input_silent_files() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) set_input_streams() (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) set_input_tags() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_insert_flexibility() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_insert_region() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) set_insertion_prob() (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) set_instruction_file() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_int_t (class in pyrosetta.rosetta.std) set_integer_msg() (pyrosetta.rosetta.utility.SimulateMPIMessage method) set_integer_option() (in module pyrosetta.rosetta.basic.options) set_integer_vector_option() (in module pyrosetta.rosetta.basic.options) set_integers_msg() (pyrosetta.rosetta.utility.SimulateMPIMessage method) set_integration_test() (pyrosetta.rosetta.protocols.magnesium.MgScanner method) set_integration_test_mode() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_intensity() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) set_inter_atr() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_inter_rep() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_interaction_graph_threads() (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) set_interface() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) set_interface_chains() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) set_interface_definition_task_operation() (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.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockTaskFactory method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) set_interface_dis() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_interface_dist() (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) set_interface_distance() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_interface_jump() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_interface_moves() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_interface_packing_distance() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) set_interface_sasa_filter() (pyrosetta.rosetta.protocols.simple_ddg.InterfaceBindingEnergyDensityFilter method) set_interfaces() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) set_intermediate_structs() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) set_internal_cycles() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) set_interval() (pyrosetta.rosetta.protocols.checkpoint.Timer method) set_interval_data_dump() (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) set_interval_pose_dump() (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) set_intra_atr() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_intra_rep() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_inverse() (pyrosetta.rosetta.core.select.residue_selector.BlockSelector method) set_inversion_random() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) set_inversion_setting() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) set_invert() (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) set_invert_task() (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) set_involves_current_pose() (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.GaussianChainFuncPotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.LoopClosePotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.SixDTransRotPotentialEvaluator method) set_invrots_for_listnum() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) set_ion_label() (pyrosetta.rosetta.core.io.nmr.ParaIon method) set_ios_hook() (pyrosetta.rosetta.basic.MemTracer static method) (pyrosetta.rosetta.basic.MemTracerImpl static method) (pyrosetta.rosetta.basic.Tracer static method) (pyrosetta.rosetta.basic.TracerImpl static method) set_is_do_minimize() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_is_dump_cyclic_poses() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_is_dump_peptide_pose() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_is_dump_prepared_pose() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_is_dump_report_file() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_is_in_Assembly() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) set_is_internal() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_is_ligand_residue() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_is_moving_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_is_prepend() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_is_prepend_map() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_is_report_gzip() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_is_rna_and_protein() (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) set_is_simple_full_length_job_params() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_is_skip_zero_isc() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_is_vital() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) set_is_working_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_iteration() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) set_iterations() (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) set_iterations_per_phase() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) set_J() (pyrosetta.rosetta.core.io.nmr.ParaIon method) set_job_data() (pyrosetta.rosetta.core.chemical.sdf.MolWriter method) set_job_id() (pyrosetta.rosetta.protocols.trajectory.DbTrajectoryReader method) set_job_inputter() (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.JobsContainer 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) set_job_outputter() (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) set_job_queen() (pyrosetta.rosetta.protocols.jd3.job_distributors.JobExtractor method) set_job_tag() (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric method) set_jobindex_on_originating_node() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_RMSDToBestSummary method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary method) set_jump() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.DownJumpSRFD method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilter method) set_jump_atom() (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim method) set_jump_atom_stub_id() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) set_jump_atoms() (pyrosetta.rosetta.core.kinematics.FoldTree method) set_jump_change_frequency() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_jump_histogram() (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) set_jump_histogram_binwidth() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_jump_histogram_binwidth_rotvector() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_jump_histogram_boxsize() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_jump_library_file() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_jump_mover() (pyrosetta.rosetta.protocols.abinitio.CoordinateConstraintKC method) (pyrosetta.rosetta.protocols.abinitio.KinematicControl method) set_jump_name() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) set_jump_now() (pyrosetta.rosetta.core.kinematics.AtomTree method) set_jump_num() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_jump_point_pair_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_jump_res() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_jump_sample() (pyrosetta.rosetta.protocols.jumping.JumpSetup method) set_jump_selector() (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) set_jumpAtoms() (pyrosetta.rosetta.protocols.jumping.ResiduePairJump method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) set_just_min_after_mutation_frequency() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_just_polar_hydrogens() (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_just_rna_backbone() (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_K() (pyrosetta.rosetta.protocols.relax.LocalRelax method) set_Kappa() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_kbt() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) set_keep_base_fixed() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) set_keep_covalent() (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) set_keep_current_ds() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) set_keep_existing_networks() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_keep_filters() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_keep_input_foldtree() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) set_keep_input_protonation_state() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_keep_pdb_info_labels() (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) set_keep_pose_in_memory() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_keep_top_designs() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_keep_virtual_residues() (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) set_kic_modeler_if_relevant() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_kic_sampling() (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) set_kids_naming_func() (pyrosetta.rosetta.utility.tag.XMLSchemaRepeatableCTNode method) set_kin_writer() (pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter method) set_kinemage_file() (pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage method) set_kinemage_file_name() (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) set_kinematic_defaults() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) set_kinematics() (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) set_kinetic_energy() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_kinmover() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) set_kt() (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) set_kT() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) set_L() (pyrosetta.rosetta.core.io.nmr.ParaIon method) set_L_alpha_compfile_contents() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_L_beta_compfile_contents() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_label() (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage 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.RigidChunkClaimer.CM_SuggestFixResidue method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SuggestValueMessage 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) set_labels() (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) set_landing_domain() (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) set_landing_pos() (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) set_large_frag_file() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) set_large_frag_size() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) set_last_accepted() (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) set_last_accepted_pose() (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) set_last_change() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) set_last_change_was_n_terminal() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) set_last_chimaera() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) set_last_chimaera_deleted() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) set_last_score() (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) (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandAssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorer method) set_last_status() (pyrosetta.rosetta.core.chemical.modifications.ChemistryBase method) (pyrosetta.rosetta.protocols.chemistries.Chemistry method) (pyrosetta.rosetta.protocols.chemistries.PatchChemistry method) (pyrosetta.rosetta.protocols.chemistries.WrappedBaseChemistry method) set_layer() (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) set_layer_as_greater_than_or_equal_to() (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) set_layer_as_less_than_or_equal_to() (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) set_layer_mode() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_layer_operation() (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) set_layer_residues() (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) set_layer_size() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) set_layer_specification() (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) set_layered_sasa() (pyrosetta.rosetta.protocols.buns.BuriedUnsatisfiedPolarsCalculator2 method) set_layers() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) set_lazy() (pyrosetta.rosetta.protocols.pose_metric_calculators.RotamerBoltzCalculator method) set_lb_function() (pyrosetta.rosetta.numeric.interpolation.spline.CompoundInterpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.Interpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.SimpleInterpolator method) set_legacy() (pyrosetta.rosetta.protocols.hbnet.UnsatSelector method) set_legacy_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) set_legacy_turner_mode() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_length() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) set_length_event_link() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) set_lengths() (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) set_lib_chi_val() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_ligand() (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.sewing.hashing.LigandBindingResPlacer method) set_ligand_atom_id() (pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue method) set_ligand_atom_name() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue method) set_ligand_atom_xyz() (pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue method) set_ligand_id() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) set_ligand_jump_id() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_ligand_mode() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) set_ligand_prob() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) set_ligand_requirements() (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_ligand_resnum() (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_ligand_resnum_string() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ligand_selector() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_ligand_weight() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_ligandchi() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) set_ligands() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_light_chain() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_light_chain_type() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) set_ligpose_rotamer() (in module pyrosetta.rosetta.protocols.match) set_ligres() (pyrosetta.rosetta.protocols.match.MatcherMover method) set_limit() (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) set_limit_for_rotamer_combo() (pyrosetta.rosetta.protocols.match.output.LimitHitsPerRotamerFilter method) set_limit_only_to_length() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) set_line_color() (pyrosetta.rosetta.protocols.match.Bool3DGridKinemageWriter method) set_linear_chainbreak_weight() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_linecount_offset() (pyrosetta.rosetta.protocols.loops.JSONFormattedLoopsFileReader method) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader method) set_link() (pyrosetta.rosetta.protocols.moves.PyMOLMover method) set_link_cutoff() (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorer method) set_linker_name() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_links() (pyrosetta.rosetta.core.pack.task.operation.SetRotamerLinks method) set_linmin_only() (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) set_live() (pyrosetta.rosetta.core.scoring.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) set_lj_atr_weight() (pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_lj_cutoff() (pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_lj_ramp_cycles() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_lj_ramp_inner_cycles() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_lj_rep_weight() (pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_lj_sol_weight() (pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_lkb_clust_rad() (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) set_lkb_overlap_dist() (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) set_lkb_rotset_radius() (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) set_local_movemap() (in module pyrosetta.rosetta.protocols.vip) set_local_positions() (pyrosetta.rosetta.protocols.environment.claims.EnvLabelSelector method) set_local_print_channel_name() (pyrosetta.rosetta.basic.MemTracer method) (pyrosetta.rosetta.basic.MemTracerImpl method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerImpl method) set_local_redock_only() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_local_refine() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_local_rotamer_id() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) set_localstrandpair_penalty() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_location_in_parent_node() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleResidueInvrotTarget method) set_logging_sink() (in module pyrosetta.logging_support) set_long_range_container() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) set_loop() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (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) (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) set_loop_ang() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_loop_angle_conf() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) set_loop_begin_and_end() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_loop_closure_energy() (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.GaussianChainFuncPotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.LoopClosePotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.SixDTransRotPotentialEvaluator method) set_loop_cluster_radius() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_loop_combine_rate_() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover 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) set_loop_cutpoint_in_pose_fold_tree() (in module pyrosetta.rosetta.protocols.loops) set_loop_dih() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_loop_file_name_and_reset() (pyrosetta.rosetta.protocols.loops.Loops method) set_loop_length_change() (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) set_loop_mover() (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) set_loop_pose() (in module pyrosetta.rosetta.protocols.generalized_kinematic_closure) set_loop_residues() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_loop_segments() (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) set_loop_size() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_loop_start() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMover method) set_loop_stop() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMover method) set_loopnumber() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_loopres_base2_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_loopres_base_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_loops() (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.loop_grower.LoopComparator 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.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoops method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) set_loops_and_anchor() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_loops_from_file() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoops method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) set_loops_pointer() (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) set_loose_rep_cutoff() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker method) set_lores() (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) set_lores_scorefxn() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) set_low_energy_ring_conformers() (pyrosetta.rosetta.core.chemical.MutableResidueType method) set_low_memory_mode() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) set_low_res_protocol_only() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) set_lower() (pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t method) set_lower_bfactor_threshold() (pyrosetta.rosetta.core.select.residue_selector.BFactorSelector method) set_lower_bound() (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) set_lower_connect_atom() (pyrosetta.rosetta.core.chemical.MutableResidueType method) set_lower_dihedrals() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_lower_residue() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_lower_residues() (pyrosetta.rosetta.core.select.residue_selector.BFactorSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) set_lower_segment() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_lower_threshold() (pyrosetta.rosetta.protocols.filters.IfThenFilter method) set_lowest() (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) set_lowest_energy_ring_conformer() (pyrosetta.rosetta.core.chemical.MutableResidueType method) set_lowest_score() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_lowest_score_pose() (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) set_lowres_score_func() (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) set_lowres_scorefxn() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_lowtemp() (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.flexpack.annealer.FlexbbSimAnnealer method) set_lt_dih() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_magnitude() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) set_magnitude_rotation() (pyrosetta.rosetta.protocols.rigid.RigidBodyMotionMover method) set_magnitude_translation() (pyrosetta.rosetta.protocols.rigid.RigidBodyMotionMover method) set_main_task_factory() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) set_mainchain_atoms() (pyrosetta.rosetta.core.chemical.MutableResidueType method) set_mainchain_torsions() (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) set_mainchain_torsions_covered() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) set_maintain_links() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_make_movie() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_make_pre_proline_potential() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) set_manager() (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) set_map_cst_from_centroid_to_fa() (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) set_map_index() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore method) set_map_type() (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) set_mapfile() (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) set_mapfile_activated() (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) set_mass() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_master() (pyrosetta.rosetta.protocols.match.Bool3DGridKinemageWriter method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage method) set_master_beam_cutoff() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_master_beam_width() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_master_packer() (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) set_match_algorithm() (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) set_match_mode() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) set_match_positions() (pyrosetta.rosetta.protocols.match.MatcherMover method) set_match_rt_limit() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) set_match_score_writer() (pyrosetta.rosetta.protocols.match.output.MatchConsolidator method) (pyrosetta.rosetta.protocols.match.output.MatchOutputter method) (pyrosetta.rosetta.protocols.match.output.MatchProcessor method) set_match_string() (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_matrix_A() (pyrosetta.rosetta.basic.svd.SVD_Solver method) set_matrix_entry() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) set_max_accepted_trials() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_max_allowed_conserved_pos_mutations() (pyrosetta.rosetta.protocols.calc_taskop_filters.ConservedPosMutationFilter method) set_max_allowed_oversaturated() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) set_max_angle_disp_4() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_max_angle_disp_7() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_max_angle_disp_slope() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_max_atoms() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_max_attempts() (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) set_max_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_max_bond_length() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_max_chi_considered() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerChiDiff method) set_max_cycles() (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_max_decoys() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer method) set_max_dist() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) set_max_distance() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) set_max_disulf_score() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) set_max_disulfides() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) set_max_dslf_energy() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_max_dslf_pot() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_max_gaplength_to_model() (pyrosetta.rosetta.protocols.hybridization.MRMover method) set_max_generations() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) set_max_hb_energy() (pyrosetta.rosetta.protocols.simple_pose_metric_calculators.NumberHBondsCalculator method) set_max_hbond_energy() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_max_insertion() (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) set_max_iter() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) set_max_kic_build_attempts() (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC method) set_max_missing_weight() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_max_mutations() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) set_max_networks_size() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_max_nstruct() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_max_ntries() (pyrosetta.rosetta.protocols.stepwise.StepWiseSampleAndScreen method) set_max_num_results() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob method) set_max_num_results_with_same_token_per_partition() (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.NodeManagerStorageMatrix method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) set_max_num_segments() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_max_pop_size() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) set_max_radius() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_max_range() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) set_max_registry_shift() (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_max_repeats() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_max_rms() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_max_rot_bumpenergy() (pyrosetta.rosetta.core.pack.rotamer_set.BumpSelector method) set_max_rot_cumulative_prob() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GAOptimizer method) set_max_rounds() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_FinalFullatomRefinementMoveGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_HelixCoilMoveGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_SigmoidalTemperatureScheduleGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator method) set_max_sample_iterations() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) set_max_samples() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) set_max_segment_length() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_max_seq_sep() (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) set_max_small_angle() (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) set_max_strand_dist_cutoff() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_max_struct() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) set_max_struct_per_radius() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_max_temperature() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_SigmoidalTemperatureScheduleGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator method) set_max_threads() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_max_trial_num() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) set_max_tries() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) set_max_tries_multiplier_for_ccd() (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) set_max_try() (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) set_max_unsat() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_maxfrac() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) set_maxfrac_crossover() (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) set_maximum_clashes_allowed() (pyrosetta.rosetta.protocols.sewing.requirements.ClashRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandClashRequirement method) set_maximum_jobs_to_hold_in_memory() (pyrosetta.rosetta.protocols.jd3.job_distributors.JobExtractor method) set_maximum_length() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.SegmentEnvelope method) (pyrosetta.rosetta.protocols.sewing.requirements.DsspSpecificLengthRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LengthInResiduesRequirement method) set_maximum_size() (pyrosetta.rosetta.protocols.sewing.requirements.SizeInSegmentsRequirement method) set_maximum_unpenalized_variance() (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) set_maxiter_minimize() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) set_maxtrials() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_mc() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio 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) set_MC() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) set_mc() (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) set_mc_kt() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) set_mc_scorefunction() (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) set_mc_temperature() (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) set_MCA() (pyrosetta.rosetta.protocols.pack_daemon.DenseIGRepacker method) set_mcfi() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) set_md_energy_report_stepsize() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_md_report_stepsize() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_md_rsr_update_stepsize() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_mdsch() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_mean() (pyrosetta.rosetta.protocols.ddg.ddGMover method) set_membrane() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_membrane_geometry() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) set_membrane_info() (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) set_membrane_jump() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) set_memory_limit() (pyrosetta.rosetta.protocols.wum.WorkUnitQueue method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue_Swapped method) set_memory_max_for_rpes() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) set_merge_chains() (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) set_merge_split_behavior_manager() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) set_metal_bond_angle_constraint_multiplier() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_metal_bond_dist_constraint_multiplier() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_metal_bond_LJ_multiplier() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_metal_center() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) set_metal_coord_bounds() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) set_metal_dist_cutoff() (pyrosetta.rosetta.protocols.buns.BuriedUnsatisfiedPolarsCalculator2 method) set_metal_resnums_string() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_metal_selector() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_metal_type() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_metal_type_from_name() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper method) set_metals_angle_constraint_multiplier() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_metals_detection_LJ_multiplier() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_metals_distance_constraint_multiplier() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_metapatched() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) set_method_weights() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions 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) set_metric() (pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelector method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities method) set_metropolis_hastings_mover() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover 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.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) set_mg_calculation_annotated_sequence() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) set_mg_coord_cst_dist() (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) set_mg_res() (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) set_mhc_epitope_setup_files() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_middle_pack_min() (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) set_min() (pyrosetta.rosetta.protocols.ddg.ddGMover method) set_min_allowed_score() (pyrosetta.rosetta.protocols.frag_picker.scores.ABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.RDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) set_min_atoms() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_min_bb() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) set_min_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_min_bond_length() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_min_chi() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_min_contiguous_res() (pyrosetta.rosetta.core.select.residue_selector.BFactorSelector method) set_min_cst() (pyrosetta.rosetta.protocols.ddg.ddGMover method) set_min_cycles() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_min_dist() (pyrosetta.rosetta.protocols.splice.RotLibOut method) set_min_distance() (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) set_min_disulfides() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) set_min_dwell() (pyrosetta.rosetta.core.pack.annealer.FixbbPwatSimAnnealer method) set_min_eps() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_min_frag_length() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) set_min_helix_length() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) set_min_lig() (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) set_min_loop() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) set_min_max_angles() (pyrosetta.rosetta.protocols.rigid.RollMover method) set_min_networks_size() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_min_num_south_sugar_filter() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_min_omg() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_min_options() (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) set_min_overlap() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) set_min_rb() (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) set_min_rings() (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) set_min_rms() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_min_sc() (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) set_min_scorefunction() (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) set_min_seq_sep() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) set_min_sfxn() (pyrosetta.rosetta.protocols.relax.LocalRelax method) set_min_solution_count() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) set_min_temperature() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_SigmoidalTemperatureScheduleGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator method) set_min_tol() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) set_min_tolerance() (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) set_min_type() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) set_min_VC_to_write() (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) set_minE() (pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector method) set_minfrac() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) set_minfrac_crossover() (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) set_minH() (pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector method) set_minimization_graph() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) set_minimization_score_function() (pyrosetta.rosetta.protocols.ddg.ddGMover method) set_minimization_threshold() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) set_minimization_type() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) set_minimize() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) set_minimize_after_delete() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_minimize_all() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) set_minimize_all_protein() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) set_minimize_and_score_native_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_minimize_and_score_sugar() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_minimize_at_end() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_minimize_bps() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) set_minimize_during_scoring() (pyrosetta.rosetta.protocols.magnesium.MgScanner method) set_minimize_mg_coord_constraint_distance() (pyrosetta.rosetta.protocols.magnesium.MgScanner method) set_minimize_options() (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) set_minimize_protein_sc() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) set_minimize_res() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.TransientCutpointHandler method) set_minimize_rna() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) set_minimize_rounds() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) set_minimize_scorefxn() (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) set_minimize_sf() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_minimize_single_res() (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.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) set_minimize_single_res_frequency() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_minimize_structure() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_minimize_w_pre_csts() (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) set_minimize_waters() (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) set_minimize_with_cst() (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) set_minimizer() (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) set_minimizer_mode() (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) set_minimizer_options() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) set_minimizer_rename_tag() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_minimizer_use_coordinate_constraints() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) set_minimum_length() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.SegmentEnvelope method) (pyrosetta.rosetta.protocols.sewing.requirements.DsspSpecificLengthRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LengthInResiduesRequirement method) set_minimum_peak_intensity() (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) set_minimum_size() (pyrosetta.rosetta.protocols.sewing.requirements.SizeInSegmentsRequirement method) set_minmelt() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_minmover() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) set_minoption() (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) set_minor_helix_params_from_file() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) set_mintolerance() (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) set_mintype() (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_mirror_symm() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) set_mirror_z() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryTransform method) (pyrosetta.rosetta.core.conformation.symmetry.VirtualCoordinate method) set_mirrored_relative_to_type() (pyrosetta.rosetta.core.conformation.Residue method) set_mismatch_probability() (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter method) set_missing_dens_as_jump() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_mixed_sliding_window() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) set_mm() (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) set_mmtf_default_options() (in module pyrosetta.rosetta.core.io.mmtf) set_mmtf_extra_data_io() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_mode() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelector method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) set_mode_from_string() (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) set_model_and_remove_capping_residues() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) set_model_file() (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) set_model_file_name() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_model_group() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) set_model_tag() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) set_model_with_density() (pyrosetta.rosetta.core.import_pose.options.RNA_BasicOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_ModelH3() (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) set_models_per_file() (pyrosetta.rosetta.protocols.contact_map.ContactMap method) set_modes() (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) set_modifiable_terminus() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_moltenres() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) set_monte_carlo() (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) set_monte_carlo_branch() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_monte_carlo_cycles() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_monte_carlo_seed_must_be_buried() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_monte_carlo_seed_must_be_fully_buried() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_monte_carlo_seed_threshold() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_motif() (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation method) set_motif_library() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) set_motifs() (pyrosetta.rosetta.protocols.denovo_design.architects.MotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) set_movable_chains() (pyrosetta.rosetta.protocols.simple_task_operations.InterfaceTaskOperation method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterface method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) set_movable_group() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) set_movable_jumps() (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.DockingProtocol 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) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.simple_task_operations.InterfaceTaskOperation method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterface method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) set_move() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) set_move_element() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) set_move_first_rigid_body() (pyrosetta.rosetta.core.import_pose.options.RNA_BasicOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) set_move_jump_points_away() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.TransientCutpointHandler method) set_move_jumps_between_chains() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) set_move_map() (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) set_move_map_for_centroid_loop() (in module pyrosetta.rosetta.protocols.loops) set_move_takeoff_torsions() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) set_move_type() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) set_moveable_jumps() (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) set_movemap() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.CoordinateConstraintKC method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicControl method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.parser.BluePrint 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) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) set_movemap_disables_packing_of_fixed_chi_positions() (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.relax.FastRelax method) set_movemap_factory() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign 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) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_movemap_from_kic_segment() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) set_movemap_smallmover() (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) set_movemaps() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_movement() (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) set_mover() (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.jd3.jobs.MoverJob method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer 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.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) set_mover_cycles() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_mover_mode() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) set_mover_tag() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer 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.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) set_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) set_moverkey() (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) set_moves() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) set_moving_lattice() (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) set_moving_partition_res() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) set_moving_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_moving_res_and_reset() (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) set_moving_res_list() (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) set_moving_residues() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_moving_scs() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) set_mpi_rank() (pyrosetta.rosetta.utility.SimulateMPI static method) set_mu() (pyrosetta.rosetta.core.pose.Pose method) set_mulfactor() (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) set_multi_template_regions() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) set_multicomponent_info() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) set_multifunc() (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) set_multiple_origin() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) set_multiplicity() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams method) set_must_switch_bins() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) set_mut_aa() (pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData method) set_mut_pose() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) set_mut_unfolded_energies_emap() (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData method) set_mutate() (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) set_mutate_gly() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) set_mutate_pro() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) set_mutate_to_glycine() (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) set_mutation_rate() (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) set_mutation_sets() (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) set_my_rank() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_N() (pyrosetta.rosetta.core.select.residue_selector.FractionSelector method) set_n_atom() (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) set_n_bins() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) set_n_candidates() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) set_n_chi_bins() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) set_n_cycle() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_n_cycles() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) set_n_cyd_seqpos() (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_n_dof() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_n_dof_temp() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_n_downstream_to_output() (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) set_n_dump() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_n_frags() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) set_n_geomcst() (pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter method) set_n_geometric_constraints() (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.LimitHitsPerRotamerFilter 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) set_n_helices() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) set_n_mainchain_torsions_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) set_n_mainchain_torsions_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) set_n_max_cluster() (pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle method) set_n_max_conf_iterations() (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) set_n_max_confs() (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) set_n_max_mutate_attempts() (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) set_n_orientational_templates() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD method) set_n_partners() (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) set_n_repeats() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) set_n_rigid_body_rounds() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) set_n_sample() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_n_samples_per_side_of_nrchi_bin() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_n_samples_wi_sd_range() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_n_tail_res() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) set_N_term_DSSP() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) set_N_term_length() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) set_n_terminal_neighbor() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) set_n_terminal_parent() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) set_n_terminal_segment() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) set_n_to_output_per_group() (pyrosetta.rosetta.protocols.match.output.MatchConsolidator method) set_n_torsion_rounds() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) set_name() (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) (pyrosetta.rosetta.core.io.rna.RDAT method) (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) (pyrosetta.rosetta.protocols.pockets.SmallMol 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.simple_moves.AddSapConstraintMover method) set_name1() (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) set_names() (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) set_natbias_helices_sheet_pot() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) set_natbias_hpairpot() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) set_natbias_spairpot() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) set_native() (pyrosetta.rosetta.protocols.abinitio.Templates method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GAOptimizer method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.PerNativeRRReporterHuman method) set_native_aa() (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) set_native_alignment() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_native_alignment_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_native_cdr_sequence() (in module pyrosetta.rosetta.protocols.antibody.design) set_native_chi_periodicity() (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) set_native_cst_set() (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) set_native_distance_viol() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) set_native_edensity_score_cutoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_native_flag() (pyrosetta.rosetta.protocols.match.upstream.ProteinUpstreamBuilder method) set_native_in_mover() (in module pyrosetta.rosetta.protocols.jd2) set_native_pose() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric method) (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.loop_modeling.utilities.TrajectoryLogger 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.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore method) (pyrosetta.rosetta.protocols.residue_selectors.NativeSelector 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) set_native_rotamer_chi() (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) set_native_rotamer_index() (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) set_native_sequence() (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) set_native_spairset() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential method) set_native_task() (pyrosetta.rosetta.core.pack.task.operation.ReplicateTask method) set_native_topology() (pyrosetta.rosetta.protocols.abinitio.PairingStatistics method) set_native_virtual_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) set_nativegrow() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_nativeness_high() (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData static method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData static method) set_nativeness_low() (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData static method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData static method) set_natoms_for_residue() (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) set_nblist() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) set_nblist_auto_update() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) set_nbr() (pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler method) (pyrosetta.rosetta.core.chemical.rdkit.RDMolToRestype method) set_nbrs() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) set_nchi() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) set_ncluster() (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) set_ncopies() (pyrosetta.rosetta.core.fragment.FragmentIO method) set_ncyc() (pyrosetta.rosetta.protocols.relax.LocalRelax method) set_ncyc_postmin() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_ncyc_premin() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_ncycle() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) set_ncycles() (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) set_negTds() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) set_neighbor_count() (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) set_neighbor_dis() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_neighbor_distance() (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) set_neighborhood_parameters() (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) set_netcharge_setup_files() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_network_anchoring() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) set_network_anchoring_per_residue() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) set_network_state() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase 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.MultiplexedAnnealableGraph 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.ResidueArrayAnnealingEvaluator 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) set_new_chain_order() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) set_new_conformation() (pyrosetta.rosetta.core.pose.Pose method) set_new_energies_object() (pyrosetta.rosetta.core.pose.Pose method) set_new_final_stream() (pyrosetta.rosetta.basic.MemTracerImpl static method) (pyrosetta.rosetta.basic.TracerImpl static method) set_new_fold_tree_initializer() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_new_move_selector() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_new_rots() (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.SpecialRotamerRSO method) set_new_upper_bounds() (pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.PeakCalibratorMap method) (pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator method) set_nexp() (pyrosetta.rosetta.protocols.relax.LocalRelax method) set_next() (pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t method) set_next_angle() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_next_correspondence() (pyrosetta.rosetta.utility.subset_mapping method) set_next_segment_id() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) set_nfrags() (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) set_nhits_per_match() (pyrosetta.rosetta.protocols.match.HitHasher method) set_niter() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.EntropyEstimator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) set_nminsteps() (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) set_nmoves() (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) set_no_CCD_on_name3_match() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) set_no_chainend_ter() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_no_design_cys() (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) set_no_detect_pseudobonds() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_no_filters() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) set_no_frags() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_no_global_frame() (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) set_no_longer_perturbed() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) set_no_optH() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_no_output_cen() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_no_probability() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_no_stem_copy() (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) set_node_label() (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) set_non_ligand_requirements() (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_non_main_chain_sugar_coords() (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) set_non_standard_residue_map() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) set_noncanonical_connection() (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) set_nonideal() (pyrosetta.rosetta.core.pack.RTMin method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRelax method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRTMin method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) set_nonpivot_bb_torsion_id() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) set_nonpivot_res_to_sweep() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) set_nonpivot_torsion_sampling() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) set_nonrotameric_chi_bbdep_scoring_step_size() (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) set_nonrotameric_chi_bbind_scoring_step_size() (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) set_nonrotameric_chi_start_angle() (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) set_norepack1() (pyrosetta.rosetta.protocols.docking.DockTaskFactory method) set_norepack2() (pyrosetta.rosetta.protocols.docking.DockTaskFactory method) set_normal() (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) set_normalization_function() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) set_normalize() (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric method) set_normalize_by_residues() (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric method) set_normalize_decoy_stddev() (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData method) set_normalize_per_atom() (pyrosetta.rosetta.protocols.simple_filters.HolesFilter method) set_normalize_per_residue() (pyrosetta.rosetta.protocols.simple_filters.HolesFilter method) set_normalize_to_thk() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_not_to_quench() (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.flexpack.annealer.FlexbbSimAnnealer method) set_nr_fragments() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ShortLoopClosure method) set_nrchi_lower_boundary() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) set_nrchi_periodicity() (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) set_nrchi_prob_minimum_for_extra_samples() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_nrchi_probability() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) set_nrchi_sample() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) set_nrchi_upper_boundary() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) set_nread_limit_for_file() (pyrosetta.rosetta.utility.io.FileContentsMap method) set_nremain_reset() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) set_nrepeat() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) set_nres() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) set_nres_subunit() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) set_nrounds() (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) set_nRsteps_from_pose() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) set_nseq() (pyrosetta.rosetta.core.scoring.TMscoreStore method) set_nstep() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_nsteps() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) set_nstruct() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup method) (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) set_nstruct_centroid() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_nstruct_mode() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) set_nstruct_repeats() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) set_nterm_included() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_ntrial() (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) set_ntrials() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) set_ntries_before_giving_up() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) set_nu() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_nu_true_range() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_nucleation_prob() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix method) set_nucleotide_to_A_form() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) set_num_bbs() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_num_chi() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_num_clash_atom_cutoff() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker method) set_num_clusters() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_num_cycles() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) set_num_decoys_used_in_calculations() (pyrosetta.rosetta.protocols.ddg.ddGMover method) set_num_distinct_backbones() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) set_num_entities() (pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence method) set_num_entity_elements() (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction method) (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunctionDriver method) (pyrosetta.rosetta.protocols.pack_daemon.EntityFunc method) set_num_geometric_constraints() (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_num_input_pose_ids() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.TagManager method) set_num_jobs() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.EvenlyPartitionedNodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) set_num_neighbors_counting_self_static() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.utility.graph.Node method) set_num_nodes() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintGraph method) (pyrosetta.rosetta.core.scoring.constraints.CstEnergyContainer method) (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) (pyrosetta.rosetta.core.scoring.LREnergyContainer method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) (pyrosetta.rosetta.protocols.jd3.JobDigraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t method) set_num_npd_properties() (pyrosetta.rosetta.protocols.pack_daemon.MPIMultistateFitnessFunction method) set_num_pack_daemons() (pyrosetta.rosetta.protocols.pack_daemon.MPIMultistateFitnessFunction method) set_num_packs() (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) set_num_pose_kept() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection method) set_num_pose_minimize() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) set_num_random_samples() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) (pyrosetta.rosetta.protocols.stepwise.StepWiseSampleAndScreen method) set_num_repeats() (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilter method) set_num_restypes() (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) set_num_sa() (pyrosetta.rosetta.protocols.pack_daemon.FASTER_IG_Repacker method) set_num_sa_trajectories() (pyrosetta.rosetta.core.pack.annealer.FASTERAnnealer method) set_num_shells() (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector method) set_num_states_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) set_num_states_per_backbone() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) set_num_target_rotamers() (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) set_num_to_propagate() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) set_num_trials() (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) set_num_vertices() (pyrosetta.rosetta.core.conformation.PointGraphPy method) (pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) set_number_ligands() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) set_number_of_energy_sum_vertex_groups() (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) set_number_of_moves() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) set_numbered_pdb_output() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_numbering_scheme() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeatures method) set_nus() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_o2prime_legacy_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_obey_ENDMDL() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) set_obligate_pairing_sets() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) set_occupied_space_bounding_box() (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.MatcherTask method) set_occupied_space_hash() (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) set_ocd_cutoff() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD method) set_octahedral_metal_positions_from_string_vector() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_offset() (pyrosetta.rosetta.core.id.SequenceMapping method) (pyrosetta.rosetta.core.io.rna.RDAT method) (pyrosetta.rosetta.core.scoring.GenTorsionParams method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) set_ok_to_increment() (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.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) set_old_last_score() (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandAssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorer method) set_omega() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilter method) set_omega0_max() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters method) set_omega0_min() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters method) set_omg() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_omit_AAs() (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) set_one_body_energy() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) set_one_body_energy_for_node_state() (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) set_onebody_energies_multithreaded() (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) set_only_enumerate_non_match_redundant_ligand_rotamers() (pyrosetta.rosetta.protocols.match.MatcherTask method) set_only_extend_existing() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_only_report_these_options() (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric method) set_only_stage4() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) set_open_mode() (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) set_optimize_cdrs() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_optimize_cyclic_threshold() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_optimize_memory_usage() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_optimum_distance() (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) set_options() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAligner method) (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash 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.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler 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.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo 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) set_options_from_tag() (pyrosetta.rosetta.protocols.sewing.requirements.AssemblyRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.ClashRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.DsspSpecificLengthRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.KeepLigandContactsRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LengthInResiduesRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandAssemblyRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandClashRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.NonTerminalStartingSegmentRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.SizeInSegmentsRequirement method) (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandAssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorer method) set_options_string() (in module pyrosetta.rosetta.utility) set_OrbH_features_data() (pyrosetta.rosetta.protocols.features.OrbitalsFeatures method) set_orbital_icoor_id() (pyrosetta.rosetta.core.chemical.MutableResidueType method) set_orbital_typeset() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) set_orbital_xyz() (pyrosetta.rosetta.core.conformation.Residue method) set_OrbOrb_features_data() (pyrosetta.rosetta.protocols.features.OrbitalsFeatures method) set_order() (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) set_order_by_energy() (pyrosetta.rosetta.core.import_pose.pose_stream.SilentFilePoseInputStream method) set_orient1() (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing method) set_orient2() (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing method) set_orientation() (pyrosetta.rosetta.core.pose.rna.BasePair method) (pyrosetta.rosetta.core.pose.rna.BaseStack method) set_orig_pose() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_origin() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) set_origin_away_from_eggshell() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) set_origin_away_from_eggshell_plane() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) set_origin_away_from_protein_center() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) set_origin_from_option_() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) set_origin_from_residue() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) set_original_pose() (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) set_original_scaffold_build_points() (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.MatcherTask method) set_original_scaffold_build_points_for_constraint() (pyrosetta.rosetta.protocols.match.Matcher method) set_original_scaffold_build_points_for_geometric_constraint() (pyrosetta.rosetta.protocols.match.MatcherTask method) set_originating_node_MPI_rank() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_RMSDToBestSummary method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary method) set_other_pose_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) set_out() (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) set_out_file_prefix() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) set_out_file_tag() (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) set_out_of_bound_e() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) set_out_of_bounds_behavior() (pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector method) set_out_path() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) set_out_prefix() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_out_torsions() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_outer_ca_only() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_outer_cycles() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) set_outer_loop_cycles() (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) set_outer_max_distance() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_outer_radius() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) set_outer_sd() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_outer_unweighted_function() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_outer_use_harmonic_function() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_outer_weight() (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) set_outlier_use() (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) set_output() (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) set_output_alternate_atomids() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_output_as_pdb_nums() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) set_output_cluster_size() (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) set_output_extra_RMSDs() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_output_file_name() (pyrosetta.rosetta.protocols.jobdist.BasicJob method) set_output_filename() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer method) set_output_filters() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_output_format() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication method) set_output_frag_files() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) set_output_histogram_file() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_output_in_rosetta_num() (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) set_output_jump_chainbreak() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_output_jump_o3p_to_o5p() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_output_jump_reference_RT_string() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_output_jump_res() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_output_jump_target_xyz() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_output_level() (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSQLite method) set_output_ligands_as_separate_chains() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_output_lores_silent_file() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_output_min_pose() (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) set_output_minimized_pose_list() (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) set_output_mode() (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) set_output_name() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) set_output_only_asymmetric_unit() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_output_partner() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_output_pdb() (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker method) set_output_period() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) set_output_pose_cache_data() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_output_pose_energies_table() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_output_pose_per_move() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_output_prefix() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastPlus method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) set_output_prefix_and_suffix() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication method) set_output_res_and_chain() (in module pyrosetta.rosetta.core.pose) set_output_rotation_vector() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_output_score_file() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_output_score_frequency() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_output_secondary_structure() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_output_simple_text_files() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_output_torsions() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_output_virtual() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_output_virtual_zero_occ() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_output_writer() (pyrosetta.rosetta.protocols.match.output.MatchConsolidator method) (pyrosetta.rosetta.protocols.match.output.MatchOutputter method) (pyrosetta.rosetta.protocols.match.output.MatchProcessor method) set_outputter() (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) set_overall_aa_probabilities() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_overhang() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) set_overlap() (pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) set_override() (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) set_override_refine_pose_rounds() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_overwrite() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) set_owner() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) (pyrosetta.rosetta.protocols.environment.claims.CutBiasClaim method) (pyrosetta.rosetta.protocols.environment.claims.EnvClaim method) (pyrosetta.rosetta.protocols.environment.claims.JumpClaim method) (pyrosetta.rosetta.protocols.environment.claims.TorsionClaim method) (pyrosetta.rosetta.protocols.environment.claims.VirtResClaim method) (pyrosetta.rosetta.protocols.environment.claims.XYZClaim method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) set_owner_segment() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) set_pack() (pyrosetta.rosetta.protocols.scoring.Interface method) set_pack_all_side_chains() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) set_pack_distance() (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) set_pack_input() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_pack_interface_separated() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) set_pack_min() (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) set_pack_min_cycles() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_pack_missing_sidechains() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_pack_neighbors() (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) set_pack_o2prime_hydrogens() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) set_pack_protein_side_chains() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_pack_rounds() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) set_pack_score_func() (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) set_pack_scorefunction() (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) set_pack_separated() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) set_pack_sfxn() (pyrosetta.rosetta.protocols.relax.LocalRelax method) set_pack_shell() (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) set_pack_together() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) set_pack_weights() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) set_packer() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) set_packer_cycles() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) set_packer_palette() (pyrosetta.rosetta.core.pack.task.TaskFactory method) set_packer_problem_string() (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) set_packer_task() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_packertask() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) set_packing() (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) set_packing_correction() (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) set_packonly_after_graft() (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) set_pair_overlap_tolerance() (pyrosetta.rosetta.protocols.match.BumpGrid method) set_pairings_file() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_parallel() (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing method) set_parallel_weight() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_param_cache() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) set_param_from_options() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) set_param_index() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) set_parameter() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.MMAtomType method) (pyrosetta.rosetta.core.chemical.orbitals.OrbitalType method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) set_parameter_as_res_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) set_parameter_as_res_list_in_pairs() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) set_parameter_as_res_lists() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) set_parameter_description() (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) set_parameter_name() (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) set_parameter_type() (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) set_parameter_units() (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) set_parametercheck() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_parameters() (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) set_parameters_index() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) set_parameters_set_index() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) set_params() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential method) set_params_angle_pot() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential method) set_params_distance_pot() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential method) set_paratope_cdrs() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_parent() (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap method) (pyrosetta.rosetta.core.optimization.DOF_Node method) (pyrosetta.rosetta.protocols.pockets.SmallMol method) set_parent_full_model_parameters() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) set_parent_name() (pyrosetta.rosetta.core.chemical.ResidueProperties method) set_parin_favorite_output() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer method) set_partial() (pyrosetta.rosetta.core.id.PartialAtomID method) set_partition_definition() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_partner() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) set_partner_ligand() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) set_partner_ligands() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) set_partner_pdb() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_partner_residue() (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) set_partners() (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.DockingProtocol 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.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_path_option() (in module pyrosetta.rosetta.basic.options) set_path_to_distance_potential_histogram() (pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry method) set_path_to_distance_potential_histogram_file() (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel method) set_path_to_ensemble_conformers() (pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry method) set_path_vector_option() (in module pyrosetta.rosetta.basic.options) set_PBP_clustering_at_chain_closure() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_pcount() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_pcs_calc() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingle method) set_pcs_err() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingle method) set_pcs_exp() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingle method) set_pdb_author() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_pdb_comments() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_pdb_names() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_pdbid method) set_pdb_output() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) set_pdb_parents() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_pdb_prefix() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) set_pdb_source() (pyrosetta.rosetta.protocols.features.strand_assembly.StrandFragment method) set_peak_id() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) set_penalty() (pyrosetta.rosetta.core.scoring.MembraneEmbed method) set_penalty_per_sap() (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) set_penalty_per_unit() (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) set_pep_lengths() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_peptide_chain() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) set_per_atom_lipid_accessibility() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) set_per_chain_renumbering() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_per_residue_controls() (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) set_perform_filters() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_perform_minimizer_run() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) set_perform_score_diff_cut() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_perform_VDW_rep_screen() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_permissible_secondary_structures() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.SegmentEnvelope method) set_permissible_segment_ends() (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) set_permitted_overlap() (pyrosetta.rosetta.protocols.match.MatcherTask method) SET_PERMUTATION (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMoverMode attribute) set_permutation_setting() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) set_perturb_CCD_off() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) set_perturb_cycles() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) set_perturb_KIC_off() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) set_perturb_show() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) set_perturb_temp() (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) set_perturbation_options() (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) set_perturbation_type() (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) set_perturbation_type_globally() (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) set_perturbed_state() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) set_perturber() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_perturber_attach_boinc_ghost_observer() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) set_perturber_bin() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) set_perturber_custom_rama_table() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) set_perturber_effect() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) set_perturber_iterations() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) set_perturber_must_switch_bins() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) set_pH() (pyrosetta.rosetta.core.energy_methods.pHEnergy static method) set_pharmacophore_reference() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner method) set_phi() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) (pyrosetta.rosetta.core.scoring.SAnode method) (pyrosetta.rosetta.protocols.make_rot_lib.RotData 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.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) set_phosphate() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) set_phosphate_domain() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) set_phosphate_move_list() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) set_physical_pose_clash_dist_cutoff() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker method) set_picked_positions() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_picking_rounds() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_piece() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) set_pivot_atoms() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) set_pivot_picker() (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) set_pivot_residue_selector() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) set_pivot_residues() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) set_pivots() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_pivots_from_residue_subset() (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) set_placeholder() (pyrosetta.rosetta.core.scoring.facts.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) set_plaintext() (pyrosetta.rosetta.protocols.sparta.GDB method) set_point() (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) (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.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid 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.VdwGrid method) set_polar_charge_cutoff() (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) set_polymeric_connection() (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) set_pool() (pyrosetta.rosetta.cppdb.backend.connection method) set_pool_name() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) set_poolrmsd() (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) set_population_based_conformer_sampling() (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) set_population_weight() (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) set_pos() (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) set_pos_in_node_edgevector() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) set_pos_in_owners_list() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.TenANeighborEdge method) (pyrosetta.rosetta.core.scoring.TwelveANeighborEdge method) (pyrosetta.rosetta.protocols.jd3.JobDirectedEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) (pyrosetta.rosetta.utility.graph.DirectedEdge method) (pyrosetta.rosetta.utility.graph.Edge method) set_pos_list() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) set_pos_temp() (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) set_pose() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob method) (pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) set_pose0() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_pose_after_closure() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) set_pose_and_scorefxn_for_edens_scoring() (in module pyrosetta.rosetta.protocols.electron_density) set_pose_and_task() (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) set_pose_energy() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary method) set_pose_from_broker() (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) set_pose_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) set_pose_minobj() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_pose_no_initialize() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) set_pose_reactive_sites() (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) set_pose_secstruct() (pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector method) set_pose_segment_dssp() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_pose_segment_ends_string() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_pose_segment_starts_string() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_pose_start() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_pose_tag() (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) set_poses() (pyrosetta.rosetta.protocols.filters.VectorPoseFilter method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.FitnessFilter method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) set_position() (pyrosetta.rosetta.core.pose.rna.RNA_Datum method) (pyrosetta.rosetta.core.pose.rna.RNA_Reactivity method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) set_position_for_missing_res() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache method) set_position_for_missing_res_in_parameter_block() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) set_position_from_index() (pyrosetta.rosetta.utility.LexicographicalIterator method) set_position_in_pose() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache method) set_positions() (pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilter method) set_positions_as_start_of_sequon() (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) set_potential_energy() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_pq_schema() (pyrosetta.rosetta.utility.sql_database.session method) set_pr_idx() (pyrosetta.rosetta.core.scoring.packstat.MultiProbePerSphereAccumulator method) (pyrosetta.rosetta.core.scoring.packstat.MultiProbePoseAccumulator method) set_pre_calc() (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingle method) set_pre_data() (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) set_pre_err() (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingle method) set_pre_exp() (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingle method) set_pre_ligand_atom_id() (pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue method) set_pre_pre_ligand_atom_id() (pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue method) set_preapply() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_precision() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) set_precomputed_library_mover() (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) set_predicted_report_to_db() (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSQLite method) set_preferred_root_res() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) set_prefix() (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) set_prefix_each_output_pdb() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_prefix_name() (pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) set_prefix_suffix() (pyrosetta.rosetta.protocols.features.SimpleMetricFeatures method) set_preminimize() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_prepack() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) set_prepack_only() (pyrosetta.rosetta.protocols.docking.DockTaskFactory method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) set_prepend() (pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover method) set_presample_added_residue() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) set_presample_by_swa() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) set_prescoring_filter() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) set_prescoring_mover() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) set_preselection_filter() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) set_preselection_mover() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) set_preserve_atom_coords() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) set_preserve_crystinfo() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_preserve_datacache() (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) set_preserve_detailed_balance() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover 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.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) set_preserve_header() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_preserve_whole_input_tag() (pyrosetta.rosetta.protocols.jobdist.BasicJob method) set_prevent_pruning() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) set_previous_mover() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) set_primary_cdrs() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_primary_strategy() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_print_out_info_to_pdb() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_private_data() (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) (pyrosetta.rosetta.protocols.sewing.hashing.EdgeMapGenerator method) set_prob() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) set_prob_cutoff() (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities method) set_prob_random_pert_current() (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) set_prob_uniform() (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) set_prob_withinrot() (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) set_probabilities_from_lines() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric method) set_probability() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_probability_data_cutoff() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) set_probe_atom_type() (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) set_probe_radius() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_probe_radius_apo() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_proc_id() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) set_ProCorrection_values() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) set_ProCorrection_values_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) set_profile() (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) set_profile_save_name() (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) set_profile_wgt() (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) set_properties() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToResidueProperties method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector method) set_property() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.core.chemical.orbitals.OrbitalType method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector method) set_protein_chis() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) set_protein_esp_to_zero() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) set_protein_linkage_prob_sampling() (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) set_protein_mass() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) set_protein_pack_all() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) set_protein_packing() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) set_protein_packing_distance() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) set_protein_prepack() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_protein_restype() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) set_protein_slice_diameter() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) set_protocol() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GAOptimizer method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) set_protocol_and_batch_id() (in module pyrosetta.rosetta.protocols.features) set_protocol_info() (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) set_protocol_options() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) set_proton() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) set_proton_chi() (pyrosetta.rosetta.core.chemical.MutableChiRecord method) (pyrosetta.rosetta.core.chemical.MutableResidueType method) set_protonated_H1_adenosine_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_prv_eqxyz() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_pseudobonds_to_residue() (pyrosetta.rosetta.core.conformation.Residue method) set_psi() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.make_rot_lib.RotData 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.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) set_psipred_assignment_file_contents() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) set_psipred_file() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) set_psipred_interface() (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter method) set_pssm_probabilities() (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) set_pucker_flip_rate() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) set_pucker_state() (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_SugarStepWiseSampler method) set_PyExitCallBack() (pyrosetta.PythonPyExitCallback static method) (pyrosetta.rosetta.utility.py.PyExitCallback static method) set_PyMOL_model_name() (pyrosetta.rosetta.protocols.moves.PyMOLMover method) set_qsar_map() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) set_quench_mode() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) set_query_phi() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_query_phi_conf() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_query_profile() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_query_psi() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_query_psi_conf() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_query_sa() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_query_seq() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_quick_alignment() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_quota_score() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) set_quote_options() (pyrosetta.rosetta.utility.tag.Tag method) set_r0_max() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters method)

set_r0_min() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters method) set_r1_guesses() (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) set_r_array() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) set_r_inv_array() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) set_radial_disp_ranges() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) set_radial_disps() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) set_radii_set() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) set_radius() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle method) set_radius_exp() (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) set_rama_check() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_rama_cutoff_energy() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) set_rama_power() (pyrosetta.rosetta.core.scoring.Ramachandran method) set_rama_prepro_mainchain_torsion_potential_name() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) set_rama_prepro_map_file_name() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) set_rama_prepro_multiplier() (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) set_rama_term_ramping() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_ramp_fa_rep() (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) set_ramp_rama() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) set_ramp_rnp_vdw() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_ramp_scorefxn() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) set_ramp_vdw() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) set_rand() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) set_rand_dihed_prob() (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) set_rand_glycan_jump_res() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) set_random() (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler 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) set_random_confomer() (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) set_random_loop_flag() (pyrosetta.rosetta.protocols.LoopRebuild method) set_random_membrane_flip_angle() (pyrosetta.rosetta.protocols.membrane.FlipMover method) set_random_membrane_tilt_angle() (pyrosetta.rosetta.protocols.membrane.TiltMover method) set_random_mode() (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) set_random_order_() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover 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) set_random_orientation_perturbation() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) set_random_position_offset() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) set_random_sheets() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_random_start() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_randomize() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) set_randomize1() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_randomize2() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_randomize_first() (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) set_randomize_init_rnp() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_randomize_input_sequence() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) set_randomize_missing_coords() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_randomize_resnum() (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover method) set_randomize_substrate_torsions() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_range() (pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) set_ranges() (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) set_ranges_unmodifiable() (pyrosetta.rosetta.core.kinematics.MoveMap method) set_rank_score() (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) set_rb_center() (pyrosetta.rosetta.core.kinematics.Jump method) set_rb_constraints() (in module pyrosetta.rosetta.protocols.rbsegment_relax) set_rb_delta() (pyrosetta.rosetta.core.kinematics.Jump method) set_rb_deltas() (pyrosetta.rosetta.core.kinematics.Jump method) set_rb_jump() (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) set_rb_trial() (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) set_rcgs() (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) set_rdc_calc() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingle method) set_rdc_err() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingle method) set_rdc_exp() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingle method) set_rdd() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFrag method) set_reactivity() (pyrosetta.rosetta.core.io.rna.RDAT method) set_reactivity_error() (pyrosetta.rosetta.core.io.rna.RDAT method) set_read_annotation() (pyrosetta.rosetta.core.fragment.FragmentIO method) set_read_fold_tree() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_read_from_file() (pyrosetta.rosetta.protocols.loop_grower.LoopComparator method) set_read_only_ATOM_entries() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_read_pdb_header() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) set_readbeams() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_real_option() (in module pyrosetta.rosetta.basic.options) set_real_vector_option() (in module pyrosetta.rosetta.basic.options) set_reasonable_fold_tree() (in module pyrosetta.rosetta.core.pose) set_rebuild_bulge_mode() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_recces_turner_mode() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_recent_history_size() (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) set_receptor_chain() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) set_rechain() (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) set_reconstruct() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) set_record_source() (pyrosetta.rosetta.core.import_pose.pose_stream.SilentFilePoseInputStream method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) set_record_statistics() (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) set_recover_low() (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) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_recover_lowest_assembly() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_recover_sidechains_filename() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) set_recovery_threshold() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerChiDiff method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerElecDensDiff method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerRotBins method) set_recursion_limit() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) set_redesign_loop() (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) set_ref_pose_from_filename() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) set_ref_xyz() (pyrosetta.rosetta.core.pose.rna.VDW_Grid method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_reference_atom() (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) set_reference_energies() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) set_reference_energy() (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) set_reference_pose() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterface method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) set_reference_pose_name() (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) set_reference_residue() (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) set_reference_round_task_factory() (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) set_refinable_lattice() (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) set_refine() (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) set_refine_CCD_off() (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) set_refine_cycles() (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) set_refine_h3() (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) set_refine_KIC_off() (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) set_refine_native_get_good_FT() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_refine_only() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) set_refine_pose() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) set_refine_pose_list() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) set_refine_repack_cycles() (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) set_refine_temp() (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) set_refstruct() (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) set_region() (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.pose_metric_calculators.FragQualCalculator method) set_region2_all_atom() (pyrosetta.rosetta.protocols.contact_map.ContactMap method) set_region_end() (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) set_region_start() (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) set_regions() (pyrosetta.rosetta.protocols.contact_map.ContactMap method) set_registry_shift() (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) set_reinitialize_CCD_torsions() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) set_rejection_thresh() (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter method) set_relative() (pyrosetta.rosetta.protocols.environment.claims.XYZClaim method) set_relax_cycles() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_relax_structure() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_relaxmode() (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) set_relaxtype() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) set_relevant_atom_ids() (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) set_relevant_residues() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) set_relevant_residues_mode() (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.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.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) set_relevant_residues_task_factory() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) set_remember_unrecognized_res() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_remember_unrecognized_water() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_removable() (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) set_remove() (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) set_remove_any_set_forced_cluster() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_remove_cterminus_variant() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_remove_hydrogens() (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) set_remove_nterminus_variant() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_remove_pre_pose() (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) set_remove_target_types() (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) set_rename_tags() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_renumber_pdb() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_rep_cutoff() (pyrosetta.rosetta.protocols.moves.SimulatedTempering method) set_repack() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) set_repack_list() (pyrosetta.rosetta.core.scoring.facts.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) set_repack_neighborhood() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_repack_period() (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) set_repack_separated() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) set_repack_shell() (pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator method) (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) set_repeat_tail_length() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) set_repeats() (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) set_rephasemap() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_replacement_resid() (pyrosetta.rosetta.protocols.match.output.PoseInserter method) set_repldist_params_helix_sheet() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) set_report_all_heavy_atom_unsats() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_report_all_unsats() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_report_as() (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) set_report_as_silent() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_report_bb_heavy_atom_unsats() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_report_crd() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) set_report_format() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_report_heavy_acceptors_and_hpols() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_report_mean_median() (pyrosetta.rosetta.protocols.simple_filters.Worst9merFilter method) set_report_nonheavy_unsats() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_report_sc_heavy_atom_unsats() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_report_scorecomp() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_report_sequence() (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) set_reporting() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) set_repulsive_term_ramping() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_require_mm_bend() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) set_required_atoms() (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) set_required_connections_for_residue() (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) set_required_resnums() (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_required_selector() (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_requirements() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_res1() (pyrosetta.rosetta.core.pose.rna.BasePair method) (pyrosetta.rosetta.core.pose.rna.BaseStack method) (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBondsTrieVsTrieCachedDataContainer method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) set_res1_nb() (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBondsTrieVsTrieCachedDataContainer method) set_res2() (pyrosetta.rosetta.core.pose.rna.BasePair method) (pyrosetta.rosetta.core.pose.rna.BaseStack method) (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBondsTrieVsTrieCachedDataContainer method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) set_res2_nb() (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBondsTrieVsTrieCachedDataContainer method) set_res_denominator() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) set_res_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) set_res_name() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) set_res_type_set() (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) set_rescoords() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) set_rescore_only() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) set_rescorebeams() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_reserve_size() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HPool_RMSD method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.Pool_RMSD method) set_reset_filters() (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) set_reset_mode() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) set_reset_pose() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) set_resfile() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMover method) set_resfile_1() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_resfile_2() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_resfile_AvNAPSA() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) set_resi_chosen() (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) set_resi_len() (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) set_resid() (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.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) (pyrosetta.rosetta.protocols.moves.ResId method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) set_resid_2_connection_entry() (pyrosetta.rosetta.core.scoring.trie.RotamerTrieBase method) set_residue() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.FragData method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) set_residue_base2_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_residue_base_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_residue_label() (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) set_residue_mapping() (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) set_residue_name() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) set_residue_name3() (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) set_residue_name_for_helix() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) set_residue_names() (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) set_residue_numbers() (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) set_residue_pair_xform() (in module pyrosetta.rosetta.core.scoring.motif) set_residue_range() (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) set_residue_range_not_surface() (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) set_residue_sampling_from_pose_and_movemap() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_residue_selector() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfile method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.select.jump_selector.ExclusivelySharedJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpForResidue method) (pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator 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.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.pose_metric_calculators.RotamerBoltzCalculator method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) (pyrosetta.rosetta.protocols.residue_selectors.NativeSelector method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.HolesFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.Worst9merFilter method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation method) set_residue_selector1() (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) set_residue_selector2() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) set_residue_selector_ref() (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric method) set_residue_selector_reference() (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) set_residue_selector_super() (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) set_residue_selector_super_reference() (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) set_residue_selectors() (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric method) set_residue_subset() (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) set_residue_surface_cutoff() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_residue_type() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) set_residue_type_set() (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) set_residue_type_set_mode() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_residue_vector() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) set_residues() (pyrosetta.rosetta.core.scoring.rna.RNA_Motif method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation method) set_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) set_residues_adjacent_for_subunit_pair_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) set_residues_for_atom_name_remapping() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_residues_per_repeat() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) set_residues_to_preglycosylate() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_resinfo() (pyrosetta.rosetta.core.pose.PDBInfo method) set_resname() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) set_resnum() (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TryRotamers method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover method) set_resnum_string() (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) set_resnums() (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) set_resolution() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbAcc_t method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbDon_t method) set_resolution_cutoff() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_resolution method) set_resolution_damping() (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) set_resonances() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) set_restore_csts() (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) set_restrict_only_design_to_loops() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoops method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) set_restrict_partners_to_chains() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_restrict_receptors_to_chains() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_restrict_restypes() (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) set_restrictions_aa() (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) set_restrictions_append() (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) set_restrictions_exclude() (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) set_restype() (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) set_restype_index() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) set_retraction_prob() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix method) set_return_results_depth_first() (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.NodeManagerStorageMatrix method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) set_return_single_random_match() (pyrosetta.rosetta.protocols.match.MatcherMover method) set_rh() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) set_rho_to_zero() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) set_rigid_body_confs() (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) set_rigid_body_confs_for_lig() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver method) set_rigid_body_mover() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_ring() (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.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid 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.VdwGrid method) set_ring_conformation() (pyrosetta.rosetta.core.pose.Pose method) set_rise() (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilter method) set_rm_virt_phosphate() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_rmax() (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) set_rms() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) set_rms_cutoff() (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) set_rms_group_cutoff() (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) set_rms_offset() (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) set_rmscutoff() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_rmsd() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary method) set_rmsd_cutoff() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) set_RMSD_only_this() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) set_rmsd_residues_to_ignore_native() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) set_rmsd_residues_to_ignore_prediction() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) set_rmsd_screen() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions 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) set_rmsd_target_tolerance() (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) set_rmsd_to_best() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_RMSDToBestSummary method) set_rmsd_type() (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) set_rmsd_unique_cutoff() (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) set_rmsdcut() (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) set_rmswindow() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_rna_and_protein() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) set_rna_anti_chi() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) set_rna_base_pair_handler() (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) set_rna_de_novo_pose_initializer() (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) set_rna_helix_mover() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) set_rna_legacy_output_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_rna_north_sugar() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) set_rna_pairing_list() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) (pyrosetta.rosetta.core.import_pose.RNA_JumpMover method) set_rna_protein_docking() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_rna_protein_docking_freq() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_rna_protein_docking_legacy() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_rna_sample_sugar() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) set_rna_secstruct() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_rna_secstruct_legacy() (in module pyrosetta.rosetta.core.pose.rna.secstruct_legacy) (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) set_rna_south_sugar() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) set_rna_syn_chi() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) set_rnp_high_res_cycles() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_rnp_high_res_relax() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_rnp_min_first() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_rnp_pack_first() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_rnp_ramp_rep() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_root() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) set_root_at_first_rigid_body() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) set_root_atom() (pyrosetta.rosetta.core.energy_methods.GoapRsdType method) set_root_node_naming_func() (pyrosetta.rosetta.utility.tag.XMLSchemaRepeatableCTNode method) set_root_partition_res() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner method) set_root_prob_sampling() (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) set_roots() (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) set_rosetta_restype() (pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler method) set_rosetta_scripts_tag() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) set_rot_energy_cutoff() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GAOptimizer method) set_rot_mag() (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) set_rot_magnitude() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) set_rot_step() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) set_rotamer() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) set_rotamer_operation() (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) set_rotamer_sampling_data_for_RLT() (in module pyrosetta.rosetta.core.pack.task.operation) set_rotamer_selection_string() (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) set_rotamer_seq_sep() (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBondsTrieVsTrieCachedDataContainer method) set_rotamer_set_operation() (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) set_rotamer_well_counts() (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) set_rotamers() (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) set_rotation() (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.RT method) set_rotation_mag() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) set_rotation_magnitude() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_rotation_matrix() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) set_rotation_range() (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) set_rotation_std_dev() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover method) set_rottrial() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_rottrials_from_kic_segment() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) set_rotwell() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) set_rotwidth() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) set_rounds() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) set_row_format() (pyrosetta.rosetta.protocols.contact_map.ContactMap method) set_rsd() (pyrosetta.rosetta.core.io.nmr.AtomSelection method) set_rsd_id() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) set_rsd_neighbor_denominator() (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) set_rsd_set() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) set_rsd_type_name3() (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) set_rsd_type_set() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_rsd_wdw_to_assign_prob() (pyrosetta.rosetta.protocols.hybridization.FragmentBiasAssigner method) set_rsrfilename() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_rt_min() (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (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.DockingProtocol 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) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) set_rtmin() (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) set_rtmutrate() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) set_run_superimpose() (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) set_rv_infos() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) set_S() (pyrosetta.rosetta.core.io.nmr.ParaIon method) set_sa_length_scale() (pyrosetta.rosetta.core.pack.annealer.FASTERAnnealer method) set_sa_scale() (pyrosetta.rosetta.protocols.pack_daemon.FASTER_IG_Repacker method) set_safe() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_salt_bridge_distance_cutoff() (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilter method) set_salt_bridge_mode() (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilter method) set_sample_all_chi() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions 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_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) set_sample_bb() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) set_sample_beta() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) set_sample_both_sugar_base_rotamer() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_sample_chirality() (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) set_sample_cis_pro_frequency() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_sample_five_prime_phosphate() (pyrosetta.rosetta.core.pack.task.rna.RNA_ResidueLevelTask method) set_sample_index() (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) set_sample_jump() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_sample_level() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_sample_lower_nucleoside() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) set_sample_near_a_form() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) set_sample_nonpivot_torsions() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_sample_nucleoside() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) set_sample_nucleoside_lower() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) set_sample_nucleoside_upper() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) set_sample_ONLY_multiple_virtual_sugar() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_sample_pH() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) set_sample_range_large() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) set_sample_range_small() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) set_sample_res() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) set_sample_residues() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_sample_ring_conformers() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) set_sample_rna_chi() (pyrosetta.rosetta.core.pack.task.rna.RNA_ResidueLevelTask method) set_sample_startegy_for_constraint() (pyrosetta.rosetta.protocols.match.Matcher method) set_sample_strategy_for_chi() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) set_sample_three_prime_phosphate() (pyrosetta.rosetta.core.pack.task.rna.RNA_ResidueLevelTask method) set_sample_type() (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler2D method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler3D method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerND method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) set_sample_upper_nucleoside() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) set_sample_zero_probs_at() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) set_sampler() (pyrosetta.rosetta.protocols.match.upstream.ProteinUpstreamBuilder method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) set_sampler_assert_no_virt_sugar_sampling() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_sampler_extra_beta_rotamer() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_sampler_extra_epsilon_rotamer() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_sampler_gaussian_stdev() (in module pyrosetta.rosetta.protocols.recces) set_sampler_include_torsion_value_in_tag() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_sampler_max_centroid_distance() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_sampler_num_pose_kept() (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) set_sampler_perform_phosphate_pack() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_sampler_silent_file() (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) set_sampler_try_sugar_instantiation() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_sampler_values() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) set_samplesheets() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_sampletype() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_sampling_fold_tree() (pyrosetta.rosetta.protocols.abinitio.CoordinateConstraintKC method) (pyrosetta.rosetta.protocols.abinitio.KinematicControl method) set_sampling_options() (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) set_sampling_temperature() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) set_sap_calculate_selector() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) set_sap_goal() (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) set_sap_lb_goal() (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) set_sasa_burial_cutoff() (pyrosetta.rosetta.protocols.buns.BuriedUnsatisfiedPolarsCalculator2 method) set_sasa_cutoff() (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter method) set_sasa_method_hp_mode() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) set_sasa_metric_mode() (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) set_sasa_selector() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) set_SASAfilter() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) set_save_jump_histogram() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_save_scores() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_save_times() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_sc_min() (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (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.DockingProtocol 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) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) set_sc_neighbor_angle_exponent() (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) set_sc_neighbor_angle_shift_factor() (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) set_sc_neighbor_denominator() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) set_sc_neighbor_dist_exponent() (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) set_sc_neighbor_dist_midpoint() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) set_sc_scale() (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_scaffold_flexibility() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_scaffold_status() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStub method) set_scale_by_length() (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric method) set_scaling() (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) set_scheduled() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_schema() (pyrosetta.rosetta.utility.tag.XMLValidator method) set_scheme_conversion() (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) set_scmin() (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) set_score() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.FragData method) (pyrosetta.rosetta.core.optimization.Particle method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge method) (pyrosetta.rosetta.core.scoring.motif.XformScore method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) set_score_against_internal_contacts() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_score_component() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) set_score_cut() (pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) set_score_cut_PDB() (pyrosetta.rosetta.protocols.magnesium.MgScanner method) set_score_cutoff() (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorer method) set_score_diff_cut() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_score_file() (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) set_score_filter() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) set_score_function() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover 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.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder 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.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.pack_daemon.DaemonSet method) (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction method) (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunctionDriver method) (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) set_score_fxn() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_score_margin() (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) set_score_multiply() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) set_score_multiply_from_subunit_factors() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) set_score_multiply_subunit() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) set_score_only() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_score_or_matchrt() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) set_score_selector() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) set_score_sphere_for_atom() (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.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid 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.VdwGrid method) set_score_threshold() (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.hybridization.FragmentBiasAssigner method) set_score_tolerance() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) set_score_type() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreCutoffFilter method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreLoopsFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreTypeFilter method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) set_score_type_threshold() (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) set_score_weight() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler 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.MembraneAbinitio method) set_scorefile_reporting_prefix() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_scorefilter() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) set_scorefunction() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector 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.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.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) set_scorefunction_min() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) set_scorefunction_ptr() (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) set_scorefxn() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector method) (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover 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.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble 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) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.RepackWithoutLigandFilter method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelector method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover 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.MgScanner method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.multistate_design.MultiStateFitnessFunction method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) (pyrosetta.rosetta.protocols.pose_metric_calculators.RotamerBoltzCalculator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TryRotamers method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer 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) (pyrosetta.rosetta.protocols.residue_selectors.HBondSelector method) (pyrosetta.rosetta.protocols.score_filters.ScoreTypeFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWiseMasterPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler 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.monte_carlo.mover.StepWiseMasterMover method) set_scorefxn_deriver() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) set_scorefxn_design() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_scorefxn_filename() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) set_scorefxn_low() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_scorefxn_minimize() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize 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) set_scorefxn_obj() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_scorefxn_pack() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (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) set_scorefxn_relax() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_scorefxn_repack() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize 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) set_scores() (pyrosetta.rosetta.protocols.loop_grower.LoopComparator method) set_scores_to_keep() (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorer method) set_scorescale() (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) set_scoretype() (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) set_scoretypes() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) set_screen_all() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) set_script_from_lines() (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.relax.FastRelax method) set_script_to_batchrelax_default() (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.relax.FastRelax method) set_sd() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) set_sd_ang() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) set_sd_degree() (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) set_sd_dih() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) set_sd_dis() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) set_sd_range() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_seal_foldtree() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) set_search_paths() (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) set_search_responsibilities() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) set_sec_str() (pyrosetta.rosetta.protocols.toolbox.IGInterfaceEdgeUpweighter method) set_second_cycle() (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) set_second_expression() (pyrosetta.rosetta.numeric.expression_parser.AddExpression method) (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.BinaryExpression method) (pyrosetta.rosetta.numeric.expression_parser.DivideExpression method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.MaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MinExpression method) (pyrosetta.rosetta.numeric.expression_parser.MultiplyExpression method) (pyrosetta.rosetta.numeric.expression_parser.OrExpression method) (pyrosetta.rosetta.numeric.expression_parser.SubtractExpression method) (pyrosetta.rosetta.protocols.pack_daemon.PowExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VectorFunction2 method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) set_second_selector() (pyrosetta.rosetta.protocols.pose_sewing.filters.HasDisulfideFilter method) set_secondary_residue_selector() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) set_secondary_structure() (pyrosetta.rosetta.protocols.star.Extender method) set_secstruct() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.fragment.BBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.SecstructSRFD method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.rna.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilter method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) set_secstruct_from_blueprint() (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation method) set_secstruct_from_bp() (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) set_secstruct_from_dssp() (in module pyrosetta.rosetta.protocols.loops) set_secstruct_from_psipred_ss2() (in module pyrosetta.rosetta.protocols.loops) set_seed() (pyrosetta.rosetta.numeric.random.RandomGenerator method) set_segdef() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) set_segfile_path() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) set_segment() (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) set_segment1_ids() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) set_segment2_ids() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) set_segment_distance_cutoff() (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_segment_envelopes() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector method) set_segment_file_paths() (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) set_segment_id() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) set_segment_IDs() (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) set_segment_name() (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) set_segment_names() (pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover method) set_segment_names_ordered() (pyrosetta.rosetta.protocols.splice.Splice method) set_segment_size() (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) set_segment_vector() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_segments() (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing method) set_segments_from_dssp() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_select_designable() (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) set_select_fixed() (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) set_select_from_branch_residue() (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) set_select_from_branch_residues() (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) set_select_from_residue_position() (pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector method) set_select_in_membrane() (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector method) set_select_only_alpha_aas() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) set_select_only_FAMILYVW() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) set_select_packable() (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) set_select_positive_phi() (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) set_select_range() (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) set_select_to_residue_position() (pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector method) set_selected_ss() (pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector method) set_selection() (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilter method) set_selection_logic() (pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector method) set_selection_low() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) set_selectmode() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_selector() (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToResidueProperties method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToSpecifiedBaseResidueTypes method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.core.select.residue_selector.BlockSelector method) (pyrosetta.rosetta.core.select.residue_selector.FractionSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorer method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) set_selector_for_res1() (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) set_selector_for_res2() (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) set_selector_kbt() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) set_selector_name() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) set_selector_scorefunction() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) set_selector_type() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) set_selectors() (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric method) set_semi_energy_dist() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_semi_prob_dist() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_separate_prt_ligand() (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) set_seq1() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_seq2() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_seq_design_cdrs() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_seq_design_options() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_seq_recovery_cache() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver method) set_seq_sep_ramping() (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) set_seq_sep_scale() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_seqfrags_only() (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) set_seqmap() (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) set_seqpos() (pyrosetta.rosetta.core.io.rna.RDAT method) (pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue method) set_seqpos1() (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) set_seqpos2() (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) set_seqprof() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation method) set_sequence() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.fragment.BBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.DownJumpSRFD method) (pyrosetta.rosetta.core.fragment.FragData 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.io.rna.RDAT method) (pyrosetta.rosetta.core.io.silent.SimpleSequenceData method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.loop_grower.LoopComparator method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.SequenceMetric method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesSeqRecoveryCache method) set_sequence_alignment_cut_max() (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) set_sequence_coupling() (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint method) set_sequence_file() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) set_sequence_file_contents() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) set_sequence_mask_selector_rs() (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) set_sequence_mode() (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) set_sequence_profile() (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) set_sequence_strings() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) set_sequences() (pyrosetta.rosetta.core.io.rna.RDAT method) set_set1_selector() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) set_set2_selector() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) set_set_up_metal_bonds() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_setting() (pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry method) set_setup_base_pair_constraints() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_sf() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) set_sfxn() (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) set_sfxn_cycles() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_shadowing_atom() (pyrosetta.rosetta.core.chemical.MutableResidueType method) set_shallow_copy() (pyrosetta.rosetta.basic.datacache.CacheableResRotPairFloatMap method) set_shared_silent_data() (pyrosetta.rosetta.core.io.silent.SilentFileData method) set_sharpen_b() (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) set_sheet_db_path() (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) set_sheet_tolerance() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_sheet_topology() (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) set_sheetbonus() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_sheetcriteria() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_sheetlist() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) set_sheetlist_as_is() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) set_sheets() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_shift() (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing method) set_short_backrub_mover() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_short_parameter_description() (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) set_short_version() (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric method) set_show_accessed_options_flag() (pyrosetta.rosetta.utility.options.OptionCollection method) set_show_all_fixes() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_show_crash_report_on_console() (in module pyrosetta.rosetta.utility) set_show_extended() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) set_show_more_pose_scores() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_show_unused_options_flag() (pyrosetta.rosetta.utility.options.OptionCollection method) set_show_viol_level() (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) set_shrink_factor() (pyrosetta.rosetta.protocols.match.Bool3DGridKinemageWriter method) set_sid_cutoff_cdr() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity method) set_sid_cutoff_fr() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity method) set_sidechain() (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) set_sidechain_frlx_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_sigmoidal_die() (pyrosetta.rosetta.core.scoring.etable.coulomb.Coulomb method) set_silent_file() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) set_silent_file_data() (pyrosetta.rosetta.core.import_pose.pose_stream.SilentFilePoseInputStream method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) set_silent_file_name() (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) set_silent_file_out() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) set_silent_files_in() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer method) set_silent_output() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication method) set_silentname() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_silentout_file_name() (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) set_sim() (pyrosetta.rosetta.protocols.cluster.APCluster method) set_simple_append_map() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_simple_metric() (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_simple_metrics() (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeatures method) set_simple_rmsd_cutoff_relax() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_single_loop_fold_tree() (in module pyrosetta.rosetta.protocols.forge.methods) (in module pyrosetta.rosetta.protocols.loops) set_single_pre_weighting_scheme() (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingleSet method) set_single_rdc_weighting_scheme() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingleSet method) set_single_resnum() (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) set_size() (pyrosetta.rosetta.cppdb.backend.statements_cache method) (pyrosetta.rosetta.protocols.pockets.SmallMol method) (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) set_size_and_nbb() (pyrosetta.rosetta.protocols.frags.TorsionFragment method) set_size_msg() (pyrosetta.rosetta.utility.SimulateMPIMessage method) set_sizes_msg() (pyrosetta.rosetta.utility.SimulateMPIMessage method) set_skeletonfile() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_skip_bulge_frequency() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_skip_chi_min() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) set_skip_clustering() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_skip_completely_buried_positions() (pyrosetta.rosetta.protocols.match.Bool3DGridKinemageWriter method) set_skip_complicated_stuff() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) set_skip_connect_info() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_skip_coord_constraints() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_skip_deletions() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_skip_last_accept() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_skip_long_min() (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) set_skip_loop_chains() (pyrosetta.rosetta.protocols.pack_interface.ProteinProteinInterfaceUpweighter method) (pyrosetta.rosetta.protocols.toolbox.IGInterfaceEdgeUpweighter method) set_skip_low_temp_phase() (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) set_skip_lr() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) set_skip_minimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) set_skip_o2prime_trials() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) set_skip_preminimize() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_skip_redundant() (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) set_skip_reporting() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_skip_ring_closure() (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) set_skip_ring_closure_from_flags() (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) set_skip_same_pucker() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler 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) set_skip_sampling() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) set_skip_set_reasonable_fold_tree() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_skip_stage1() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) set_skip_stage2() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) set_skip_unknown_mutant() (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) set_sl_weights() (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) set_SlaveCanOpenFile() (pyrosetta.rosetta.protocols.jd2.DebugOut_MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd2.MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd2.WriteOut_MpiFileBuffer method) set_slice_mode() (pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector method) set_slice_res() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) set_slice_res_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) set_slice_width() (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) set_slide_axis() (pyrosetta.rosetta.protocols.surface_docking.SurfaceParameters method) set_slide_criteria() (pyrosetta.rosetta.protocols.symmetry.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SymmetrySlider method) set_slide_glycan_into_contact() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) set_slide_info() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) set_slide_order() (pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo method) set_slide_threshold() (pyrosetta.rosetta.protocols.symmetry.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SymmetrySlider method) set_slide_type() (pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo method) set_SlideCriteriaType() (pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo method) set_SlideCriteriaVal() (pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo method) set_sliding_window_size() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) set_slope() (pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction method) set_small_docking_moves() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_small_frag_file() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) set_small_frag_insertion_weight() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_small_frag_size() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) set_small_fragments() (pyrosetta.rosetta.protocols.hybridization.MRMover method) set_smart_annealer() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) set_smart_annealer_cutoff() (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) set_smart_annealer_disable_during_quench() (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) set_smart_annealer_model() (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) set_smart_annealer_pick_again() (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) set_smoothing() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) set_snugdock_foldtree() (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) set_SnugFit() (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) set_soft_dampening() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) set_solution_picker() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) set_solvation() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_sort_scorefxn() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) set_sorter() (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) set_source_from_to_res() (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) set_source_pose() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseSegment method) (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) set_source_size() (pyrosetta.rosetta.utility.subset_mapping method) set_spacegroup() (pyrosetta.rosetta.protocols.cryst.Spacegroup method) set_span() (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) set_spanfile1() (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) set_spanfile2() (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) set_sparse_aa_info() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) set_sparse_aa_info_for_edge() (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.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) set_special_edges() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) set_special_region() (pyrosetta.rosetta.protocols.simple_pose_metric_calculators.BuriedUnsatisfiedPolarsCalculator method) (pyrosetta.rosetta.protocols.simple_pose_metric_calculators.NumberHBondsCalculator method) set_species() (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) set_specific_conformer() (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) set_speed() (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) set_sphere() (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.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid 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.VdwGrid method) set_spin() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_spinlabel() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) set_square_planar_metal_positions_from_string_vector() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_square_pyramidal_metal_positions_from_string_vector() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_ss() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) set_ss_cutoff() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_ss_defaults() (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) set_ss_from_phipsi() (in module pyrosetta.rosetta.core.pose) set_ss_from_str() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) set_ss_lowstrand() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_ssid() (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) set_SSorient() (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) set_st_weights() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_stage1_1_cycles() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_stage1_2_cycles() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_stage1_3_cycles() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_stage1_4_cycles() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_stage1_increase_cycles() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) set_stage1_perturb_glycan_com_rot_mag() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) set_stage1_perturb_glycan_com_trans_mag() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) set_stage1_rotate_glycan_about_com() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) set_stage1_scorefxn() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) set_stage1_torsion_uniform_pert_mag() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) set_stage2_cycles() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_stage2_increase_cycles() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) set_stage2_repack_period() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_stage2_rot_mag() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) set_stage2_scorefxn() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) set_stage2_trans_mag() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) set_stage2min_scorefxn() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) set_stage2pack_scorefxn() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) set_stage3_cycles() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_stage4_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler 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.MembraneAbinitio method) set_staged_constraints() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_standard_bb_stdev() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_standard_stub_atoms() (pyrosetta.rosetta.core.fragment.DownJumpSRFD method) set_start() (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) set_start_added_residue_in_aform() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) set_start_graft() (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) set_start_node_vital_segments() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_start_position() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix method) set_start_rep_weight() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_start_res() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_start_res_vec() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_start_resnums() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_start_segments() (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) set_start_temperature() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_starting_reference_energies() (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) set_starting_rep() (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) set_starting_residue() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseSegment method) set_starting_segment() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) set_starts_and_ends() (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) set_state() (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) set_state_for_node() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase 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.MultiplexedAnnealableGraph 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.ResidueArrayAnnealingEvaluator 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) set_state_ind_for_this_aa_type() (pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex method) set_states() (pyrosetta.rosetta.core.pack.task.operation.UseMultiCoolAnnealer method) set_statistics_filename() (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) set_stats_cutoff() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_status() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) set_status_prefix() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) set_status_suffix() (pyrosetta.rosetta.protocols.jd3.LarvalJob method) set_std_dev() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_std_pair_std_string_std_string_t (class in pyrosetta.rosetta.std) set_std_pair_unsigned_long_unsigned_long_t (class in pyrosetta.rosetta.std) set_std_set_unsigned_long_t (class in pyrosetta.rosetta.std) set_std_shared_ptr_protocols_environment_ClientMover_t (class in pyrosetta.rosetta.std) set_std_string_std_less_std_string_std_allocator_std_string_t (in module pyrosetta.rosetta.std) set_std_string_t (class in pyrosetta.rosetta.std) set_steal_large_frags() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) set_steal_small_frags() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) set_stem_optimize() (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) set_stem_pairing_sets() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) set_stem_size() (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) set_step_size() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_steps() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_stepsize() (pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch method) set_stepwise_modeler() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover 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) set_stop() (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.protocols.loops.Loop method) set_stop_after_closure() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_stop_res() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) set_stop_sampling() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_stop_segments() (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) set_store_silents() (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) set_store_trj() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_storedbeams() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_strand_dist_cutoff() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_strand_extensions() (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) set_strand_pairings() (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilter method) set_strand_pairs() (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) set_strand_strand_weights() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) set_strategy() (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) set_stretch_strand_dist_cutoff() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) set_strict_dssp_changes() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_strict_looprelax_checks() (pyrosetta.rosetta.protocols.loops.Loops method) set_strict_loops() (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover 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) set_strict_movemap() (pyrosetta.rosetta.protocols.abinitio.CoordinateConstraintKC method) (pyrosetta.rosetta.protocols.abinitio.KinematicControl method) set_stride() (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) set_string_msg() (pyrosetta.rosetta.utility.SimulateMPIMessage method) set_string_option() (in module pyrosetta.rosetta.basic.options) set_string_vector_option() (in module pyrosetta.rosetta.basic.options) set_strip_existing_glycans() (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) set_struct_id1() (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSQLite method) set_struct_ids_from_sql() (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) set_struct_ids_from_strings() (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) set_structure() (pyrosetta.rosetta.core.io.rna.RDAT method) set_structure_input_tag() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) set_structure_tag() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) set_structures() (pyrosetta.rosetta.core.io.rna.RDAT method) set_stub_atoms() (pyrosetta.rosetta.core.fragment.DownJumpSRFD method) set_stub_transform() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) set_subbin_type_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) set_subbin_type_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) set_subchemistry() (pyrosetta.rosetta.protocols.chemistries.WrappedBaseChemistry method) set_subelements_pick_one() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) set_subelements_pick_one_or_none() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) set_subelements_repeatable() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) set_subelements_single_appearance_optional() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) set_subelements_single_appearance_required() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) set_subelements_single_appearance_required_and_ordered() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) set_submotif_frequency() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_submotif_library() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) set_subset() (pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) set_substrate_chain() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_substrate_foldtree() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) set_substrate_type() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_subunits() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) set_suffix() (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) set_sugar() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) set_sugar_domain() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) set_sugar_donor() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_sugars_to_preglycosylate() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_suite_cluster_radius() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_sulph_dist_cutoff() (pyrosetta.rosetta.protocols.buns.BuriedUnsatisfiedPolarsCalculator2 method) set_sum() (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorer method) set_super_secret_fixed_interface_mode() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_superimpose_over_all() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions 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.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_superimpose_over_all_instantiated() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner method) set_superimpose_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) set_suppress_bp_constraint() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_suppress_checkpoints() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_suppress_sampler_display() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_suppress_zero_occ_pdb_output() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_surf() (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) set_surface() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) set_surface_contact_mover() (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) set_surface_esp_to_zero() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) set_surface_orient_mover() (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) set_surface_parameters() (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) set_sweep_nonpivot_torsions() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_sweep_nsteps() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) set_sweep_start_angle() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) set_sweep_step_size() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) set_switch_focus_frequency() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_sym_dof_names() (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) set_symm() (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilter method) set_symm_count() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_symm_hack_arity() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_symm_info() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_symm_repeats() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) set_symm_transforms() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) set_symm_type() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) set_symmdef_file() (pyrosetta.rosetta.protocols.hybridization.MRMover method) set_symmetric_pack() (pyrosetta.rosetta.protocols.scoring.Interface method) set_symmetric_sequence() (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) set_symmetrize_gly() (pyrosetta.rosetta.core.chemical.mainchain_potential.MainchainScoreTable method) set_symmetrize_output() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) set_symmetry() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) set_symmetry_copies() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) set_symmetry_name() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) set_symmetry_options_from_tag() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) set_symmetry_type() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) set_T_xx() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) set_T_xy() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) set_T_xz() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) set_T_yy() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) set_T_yz() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) set_table_name() (pyrosetta.rosetta.protocols.features.SimpleMetricFeatures method) set_tag() (pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) set_tag_along_chains() (pyrosetta.rosetta.protocols.ligand_docking.Rotate_info method) set_tag_from_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) set_takeoff_domain() (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) set_takeoff_pos() (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) set_targ_ang() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_targ_dih() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) set_target() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) set_target_and_tolerance() (pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.PeakCalibratorMap method) (pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator method) set_target_atom_name() (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) set_target_attractive_weight() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) set_target_filename() (pyrosetta.protocols.h5_fragment_store_provider.H5PyFragmentStoreProvider method) (pyrosetta.rosetta.protocols.indexed_structure_store.BinaryFragmentStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreProvider method) set_target_function() (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) set_target_geomcst_id() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) set_target_proximity_to_starting_conformation() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) set_target_range() (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) set_target_repulsive_weight() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) set_target_res() (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) set_target_res_index() (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) set_target_res_pdb() (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) set_target_residue() (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) set_target_sequences() (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) set_target_type() (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) set_task() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.task_operations.STMStoredTask method) set_task_and_movemap() (in module pyrosetta.rosetta.protocols.hydrate) set_task_factory() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler 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.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign 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.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle 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) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner 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.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.pack_daemon.DaemonSet method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric 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) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) set_task_for_filters() (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) set_task_scaling() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) set_task_segments() (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) set_task_with_de_novo_water_using_resfile() (in module pyrosetta.rosetta.protocols.hydrate) set_taskfactory() (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) set_taskop() (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) set_tau() (pyrosetta.rosetta.core.conformation.Residue method) set_tau_c() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) set_tau_c_limits() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) set_tau_e() (pyrosetta.rosetta.core.io.nmr.ParaIon method) set_tau_r() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) set_tau_t() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) set_tcr_loop_model() (pyrosetta.rosetta.protocols.tcr.TCRloopRefine method) set_temp() (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.multistate_design.PartitionAggregateFunction method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) set_temp0() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_temp_cycles() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_temperature() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions 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.core.scoring.nmr.pre.PREMultiSet method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.flexpack.annealer.FlexbbSimAnnealer method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover 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.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_temperature_observer() (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) set_temperature_ramping() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_temperature_schedule() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) set_temperatures() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_tempering() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) set_template() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerLinks method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) set_template_pose() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) set_template_res_index() (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) set_templates_to_ignore() (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) set_temps() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) set_tensor() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) set_tensor_in_arbitrary_frame() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) set_tensor_in_pas() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) set_term_name() (pyrosetta.rosetta.protocols.simple_filters.ReadPoseExtraScoreFilter method) set_terminal_res() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_terminus() (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) set_terminus_selector() (pyrosetta.rosetta.core.select.residue_selector.ConfluentSelector method) set_test_all_mg_hydration_frames() (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) set_test_all_moves() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_tether_jump() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_tether_to_closest_res() (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.SampleGrid method) set_tetrahedral_metal_positions_from_string_vector() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_thermal_sampler_mode() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_thermal_sampler_output_min_pose() (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) set_theta() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) (pyrosetta.rosetta.core.pose.Pose method) set_thread_limit() (pyrosetta.rosetta.core.pack.task.operation.RestrictInteractionGraphThreadsOperation method) set_three_prime_phosphate_res() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) set_thresh() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorMatrix method) set_threshold() (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.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreTypeFilter method) (pyrosetta.rosetta.protocols.simple_filters.HolesFilter method) (pyrosetta.rosetta.protocols.simple_filters.ReadPoseExtraScoreFilter method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) set_threshold_distance() (pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore method) set_thresholds() (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilter method) set_throw_on_double_registration() (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) (pyrosetta.rosetta.core.select.jump_selector.JumpSelectorFactory method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorFactory method) (pyrosetta.rosetta.protocols.chemistries.ChemistryFactory method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputterFactory method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputterFactory method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterFactory method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricFactory method) set_throw_on_fail() (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) set_tied_pos_rs() (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) set_tilt() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_tilt1_center() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_tilt2_center() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_time_minobj() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_titrate_stack_bonus() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_tmh_inserted() (pyrosetta.rosetta.core.scoring.MembraneTopology method) set_tmh_jump() (pyrosetta.rosetta.protocols.jumping.PairingLibrary method) (pyrosetta.rosetta.protocols.jumping.SpecificGeometryLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) set_to() (pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector method) set_to_default() (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.relax.FastRelax method) set_to_origin() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) set_to_pose() (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) set_to_quench() (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.flexpack.annealer.FlexbbSimAnnealer method) set_token_type() (pyrosetta.rosetta.numeric.expression_parser.SimpleToken method) set_tol() (pyrosetta.rosetta.protocols.nmr.pre.PREDistanceRecord method) set_tolerance() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) set_tolerated_overlap() (pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) set_top_frag_num() (pyrosetta.rosetta.core.fragment.FragmentIO method) set_top_n_big_frag() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_top_n_small_frag() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_topology() (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) set_tor_U1D3_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_tor_U2D2_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_tor_U3D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) set_torsion() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.fragment.BBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) set_torsion_and_align() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAligner method) set_torsion_angle() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) set_torsion_id() (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) set_torsion_screen() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) set_torsion_to_pose() (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) set_torsion_type() (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler2D method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler3D method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerND method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler method) (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler method) set_torsion_values() (pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1 method) set_torsions() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) set_torsions_using() (pyrosetta.rosetta.protocols.normalmode.NormalMode method) set_torsmutrate() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) set_total_energy_cutoff() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_total_jobs() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) set_total_num_mc_runs() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_total_residue() (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData method) set_total_score_last_considered() (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) set_total_weight() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) set_trace() (pyrosetta.rosetta.core.io.rna.RDAT method) set_tracer_options() (pyrosetta.rosetta.basic.MemTracerImpl static method) (pyrosetta.rosetta.basic.TracerImpl static method) set_trackfragments() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_traits() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.multistate_design.MultiStateEntity method) set_traits_size() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.multistate_design.MultiStateEntity method) set_trans_mag() (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) set_trans_magnitude() (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) set_trans_step() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) set_transaction_mode() (pyrosetta.rosetta.utility.sql_database.session method) set_transform() (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) set_translation() (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.RT method) set_translation_mag() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) set_translation_magnitude() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) set_translation_matrix() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) set_transparent_facets() (pyrosetta.rosetta.protocols.match.Bool3DGridKinemageWriter method) set_transwidth() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) set_trial_positions() (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) set_trigonal_planar_metal_positions_from_string_vector() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_trigonal_pyramidal_metal_positions_from_string_vector() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_trim_info() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) set_trivial_decoy_compatibility_score() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList method) set_trj() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_trj_score_only() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_trj_scratch() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_try_all_pairs() (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) set_turn_off_rna_chem_map_during_optimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_turnoff_minimization() (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) set_twist() (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) set_two_body_energy() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge method) set_two_body_energy_for_edge() (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.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) set_two_stage_clustering() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_twobody_energies_multithreaded() (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.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) set_twoprime() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) set_twoprime_res() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) set_type() (pyrosetta.rosetta.core.pose.rna.RNA_Reactivity method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_Motif method) (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.checkpoint.CheckPointer 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.PyMOLObserver 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.network.UIObserver 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.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.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid 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.VdwGrid 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.data_storage.LigandResidue method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSewingResidue 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) set_ub_function() (pyrosetta.rosetta.numeric.interpolation.spline.CompoundInterpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.Interpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.SimpleInterpolator method) set_UBQpdb() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) set_unbound_mode() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_undercount_sugar_rotamers() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer method) set_unfolded_energy_emap_vector() (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) set_uniform_backrub() (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover method) set_uniform_coord_constrained() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_uniform_euler_angle_bin_width() (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) set_uniform_modeler() (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) set_uniform_trans() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_uniform_xyz_bin_width() (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) set_unit() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) set_unseen_score() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorExternal method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded method) set_unselectable() (pyrosetta.rosetta.protocols.match.Bool3DGridKinemageWriter method) set_unsigned_long_t (class in pyrosetta.rosetta.std) set_unweighted() (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilter method) set_unweighted_function() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) set_up_assembly() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_up_default_special_behaviours() (pyrosetta.rosetta.core.pack.palette.CustomBaseTypePackerPalette method) (pyrosetta.rosetta.core.pack.palette.DefaultPackerPalette method) (pyrosetta.rosetta.core.pack.palette.NCAADefaultPackerPalette method) (pyrosetta.rosetta.core.pack.palette.NoDesignPackerPalette method) (pyrosetta.rosetta.core.pack.palette.PackerPalette method) set_up_default_task_factory() (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) set_up_hashing() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_up_mapfile_reassignments_from_commandline() (in module pyrosetta.rosetta.core.chemical) set_up_metal_bonds() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_up_metal_constraints() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) set_up_packer_palette() (in module pyrosetta.rosetta.core.pack.task) set_up_peptide_stub_mover() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) set_up_quota_nnmake_style() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_up_residuearrayannealableenergy_for_packing() (pyrosetta.rosetta.core.energy_methods.AACompositionEnergy method) (pyrosetta.rosetta.core.energy_methods.AARepeatEnergy method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergy method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PartitionEnergy 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.scoring.annealing.ResidueArrayAnnealableEnergy method) set_up_residues() (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) set_up_ss_abego_quota() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_up_target_sequence() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) set_up_thioether_bond_mover() (in module pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) set_up_thioether_constraints() (in module pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) set_up_thioether_variants() (in module pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) set_up_user_helix_assignments() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_HelixCoilMoveGenerator method) set_up_user_helix_assignments_from_psipred_predictions() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_HelixCoilMoveGenerator method) set_up_voxel_grid_and_compute_burial() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) set_update_boinc() (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) set_update_pdb_numbering_mode() (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) set_update_polymer_bond_dependent_atoms() (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) set_update_polymer_dependent() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) set_update_pose() (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) set_update_tolerance() (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) set_upper() (pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t method) set_upper_bfactor_threshold() (pyrosetta.rosetta.core.select.residue_selector.BFactorSelector method) set_upper_bound() (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) set_upper_connect_atom() (pyrosetta.rosetta.core.chemical.MutableResidueType method) set_upper_dihedrals() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_upper_residue() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_upper_residues() (pyrosetta.rosetta.core.select.residue_selector.BFactorSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) set_upper_segment() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) set_upper_threshold() (pyrosetta.rosetta.protocols.simple_ddg.InterfaceBindingEnergyDensityFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_upstream_chain() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) set_upstream_pose() (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.MatcherTask method) set_upweight_starting_twobody() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) set_use_6D_potential() (pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph method) set_use_ave_pssm() (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric method) set_use_basic_enhanced_n_linked_sequon() (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) set_use_big_polar_hydrogen() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod method) set_use_cached_data() (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeatures method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities method) set_use_centroid_dG() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_use_chainbreak_energy() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_use_chem_shift_data() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_use_cluster_csts() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_use_cluster_for_H3() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_use_confidence() (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter method) set_use_conformer_population_stats() (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) set_use_conformer_probabilities() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) set_use_constraints() (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) set_use_contact_selector() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_use_coordinate_constraints() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) set_use_custom_dihedral_angle() (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) set_use_ddG_style() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_use_degrees() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) set_use_delta() (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) set_use_dssp() (pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilter method) (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) set_use_dssp_reduced() (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) set_use_ellipsoidal_randomization() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) set_use_epitope_constraints() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) set_use_fast_frame_heuristic() (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) set_use_fast_heuristic() (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) set_use_first_jump_for_submotif() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_use_fold_tree_from_silent_file() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) set_use_gaussian_sampling() (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) set_use_general_csts_on_cluster_failure() (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) set_use_gma_templates() (pyrosetta.rosetta.protocols.tcr.TCRmodel method) set_use_gmb_templates() (pyrosetta.rosetta.protocols.tcr.TCRmodel method) set_use_green_packer() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) set_use_harmonic_function() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) set_use_hbnet_behavior() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_use_hh_abego_rules() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) set_use_hydrogens() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) set_use_increased_vdw_radii() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) set_use_input_sidechain() (pyrosetta.rosetta.protocols.match.upstream.ProteinUpstreamBuilder method) set_use_jobname() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_use_legacy_protocol() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) set_use_legacy_setup() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) set_use_ligand_selector() (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) set_use_nblist() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) set_use_outliers() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) set_use_packer_instead_of_rotamer_trials() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) set_use_pdb_format_HETNAM_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_use_pharmacophore() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner method) set_use_phenix_geo() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_use_pose_name() (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) set_use_precomputed_library() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_use_probability() (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter method) set_use_rama2b() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) set_use_rama_power() (pyrosetta.rosetta.core.scoring.Ramachandran method) set_use_rama_prepro_for_sampling() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) set_use_relevant_residues_as_loop_length() (pyrosetta.rosetta.protocols.features.LoopAnchorFeatures method) set_use_reporter_behavior() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_use_resfile() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) set_use_rosetta_numbering() (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) set_use_sc_neighbors() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_use_secondary_graft_mover_if_needed() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) set_use_selector_as_zscore_mask() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) set_use_seqprof_constraints() (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) set_use_shear() (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) set_use_sidechain_neighbors() (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) set_use_single_residue_to_define_anchor_transfrom() (pyrosetta.rosetta.protocols.features.LoopAnchorFeatures method) set_use_soft_clash() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) set_use_statistical_potential() (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter method) set_use_stored_energy() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) set_use_sugar_bb_data_if_needed() (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) set_use_sum_for_per_residue_real() (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) set_use_svm() (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter method) set_use_symmetry() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) set_use_threeletter() (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) set_use_tracer() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) set_use_trRosetta_constraints() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (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) set_use_virtual_waters_as_placeholders() (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) set_use_vsasa() (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) set_user_chain1() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) set_user_chain2() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) set_user_csts() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) set_user_defined_calc_rms_res() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner method) set_user_defined_cycles() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_user_defined_name() (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) set_user_defined_peptide() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) set_user_defined_receptor() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) set_user_input() (pyrosetta.rosetta.core.import_pose.libraries.ChunkSet method) set_user_input_chunk_initialization_library() (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) set_user_input_chunk_library() (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) set_user_input_VDW_bin_checker() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) set_user_provided_movers() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) set_userpos() (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) set_using() (pyrosetta.rosetta.core.energy_methods.GoapRsdType method) set_using_a_resselect() (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) set_valid() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.FragData method) set_valid_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) set_validate_lattice() (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) set_vall() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) set_vall_file() (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) set_vall_torsions_file() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_value() (pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter 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.core.pose.rna.RNA_Reactivity method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricData method) (pyrosetta.rosetta.numeric.expression_parser.LiteralExpression method) (pyrosetta.rosetta.numeric.expression_parser.VariableExpression method) (pyrosetta.rosetta.numeric.MathNTensor_bool_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_1_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_2_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_4_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_5_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_6_t method) (pyrosetta.rosetta.numeric.MathNTensorBase_bool_t method) (pyrosetta.rosetta.numeric.MathNTensorBase_double_t method) (pyrosetta.rosetta.protocols.filters.ContingentFilter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) (pyrosetta.rosetta.protocols.optimize_weights.OptEVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.qsar.qsarPoint method) (pyrosetta.rosetta.utility.libsvm.Svm_node_rosetta method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.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) set_value_for_bin() (pyrosetta.rosetta.protocols.match.Bool3DGrid method) set_value_from_pdb_line() (pyrosetta.rosetta.core.io.pdb.Field method) set_values() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) set_variant_type() (pyrosetta.rosetta.core.chemical.ResidueProperties method) set_vary_bond_geometry() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) set_vary_bondangles() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) set_vary_ca_bond_angles() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) set_vary_cutpoints() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) set_vary_loop_length_frequency() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_vary_polar_hydrogen_geometry() (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) set_vary_rna_bond_geometry() (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) set_vdw_cached_rep_screen_info() (in module pyrosetta.rosetta.protocols.scoring) set_vdw_cached_rep_screen_info_from_pose() (in module pyrosetta.rosetta.protocols.scoring) set_vdw_calculation_annotated_sequence() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) set_vdw_grid() (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) set_VDW_rep_alignment_RMSD_CUTOFF() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker method) set_VDW_rep_delete_matching_res() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker method) set_vdw_rep_screen_include_sidechains() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) set_VDW_rep_screen_info() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer 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) set_VDW_rep_screen_physical_pose_clash_dist_cutoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_vdw_sf() (pyrosetta.rosetta.protocols.loop_grower.LoopComparator method) set_VDW_weight() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) set_vector_b() (pyrosetta.rosetta.basic.svd.SVD_Solver method) set_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) set_vector_name_and_weight() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter 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) set_vel() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_verbose() (pyrosetta.rosetta.core.import_pose.options.RNA_BasicOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.scoring.rna.RNA_TorsionPotential method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter method) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.StepWiseSampleAndScreen method) set_verbose_sampler() (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) set_verbose_scorefile() (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) set_verbose_scores() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_version() (pyrosetta.rosetta.core.io.rna.RDAT method) (pyrosetta.rosetta.protocols.sewing.hashing.SegmentVector method) set_vertex_member_of_group() (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) set_vh_vl_jump() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) set_vicinity_degree() (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) set_vicinity_sampling() (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) set_view() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) set_virtual_anchor_attachment_points() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) set_virtual_res() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) set_virtual_sugar_do_minimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_virtual_sugar_do_screens() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_virtual_sugar_is_from_prior_step() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) set_virtual_sugar_keep_base_fixed() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) set_virtual_sugar_legacy_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) set_virtual_sugar_res() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) set_virtualize_packable_moieties_in_screening_pose() (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) set_visited() (pyrosetta.rosetta.numeric.ClusteringTreeNode method) (pyrosetta.rosetta.protocols.pockets.SmallMol method) set_vital_residues() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) set_vital_selector() (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) set_vlb() (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) set_volume() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) set_voxel_size_and_padding() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) set_voxel_spacing() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) set_w_rep() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) set_wallpaper_group() (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) set_warn_empty_list() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) set_watch_in_pymol() (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) set_water_info_and_add_de_novo_water() (in module pyrosetta.rosetta.protocols.hydrate) set_watlim_scale() (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) set_wdw_to_freeze() (pyrosetta.rosetta.protocols.hybridization.FragmentBiasAssigner method) set_weak_pointer_to_self() (pyrosetta.rosetta.core.kinematics.AtomTree method) set_weight() (pyrosetta.rosetta.core.pose.rna.RNA_Datum method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingle method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingle method) (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingleSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingle method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingleSet method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.numeric.random.WeightedSampler method) (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.abinitio.PairingStatEntry method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) (pyrosetta.rosetta.protocols.pack_interface.ProteinProteinInterfaceUpweighter method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandAssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorer method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) set_weight_constraints_NtoC() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_weight_constraints_sheet() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) set_weight_if_zero() (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) set_weighted_average() (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) set_weights() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilter method) (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) set_well_depth() (pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction method) set_which_side() (pyrosetta.rosetta.core.pose.rna.BaseStack method) set_width() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) set_window() (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.noesy_assign.FoldResonance method) set_window_size() (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) set_window_width() (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorer method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric method) (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) set_windowdensweight() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_working_best_alignment() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_working_bridge_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_working_calc_rms_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_working_fixed_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_working_minimize_res() (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) set_working_moving_partition_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_working_moving_res_list() (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.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_working_native_alignment() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_working_native_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_working_pack_res() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWiseMasterPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) set_working_parameters() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) set_working_parameters_exist() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) set_working_prepack_res() (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) set_working_res() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) set_working_superimpose_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) set_worst() (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) set_wrapping_optE_multifunc() (pyrosetta.rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator method) set_write_all_connect_info() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_write_atom_names() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) set_write_dynamic_rsr() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_write_empty_voxels() (pyrosetta.rosetta.protocols.match.Bool3DGridKinemageWriter method) set_write_facets() (pyrosetta.rosetta.protocols.match.Bool3DGridKinemageWriter method) set_write_glycan_pdb_codes() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_write_no_structures() (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) set_write_only_highest_VC() (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) set_write_pdb_link_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_write_pdb_parametric_info() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_write_pdb_title_section_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_write_potentials_for_individual_scoreterms() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) set_write_separate_scorefile() (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) set_write_seqres_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) set_writebeams() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_writelps() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) set_wt_aa() (pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData method) set_wt_adp() (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) set_wt_dens() (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) set_wt_pose() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) set_wt_unfolded_energies_emap() (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData method) set_wu_type() (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash 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.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore 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) set_x() (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover method) set_x_middle() (pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction method) set_x_values() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) set_xaxis_rotation_deg() (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) set_xaxis_rotation_rad() (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) set_xsel() (pyrosetta.rosetta.core.io.rna.RDAT method) set_xsel_refine() (pyrosetta.rosetta.core.io.rna.RDAT method) set_xyz() (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.core.io.ResidueInformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) set_xyz_bin() (pyrosetta.rosetta.core.pose.rna.VDW_Grid method) set_xyz_bin_widths() (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) set_xyz_file() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) set_xyz_step() (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.SampleGrid method) set_xyz_target() (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraint method) set_y() (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover method) set_y_values() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) set_yaxis_rotation_deg() (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) set_yaxis_rotation_rad() (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) set_year_and_article() (pyrosetta.rosetta.basic.citation_manager.Citation method) set_z() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.EulerAngles method) set_z_values() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) set_zaxis_rotation_deg() (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) set_zaxis_rotation_rad() (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) set_zero() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) set_zero_prob_weight_at() (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) set_zeta() (pyrosetta.rosetta.core.pose.Pose method) SetAACompositionPotential (class in pyrosetta.rosetta.protocols.fldsgn.potentials) SetAACompositionPotentialCreator (class in pyrosetta.rosetta.protocols.fldsgn.potentials) setAccessed() (pyrosetta.rosetta.utility.tag.Tag method) setActiveAtom() (pyrosetta.rosetta.RDKit.RWMol method) setAlgorithm() (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) setall() (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) SetAllAtomsRepulsive (class in pyrosetta.rosetta.core.chemical) setAtomBookmark() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) SetAtomicCharge (class in pyrosetta.rosetta.core.chemical) setAtomicNum() (pyrosetta.rosetta.RDKit.Atom method) setAtomMapNum() (pyrosetta.rosetta.RDKit.Atom method) setAtomMask() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) setAtomPos() (pyrosetta.rosetta.RDKit.Conformer method) SetAtomTree (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) SetAtomTreeCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) SetAtomType (class in pyrosetta.rosetta.core.chemical) setB() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) SetBackboneHeavyatom (class in pyrosetta.rosetta.core.chemical) setBase() (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) SetBaseName (class in pyrosetta.rosetta.core.chemical) setBeginAtom() (pyrosetta.rosetta.RDKit.Bond method) setBeginAtomIdx() (pyrosetta.rosetta.RDKit.Bond method) setBondBookmark() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) setBondDir() (pyrosetta.rosetta.RDKit.Bond method) setBondType() (pyrosetta.rosetta.RDKit.Bond method) setCartRef() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) SetCatalyticResPackBehavior (class in pyrosetta.rosetta.protocols.enzdes) SetCatalyticResPackBehaviorCreator (class in pyrosetta.rosetta.protocols.enzdes) setCenterOnMiddleCA() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) setCentroidSilentOut() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setCheatNativeCOM() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setCheatNativeMCA() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) SetChiMover (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) SetChiMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) setChiralTag() (pyrosetta.rosetta.RDKit.Atom method) setClusterOversamp() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setClusterRadius() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setCombinedSearchResultsFname() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setConstrainRefinement() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setConvoluteSingleR() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setCoreIdx() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) SetCrystWeightMover (class in pyrosetta.rosetta.protocols.cryst) SetCrystWeightMoverCreator (class in pyrosetta.rosetta.protocols.cryst) setData() (pyrosetta.rosetta.protocols.sparta.GDB method) setdefault() (pyrosetta.bindings.pose.PoseScoreAccessor method) (pyrosetta.io.silent_file_map.SilentFileMap method) setDefaultAnchors() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) setDelR() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setDimensions() (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) SetDisulfideAtomName (class in pyrosetta.rosetta.core.chemical) setDoRefine() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setDumpInter() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setDumpInterSilent() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setEndAtom() (pyrosetta.rosetta.RDKit.Bond method) setEndAtomIdx() (pyrosetta.rosetta.RDKit.Bond method) setEntry() (pyrosetta.rosetta.protocols.sparta.GDB method) setf() (pyrosetta.rosetta.std.ios_base method) setfilterparams() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) setFinalChain() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) SetFormalCharge (class in pyrosetta.rosetta.core.chemical) setFormalCharge() (pyrosetta.rosetta.RDKit.Atom method) setFragDens() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setFullOccupied() (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) setGaussianBlur() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setGridStep() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setHybridization() (pyrosetta.rosetta.RDKit.Atom method) SetICoor (class in pyrosetta.rosetta.core.chemical) setId() (pyrosetta.rosetta.RDKit.Conformer method) setIdx() (pyrosetta.rosetta.RDKit.Atom method) (pyrosetta.rosetta.RDKit.Bond method) SetIGTypeOperation (class in pyrosetta.rosetta.protocols.task_operations) SetIGTypeOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) SetInterchangeabilityGroup_String (class in pyrosetta.rosetta.core.chemical) SetIO_String (class in pyrosetta.rosetta.core.chemical) setIsAromatic() (pyrosetta.rosetta.RDKit.Atom method) (pyrosetta.rosetta.RDKit.Bond method) setIsConjugated() (pyrosetta.rosetta.RDKit.Bond method) setIsotope() (pyrosetta.rosetta.RDKit.Atom method) setK() (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) setLaplacianOffset() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setMaxRotPerTrans() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) SetMembraneCenterMover (class in pyrosetta.rosetta.protocols.membrane) SetMembraneCenterMoverCreator (class in pyrosetta.rosetta.protocols.membrane) SetMembraneNormalMover (class in pyrosetta.rosetta.protocols.membrane) SetMembraneNormalMoverCreator (class in pyrosetta.rosetta.protocols.membrane) SetMembranePositionMover (class in pyrosetta.rosetta.protocols.membrane) SetMembranePositionMoverCreator (class in pyrosetta.rosetta.protocols.membrane) setMinBackbone() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setMinDist() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) SetMMAtomType (class in pyrosetta.rosetta.core.chemical) setMultiNative() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setName() (pyrosetta.rosetta.utility.tag.Tag method) setNames() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) setNative() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) SetNbrAtom (class in pyrosetta.rosetta.core.chemical) SetNbrRadius (class in pyrosetta.rosetta.core.chemical) setNCyc() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setNeighbors() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) SetNetFormalCharge (class in pyrosetta.rosetta.core.chemical) setNoImplicit() (pyrosetta.rosetta.RDKit.Atom method) setNRsteps() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setNumExplicitHs() (pyrosetta.rosetta.RDKit.Atom method) setNumRadicalElectrons() (pyrosetta.rosetta.RDKit.Atom method) setOptions() (pyrosetta.rosetta.utility.tag.Tag method) SetOrientAtom (class in pyrosetta.rosetta.core.chemical) setOrigin() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) setOutputSilent() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setOverwrite() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setOwningMol() (pyrosetta.rosetta.RDKit.Bond method) setPassThrough() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setPdbCodes() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) setPODVal() (pyrosetta.rosetta.RDKit.Dict method) setPointRadius() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setPointSearchResultsFname() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setPointsToSearchFname() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setPointsToSearchPDBFname() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) SetPolymerConnectAtom (class in pyrosetta.rosetta.core.chemical) setPose() (pyrosetta.rosetta.protocols.match.downstream.ScoringSecMatchRPE method) setPoseExtraScore() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure 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.relax.ClassicRelax method) SetPoseSecstructFromStructureDataMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) setProp() (pyrosetta.rosetta.RDKit.Atom method) (pyrosetta.rosetta.RDKit.Bond method) (pyrosetta.rosetta.RDKit.Conformer method) (pyrosetta.rosetta.RDKit.RDProps method) (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) setRefineEnd() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) SetRefinementOptionsMover (class in pyrosetta.rosetta.protocols.cryst) SetRefinementOptionsMoverCreator (class in pyrosetta.rosetta.protocols.cryst) setRefineStart() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) SetResidueAliasMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) SetResidueAliasMoverCreator (class in pyrosetta.rosetta.protocols.denovo_design.movers) setResidueRange() (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) setResLimits() (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) SetReturningPackRotamersMover (class in pyrosetta.rosetta.protocols.minimization_packing) SetRotamerCouplings (class in pyrosetta.rosetta.core.pack.task.operation) SetRotamerCouplingsCreator (class in pyrosetta.rosetta.core.pack.task.operation) SetRotamerLinks (class in pyrosetta.rosetta.core.pack.task.operation) SetRotamerLinksCreator (class in pyrosetta.rosetta.core.pack.task.operation) setRotateMiddleCA() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setRotateOnSeqCenter() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setRotateSeqCenter() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) sets() (pyrosetta.rosetta.utility.graph.DisjointSets method) setScoreNatives() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setScoreWindowContext() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) setSCscaling() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) SetSDFType() (pyrosetta.rosetta.core.chemical.Bond method) setSearchEnd() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setSearchStart() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setSecStruct() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) SetSecStructEnergies (class in pyrosetta.rosetta.protocols.fldsgn.potentials) SetSecStructEnergiesCreator (class in pyrosetta.rosetta.protocols.fldsgn.potentials) setSeed() (pyrosetta.rosetta.numeric.random.mt19937_RG method) (pyrosetta.rosetta.numeric.random.standard_RG method) (pyrosetta.rosetta.numeric.random.uniform_RG method) setStartModel() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setStereo() (pyrosetta.rosetta.RDKit.Bond method) setStereoAtoms() (pyrosetta.rosetta.RDKit.Bond method) setSymminfo() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) setTag() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) SetTemperatureFactor (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) SetTemperatureFactorCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) setting() (pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry method) (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) setTopN() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) SetTorsion (class in pyrosetta.rosetta.protocols.simple_moves) SetTorsionCreator (class in pyrosetta.rosetta.protocols.simple_moves) SetToType() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) setTwinLaw() (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) setup() (pyrosetta.rosetta.core.optimization.CartesianMinimizerMap method) (pyrosetta.rosetta.core.optimization.MinimizerMap 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.rna.VDW_Grid method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.DataBuffer method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.PoolData method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator method) (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.SlicedPoseWorkingParameters method) (pyrosetta.rosetta.protocols.symmetry.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SymmetrySlider method) setUp() (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) setup_A_LH_foldtree() (in module pyrosetta.rosetta.protocols.antibody) setup_ab_ag_foldtree() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) setup_after_edge_addition() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) setup_alignment_map() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) setup_atom_id_map() (in module pyrosetta.rosetta.core.pose.copydofs) setup_atom_id_map_match_atom_names() (in module pyrosetta.rosetta.core.pose.copydofs) setup_atom_type_reassignments_from_commandline() (in module pyrosetta.rosetta.core.chemical) setup_atomic_charge_reassignments_from_commandline() (in module pyrosetta.rosetta.core.chemical) setup_attlist_for_derived_classes() (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover static method) setup_base_pair_constraints() (in module pyrosetta.rosetta.core.pose.rna) (pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler method) (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) setup_bbmin_ft_and_csts() (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) setup_bulge_jump_point() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) setup_CDR_cluster() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) setup_CDR_clusters() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) setup_cdr_template() (in module pyrosetta.rosetta.protocols.tcr) setup_cdr_template_from_db() (in module pyrosetta.rosetta.protocols.tcr) setup_cdr_template_from_pdbid() (in module pyrosetta.rosetta.protocols.tcr) setup_centroid_constraints() (in module pyrosetta.rosetta.protocols.hybridization) setup_centroid_scatter() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) setup_centroid_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) setup_chain_break_jump_point() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) setup_chain_break_variants() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) setup_chainbreak_variants() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) setup_chunks_for_output() (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) setup_CM_helical_constraint() (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) setup_coarse_chainbreak_constraints() (in module pyrosetta.rosetta.protocols.rna.denovo) setup_complex_fold_tree() (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) setup_conformer_map() (in module pyrosetta.rosetta.protocols.motifs) setup_conformers() (pyrosetta.rosetta.protocols.ligand_docking.Transform method) setup_connectivity() (pyrosetta.rosetta.core.energy_methods.GoapRsdType method) setup_constraints() (in module pyrosetta.rosetta.protocols.hybridization) (pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential method) setup_convergence_checks_from_cmdline() (in module pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks) setup_copy_DOF_input() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) setup_corresponding_atoms() (in module pyrosetta.rosetta.core.conformation) setup_coupled_mover() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) setup_coupled_mover_for_ligand() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) setup_csts() (pyrosetta.rosetta.core.scoring.constraints.FabConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) setup_cylindrical_coords() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) setup_d2_bounds() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) setup_daemons() (pyrosetta.rosetta.protocols.pack_daemon.DaemonSet method) setup_data_map() (pyrosetta.rosetta.protocols.qsar.qsarOptFunc method) setup_default_evaluators() (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) setup_defaults() (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib method) setup_disconnected() (in module pyrosetta.rosetta.protocols.rbsegment_relax) setup_dock_into_density_mover() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) setup_dof_mask_from_move_map() (in module pyrosetta.rosetta.core.pose) setup_dof_to_torsion_map() (in module pyrosetta.rosetta.core.pose) setup_element2name() (in module pyrosetta.rosetta.core.chemical.element) setup_empty_config() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) setup_favor_native_constraints() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver method) setup_filter_stats() (in module pyrosetta.rosetta.protocols.ncbb) setup_finalPose_copy_labels() (pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop method) setup_finalPose_copy_rotamers() (pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop method) setup_fold() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) setup_fold_tree() (pyrosetta.rosetta.protocols.jumping.MembraneJump method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover 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.rna.movers.ErraserMinimizerMover method) setup_fold_tree_and_jumps_and_variants() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) setup_foldtree() (in module pyrosetta.rosetta.protocols.docking) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) setup_foldtree_around_anchor_invrot() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) setup_foldtree_from_anchors() (in module pyrosetta.rosetta.protocols.membrane) setup_foldtree_pose_com() (in module pyrosetta.rosetta.protocols.membrane) setup_for_density_scoring() (in module pyrosetta.rosetta.core.import_pose) setup_for_derivatives() (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.DunbrackConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint 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.SapConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint 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.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy 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.Constraints method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy 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.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.DockingScoreFunction 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.facts.FACTSPotential 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.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint 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.ScoreFunction method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy 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.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction 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.pockets.PocketConstraint 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) setup_for_derivatives_for_residue() (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) setup_for_derivatives_for_residue_pair() (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) setup_for_dna() (in module pyrosetta.rosetta.protocols.relax) setup_for_lr2benmeth_minimization_for_respair() (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) setup_for_mc() (pyrosetta.rosetta.core.pack.annealer.AnnealerObserver method) setup_for_minimizing() (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.DockingScoreFunction 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.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction 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.ScoreFunction method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction 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.flexpack.OtherContextScoreFunction 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) setup_for_minimizing_for_node() (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) setup_for_minimizing_for_residue() (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.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.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.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet 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) setup_for_minimizing_for_residue_pair() (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.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.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.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) setup_for_minimizing_sr2b_enmeths_for_minedge() (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) setup_for_packing() (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.DockingScoreFunction 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.facts.FACTSPotential method) (pyrosetta.rosetta.core.scoring.GenBornPotential 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.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.MultipoleElecPotential 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.ScoreFunction method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction 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) setup_for_packing_with_rotsets() (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.DockingScoreFunction 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.MinScoreScoreFunction 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.ScoreFunction method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction 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.flexpack.OtherContextScoreFunction 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) setup_for_residue_pair_energies() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) setup_for_run() (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) setup_for_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.DunbrackConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint 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.SapConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint 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.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy 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.Constraints method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy 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.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.DockingScoreFunction 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.facts.FACTSPotential method) (pyrosetta.rosetta.core.scoring.GenericBondedPotential 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.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint 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.ProQPotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.SASAPotential method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.SecondaryStructurePotential method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential 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.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction 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.pockets.PocketConstraint 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) (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib method) setup_for_scoring_() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) setup_for_scoring_for_residue() (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) setup_for_scoring_for_residue_energy_methods() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph 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) setup_for_scoring_for_residue_pair() (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) setup_fragment_picker() (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) setup_from_ConnollySurface() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) setup_from_eggshell_pdb_file() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) setup_from_eggshell_triplet_file() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) setup_from_EggshellGrid() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) setup_from_espGrid() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) setup_from_kill_hairpins_file() (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) setup_from_options() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) setup_from_PlaidFingerprint() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) setup_from_PocketGrid() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) setup_from_PocketGrid_and_known_ligand() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) setup_from_PocketGrid_using_bound_ligand() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) setup_from_psipred() (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) setup_from_rotamer_dots() (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) setup_from_xml_file() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) setup_from_xml_string() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) setup_from_xml_tag() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) setup_full_model_info() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) setup_fullatom_constraints() (in module pyrosetta.rosetta.protocols.hybridization) setup_fw_template() (in module pyrosetta.rosetta.protocols.tcr) setup_fw_template_from_db() (in module pyrosetta.rosetta.protocols.tcr) setup_fw_template_from_pdbid() (in module pyrosetta.rosetta.protocols.tcr) setup_glycan_nodes() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) setup_glycan_trees() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (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) setup_GlycanDock_movemap() (in module pyrosetta.rosetta.protocols.glycan_docking) setup_GlycanDock_stage1_rb_seqmover() (in module pyrosetta.rosetta.protocols.glycan_docking) setup_GlycanDock_stage2_rb_randmover() (in module pyrosetta.rosetta.protocols.glycan_docking) setup_GlycanDock_stage2_tor_randmover() (in module pyrosetta.rosetta.protocols.glycan_docking) setup_GlycanDock_taskfactory() (in module pyrosetta.rosetta.protocols.glycan_docking) setup_glycoligand_selector() (in module pyrosetta.rosetta.protocols.glycan_docking) setup_glycosylation_foldtree() (in module pyrosetta.rosetta.protocols.glycopeptide_docking) setup_hash_maps() (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) setup_helical_constraint() (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) setup_icoor_reassignments_from_commandline() (in module pyrosetta.rosetta.core.chemical) setup_info() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) setup_info_for_mg_calculation() (pyrosetta.rosetta.core.scoring.magnesium.MgKnowledgeBasedPotential method) setup_iterations() (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.flexpack.annealer.FlexbbSimAnnealer method) setup_jumps() (in module pyrosetta.rosetta.core.import_pose) setup_key_residues() (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) setup_kic_config() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) setup_kic_with_fragments_config() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) setup_killhairpins() (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) setup_LH_A_foldtree() (in module pyrosetta.rosetta.protocols.antibody) setup_list() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) setup_loophash_kic_config() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) setup_matching_atoms_with_given_names() (in module pyrosetta.rosetta.core.scoring) setup_matching_CA_atoms() (in module pyrosetta.rosetta.core.scoring) setup_matching_heavy_atoms() (in module pyrosetta.rosetta.core.scoring) setup_matching_protein_backbone_heavy_atoms() (in module pyrosetta.rosetta.core.scoring) setup_membrane_topology() (in module pyrosetta.rosetta.protocols.relax) setup_min_map() (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) setup_modeler_options() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) setup_move_and_design_positions() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) setup_move_maps() (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) setup_move_type() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) setup_movemap() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) setup_mover() (pyrosetta.rosetta.protocols.recon_design.MSDMover method) setup_native_pose() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) SETUP_NBLIST (pyrosetta.rosetta.basic.ProfTag attribute) setup_options_for_VDW_bin_checker() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) setup_orientation_template() (in module pyrosetta.rosetta.protocols.tcr) setup_other_poses() (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) setup_pack() (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) setup_pack_operation_movers() (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) setup_packer() (in module pyrosetta.rosetta.protocols.mpi_refinement) setup_packer_and_movemap() (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) setup_packer_task() (in module pyrosetta.rosetta.protocols.antibody) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) setup_packer_task_and_starting_residues() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) setup_parallel_antiparallel_weights() (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) setup_params_for_runmode() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) setup_pert_foldtree() (in module pyrosetta.rosetta.protocols.ncbb) setup_poly_params() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) setup_pose() (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) setup_pose_from_rbsegs() (in module pyrosetta.rosetta.protocols.rbsegment_relax) setup_pose_input_stream() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) setup_pose_rbsegs_keep_loops() (in module pyrosetta.rosetta.protocols.rbsegment_relax) setup_pose_setup_class() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) setup_pose_with_moving_residue_alternative_list() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body) setup_protein_backbone_atom_id_map() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) setup_relax_foldtree() (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) setup_relevant_chains() (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) setup_repeat_pose() (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) setup_repeat_pose_jumping() (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) setup_repeat_symminfo() (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) setup_resnum() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) setup_rigid_body_mover() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) setup_rmsd_atom_names() (in module pyrosetta.rosetta.core.scoring) setup_rna_protein_docking_mover() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) setup_rna_working_parameters() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) setup_rnp_fold_tree() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) setup_rsdtype() (pyrosetta.rosetta.core.energy_methods.GoapRsdType method) setup_sampler() (in module pyrosetta.rosetta.protocols.stepwise.sampler.rna) setup_scorefunctions() (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) setup_sequence_recovery_cache() (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) setup_simple_fold_tree() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) setup_simple_full_length_rna_working_parameters() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) setup_single_loop_double_arm_remodeling_foldtree() (in module pyrosetta.rosetta.protocols.grafting) setup_single_loop_single_arm_remodeling_foldtree() (in module pyrosetta.rosetta.protocols.grafting) setup_spline() (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter method) setup_stage() (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) setup_star_topology() (in module pyrosetta.rosetta.protocols.rbsegment_relax) setup_sugar_ring_closure_constraints() (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) setup_suite_atom_id_map() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) setup_summary() (pyrosetta.rosetta.protocols.frag_picker.QuotaDebug method) setup_svm() (pyrosetta.rosetta.protocols.helix_capper.HelixNCapperMover method) setup_symmetric_conformation() (in module pyrosetta.rosetta.core.conformation.symmetry) setup_temperature() (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.flexpack.annealer.FlexbbSimAnnealer method) setup_template_from_pdbfile() (in module pyrosetta.rosetta.protocols.tcr) setup_templates_and_sampling_options() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) setup_tf() (pyrosetta.rosetta.protocols.pose_metric_calculators.SequenceComparison method) setup_three_prime_phosphate_based_on_next_residue() (in module pyrosetta.rosetta.core.pose.rna) setup_topology() (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) setup_unified_stepwise_modeler() (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) setup_user_coordinate_constraints() (in module pyrosetta.rosetta.protocols.hybridization) setup_user_defined_jumps() (in module pyrosetta.rosetta.core.import_pose) setup_using_user_input_VDW_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker method) setup_using_working_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker method) setup_vall_cheating_fragments() (in module pyrosetta.rosetta.protocols.frags) setup_vall_fragments() (in module pyrosetta.rosetta.protocols.frags) setup_vary_polar_hydrogen_geometry() (in module pyrosetta.rosetta.protocols.simple_moves) setup_vary_rna_bond_geometry() (in module pyrosetta.rosetta.protocols.simple_moves) setup_vdw_cached_rep_screen_info() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) setup_water_bank_for_magnesiums() (in module pyrosetta.rosetta.core.import_pose) setup_working_alignment() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker method) setup_working_parameters_explicit() (in module pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters) setup_working_parameters_for_swa() (in module pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters) setup_xtal_symminfo() (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) setupBesselOrder() (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffraction method) setUpClass() (pyrosetta.tests.bindings.core.test_pose.TestPoseIO class method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor class method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor class method) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor class method) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent class method) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs class method) SetupForDensityScoringMover (class in pyrosetta.rosetta.protocols.electron_density) SetupForDensityScoringMoverCreator (class in pyrosetta.rosetta.protocols.electron_density) SetupForFibrilMover (class in pyrosetta.rosetta.protocols.fibril) SetupForSequenceSymmetryMover (class in pyrosetta.rosetta.protocols.symmetry) SetupForSequenceSymmetryMoverCreator (class in pyrosetta.rosetta.protocols.symmetry) SetupForSymmetryMover (class in pyrosetta.rosetta.protocols.symmetry) SetupForSymmetryMoverCreator (class in pyrosetta.rosetta.protocols.symmetry) SetupHotspotConstraintsLoopsMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) SetupHotspotConstraintsLoopsMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) SetupHotspotConstraintsMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) SetupHotspotConstraintsMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) SetupMetalsMover (class in pyrosetta.rosetta.protocols.simple_moves) SetupMetalsMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) SetupNCSMover (class in pyrosetta.rosetta.protocols.symmetry) SetupNCSMoverCreator (class in pyrosetta.rosetta.protocols.symmetry) SetupPoissonBoltzmannPotential (class in pyrosetta.rosetta.protocols.pb_potential) SetupPoissonBoltzmannPotentialCreator (class in pyrosetta.rosetta.protocols.pb_potential) SetupRamaTables() (pyrosetta.rosetta.protocols.frag_picker.scores.RamaScore method) setupZones() (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) setVal() (pyrosetta.rosetta.RDKit.Dict method) setValue() (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) setVAR() (pyrosetta.rosetta.protocols.sparta.GDB method) SetVirtualShadow (class in pyrosetta.rosetta.core.chemical) setWindow() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) sever_chemical_bond() (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) SewAnythingAddMover (class in pyrosetta.rosetta.protocols.pose_sewing.movers) SewAnythingAddMoverCreator (class in pyrosetta.rosetta.protocols.pose_sewing.movers) SewAtom (class in pyrosetta.rosetta.protocols.legacy_sewing) SewGraph (class in pyrosetta.rosetta.protocols.legacy_sewing) SewResidue (class in pyrosetta.rosetta.protocols.legacy_sewing) SewSegment (class in pyrosetta.rosetta.protocols.legacy_sewing) sf_opts() (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification method) SF_Replica (class in pyrosetta.rosetta.protocols.toolbox) SFHEADER_SCORE_LINE (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine attribute) SFHEADER_SCORE_TYPE_LINE (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine attribute) SFHEADER_SEQUENCE_LINE (pyrosetta.rosetta.core.io.silent.SilentFileHeaderLine attribute) sformat_idxof() (in module pyrosetta.rosetta.numeric.random) sfr() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) sfr_opts() (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputSpecification method) sfxn() (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.recon_design.FitnessFilter method) sfxn_set() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) sfxn_specialized (pyrosetta.rosetta.protocols.relax.DatabaseRelaxScript property) sfxn_wt_ (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBond property) sfxns_supported (pyrosetta.rosetta.protocols.relax.DatabaseRelaxScript property) Sg (pyrosetta.rosetta.core.chemical.element.Elements attribute) sg() (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) SG_CONNECT (pyrosetta.rosetta.core.chemical.VariantType attribute) SG_Dist_Func (class in pyrosetta.rosetta.core.scoring.disulfides) sgetc() (pyrosetta.rosetta.std.filebuf method) (pyrosetta.rosetta.std.streambuf method) (pyrosetta.rosetta.std.stringbuf method) (pyrosetta.rosetta.std.wstreambuf method) (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) sgetn() (pyrosetta.rosetta.std.filebuf method) (pyrosetta.rosetta.std.streambuf method) (pyrosetta.rosetta.std.stringbuf method) (pyrosetta.rosetta.std.wstreambuf method) (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) sgn() (in module pyrosetta.rosetta.core.io.pose_from_sfr) SGSG_Dihedral_Func (class in pyrosetta.rosetta.core.scoring.disulfides) shadow_atoms() (pyrosetta.rosetta.core.chemical.MutableResidueType method) ShakeStructureMover (class in pyrosetta.rosetta.protocols.simple_moves) shallow_clone() (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) SHAPE_1M7 (pyrosetta.rosetta.core.pose.rna.RNA_ReactivityType attribute) ShapeComplementarityCalculator (class in pyrosetta.rosetta.core.scoring.sc) ShapeComplementarityCalculatorException (class in pyrosetta.rosetta.core.scoring.sc) ShapeComplementarityFilter (class in pyrosetta.rosetta.protocols.simple_filters) ShapeComplementarityFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) ShapeGrid (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) ShapeGridCreator (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) ShapeSimilarityCalculator (class in pyrosetta.rosetta.core.scoring.sc) ShapeSimilarityMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) ShapeSimilarityMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.metrics) share_axis_atoms() (in module pyrosetta.rosetta.core.scoring.power_diagram) share_packer_data_from() (pyrosetta.rosetta.protocols.multistate_design.PackingState method) shared_from_this() (pyrosetta.rosetta.basic.datacache.CacheableResRotPairFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringIntegerMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.CacheableUint64MathMatrixFloatMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricData method) (pyrosetta.rosetta.protocols.abinitio.abscript.JumpSampleData method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.environment.AutoCutData method) (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.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer 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.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer 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) SharedSilentData (class in pyrosetta.rosetta.core.io.silent) SharedSilentDataType (class in pyrosetta.rosetta.core.io.silent) sharm_invTransform() (pyrosetta.rosetta.numeric.fourier.SHT method) sharm_transform() (pyrosetta.rosetta.numeric.fourier.SHT method) shear() (pyrosetta.rosetta.protocols.dna.DNABasepair method) ShearFreePeptideMover (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers) ShearMinCCDTrial (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) ShearMinCCDTrialCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) ShearMover (class in pyrosetta.rosetta.protocols.simple_moves) ShearMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) Sheet (class in pyrosetta.rosetta.protocols.fldsgn.topology) SHEET (pyrosetta.rosetta.core.io.pdb.RecordType attribute) sheet (pyrosetta.rosetta.core.scoring.ScoreType attribute) sheet() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet method) sheet_dis_by_terminals() (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) sheet_fraction() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) sheet_torsion() (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) SheetBuilder (class in pyrosetta.rosetta.protocols.jumping) SheetConstraintGenerator (class in pyrosetta.rosetta.protocols.fldsgn) SheetConstraintGeneratorCreator (class in pyrosetta.rosetta.protocols.fldsgn) SheetDB (class in pyrosetta.rosetta.protocols.denovo_design.components) SheetFilter (class in pyrosetta.rosetta.protocols.simple_filters) SheetFoldType (class in pyrosetta.rosetta.protocols.fldsgn.topology) SheetFoldTypeManager (class in pyrosetta.rosetta.protocols.fldsgn.topology) sheethbonds() (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) sheetID (pyrosetta.rosetta.core.io.SHEETInformation property) SHEETInformation (class in pyrosetta.rosetta.core.io) SHEETInformations() (pyrosetta.rosetta.core.io.StructFileRep method) SheetPositions (class in pyrosetta.rosetta.protocols.loop_grower) SheetRemodelConstraintGenerator (class in pyrosetta.rosetta.protocols.fldsgn) SheetRemodelConstraintGeneratorCreator (class in pyrosetta.rosetta.protocols.fldsgn) sheets() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet method) SheetSampler (class in pyrosetta.rosetta.protocols.loop_grower) sheetscore() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) SheetSet (class in pyrosetta.rosetta.protocols.fldsgn.topology) SheetTopologyFilter (class in pyrosetta.rosetta.protocols.fldsgn.filters) SheetTopologyFilterCreator (class in pyrosetta.rosetta.protocols.fldsgn.filters) shell_radius_for_atom() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) shift() (pyrosetta.rosetta.core.conformation.membrane.Span method) (pyrosetta.rosetta.core.scoring.SmoothScoreTermCoeffs method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing method) (pyrosetta.rosetta.protocols.dna.DNABasestep method) (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) shift_ (pyrosetta.rosetta.ObjexxFCL.FArray1_bool_t property) (pyrosetta.rosetta.ObjexxFCL.FArray1_char_t property) (pyrosetta.rosetta.ObjexxFCL.FArray1_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray1_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray1_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray1_ObjexxFCL_FArray1D_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray1_std_string_t property) (pyrosetta.rosetta.ObjexxFCL.FArray1_unsigned_long_t property) (pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t property) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t property) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t property) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepNRChiSample_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_1_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_2_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_3_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_4_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_5_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBIndNRChiSample_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_numeric_xyzVector_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_FArray2D_float__star__t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_ubyte_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_std_string_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_char_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_long_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_double_std_allocator_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2A_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_1_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_2_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_3_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_4_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_5_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_complex_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_vector_unsigned_long_std_allocator_unsigned_long_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_char_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_long_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_double_std_allocator_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_unsigned_int_std_allocator_unsigned_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3A_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray4_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray4_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray4_unsigned_char_t property) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t property) (pyrosetta.rosetta.ObjexxFCL.FArray5_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray5_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray5_int_t property) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t property) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t property) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t property) shift_by() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragSetCollection method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.MinimalFragSet method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.OrderedFragSet method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) SHIFT_DIR (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) shift_jump_numbers_in_dofs() (in module pyrosetta.rosetta.core.conformation.symmetry) shift_jumps() (in module pyrosetta.rosetta.protocols.forge.methods) shift_set() (pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_float_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.FArray3A_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) shift_span() (pyrosetta.rosetta.core.scoring.MembraneTopology method) shift_to() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) shifts() (pyrosetta.rosetta.protocols.frag_picker.CS2ndShift method) SHOBuriedUnsatisfiedPolarsCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) short_affix (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow property) short_desc() (pyrosetta.rosetta.core.pose.PDBInfo method) short_description() (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) short_frag_cycle_ratio() (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) short_name() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) short_name_w_linkage_notation() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) short_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) short_parameter_description() (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) short_parameter_description_from_enum() (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator static method) short_range_interactions_exist() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) short_ss_loop_filter() (in module pyrosetta.rosetta.protocols.evolution.AlignmentCleanerTools) short_version() (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric method) ShortBackrubMover (class in pyrosetta.rosetta.protocols.simple_moves) ShortBackrubMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) shortd() (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.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_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_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) shortDescription() (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) shorten_target_list() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) shorter() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) shorter_or_equal() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) shortest_dis_sidechain() (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) shortest_path() (in module pyrosetta.rosetta.core.chemical) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) shortest_path_bfs() (pyrosetta.rosetta.protocols.loop_grower.DensSkeleton method) ShortestPathInFoldTree (class in pyrosetta.rosetta.core.kinematics) ShortLoopClosure (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) ShortRangeTwoBodyEnergy (class in pyrosetta.rosetta.core.scoring.methods) ShortToRealAngle() (in module pyrosetta.rosetta.protocols.loophash) SHOVE_BB (pyrosetta.rosetta.core.chemical.VariantType attribute) ShoveResidueMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) ShoveResidueMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) Show (class in pyrosetta.rosetta.utility) show() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (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.chemical.carbohydrates.CarbohydrateInfo method) (pyrosetta.rosetta.core.chemical.MutableICoorRecord method) (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.chemical.rings.RingConformerSet method) (pyrosetta.rosetta.core.conformation.Atom method) (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.conformation.membrane.ImplicitLipidInfo method) (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) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) (pyrosetta.rosetta.core.conformation.membrane.Span method) (pyrosetta.rosetta.core.conformation.membrane.SpanningTopology method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) (pyrosetta.rosetta.core.environment.DofPassport method) (pyrosetta.rosetta.core.environment.EXCN_Env_Exception method) (pyrosetta.rosetta.core.environment.EXCN_FTSketchGraph method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.fragment.BBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.DownJumpSRFD method) (pyrosetta.rosetta.core.fragment.FragData method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.fragment.SecstructSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.UpJumpSRFD method) (pyrosetta.rosetta.core.id.EXCN_AtomNotFound method) (pyrosetta.rosetta.core.id.SequenceMapping method) (pyrosetta.rosetta.core.io.nmr.AtomSelection method) (pyrosetta.rosetta.core.io.nmr.ParaIon method) (pyrosetta.rosetta.core.kinematics.EXCN_InvalidFoldTree method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint 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.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResfileReaderException method) (pyrosetta.rosetta.core.pack_basic.RotamerSetsBase method) (pyrosetta.rosetta.core.pose.PDBInfo method) (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) (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy 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.Constraints 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.DOF_Constraint 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.CSA method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.DistanceFunc method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.DipolarCoupling 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.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.etable.EtableOptions method) (pyrosetta.rosetta.core.scoring.etable.etrie.EtableAtom 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.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.hbonds.FadeInterval method) (pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple method) (pyrosetta.rosetta.core.scoring.hbonds.HBond method) (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.Polynomial_1d method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.mm.mmtrie.MMEnergyTableAtom method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSData method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingle method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREData method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingle method) (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingleSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCData method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingle method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingleSet method) (pyrosetta.rosetta.core.scoring.packstat.MultiProbePerSphereAccumulator method) (pyrosetta.rosetta.core.scoring.packstat.MultiProbePoseAccumulator method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping 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.core.simple_metrics.SimpleMetricData method) (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) (pyrosetta.rosetta.numeric.kdtree.HyperRectangle method) (pyrosetta.rosetta.numeric.kdtree.KDPoint method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.numeric.Polynomial_1d method) (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.AlternativePairings 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.PairingStatEntry method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.abinitio.StrandConstraints 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.Ab_TemplateInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo 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.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.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.mc_convergence_checks.EXCN_Heat_Converged method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Pool_Converged method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter 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.IgnoreSubsetConstraintSet 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.ThreadingJob method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.EXCN_RemoveCstsFailed 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.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.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.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary method) (pyrosetta.rosetta.protocols.ddg.ddGMover 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.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.connection.EXCN_ConnectionSetupFailed 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.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_NothingToFold 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.claims.CutBiasClaim method) (pyrosetta.rosetta.protocols.environment.claims.EnvClaim method) (pyrosetta.rosetta.protocols.environment.claims.JumpClaim method) (pyrosetta.rosetta.protocols.environment.claims.TorsionClaim method) (pyrosetta.rosetta.protocols.environment.claims.VirtResClaim method) (pyrosetta.rosetta.protocols.environment.claims.XYZClaim method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Passport method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Security_Exception 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.EnzdesFlexibleRegion 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.evaluation.PCA 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.potentials.sspot.NatbiasHelixPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets 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.EXCN_RemoveCstsFailed 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.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags 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.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.jd2.archive.EXCN_Archive method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.InnerMultiThreadingJob method) (pyrosetta.rosetta.protocols.jd2.JD2Failure method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) (pyrosetta.rosetta.protocols.jd3.standard.StandardInnerLarvalJob method) (pyrosetta.rosetta.protocols.jumping.ChainbreakDistFunc method) (pyrosetta.rosetta.protocols.jumping.SameStrand 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.legacy_sewing.sampling.requirements.LegacyGlobalLengthRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyIntraSegmentRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementSet method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyResidueRetentionRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentDsspRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentLengthRequirement 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.AtomProperties method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore 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.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.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.EXCN_Loop_not_closed method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.Loop 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.RamaCheck1B method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure 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.MakeRotLibJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter 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.AAMatrix method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.EnergiesByTaskCalculator method) (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover 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.MeanField method) (pyrosetta.rosetta.protocols.mean_field.ResHashMap method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.mean_field.RotProb 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.geometry.Embedding method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef 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.EXCN_Converged 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.TrialCounter method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.multistate_design.MultiStateEntity 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.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover 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.noesy_assign.FoldResonance method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters 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.pockets.PocketConstraint 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_metric_calculators.DecomposeAndReweightEnergiesCalculator 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.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) (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.rosetta_scripts.XmlObjects method) (pyrosetta.rosetta.protocols.rotamer_recovery.PerNativeRRReporterHuman method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecovery method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover 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) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.scoring.Interface method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments 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.sic_dock.BuriedPolarScore method) (pyrosetta.rosetta.protocols.sic_dock.CBScore method) (pyrosetta.rosetta.protocols.sic_dock.ConstraintSetScore method) (pyrosetta.rosetta.protocols.sic_dock.EdgeStandScore method) (pyrosetta.rosetta.protocols.sic_dock.HelixScore method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.sic_dock.LinkerScore method) (pyrosetta.rosetta.protocols.sic_dock.RigidScore method) (pyrosetta.rosetta.protocols.sic_dock.scores.MotifHashRigidScore method) (pyrosetta.rosetta.protocols.sic_dock.scores.TrisBpyScore method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed 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.BBMatching 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.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions 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.options.StepWiseMonteCarloOptions 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.ClusterBase method) (pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage 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) (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.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer.CM_SuggestFixResidue method) (pyrosetta.rosetta.protocols.topology_broker.SuggestValueMessage 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) (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) (pyrosetta.rosetta.utility.Show method) show_accessed_options() (pyrosetta.rosetta.utility.options.OptionCollection method) show_additional() (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) show_additional_info() (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) show_adjacent_nt_connections() (in module pyrosetta.rosetta.core.pose) show_all() (pyrosetta.rosetta.utility.options.OptionCollection method) show_all_atom_names() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) show_all_fixes() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) show_all_hier() (pyrosetta.rosetta.utility.options.OptionCollection method) show_all_residue_tasks() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) SHOW_ALL_TRIALS (pyrosetta.rosetta.protocols.viewer.graphics_states_param.TrajectoryState attribute) show_atom_tree() (in module pyrosetta.rosetta.core.conformation) show_availability() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) show_available_silent_struct_types() (pyrosetta.rosetta.core.io.silent.SilentStructFactory method) SHOW_BACKBONE (pyrosetta.rosetta.protocols.viewer.graphics_states_param.BBdisplayState attribute) show_base_pair_params() (in module pyrosetta.rosetta.core.scoring.dna) show_base_step_params() (in module pyrosetta.rosetta.core.scoring.dna) SHOW_BBSPHERES (pyrosetta.rosetta.protocols.viewer.graphics_states_param.BBdisplayState attribute) SHOW_BEST (pyrosetta.rosetta.protocols.viewer.graphics_states_param.TrajectoryState attribute) SHOW_CARTOON (pyrosetta.rosetta.protocols.viewer.graphics_states_param.BBdisplayState attribute) show_classic() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.FragData method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) show_cluster_assignments() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) show_contents() (pyrosetta.rosetta.utility.Inline_File_Provider method) show_counters() (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover 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.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) show_cst_definitions() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) show_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) show_def_nopose() (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedDihedralConstraint method) show_definition() (pyrosetta.rosetta.core.scoring.constraints.BoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.Constraints method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc 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.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) (pyrosetta.rosetta.protocols.jumping.ChainbreakDistFunc method) show_definitions() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) show_dna_geometry() (in module pyrosetta.rosetta.protocols.dna) show_dna_geometry_extra_details() (in module pyrosetta.rosetta.protocols.dna) show_foldtree() (in module pyrosetta.rosetta.core.conformation.symmetry) SHOW_H (pyrosetta.rosetta.protocols.viewer.graphics_states_param.ShowHState attribute) show_H_state (pyrosetta.rosetta.protocols.viewer.GraphicsState property) show_header() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) show_help() (pyrosetta.rosetta.utility.options.OptionCollection method) show_help_hier() (pyrosetta.rosetta.utility.options.OptionCollection method) show_if_nonzero_weight() (pyrosetta.rosetta.core.scoring.EMapVector method) show_inaccessed_user_options() (pyrosetta.rosetta.utility.options.OptionCollection method) show_internals() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) show_line() (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) show_line_headers() (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) SHOW_LOW (pyrosetta.rosetta.protocols.viewer.graphics_states_param.TrajectoryState attribute) SHOW_MC_TRIALS (pyrosetta.rosetta.protocols.viewer.graphics_states_param.TrajectoryState attribute) show_more_pose_scores() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) show_new_base_step_params() (in module pyrosetta.rosetta.core.scoring.dna) SHOW_NO_H (pyrosetta.rosetta.protocols.viewer.graphics_states_param.ShowHState attribute) SHOW_NOBB (pyrosetta.rosetta.protocols.viewer.graphics_states_param.BBdisplayState attribute) show_nonzero() (pyrosetta.rosetta.core.scoring.EMapVector method) SHOW_NOSC (pyrosetta.rosetta.protocols.viewer.graphics_states_param.SCdisplayState attribute) show_numbers() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) show_on_tracer() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters method) show_option_help() (pyrosetta.rosetta.utility.options.OptionCollection method) show_option_help_hier() (pyrosetta.rosetta.utility.options.OptionCollection method) show_params() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) show_pdb_ids() (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter method) show_pretty() (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) show_protocol() (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) show_rdc_values() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) show_residue_connections() (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) show_residue_task() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) show_scorefxn_weight_lines() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) show_scores() (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover 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) show_scoring_methods() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) SHOW_SCSPHERES (pyrosetta.rosetta.protocols.viewer.graphics_states_param.SCdisplayState attribute) show_state() (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) SHOW_STICK (pyrosetta.rosetta.protocols.viewer.graphics_states_param.SCdisplayState attribute) show_submotif_info_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) show_table_text() (pyrosetta.rosetta.utility.options.OptionCollection method) show_table_Wiki() (pyrosetta.rosetta.utility.options.OptionCollection method) show_tensor_matrix() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) show_tensor_stats() (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) show_tensor_stats_nls() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) show_time() (in module pyrosetta.rosetta.basic) show_total_headers() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) show_totals() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) show_unmoved() (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged method) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged method) show_unused_options() (pyrosetta.rosetta.utility.options.OptionCollection method) show_user() (pyrosetta.rosetta.utility.options.OptionCollection method) show_valid() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) show_values() (pyrosetta.rosetta.core.scoring.hbonds.Polynomial_1d method) show_violations() (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.Constraints 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.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.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.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.jumping.ChainbreakDistFunc method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) show_water_hb_network() (in module pyrosetta.rosetta.protocols.hydrate) show_weighted() (pyrosetta.rosetta.core.scoring.EMapVector method) SHOW_WIREFRAME (pyrosetta.rosetta.protocols.viewer.graphics_states_param.SCdisplayState attribute) showClusters() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) ShowConstraintsFilter (class in pyrosetta.rosetta.protocols.constraint_filters) ShowConstraintsFilterCreator (class in pyrosetta.rosetta.protocols.constraint_filters) showGDB() (pyrosetta.rosetta.protocols.sparta.GDB method) ShowHState (class in pyrosetta.rosetta.protocols.viewer.graphics_states_param) shrink() (pyrosetta.rosetta.core.id.AtomID_Map_AtomID method) (pyrosetta.rosetta.core.id.AtomID_Map_bool method) (pyrosetta.rosetta.core.id.AtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_MP_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_Real method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_NamedAtomID method) (pyrosetta.rosetta.protocols.frags.RMSVallData method) (pyrosetta.rosetta.protocols.frags.VallData 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) shrink_cluster() (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) shrink_to_fit() (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.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.ScoreRmsPoints 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.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) (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 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(pyrosetta.rosetta.utility.vector1_utility_vector1_std_set_protocols_match_upstream_hit_std_less_protocols_match_upstream_hit_std_allocator_protocols_match_upstream_hit_std_allocator_std_set_protocols_match_upstream_hit_std_less_protocols_match_upstream_hit_std_allocator_protocols_match_upstream_hit_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_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) SHT (class in pyrosetta.rosetta.numeric.fourier) shuffle() (pyrosetta.rosetta.protocols.cluster.Cluster method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) shuffle_order() (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) ShuffleFileSystemJobDistributor (class in pyrosetta.rosetta.protocols.jd2) shutdown() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) Si (pyrosetta.rosetta.core.chemical.element.Elements attribute) SIALIC_ACID (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) SICFast (class in pyrosetta.rosetta.protocols.sic_dock) SICPatternAtTransform (class in pyrosetta.rosetta.protocols.hotspot_hashing) sid (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult property) side (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBInstruction property) side1 (pyrosetta.rosetta.protocols.analysis.InterfaceRegion attribute) side2 (pyrosetta.rosetta.protocols.analysis.InterfaceRegion attribute) side_one_tag (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info property) side_two_tag (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info property) SIDECHAIN (pyrosetta.rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE attribute) sidechain() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) SIDECHAIN_AMINE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) SIDECHAIN_CONJUGATION (pyrosetta.rosetta.core.chemical.VariantType attribute) sidechain_frlx_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) sidechain_neighbors (pyrosetta.rosetta.core.scoring.ScoreType attribute) sidechain_sidechain() (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) sidechain_sidechain_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.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) SIDECHAIN_THIOL (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) SidechainContactDistCutoff (class in pyrosetta.rosetta.protocols.frag_picker) SideChainCopier (class in pyrosetta.rosetta.protocols.stepwise.modeler.packer) SidechainMCMover (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) SIDECHAINMCMOVER (pyrosetta.rosetta.basic.ProfTag attribute) SidechainMCMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) SidechainMetropolisHastingsMover (class in pyrosetta.rosetta.protocols.canonical_sampling) SidechainMetropolisHastingsMoverCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) SidechainMinMover (class in pyrosetta.rosetta.protocols.docking) SidechainMover (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) SIDECHAINMOVER (pyrosetta.rosetta.basic.ProfTag attribute) SidechainMoverBase (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) SidechainMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) SidechainNeighborCountMetric (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) SidechainNeighborCountMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) SidechainRmsdFilter (class in pyrosetta.rosetta.protocols.simple_filters) SidechainRmsdFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) SidechainStateAssignment (class in pyrosetta.rosetta.core.pack.scmin) SIGMA (pyrosetta.rosetta.core.scoring.nmr.SINGLE_NMR_VALUE_WEIGHTING attribute) sigma() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing method) sigma1() (pyrosetta.rosetta.core.scoring.CSA method) sigma2() (pyrosetta.rosetta.core.scoring.CSA method) sigma3() (pyrosetta.rosetta.core.scoring.CSA method) SIGMA_ATOM (pyrosetta.rosetta.core.chemical.GreekDistance attribute) SigmaOrbitalElectronegativityMulliken (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) SigmaOrbitalElectronegativityPauling (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) SigmaValenceStateElectronAffinity (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) SigmaValenceStateIonizationPotential (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) Sigmoid (class in pyrosetta.rosetta.protocols.calc_taskop_filters) sigmoid() (in module pyrosetta.rosetta.core.scoring.epr_deer) (pyrosetta.rosetta.core.scoring.SmoothScoreTermCoeffs method) sigmoid_deps_dr() (pyrosetta.rosetta.core.scoring.etable.coulomb.Coulomb method) sigmoid_eps() (pyrosetta.rosetta.core.scoring.etable.coulomb.Coulomb method) sigmoid_filter() (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) SIGMOID_WEIGHTED_CEN_LIST (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) SIGMOID_WEIGHTED_D_CEN_LIST (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) SigmoidFilterCreator (class in pyrosetta.rosetta.protocols.calc_taskop_filters) SigmoidFunc (class in pyrosetta.rosetta.core.scoring.func) sign() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.ObjexxFCL) sign1() (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing method) sign2() (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing method) SignalHub_void_core_chemical_RestypeDestructionEvent_t (class in pyrosetta.rosetta.utility.signals) SignalHub_void_core_conformation_signals_ConnectionEvent_t (class in pyrosetta.rosetta.utility.signals) SignalHub_void_core_conformation_signals_GeneralEvent_t (class in pyrosetta.rosetta.utility.signals) SignalHub_void_core_conformation_signals_IdentityEvent_t (class in pyrosetta.rosetta.utility.signals) SignalHub_void_core_conformation_signals_LengthEvent_t (class in pyrosetta.rosetta.utility.signals) SignalHub_void_core_conformation_signals_XYZEvent_t (class in pyrosetta.rosetta.utility.signals) SignalHub_void_core_pose_signals_ConformationEvent_t (class in pyrosetta.rosetta.utility.signals) SignalHub_void_core_pose_signals_DestructionEvent_t (class in pyrosetta.rosetta.utility.signals) SignalHub_void_core_pose_signals_EnergyEvent_t (class in pyrosetta.rosetta.utility.signals) SignalHub_void_core_pose_signals_GeneralEvent_t (class in pyrosetta.rosetta.utility.signals) signature_ (pyrosetta.rosetta.protocols.cluster.calibur.Stru property) signature_string() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) signedAngleTo() (pyrosetta.rosetta.RDGeom.Point3D method) silent() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.MinimizerOptions method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) silent_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) silent_Es() (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) SILENT_FILE (pyrosetta.rosetta.protocols.cluster.calibur.INPUT_FILE_TYPE attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum attribute) silent_file() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.recces.options.RECCES_Options 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) silent_file_data() (pyrosetta.rosetta.core.import_pose.pose_stream.SilentFilePoseInputStream method) (pyrosetta.rosetta.protocols.jd2.LazySilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.SilentFileFullModelInputter method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputter method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) SILENT_FILL_POSE (pyrosetta.rosetta.basic.ProfTag attribute) SILENT_FILL_STRUCT (pyrosetta.rosetta.basic.ProfTag attribute) silent_in() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) silent_out() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) silent_output_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) SILENT_READ_TAG_TEST (pyrosetta.rosetta.basic.ProfTag attribute) SILENT_SET_POSE_COORDS (pyrosetta.rosetta.basic.ProfTag attribute) silent_struct_output_list() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) SilentEnergy (class in pyrosetta.rosetta.core.io.silent) SilentFileData (class in pyrosetta.rosetta.core.io.silent) SilentFileData.const_iterator (class in pyrosetta.rosetta.core.io.silent) SilentFileData.iterator (class in pyrosetta.rosetta.core.io.silent) SilentFileEnergyAccessor (class in pyrosetta.io.silent_file_map) SilentFileFullModelInputter (class in pyrosetta.rosetta.protocols.jd3.full_model_inputters) SilentFileFullModelInputterCreator (class in pyrosetta.rosetta.protocols.jd3.full_model_inputters) SilentFileHeaderLine (class in pyrosetta.rosetta.core.io.silent) SilentFileJobInputter (class in pyrosetta.rosetta.protocols.jd2) SilentFileJobInputterCreator (class in pyrosetta.rosetta.protocols.jd2) SilentFileJobOutputter (class in pyrosetta.rosetta.protocols.jd2) SilentFileJobOutputterCreator (class in pyrosetta.rosetta.protocols.jd2) SilentFileMap (class in pyrosetta.io.silent_file_map) SilentFileOptions (class in pyrosetta.rosetta.core.io.silent) SilentFilePoseAccessor (class in pyrosetta.io.silent_file_map) SilentFilePoseInputStream (class in pyrosetta.rosetta.core.import_pose.pose_stream) SilentFilePoseInputter (class in pyrosetta.rosetta.protocols.jd3.pose_inputters) SilentFilePoseInputterCreator (class in pyrosetta.rosetta.protocols.jd3.pose_inputters) SilentFilePoseOutputSpecification (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) SilentFilePoseOutputter (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) SilentFilePoseOutputterCreator (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) silentname() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) SilentObserver (class in pyrosetta.rosetta.protocols.viewer) SilentStruct (class in pyrosetta.rosetta.core.io.silent) SilentStructCreator (class in pyrosetta.rosetta.core.io.silent) SilentStructFactory (class in pyrosetta.rosetta.core.io.silent) SilentStructStore (class in pyrosetta.rosetta.protocols.wum) SilentStructureStoreBackend (class in pyrosetta.rosetta.protocols.indexed_structure_store) SilentTrajectoryRecorder (class in pyrosetta.rosetta.protocols.canonical_sampling) SilentTrajectoryRecorderCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) sim_origin() (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) sim_selector() (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) sim_type (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) SimAnnealerBase (class in pyrosetta.rosetta.core.pack.annealer) SIMANNEALING (pyrosetta.rosetta.basic.ProfTag attribute) SimPDB (class in pyrosetta.rosetta.protocols.cluster.calibur) simple_element_naming_func_has_been_set() (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) simple_fold_tree() (in module pyrosetta.rosetta.protocols.antibody) (in module pyrosetta.rosetta.protocols.antibody_legacy) (in module pyrosetta.rosetta.protocols.star) simple_ft() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) simple_mapping_from_file() (in module pyrosetta.rosetta.core.sequence) simple_metric_composite_real_data (pyrosetta.rosetta.core.io.mmtf.ExtraDataEnum attribute) simple_metric_composite_string_data (pyrosetta.rosetta.core.io.mmtf.ExtraDataEnum attribute) SIMPLE_METRIC_DATA (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) simple_metric_data() (pyrosetta.rosetta.core.io.StructFileRep method) simple_metric_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.SimpleMetricLoader static method) simple_metric_per_residue_real_data (pyrosetta.rosetta.core.io.mmtf.ExtraDataEnum attribute) simple_metric_per_residue_real_output (pyrosetta.rosetta.core.io.mmtf.ExtraDataEnum attribute) simple_metric_per_residue_string_data (pyrosetta.rosetta.core.io.mmtf.ExtraDataEnum attribute) simple_metric_per_residue_string_output (pyrosetta.rosetta.core.io.mmtf.ExtraDataEnum attribute) simple_metric_real_data (pyrosetta.rosetta.core.io.mmtf.ExtraDataEnum attribute) simple_metric_string_data (pyrosetta.rosetta.core.io.mmtf.ExtraDataEnum attribute) simple_metric_type() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric method) (pyrosetta.rosetta.protocols.filters.FilterValueMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric method) simple_metric_xml_schema_group_name() (pyrosetta.rosetta.core.simple_metrics.SimpleMetricFactory static method) simple_numeric_deriv_check() (in module pyrosetta.rosetta.core.optimization) simple_one_loop_fold_tree() (in module pyrosetta.rosetta.protocols.antibody) (in module pyrosetta.rosetta.protocols.antibody_legacy) SIMPLE_POSE_SELECTION (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) SIMPLE_RMSD (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) simple_rmsd_cutoff_relax() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) simple_tree() (pyrosetta.rosetta.core.kinematics.FoldTree method) simple_visualize_fold_tree() (in module pyrosetta.rosetta.core.kinematics) simple_visualize_fold_tree_and_movemap() (in module pyrosetta.rosetta.core.kinematics) simple_visualize_fold_tree_and_movemap_bb_chi() (in module pyrosetta.rosetta.core.kinematics) SimpleCycpepPredictApplication (class in pyrosetta.rosetta.protocols.cyclic_peptide_predict) SimpleDerivCheckResult (class in pyrosetta.rosetta.core.optimization) SimpleEdge (class in pyrosetta.rosetta.core.pack.interaction_graph) SimpleExpressionCreator (class in pyrosetta.rosetta.numeric.expression_parser) SimpleGlycosylateMover (class in pyrosetta.rosetta.protocols.carbohydrates) SimpleGlycosylateMoverCreator (class in pyrosetta.rosetta.protocols.carbohydrates) SimpleHbondsToAtomFilter (class in pyrosetta.rosetta.protocols.simple_filters) SimpleHbondsToAtomFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) SimpleInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) SimpleInterpolator (class in pyrosetta.rosetta.numeric.interpolation.spline) SIMPLEINTGRAPH (pyrosetta.rosetta.basic.ProfTag attribute) SimpleMetric (class in pyrosetta.rosetta.core.simple_metrics) (pyrosetta.rosetta.basic.citation_manager.CitedModuleType attribute) SimpleMetricCreator (class in pyrosetta.rosetta.core.simple_metrics) SimpleMetricData (class in pyrosetta.rosetta.core.simple_metrics) SimpleMetricFactory (class in pyrosetta.rosetta.core.simple_metrics) SimpleMetricFeatures (class in pyrosetta.rosetta.protocols.features) SimpleMetricFeaturesCreator (class in pyrosetta.rosetta.protocols.features) SimpleMetricFilter (class in pyrosetta.rosetta.protocols.simple_filters) SimpleMetricFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) SimpleMetricLoader (class in pyrosetta.rosetta.protocols.parser) SimpleMetricLoaderCreator (class in pyrosetta.rosetta.protocols.parser) SimpleMetricSelector (class in pyrosetta.rosetta.core.select.residue_selector) SimpleMetricSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) SimpleMetricStruct (class in pyrosetta.rosetta.core.simple_metrics) SimpleNode (class in pyrosetta.rosetta.core.pack.interaction_graph) SimpleNodeManager (class in pyrosetta.rosetta.protocols.jd3.dag_node_managers) SimplePDB (class in pyrosetta.rosetta.core.scoring.packstat) SimplePDB_Atom (class in pyrosetta.rosetta.core.scoring.packstat) SimplePoseSelection (class in pyrosetta.rosetta.protocols.stepwise.legacy.screener) SimpleRange1 (class in pyrosetta.rosetta.utility) SimpleRMSD_Screener (class in pyrosetta.rosetta.protocols.stepwise.legacy.screener) SimpleScoringScheme (class in pyrosetta.rosetta.core.sequence) SimpleSequenceCreator (class in pyrosetta.rosetta.core.sequence) SimpleSequenceData (class in pyrosetta.rosetta.core.io.silent) simplesequencedata (pyrosetta.rosetta.core.io.silent.SharedSilentDataType attribute) SimpleThreadingMover (class in pyrosetta.rosetta.protocols.simple_moves) SimpleThreadingMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) SimpleToken (class in pyrosetta.rosetta.numeric.expression_parser) simplifyWhiteSpace() (in module pyrosetta.rosetta.protocols.sparta) simulate_mpi() (pyrosetta.rosetta.utility.SimulateMPI static method) simulate_mpi_message_type (class in pyrosetta.rosetta.utility) Simulated4PDEERTrace (class in pyrosetta.rosetta.core.scoring.epr_deer) Simulated4PDEERTraceFactory (class in pyrosetta.rosetta.core.scoring.epr_deer) SimulatedTempering (class in pyrosetta.rosetta.protocols.canonical_sampling) (class in pyrosetta.rosetta.protocols.moves) SimulatedTemperingCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) SimulateMPI (class in pyrosetta.rosetta.utility) SimulateMPIData (class in pyrosetta.rosetta.utility) SimulateMPIMessage (class in pyrosetta.rosetta.utility) simultaneous_cycles() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) sin_cos_range() (in module pyrosetta.rosetta.numeric) sin_cos_tolerance() (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) sine (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder property) SINFXN() (in module pyrosetta.rosetta.numeric.crick_equations) Single (pyrosetta.rosetta.protocols.canonical_sampling.TorsionSpecStyle attribute) single (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequencesMode attribute) single_beta_sample() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) SINGLE_GLYCAN (pyrosetta.rosetta.protocols.viewer.graphics_states_param.ColorMode attribute) single_grow() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) single_ligand_motif_from_stream() (in module pyrosetta.rosetta.protocols.motifs) single_motif_from_filename() (in module pyrosetta.rosetta.protocols.motifs) single_motif_from_stream() (in module pyrosetta.rosetta.protocols.motifs) SINGLE_NMR_VALUE_WEIGHTING (class in pyrosetta.rosetta.core.scoring.nmr) single_residue_from_stream() (in module pyrosetta.rosetta.protocols.motifs) single_rotamer_rotset_original_rotmer_index() (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) single_state_design() (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) single_state_entity_data() (pyrosetta.rosetta.protocols.multistate_design.MultiStateEntity method) single_substitution() (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) single_user_input_chunk() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) single_water_atom_fractions() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) single_water_water_bridge2_fraction_1way() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) single_water_water_fraction_1way() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) SingleBasicRotamerLibrary (class in pyrosetta.rosetta.core.pack.rotamers) SingleBasicRotamerLibraryCreator (class in pyrosetta.rosetta.core.pack.rotamers) SingleBond (pyrosetta.rosetta.core.chemical.BondName attribute) SingleBondOrder (pyrosetta.rosetta.core.chemical.BondOrder attribute) SingleConstraint (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) SingleDownstreamResidueWriter (class in pyrosetta.rosetta.protocols.match.output) SingleFileBuffer (class in pyrosetta.rosetta.protocols.jd2) SingleGrid (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) SingleLigandRotamerLibrary (class in pyrosetta.rosetta.core.pack.rotamers) SingleLigandRotamerLibraryCreator (class in pyrosetta.rosetta.core.pack.rotamers) SingleLinkClusterer (class in pyrosetta.rosetta.numeric) SingleMotif (class in pyrosetta.rosetta.protocols.motifs) SingleNCAARotamerLibraryCreator (class in pyrosetta.rosetta.core.pack.rotamers) SingleResidueCenrotLibrary (class in pyrosetta.rosetta.core.pack.dunbrack.cenrot) SingleResidueCenrotLibraryCreator (class in pyrosetta.rosetta.core.pack.dunbrack.cenrot) SingleResidueDunbrackLibrary (class in pyrosetta.rosetta.core.pack.dunbrack) SingleResidueDunbrackLibraryCreator (class in pyrosetta.rosetta.core.pack.dunbrack) SingleResidueFragData (class in pyrosetta.rosetta.core.fragment) SingleResidueInvrotTarget (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) SingleResidueMultifunc (class in pyrosetta.rosetta.core.optimization) SingleResidueRotamerLibrary (class in pyrosetta.rosetta.core.pack.rotamers) SingleResidueRotamerLibraryCreator (class in pyrosetta.rosetta.core.pack.rotamers) SingleResidueRotamerLibraryFactory (class in pyrosetta.rosetta.core.pack.rotamers) SingleResidueTorsionFragmentLibrary (class in pyrosetta.rosetta.protocols.frags) SingleState (class in pyrosetta.rosetta.protocols.multistate_design) SingleStateEntityData (class in pyrosetta.rosetta.protocols.multistate_design) SingleStateFitnessFunction (class in pyrosetta.rosetta.protocols.multistate_design) SingleStructureData (class in pyrosetta.rosetta.protocols.optimize_weights) Singleton (pyrosetta.rosetta.basic.citation_manager.CitedModuleType attribute) SingletonBase_basic_citation_manager_CitationManager_t (class in pyrosetta.rosetta.utility) SingletonBase_basic_datacache_WriteableCacheableDataFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_basic_mpi_MessageListenerFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_basic_resource_manager_ResourceLoaderFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_basic_resource_manager_ResourceLocatorFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_basic_resource_manager_ResourceManagerFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_basic_sampling_orientations_QuaternionGridManager_t (class in pyrosetta.rosetta.utility) SingletonBase_basic_tensorflow_manager_RosettaTensorflowManager_t (class in pyrosetta.rosetta.utility) SingletonBase_basic_thread_manager_RosettaThreadManager_t (class in pyrosetta.rosetta.utility) SingletonBase_basic_thread_manager_RosettaThreadManagerInitializationTracker_t (class in pyrosetta.rosetta.utility) SingletonBase_core_chemical_AtomPropertiesManager_t (class in pyrosetta.rosetta.utility) SingletonBase_core_chemical_carbohydrates_CarbohydrateInfoManager_t (class in pyrosetta.rosetta.utility) SingletonBase_core_chemical_ChemicalManager_t (class in pyrosetta.rosetta.utility) SingletonBase_core_chemical_orbitals_OrbitalTypeMapper_t (class in pyrosetta.rosetta.utility) SingletonBase_core_chemical_PatchOperationFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_core_chemical_rings_RingConformerManager_t (class in pyrosetta.rosetta.utility) SingletonBase_core_chemical_rotamers_RotamerLibrarySpecificationFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_core_energy_methods_GridInfo_t (class in pyrosetta.rosetta.utility) SingletonBase_core_energy_methods_WaterWeightGridSet_t (class in pyrosetta.rosetta.utility) SingletonBase_core_enzymes_EnzymeManager_t (class in pyrosetta.rosetta.utility) SingletonBase_core_fragment_picking_old_FragmentLibraryManager_t (class in pyrosetta.rosetta.utility) SingletonBase_core_import_pose_libraries_RNA_LibraryManager_t (class in pyrosetta.rosetta.utility) SingletonBase_core_io_nmr_ParamagneticDatabaseHandler_t (class in pyrosetta.rosetta.utility) SingletonBase_core_io_nmr_SpinlabelDatabaseHandler_t (class in pyrosetta.rosetta.utility) SingletonBase_core_io_NomenclatureManager_t (class in pyrosetta.rosetta.utility) SingletonBase_core_io_pdb_RecordCollection_t (class in pyrosetta.rosetta.utility) SingletonBase_core_io_silent_SilentStructFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_core_pack_dunbrack_cenrot_CenrotLibrary_t (class in pyrosetta.rosetta.utility) SingletonBase_core_pack_dunbrack_RotamerLibrary_t (class in pyrosetta.rosetta.utility) SingletonBase_core_pack_guidance_scoreterms_sap_SapDatabase_t (class in pyrosetta.rosetta.utility) SingletonBase_core_pack_interaction_graph_RotamerDotsRadiusData_t (class in pyrosetta.rosetta.utility) SingletonBase_core_pack_interaction_graph_SurfacePotential_t (class in pyrosetta.rosetta.utility) SingletonBase_core_pack_palette_PackerPaletteFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_core_pack_rotamers_SingleResidueRotamerLibraryFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_core_pack_task_operation_ResFilterFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_core_pack_task_operation_ResLvlTaskOperationFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_core_pack_task_operation_TaskOperationFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_core_scoring_bin_transitions_BinTransitionCalculatorManager_t (class in pyrosetta.rosetta.utility) SingletonBase_core_scoring_constraints_ConstraintFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_core_scoring_constraints_ConstraintIO_t (class in pyrosetta.rosetta.utility) SingletonBase_core_scoring_lkball_LKBallDatabase_t (class in pyrosetta.rosetta.utility) SingletonBase_core_scoring_motif_MotifHashManager_t (class in pyrosetta.rosetta.utility) SingletonBase_core_scoring_nmr_NMRDataFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_core_scoring_saxs_SinXOverX_t (class in pyrosetta.rosetta.utility) SingletonBase_core_scoring_ScoreFunctionFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_core_scoring_ScoringManager_t (class in pyrosetta.rosetta.utility) SingletonBase_core_select_jump_selector_JumpSelectorFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_core_select_residue_selector_ResidueSelectorFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_core_sequence_SequenceFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_core_simple_metrics_SimpleMetricFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_numeric_model_quality_RmsData_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_antibody_grafting_RegExManager_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_antibody_grafting_SCS_Helper_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_chemistries_ChemistryFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_constraint_generator_ConstraintGeneratorFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_constraint_generator_ConstraintsManager_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_constraint_generator_HydrogenBondInfo_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_denovo_design_architects_DeNovoArchitectFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_denovo_design_components_Picker_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_denovo_design_components_StructureDataFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_denovo_design_task_operations_ConsensusLoopDatabase_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_docking_DockingHighResFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_drug_design_bcl_BCLReferenceSDFilesManager_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_drug_design_bcl_BCLSampleConfsManager_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_evaluation_EvaluatorFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_features_FeaturesReporterFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_filters_FilterFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_genetic_algorithm_EntityElementFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_indexed_structure_store_FragmentStoreManager_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_indexed_structure_store_StructureStoreManager_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_jd2_JobInputterFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_jd2_JobOutputterFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_jd3_chunk_library_inputters_ChunkLibraryInputterFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_jd3_full_model_inputters_FullModelInputterFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_jd3_pose_inputters_PoseInputterFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_jd3_pose_outputters_PoseOutputterFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_jumping_StandardDisulfPairingLibrary_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_jumping_StandardPairingLibrary_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_legacy_sewing_sampling_requirements_LegacyRequirementFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_ligand_docking_DistributionMap_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_ligand_docking_rdf_RDFFunctionFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_loops_loop_mover_refine_LoopRefineInnerCycleFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_loops_LoopMoverFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_loops_loops_definers_LoopsDefinerFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_matdes_SymDofMoverSampler_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_moves_MoverFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_multistage_rosetta_scripts_cluster_ClusterMetricFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_noesy_assign_CovalentCompliance_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_noesy_assign_MethylNameLibrary_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_parser_DataLoaderFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_qsar_scoring_grid_GridFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_qsar_scoring_grid_GridManager_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_relax_RelaxScriptManager_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_rosetta_scripts_PosePropertyReporterFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_rosetta_scripts_PoseSelectorFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_rosetta_scripts_RosettaScriptsSchemaValidator_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_rotamer_recovery_RotamerRecoveryFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_scoring_InterchainPotential_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_scoring_methods_pcs2_PcsDataCenterManagerSingleton_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_scoring_methods_pcs2_PcsEnergyParameterManager_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_scoring_methods_pcs2_PcsGridSearchParameterManager_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_scoring_methods_pcs2_PcsInputCenterManager_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_scoring_methods_pcs_PCS_data_input_manager_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_scoring_methods_pcs_PCS_Energy_parameters_manager_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_scoring_methods_pcsTs1_PCS_Energy_parameters_manager_Ts1_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_scoring_methods_pcsTs2_PCS_Energy_parameters_manager_Ts2_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_scoring_methods_pcsTs3_PCS_Energy_parameters_manager_Ts3_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_scoring_methods_pcsTs4_PCS_Energy_parameters_manager_Ts4_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_sewing_requirements_AssemblyRequirementFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_sewing_scoring_AssemblyScorerFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_protocols_topology_broker_TopologyClaimerFactory_t (class in pyrosetta.rosetta.utility) SingletonBase_utility_Inline_File_Provider_t (class in pyrosetta.rosetta.utility) SingletonBase_utility_io_GeneralFileManager_t (class in pyrosetta.rosetta.utility) SingletonBase_utility_io_GeneralFileManagerVector_t (class in pyrosetta.rosetta.utility) SingletonBase_utility_sql_database_DatabaseSessionManager_t (class in pyrosetta.rosetta.utility) singleval() (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) SingleValuePoseEvaluator_double_t (class in pyrosetta.rosetta.protocols.evaluation) SingleValuePoseEvaluator_long_t (class in pyrosetta.rosetta.protocols.evaluation) SingleValuePoseEvaluator_Size (class in pyrosetta.rosetta.protocols.evaluation) SingleValuePoseEvaluator_SSize (class in pyrosetta.rosetta.protocols.evaluation) SingleValuePoseEvaluator_unsigned_long_t (class in pyrosetta.rosetta.protocols.evaluation) SingResCnlCrea (class in pyrosetta.rosetta.protocols.constel) SinXOverX (class in pyrosetta.rosetta.core.scoring.saxs) SITE (pyrosetta.rosetta.core.io.pdb.RecordType attribute) site_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) SiteConstraint (class in pyrosetta.rosetta.core.scoring.constraints) SiteConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) SiteConstraintResidues (class in pyrosetta.rosetta.core.scoring.constraints) SiteConstraintResiduesCreator (class in pyrosetta.rosetta.core.scoring.constraints) SiteGrid (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) SiteGridCreator (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) SixDCoordinateBinner (class in pyrosetta.rosetta.numeric.geometry.hashing) SixDOffsetTree (class in pyrosetta.rosetta.numeric.geometry.hashing) SixDoFGridDockMover (class in pyrosetta.rosetta.protocols.simple_moves) SixDoFGridDockMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) SixDTransRotPotential (class in pyrosetta.rosetta.core.scoring.loop_graph.evaluator) SixDTransRotPotentialEvaluator (class in pyrosetta.rosetta.core.scoring.loop_graph.evaluator) size() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.ConstDataMap 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.basic.datacache.DataMap method) (pyrosetta.rosetta.core.chemical.rings.RingConformerSet method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.PseudoBondCollection method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragData 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.core.fragment.picking_old.concepts.Book_core_fragment_picking_old_vall_VallResidues_t method) (pyrosetta.rosetta.core.fragment.picking_old.concepts.Book_VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.concepts.Library_core_fragment_picking_old_vall_VallSections_t method) (pyrosetta.rosetta.core.fragment.picking_old.concepts.Library_VallSections method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection 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.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) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SecStruct method) (pyrosetta.rosetta.core.pose.rna.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.core.pose.rna.VDW_Grid method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraints method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraint method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.PairFuncMap method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTrace method) (pyrosetta.rosetta.core.scoring.etable.etrie.GenericResidueConnectionData method) (pyrosetta.rosetta.core.scoring.facts.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.facts.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.Hairpins method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.loop_graph.LoopCycle method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.motif.Xfrag method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.core.scoring.saxs.DistanceHistogram method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.SequenceAlignment method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) (pyrosetta.rosetta.numeric.ClusteringTreeNode method) (pyrosetta.rosetta.numeric.DiscreteIntervalEncodingTree_unsigned_long_t method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) (pyrosetta.rosetta.numeric.kdtree.KDPoint method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.numeric.kdtree.KDTree method) (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) (pyrosetta.rosetta.numeric.MathNTensor_bool_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_1_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_2_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_4_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_5_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_6_t method) (pyrosetta.rosetta.numeric.MathVector_double_t method) 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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.FArray4_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_unsigned_char_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.FArray5_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_int_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.FArray_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArraySection_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArraySection_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArraySection_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArraySection_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.protocols.abinitio.PairingStatEntry method) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds method) (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HPool_RMSD method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.Pool_Evaluator method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.Pool_RMSD method) (pyrosetta.rosetta.protocols.checkpoint.FileBuffer method) (pyrosetta.rosetta.protocols.cluster.Cluster method) (pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator method) (pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet method) (pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluator 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.SegmentPairSet 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.dna.DnaChains method) (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.evaluation.AlignEvaluator method) (pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator method) (pyrosetta.rosetta.protocols.evaluation.PoseEvaluator method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_long_t method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_Size method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_SSize method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_unsigned_long_t method) (pyrosetta.rosetta.protocols.evaluation.TimeEvaluator method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelicalFragment method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTripletSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator 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_Config method) (pyrosetta.rosetta.protocols.frag_picker.scores.AdaptiveScoreHistogram method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.frags.RMSVallData method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.JumpSample method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.PairingLibrary method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.SpecificGeometryLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) (pyrosetta.rosetta.protocols.loophash.BackboneDB method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.Loops 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.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.NoFailDataMap method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList 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.pack_daemon.IterativeVectorExpression method) (pyrosetta.rosetta.protocols.pack_daemon.TopEntitySet method) (pyrosetta.rosetta.protocols.pack_daemon.VariableVectorExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VectorExpression method) (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.PCluster method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.qsar.qsarMap method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.SourcePositions method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck method) (pyrosetta.rosetta.protocols.simple_filters.BatchEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.BatchNrEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.ExternalEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.JumpEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.LoopRmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.RDC_Evaluator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SelectGdtEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SelectMaxsubEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SelectRDC_Evaluator method) (pyrosetta.rosetta.protocols.simple_filters.SelectRmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.StructuralSimilarityEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricRmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.TruncatedScoreEvaluator method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluator method) (pyrosetta.rosetta.protocols.splice.BBMatching method) (pyrosetta.rosetta.protocols.splice.ResidueBBDofs method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeSet 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.rna.RNA_ChiStepWiseSampler 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.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.toolbox.ClusterBase method) (pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper method) (pyrosetta.rosetta.protocols.wum.SilentStructStore method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue_Swapped method) (pyrosetta.rosetta.std.array_core_kinematics_inverse_AlignmentAtom_3_t 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) (pyrosetta.rosetta.std.multimap_double_std_pair_unsigned_long_std_pair_std_shared_ptr_protocols_hotspot_hashing_HotspotStubSet_std_shared_ptr_protocols_hotspot_hashing_HotspotStub_t method) (pyrosetta.rosetta.std.multimap_double_std_shared_ptr_protocols_hotspot_hashing_HotspotStub_t method) (pyrosetta.rosetta.std.priority_queue_protocols_motif_grafting_movers_MotifMatch_std_vector_protocols_motif_grafting_movers_MotifMatch_std_less_protocols_motif_grafting_movers_MotifMatch_t method) (pyrosetta.rosetta.std.set_core_chemical_gasteiger_GasteigerAtomTypeData_AtomicOrbitalTypes_t method) (pyrosetta.rosetta.std.set_core_id_DOF_ID_t method) (pyrosetta.rosetta.std.set_core_id_PartialAtomID_t method) (pyrosetta.rosetta.std.set_double_t method) (pyrosetta.rosetta.std.set_int_t method) (pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t method) (pyrosetta.rosetta.std.set_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.set_std_set_unsigned_long_t method) (pyrosetta.rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_t method) (pyrosetta.rosetta.std.set_std_string_t method) (pyrosetta.rosetta.std.set_unsigned_long_t 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.utility.deep_copy_vector1_std_shared_ptr_core_chemical_Orbital_t method) (pyrosetta.rosetta.utility.fixedsizearray0_double_3_t method) (pyrosetta.rosetta.utility.fixedsizearray0_double_5_t method) (pyrosetta.rosetta.utility.fixedsizearray0_utility_fixedsizearray0_double_3_3_t method) (pyrosetta.rosetta.utility.fixedsizearray0_utility_fixedsizearray0_double_5_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_bool_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_bool_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_bool_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_bool_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_bool_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_bool_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepNRChiSample_float_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepNRChiSample_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepNRChiSample_float_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepNRChiSample_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepNRChiSample_float_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepScoreInterpData_1_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepScoreInterpData_2_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepScoreInterpData_3_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepScoreInterpData_4_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepScoreInterpData_5_64_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_64_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_7_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_float_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_float_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_float_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_int_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_CatmullRomSplineBoundaryType_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_CatmullRomSplineBoundaryType_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_spline_BorderFlag_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_spline_BorderFlag_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_spline_BorderFlag_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_spline_BorderFlag_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_spline_BorderFlag_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_spline_BorderFlag_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathNTensor_double_1_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathNTensor_double_2_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathNTensor_double_3_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathNTensor_double_4_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathNTensor_double_5_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathNTensor_double_6_64_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathVector_double_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathVector_double_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathVector_double_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathVector_double_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_ObjexxFCL_FArray1D_double_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_ObjexxFCL_FArray1D_double_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_ObjexxFCL_FArray1D_double_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_ObjexxFCL_FArray1D_double_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_ObjexxFCL_FArray1D_double_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_protocols_match_ProbeRadius_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_std_pair_double_double_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_std_pair_double_double_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_std_pair_double_double_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_std_pair_double_double_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_std_pair_double_double_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_std_pair_double_double_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_char_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_char_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_7_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_short_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_16_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_2_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_32_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_4_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_5_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_64_64_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_8_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_vector1_unsigned_long_std_allocator_unsigned_long_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_vector1_unsigned_long_std_allocator_unsigned_long_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_vector1_unsigned_long_std_allocator_unsigned_long_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_vector1_unsigned_long_std_allocator_unsigned_long_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_vector1_unsigned_long_std_allocator_unsigned_long_5_t method) (pyrosetta.rosetta.utility.graph.Array0_double_t method) (pyrosetta.rosetta.utility.graph.ArrayPoolElement_double_t method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) (pyrosetta.rosetta.utility.heap method) (pyrosetta.rosetta.utility.keys.KeyLookup_utility_options_OptionKey_t static 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) 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(pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_float_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.FArray3_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3A_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.FArray4_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_unsigned_char_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.FArray5_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_int_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.FArray_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) SIZED (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) sized() (in module pyrosetta.rosetta.ObjexxFCL) SIZED_ANY (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) SIZED_COMB (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) SizeInSegmentsRequirement (class in pyrosetta.rosetta.protocols.sewing.requirements) SizeInSegmentsRequirementCreator (class in pyrosetta.rosetta.protocols.sewing.requirements) sizes_msg() (pyrosetta.rosetta.utility.SimulateMPIMessage method) SizeValuedParameter (class in pyrosetta.rosetta.core.conformation.parametric) sizevector_parameter() (pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) sizevector_parameter_cop() (pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) SizeVectorValuedParameter (class in pyrosetta.rosetta.core.conformation.parametric) skeleton_filter() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) Skip (class in pyrosetta.rosetta.ObjexxFCL.format) skip() (in module pyrosetta.rosetta.ObjexxFCL.format) (in module pyrosetta.rosetta.utility.io) skip_ala_scan() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) skip_alignment() (pyrosetta.rosetta.protocols.splice.Splice method) skip_atom() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa static method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod static method) skip_best_check() (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) skip_bulge_frequency() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) skip_chi_min() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) skip_citation_info_in_schema() (pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSetCreator method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerCreator method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSetCreator method) (pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShellCreator method) (pyrosetta.rosetta.core.pack.task.operation.DesignRestrictionsCreator method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeCreator method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealerCreator method) (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealerCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentCreator method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandlineCreator method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandlineCreator method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollectionCreator method) (pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetryCreator method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfidesCreator method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResiduesCreator method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubsetCreator method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHGCreator method) (pyrosetta.rosetta.core.pack.task.operation.OptHCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepackingCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitResiduePropertiesCreator method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypesCreator method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEventsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASExceptNativeRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictInteractionGraphThreadsOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepackingCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepackingCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepackingRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToResiduePropertiesCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToSpecifiedBaseResidueTypesCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesignCreator method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosionCreator method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerCouplingsCreator method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerLinksCreator method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.UseMultiCoolAnnealerCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperationCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperationCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperationCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperationCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighborsCreator method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperationCreator method) (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterfaceCreator method) (pyrosetta.rosetta.protocols.dna.WatsonCrickRotamerCouplingsCreator method) (pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamersOperationCreator method) (pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfsCreator method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterfaceOperationCreator method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighterOperationCreator method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehaviorCreator method) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperationCreator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinksCreator method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetworkCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFileCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFileCreator method) (pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperationCreator method) (pyrosetta.rosetta.protocols.pack_interface.ProteinProteinInterfaceUpweighterTaskOperationCreator method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterfaceCreator method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighborsCreator method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsCreator method) (pyrosetta.rosetta.protocols.splice.DesignInterfacesOperationCreator method) (pyrosetta.rosetta.protocols.splice.FindEndpointsOperationCreator method) (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDBCreator method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThreadCreator method) (pyrosetta.rosetta.protocols.task_operations.DesignAroundOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosionCreator method) (pyrosetta.rosetta.protocols.task_operations.JointSequenceOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2OperationCreator method) (pyrosetta.rosetta.protocols.task_operations.LinkResiduesCreator method) (pyrosetta.rosetta.protocols.task_operations.ModifyAnnealerCreator method) (pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDBCreator method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilitiesCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3LoopCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperationCreator method) skip_connect_info() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) skip_coord_constraints() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) skip_deletions() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) skip_last_accept() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) skip_minimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) skip_o2prime_trials() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) skip_preminimize() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) skip_rate (pyrosetta.rosetta.protocols.loops.LoopConfiguration attribute) (pyrosetta.rosetta.protocols.loops.SerializedLoop property) skip_rate() (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.LoopFromFileData method) skip_redundant() (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) skip_redundant_constraints() (in module pyrosetta.rosetta.core.scoring.constraints) skip_redundant_width() (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) skip_relax() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) skip_ring_closure() (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) skip_set_reasonable_fold_tree() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) skip_unknown_mutant() (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) skipHs (pyrosetta.rosetta.core.chemical.rdkit.RestypeToRDMolOptions property) skipTest() (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) SkipViolFunc (class in pyrosetta.rosetta.core.scoring.func) sl_weights() (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) Slab (class in pyrosetta.rosetta.core.conformation.membrane.membrane_geometry) SLAB (pyrosetta.rosetta.core.conformation.membrane.MP_GEOMETRY_TRANSITION attribute) slash_char (pyrosetta.rosetta.protocols.sparta.ANN property) (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) Slice (class in pyrosetta.rosetta.core.scoring.packstat) slice() (in module pyrosetta.rosetta.protocols.stepwise.modeler) (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) slice_1base_indicies() (in module pyrosetta.bindings.utility) slice_out_pose() (in module pyrosetta.rosetta.protocols.stepwise.modeler) slice_res() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) slice_res_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) sliced_pose_best_alignment (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.SlicedPoseWorkingParameters property) sliced_pose_calc_rms_res (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.SlicedPoseWorkingParameters property) sliced_pose_full_to_sub (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.SlicedPoseWorkingParameters property) sliced_pose_is_prepend_map (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.SlicedPoseWorkingParameters property) SlicedPoseWorkingParameters (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) SliceMode (class in pyrosetta.rosetta.core.select.residue_selector.slice_enums) SliceResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) SliceResidueSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) SliceToMiniProteinMover (class in pyrosetta.rosetta.protocols.pose_creation) SliceToMiniProteinMover.Chunk (class in pyrosetta.rosetta.protocols.pose_creation) SliceToMiniProteinMover.SSElement (class in pyrosetta.rosetta.protocols.pose_creation) SliceToMiniProteinMoverCreator (class in pyrosetta.rosetta.protocols.pose_creation) slide() (pyrosetta.rosetta.core.conformation.UltraLightResidue method) (pyrosetta.rosetta.protocols.dna.DNABasestep method) (pyrosetta.rosetta.protocols.symmetry.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SymmetrySlider method) slide_away() (pyrosetta.rosetta.protocols.symmetry.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SymmetrySlider method) slide_axis() (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceParameters method) slide_back_to_origin() (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) slide_cutpoint() (pyrosetta.rosetta.core.kinematics.FoldTree method) slide_into_contact() (pyrosetta.rosetta.protocols.sic_dock.SICFast method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) slide_into_contact_and_score() (in module pyrosetta.rosetta.protocols.sic_dock) slide_into_contact_and_score_DEPRICATED() (in module pyrosetta.rosetta.protocols.sic_dock) slide_into_contact_DEPRICATED() (pyrosetta.rosetta.protocols.sic_dock.SICFast method) slide_jump() (in module pyrosetta.rosetta.protocols.denovo_design) (pyrosetta.rosetta.core.kinematics.FoldTree method) slide_jump_randomly() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) slide_lattice() (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) slide_order_ (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider property) slide_score() (pyrosetta.rosetta.protocols.symmetry.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SymmetrySlider method) SlideCriteriaType (class in pyrosetta.rosetta.core.conformation.symmetry) SlideIntoContact (class in pyrosetta.rosetta.protocols.docking) slideintocontact (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) SlideTogether (class in pyrosetta.rosetta.protocols.ligand_docking) SlideTogetherCreator (class in pyrosetta.rosetta.protocols.ligand_docking) SlideType (class in pyrosetta.rosetta.core.conformation.symmetry) SlidingWindowLoopClosure (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) slim_etable() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) slope (pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion property) (pyrosetta.rosetta.core.sequence.Line property) (pyrosetta.rosetta.numeric.interpolation.spline.LinearFunction property) slope() (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTrace method) (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTraceFactory method) (pyrosetta.rosetta.core.scoring.func.SigmoidFunc method) slurp() (in module pyrosetta.rosetta.utility) Sm (pyrosetta.rosetta.core.chemical.element.Elements attribute) small_docking_moves() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) small_fragments() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) SMALL_OVERLAP (pyrosetta.rosetta.core.scoring.motif.MotifMatchOverlapReq attribute) SmallAtNb (class in pyrosetta.rosetta.core.scoring) SmallBBSampler (class in pyrosetta.rosetta.protocols.simple_moves.bb_sampler) SMALLER (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator attribute) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator.CompareMode attribute) smallest_dscore() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) smallest_native_violation() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) SmallFragWeight (class in pyrosetta.rosetta.protocols.topology_broker.weights) SmallKeyVector_utility_options_AnyOptionKey_utility_options_VariantOption_utility_options_ScalarOption_t (class in pyrosetta.rosetta.utility.keys) SmallKeyVector_utility_options_AnyVectorOptionKey_utility_options_VariantOption_utility_options_VectorOption_t (class in pyrosetta.rosetta.utility.keys) SmallKeyVector_utility_options_BooleanOptionKey_utility_options_BooleanOption_t (class in pyrosetta.rosetta.utility.keys) SmallKeyVector_utility_options_BooleanVectorOptionKey_utility_options_BooleanVectorOption_t (class in pyrosetta.rosetta.utility.keys) SmallKeyVector_utility_options_FileOptionKey_utility_options_FileOption_t (class in pyrosetta.rosetta.utility.keys) SmallKeyVector_utility_options_FileVectorOptionKey_utility_options_FileVectorOption_t (class in pyrosetta.rosetta.utility.keys) SmallKeyVector_utility_options_IntegerOptionKey_utility_options_IntegerOption_t (class in pyrosetta.rosetta.utility.keys) SmallKeyVector_utility_options_IntegerVectorOptionKey_utility_options_IntegerVectorOption_t (class in pyrosetta.rosetta.utility.keys) SmallKeyVector_utility_options_OptionKey_utility_options_OptionTypes_t (class in pyrosetta.rosetta.utility.keys) SmallKeyVector_utility_options_PathOptionKey_utility_options_PathOption_t (class in pyrosetta.rosetta.utility.keys) SmallKeyVector_utility_options_PathVectorOptionKey_utility_options_PathVectorOption_t (class in pyrosetta.rosetta.utility.keys) SmallKeyVector_utility_options_RealOptionKey_utility_options_RealOption_t (class in pyrosetta.rosetta.utility.keys) SmallKeyVector_utility_options_RealVectorOptionKey_utility_options_RealVectorOption_t (class in pyrosetta.rosetta.utility.keys) SmallKeyVector_utility_options_ResidueChainVectorOptionKey_utility_options_ResidueChainVectorOption_t (class in pyrosetta.rosetta.utility.keys) SmallKeyVector_utility_options_StringOptionKey_utility_options_StringOption_t (class in pyrosetta.rosetta.utility.keys) SmallKeyVector_utility_options_StringVectorOptionKey_utility_options_StringVectorOption_t (class in pyrosetta.rosetta.utility.keys) smallmer_from_largemer() (in module pyrosetta.rosetta.protocols.forge.methods) SmallMinCCDTrial (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) SmallMinCCDTrialCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) SmallMol (class in pyrosetta.rosetta.protocols.pockets) SmallMover (class in pyrosetta.rosetta.protocols.simple_moves) SmallMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) smart_annealer() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) smart_annealer_cutoff() (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) smart_annealer_disable_during_quench() (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) smart_annealer_model() (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) smart_annealer_pick_again() (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) SmartAssembly (class in pyrosetta.rosetta.protocols.sewing.data_storage) SmartFixbbSimAnnealer (class in pyrosetta.rosetta.core.pack.annealer) SmartSegment (class in pyrosetta.rosetta.protocols.sewing.data_storage) SmartSewingResidue (class in pyrosetta.rosetta.protocols.sewing.data_storage) smax_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) smooth() (pyrosetta.rosetta.protocols.hybridization.TMalign method) smooth_fa_elec() (pyrosetta.rosetta.core.scoring.etable.coulomb.Coulomb method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) smooth_hb_env_dep() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) smooth_move_small() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) smooth_nb() (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) smooth_to_zero() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) SmoothCenPairEnergy (class in pyrosetta.rosetta.core.energy_methods) SmoothCenPairEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) SmoothEnvEnergy (class in pyrosetta.rosetta.core.energy_methods) SmoothEnvEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) SmoothEnvPairPotential (class in pyrosetta.rosetta.core.scoring) SmoothFragmentMover (class in pyrosetta.rosetta.protocols.simple_moves) SmoothFragWeight (class in pyrosetta.rosetta.protocols.topology_broker.weights) smoothing (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GADockStageParams property) SmoothScoreTermCoeffs (class in pyrosetta.rosetta.core.scoring) SmoothStepFunc (class in pyrosetta.rosetta.core.scoring.func) SmoothSymmetricFragmentMover (class in pyrosetta.rosetta.protocols.simple_moves) SmotifFeatures (class in pyrosetta.rosetta.protocols.features) SmotifFeaturesCreator (class in pyrosetta.rosetta.protocols.features) smove_angle_range (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) smpbe_size (pyrosetta.rosetta.core.scoring.APBSConfig.R_PARAM property) smpbe_vol (pyrosetta.rosetta.core.scoring.APBSConfig.R_PARAM property) smpi_char (pyrosetta.rosetta.utility.simulate_mpi_message_type attribute) smpi_double (pyrosetta.rosetta.utility.simulate_mpi_message_type attribute) smpi_doubles (pyrosetta.rosetta.utility.simulate_mpi_message_type attribute) smpi_integer (pyrosetta.rosetta.utility.simulate_mpi_message_type attribute) smpi_integers (pyrosetta.rosetta.utility.simulate_mpi_message_type attribute) smpi_size (pyrosetta.rosetta.utility.simulate_mpi_message_type attribute) smpi_sizes (pyrosetta.rosetta.utility.simulate_mpi_message_type attribute) smpi_string (pyrosetta.rosetta.utility.simulate_mpi_message_type attribute) Sn (pyrosetta.rosetta.core.chemical.element.Elements attribute) snextc() (pyrosetta.rosetta.std.filebuf method) (pyrosetta.rosetta.std.streambuf method) (pyrosetta.rosetta.std.stringbuf method) (pyrosetta.rosetta.std.wstreambuf method) (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) SnugDock (class in pyrosetta.rosetta.protocols.antibody.snugdock) (pyrosetta.rosetta.protocols.docking.DHR_Type attribute) SnugDockCreator (class in pyrosetta.rosetta.protocols.antibody.snugdock) SnugDockProtocol (class in pyrosetta.rosetta.protocols.antibody.snugdock) snugfit_MC_min() (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) snugfit_mcm_protocol() (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) so3_correlate() (pyrosetta.rosetta.numeric.fourier.SHT method) SO3coeffs (class in pyrosetta.rosetta.numeric.fourier) SoedingFunc (class in pyrosetta.rosetta.core.scoring.func) softmax() (pyrosetta.rosetta.protocols.esm_perplexity.EsmPerplexityTensorflowProtocol static method) softSanitize() (in module pyrosetta.rosetta.core.chemical.rdkit) sog_cst_param() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) SOGFunc (class in pyrosetta.rosetta.core.scoring.func) SOGFunc_Impl (class in pyrosetta.rosetta.core.scoring.func) sol_value (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.MyWaterHolder property) sol_weight() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) SOLID_STATE_NMR (pyrosetta.rosetta.core.io.rcsb.ExperimentalTechnique attribute) SOLUTION_NMR (pyrosetta.rosetta.core.io.rcsb.ExperimentalTechnique attribute) SOLUTION_SCATTERING (pyrosetta.rosetta.core.io.rcsb.ExperimentalTechnique attribute) SOLUTION_SCATTERING_THEORETICAL_MODEL (pyrosetta.rosetta.core.io.rcsb.ExperimentalTechnique attribute) SolutionPicker (class in pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers) SolutionPredicate (class in pyrosetta.rosetta.protocols.denovo_design.components) solv1() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) solv2() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) solvation (pyrosetta.rosetta.core.scoring.etable.AtomPairEnergy property) SolvationGrid (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) SolvationGridCreator (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) SolvationMetaGrid (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) SolvationMetaGridCreator (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) solve() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.normalmode.NormalMode method) solve_gaps() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) solve_pb() (pyrosetta.rosetta.core.scoring.PoissonBoltzmannPotential method) solve_sturm() (in module pyrosetta.rosetta.numeric.kinematic_closure) solve_tensor_and_compute_score_by_nls() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) solve_tensor_and_compute_score_by_svd() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) SOLVENT (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid attribute) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid.PtType attribute) SolventAccessibility (class in pyrosetta.rosetta.protocols.frag_picker.scores) solvF2BR() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) solvF2BR_ (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo property) solvF2d() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) solvF2d_ (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo property) some_claim_ (pyrosetta.rosetta.protocols.topology_broker.SuggestValueMessage property) sort() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) sort_by() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff static method) (pyrosetta.rosetta.protocols.wum.SilentStructStore method) sort_by_binding() (in module pyrosetta.rosetta.protocols.ligand_docking) SORT_BY_CIS_PEPTIDE_BONDS (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HIERARCHICAL_HYBRID_JD_MPI_SORT_TYPE attribute) SORT_BY_ENERGIES (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HIERARCHICAL_HYBRID_JD_MPI_SORT_TYPE attribute) SORT_BY_HBONDS (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HIERARCHICAL_HYBRID_JD_MPI_SORT_TYPE attribute) sort_by_percent_hbond_capacity (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) sort_by_rms_and_energy() (pyrosetta.rosetta.core.scoring.motif.MotifHits method) SORT_BY_RMSD (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HIERARCHICAL_HYBRID_JD_MPI_SORT_TYPE attribute) sort_by_second() (in module pyrosetta.rosetta.protocols.ligand_docking) sort_by_weighted_energy() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) sort_each_group_by_energy() (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.toolbox.ClusterBase method) (pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle method) sort_ensemble_by_designability() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) sort_fill_energies() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) sort_first_by_tot_unsat (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) sort_groups_by_energy() (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) sort_new_rotamers_into_rotset_vector() (in module pyrosetta.rosetta.core.pack.rotamer_set) sort_pair_list() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) SORT_POOL (pyrosetta.rosetta.basic.ProfTag attribute) sort_pose_by_score() (in module pyrosetta.rosetta.core.pose) sort_R_function() (pyrosetta.rosetta.core.optimization.EItem static method) sort_relaxed_poses() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) sort_residue_type_pointers_by_name() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) sort_seq_num_list() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) sort_silent_scores() (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) SortByLowEnergy (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts) sorted_res_list() (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) sorted_values() (pyrosetta.rosetta.numeric.kdtree.KDPointList method) sortrms() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) SOURCE (pyrosetta.rosetta.core.io.pdb.RecordType attribute) source_chain() (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) source_file_name() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) source_filename() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) source_from_res() (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) source_id() (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputSource method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputSource method) (pyrosetta.rosetta.protocols.jd3.InputSource method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputSource method) source_id_is_mapped() (pyrosetta.rosetta.utility.subset_mapping method) source_pdb() (pyrosetta.rosetta.protocols.splice.ResidueBBDofs 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) source_pdb_from_res() (pyrosetta.rosetta.protocols.splice.Splice method) source_pdb_name() (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) source_pdb_to_res() (pyrosetta.rosetta.protocols.splice.Splice method) source_pose() (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) source_size() (pyrosetta.rosetta.utility.subset_mapping method) source_string() (pyrosetta.rosetta.core.pose.RID_FileSource method) (pyrosetta.rosetta.core.pose.RID_Source method) source_to_res() (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) sourceName (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) SourcePositions (class in pyrosetta.rosetta.protocols.rna.denovo.coarse) sources_same() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.standard.StandardInnerLarvalJob method) SOUTH (pyrosetta.rosetta.core.chemical.rna.PuckerState attribute) SP (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.HybridOrbitalType attribute) SP2 (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.HybridOrbitalType attribute) sp2_BAH180_rise() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) SP2_HYBRID (pyrosetta.rosetta.core.chemical.Hybridization attribute) sp2_outer_width() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) SP3 (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.HybridOrbitalType attribute) SP3_HYBRID (pyrosetta.rosetta.core.chemical.Hybridization attribute) space (pyrosetta.rosetta.core.scoring.APBSConfig property) space() (in module pyrosetta.rosetta.ObjexxFCL) (in module pyrosetta.rosetta.ObjexxFCL.format) space_prefixed() (pyrosetta.rosetta.utility.options.OptionCollection static method) spaceAllocatedForRMSD (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) Spacegroup (class in pyrosetta.rosetta.protocols.cryst) spacegroup() (pyrosetta.rosetta.core.io.CrystInfo method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) SpacegroupSetting (class in pyrosetta.rosetta.protocols.cryst) spacer_positions() (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) spacing() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) spairs_from_foldtype() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) spairset() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet method) Span (class in pyrosetta.rosetta.core.conformation.membrane) span() (pyrosetta.rosetta.core.conformation.membrane.SpanningTopology method) span_begin() (pyrosetta.rosetta.core.scoring.MembraneTopology method) span_end() (pyrosetta.rosetta.core.scoring.MembraneTopology method) span_file() (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) span_ins (pyrosetta.rosetta.core.scoring.ScoreType attribute) spanfile() (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover method) spanfile_name() (in module pyrosetta.rosetta.core.conformation.membrane) spanfile_names() (in module pyrosetta.rosetta.core.conformation.membrane) SpanInfo (class in pyrosetta.rosetta.protocols.membrane) spanning() (pyrosetta.rosetta.core.conformation.membrane.SpanningTopology method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) spanning_topology() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) SpanningTopology (class in pyrosetta.rosetta.core.conformation.membrane) SpanTopologyMatchPoseFilter (class in pyrosetta.rosetta.protocols.simple_filters) SpanTopologyMatchPoseFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) SPARSE (pyrosetta.rosetta.core.select.residue_selector.slice_enums.SliceMode attribute) SparseMatrixIndex (class in pyrosetta.rosetta.core.pack.interaction_graph) Sparta (class in pyrosetta.rosetta.protocols.sparta) Sparta.SpartaLib (class in pyrosetta.rosetta.protocols.sparta) SPARTA_ANN (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) SPARTA_DIR (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) SPARTA_ERR_SURF (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) spearman() (in module pyrosetta.rosetta.protocols.ligand_docking) spearman_r() (in module pyrosetta.rosetta.numeric.statistics) SPECIAL_ROT (pyrosetta.rosetta.core.chemical.VariantType attribute) special_rot (pyrosetta.rosetta.core.scoring.ScoreType attribute) SPECIAL_SEGMENTS_OBSERVER (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType attribute) specialized_commands_exist_for_residue() (pyrosetta.rosetta.core.pack.task.ResfileContents method) SpecialPackerPaletteBehaviour (class in pyrosetta.rosetta.core.pack.palette) SpecialRotamerEnergy (class in pyrosetta.rosetta.protocols.scoring.methods) SpecialRotamerEnergyCreator (class in pyrosetta.rosetta.protocols.scoring.methods) SpecialRotamerRSO (class in pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations) SpecialSegmentsObserver (class in pyrosetta.rosetta.core.pose.datacache) specific_build_position() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) specific_name (pyrosetta.rosetta.core.chemical.rings.RingConformer property) SpecificGeometryLibrary (class in pyrosetta.rosetta.protocols.jumping) SpecificResiduesNearInterfaceFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) SpecificResiduesNearInterfaceFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) specified_check() (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) specified_report() (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) sph_standardize() (pyrosetta.rosetta.numeric.fourier.SHT method) spharm_score_ (pyrosetta.rosetta.protocols.electron_density.RefinementResult property) Sphere (class in pyrosetta.rosetta.core.scoring.packstat) sphere() (pyrosetta.rosetta.core.scoring.packstat.CavityBall method) sphere_ (pyrosetta.rosetta.core.scoring.packstat.CavityBall property) sphere_lookup() (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) SPHERE_MODE_BB (pyrosetta.rosetta.protocols.viewer.spheremode attribute) SPHERE_MODE_LIGAND (pyrosetta.rosetta.protocols.viewer.spheremode attribute) SPHERE_MODE_SC (pyrosetta.rosetta.protocols.viewer.spheremode attribute) sphere_sasa (pyrosetta.rosetta.core.scoring.packstat.SasaResult property) spheremode (class in pyrosetta.rosetta.protocols.viewer) SpherePointNo (pyrosetta.rosetta.protocols.sparta.PDB property) spheres (pyrosetta.rosetta.core.scoring.packstat.PosePackData property) spherical() (in module pyrosetta.rosetta.protocols.fldsgn.potentials.sspot) (pyrosetta.rosetta.core.kinematics.Stub method) spherical_coor_triplet (class in pyrosetta.rosetta.protocols.pockets) SphericalRotationSearchPattern (class in pyrosetta.rosetta.protocols.hotspot_hashing) spin() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) spin_axis() (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) spin_down (pyrosetta.rosetta.protocols.pack_daemon.DaemonSetMessage attribute) spin_id() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) spin_mag() (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) SpinAroundPartnerMover (class in pyrosetta.rosetta.protocols.membrane) SpinAroundPartnerMoverCreator (class in pyrosetta.rosetta.protocols.membrane) SPINLABEL (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) SpinlabelDatabaseEntry (class in pyrosetta.rosetta.core.io.nmr) SpinlabelDatabaseHandler (class in pyrosetta.rosetta.core.io.nmr) SpinMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) SpinMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) Splice (class in pyrosetta.rosetta.protocols.splice) splice_filter() (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) splice_segments() (pyrosetta.rosetta.protocols.splice.SpliceManager method) SpliceCreator (class in pyrosetta.rosetta.protocols.splice) SpliceIn (class in pyrosetta.rosetta.protocols.splice) SpliceInAntibody (class in pyrosetta.rosetta.protocols.splice) SpliceInAntibodyCreator (class in pyrosetta.rosetta.protocols.splice) SpliceInCreator (class in pyrosetta.rosetta.protocols.splice) SpliceInTail (class in pyrosetta.rosetta.protocols.splice) SpliceInTailCreator (class in pyrosetta.rosetta.protocols.splice) SpliceManager (class in pyrosetta.rosetta.protocols.splice) SpliceOut (class in pyrosetta.rosetta.protocols.splice) SpliceOutAntibody (class in pyrosetta.rosetta.protocols.splice) SpliceOutAntibodyCreator (class in pyrosetta.rosetta.protocols.splice) SpliceOutCreator (class in pyrosetta.rosetta.protocols.splice) SpliceOutFilter() (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) SpliceOutRMSDFilter() (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) SpliceOutTail (class in pyrosetta.rosetta.protocols.splice) SpliceOutTailCreator (class in pyrosetta.rosetta.protocols.splice) SpliceSegment (class in pyrosetta.rosetta.protocols.splice) spline_by_z() (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) spline_coeffs() (in module pyrosetta.rosetta.core.scoring.electron_density) spline_from_file() (in module pyrosetta.rosetta.numeric.interpolation) spline_from_stream() (in module pyrosetta.rosetta.numeric.interpolation) spline_interpolate() (in module pyrosetta.rosetta.numeric.interpolation.spline) spline_second_derivative() (in module pyrosetta.rosetta.numeric.interpolation.spline) SplineFunc (class in pyrosetta.rosetta.core.scoring.func) SplineGenerator (class in pyrosetta.rosetta.numeric.interpolation.spline) SplineParameters (class in pyrosetta.rosetta.numeric) SPLIT (pyrosetta.rosetta.core.io.pdb.RecordType attribute) split() (in module pyrosetta.rosetta.protocols.sparta) (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.protocols.hybridization.DDomainParse method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) split_axis() (pyrosetta.rosetta.numeric.kdtree.KDNode method) split_behavior_for_name3() (pyrosetta.rosetta.core.chemical.io.MergeAndSplitBehaviorManager method) split_by_ca_ca_dist() (in module pyrosetta.rosetta.protocols.loops) split_by_chain() (pyrosetta.rosetta.core.pose.Pose method) split_by_newlines() (in module pyrosetta.rosetta.utility) split_by_resSeq() (in module pyrosetta.rosetta.protocols.loops) split_chains() (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) split_existing_edge_at_residue() (pyrosetta.rosetta.core.kinematics.FoldTree method) split_line() (pyrosetta.rosetta.core.scoring.epr_deer.DEERIO method) split_line_to_polyval() (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) split_line_to_spline() (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) split_mid_ranges() (in module pyrosetta.rosetta.protocols.fold_from_loops.utils) split_pose() (in module pyrosetta.rosetta.protocols.stepwise.modeler) split_script_vars() (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric method) split_sequence_motif() (in module pyrosetta.rosetta.core.sequence) split_to_list() (in module pyrosetta.rosetta.utility) split_to_set() (in module pyrosetta.rosetta.utility) split_topology_by_jump() (in module pyrosetta.rosetta.protocols.membrane) split_topology_by_jump_noshift() (in module pyrosetta.rosetta.protocols.membrane) split_unfolded_label_type() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) split_unfolded_two_body (pyrosetta.rosetta.core.scoring.ScoreType attribute) split_unfolded_value_type() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) split_up_remark_line() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) split_WhiteSpace() (in module pyrosetta.rosetta.protocols.sparta) split_whitespace() (in module pyrosetta.rosetta.utility) SplitAndMixPoseMover (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) SplitAndMixPoseMoverCreator (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) splitString() (pyrosetta.rosetta.protocols.forge.remodel.RemodelData method) SplitUnfoldedTwoBodyEnergy (class in pyrosetta.rosetta.core.energy_methods) SplitUnfoldedTwoBodyEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) SplitUnfoldedTwoBodyPotential (class in pyrosetta.rosetta.core.scoring) spm_reference_name() (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) spring_constant_ (pyrosetta.rosetta.protocols.optimize_weights.WeightRangeConstraint property) SpringParams (class in pyrosetta.rosetta.core.scoring) SPRSDE (pyrosetta.rosetta.core.io.pdb.RecordType attribute) sputbackc() (pyrosetta.rosetta.std.filebuf method) (pyrosetta.rosetta.std.streambuf method) (pyrosetta.rosetta.std.stringbuf method) (pyrosetta.rosetta.std.wstreambuf method) (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) sputc() (pyrosetta.rosetta.std.filebuf method) (pyrosetta.rosetta.std.streambuf method) (pyrosetta.rosetta.std.stringbuf method) (pyrosetta.rosetta.std.wstreambuf method) (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) sputn() (pyrosetta.rosetta.std.filebuf method) (pyrosetta.rosetta.std.streambuf method) (pyrosetta.rosetta.std.stringbuf method) (pyrosetta.rosetta.std.wstreambuf method) (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) sq_vec_distance() (in module pyrosetta.rosetta.numeric.kdtree) sql_query() (pyrosetta.rosetta.cppdb.backend.statement method) sqlite3 (pyrosetta.rosetta.utility.sql_database.DatabaseMode attribute) (pyrosetta.rosetta.utility.sql_database.DatabaseMode.e attribute) sqr() (in module pyrosetta.rosetta.numeric.interpolation.spline) (pyrosetta.rosetta.numeric.interpolation.spline.BicubicSpline method) (pyrosetta.rosetta.numeric.interpolation.spline.CubicSpline method) sqrt_2pi() (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) square() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_float_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) square_distance() (pyrosetta.rosetta.core.scoring.EnergyEdge method) square_norm() (pyrosetta.rosetta.numeric.MathVector_double_t method) square_planar_metal (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker attribute) square_pyramidal_metal (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker attribute) SquarePlanarMetal_Helper (class in pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) SquarePyramidalMetal_Helper (class in pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) SquarerootExpression (class in pyrosetta.rosetta.numeric.expression_parser) SquareWell2Func (class in pyrosetta.rosetta.core.scoring.func) SquareWellFunc (class in pyrosetta.rosetta.core.scoring.func) Sr (pyrosetta.rosetta.core.chemical.element.Elements attribute) sraa (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet property) srad (pyrosetta.rosetta.core.scoring.APBSConfig.R_PARAM property) src() (pyrosetta.rosetta.utility.SimulateMPIMessage method) src_begin (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) src_end (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) src_pose() (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) src_pose_start() (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) srfm (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) SRI (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) SRLZ_file (pyrosetta.rosetta.core.import_pose.FileType attribute) srnbb (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet property) srnchi (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet property) ss (pyrosetta.rosetta.core.fragment.torsions property) (pyrosetta.rosetta.protocols.denovo_design.architects.SecStructInfo property) (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueEntry property) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBInstruction property) SS() (in module pyrosetta.rosetta.ObjexxFCL.format) ss() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.scoring.motif.Xfres method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) ss1() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) ss2() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) ss_around (pyrosetta.rosetta.protocols.denovo_design.task_operations.LoopInfo property) SS_Base (class in pyrosetta.rosetta.protocols.fldsgn.topology) ss_contact_worst (pyrosetta.rosetta.core.scoring.ScoreType attribute) SS_dimer (pyrosetta.rosetta.core.scoring.Strands property) ss_dist() (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet method) ss_element_id() (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) ss_from_blueprint() (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) ss_helix_nres (pyrosetta.rosetta.protocols.analysis.InterfaceData property) ss_index() (in module pyrosetta.rosetta.protocols.frag_picker.quota) ss_index_match (pyrosetta.rosetta.protocols.indexed_structure_store.BackboneStub property) SS_Info (class in pyrosetta.rosetta.core.scoring) SS_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) SS_Info2 (class in pyrosetta.rosetta.protocols.fldsgn.topology) SS_Killhairpins_Info (class in pyrosetta.rosetta.core.scoring) SS_KILLHAIRPINS_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) ss_length_check() (in module pyrosetta.rosetta.protocols.frags) ss_loop_nres (pyrosetta.rosetta.protocols.analysis.InterfaceData property) ss_orient() (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet method) ss_pair (pyrosetta.rosetta.core.scoring.ScoreType attribute) ss_penalty() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) SS_predictor (class in pyrosetta.rosetta.protocols.ss_prediction) SS_resnum (pyrosetta.rosetta.core.scoring.Strands property) ss_sheet_nres (pyrosetta.rosetta.protocols.analysis.InterfaceData property) ss_str() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) SS_strand (pyrosetta.rosetta.core.scoring.Strands property) SS_strand_end (pyrosetta.rosetta.core.scoring.Strands property) ss_strings() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo method) ss_strings_specified() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo method) ss_type (pyrosetta.rosetta.protocols.jumping.DisulfPairing property) ss_type() (pyrosetta.rosetta.protocols.comparative_modeling.features.SSFeature method) ss_type_convert() (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) SSamountFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) SSamountFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) SSBOND (pyrosetta.rosetta.core.io.pdb.RecordType attribute) ssbond_map() (pyrosetta.rosetta.core.io.StructFileRep method) SSBondInformation (class in pyrosetta.rosetta.core.io) sscomp() (pyrosetta.rosetta.core.scoring.motif.Xfrag method) ssdep_ (pyrosetta.rosetta.core.scoring.hbonds.SSWeightParameters property) sse() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) sse_contact_strength() (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) SSElementBisectddGFilter (class in pyrosetta.rosetta.protocols.simple_ddg) SSElementBisectddGFilterCreator (class in pyrosetta.rosetta.protocols.simple_ddg) SSElementLengthFilter (class in pyrosetta.rosetta.protocols.simple_filters) SSElementLengthFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) SSElementMotifContactEnergy (class in pyrosetta.rosetta.core.energy_methods) SSElementMotifContactEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) SSElementMotifContactFilter (class in pyrosetta.rosetta.protocols.simple_filters) SSElementMotifContactFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) SSElementSelector (class in pyrosetta.rosetta.core.select.residue_selector) SSElementSelector.SSElement (class in pyrosetta.rosetta.core.select.residue_selector) SSElementSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) SSFeature (class in pyrosetta.rosetta.protocols.comparative_modeling.features) SSHashedFragmentStore (class in pyrosetta.rosetta.protocols.indexed_structure_store) SSHashedFragmentStore() (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager method) SSManager (class in pyrosetta.rosetta.core.sequence) SSMotifFinder (class in pyrosetta.rosetta.protocols.simple_filters) SSMotifFinderFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) SSPairPotential (class in pyrosetta.rosetta.protocols.fldsgn.potentials.sspot) SSPredictionFilter (class in pyrosetta.rosetta.protocols.denovo_design.filters) SSPredictionFilterCreator (class in pyrosetta.rosetta.protocols.denovo_design.filters) SSShapeComplementarityFilter (class in pyrosetta.rosetta.protocols.denovo_design.filters) SSShapeComplementarityFilterCreator (class in pyrosetta.rosetta.protocols.denovo_design.filters) SSType (class in pyrosetta.rosetta.protocols.comparative_modeling.features) sstype (pyrosetta.rosetta.protocols.forge.remodel.LineObject property) SSWeightParameters (class in pyrosetta.rosetta.core.scoring.hbonds) st_atr() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) st_rep() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) st_sol() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) st_weights() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) stack_elec (pyrosetta.rosetta.core.scoring.ScoreType attribute) stack_elec_base_base (pyrosetta.rosetta.core.scoring.ScoreType attribute) stack_elec_base_bb (pyrosetta.rosetta.core.scoring.ScoreType attribute) STACK_ELEC_NBLIST (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) StackElecEnergy (class in pyrosetta.rosetta.core.energy_methods) StackElecEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) STAGE1 (pyrosetta.rosetta.basic.ProfTag attribute) stage1() (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) stage1_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler 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.MembraneAbinitio method) stage1_mover() (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) stage1_pose_setup() (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) STAGE2 (pyrosetta.rosetta.basic.ProfTag attribute) stage2() (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) stage2_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler 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.MembraneAbinitio method) stage2_mover() (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) STAGE2_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) STAGE3 (pyrosetta.rosetta.basic.ProfTag attribute) stage3_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler 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.MembraneAbinitio method) stage3_mover() (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) STAGE4 (pyrosetta.rosetta.basic.ProfTag attribute) stage4_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler 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.MembraneAbinitio method) stage4_mover() (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) STAGE5 (pyrosetta.rosetta.basic.ProfTag attribute) stage5_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) STAGE_1 (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper attribute) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.StageID attribute) STAGE_2 (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper attribute) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.StageID attribute) STAGE_3 (pyrosetta.rosetta.protocols.abinitio.StageID attribute) STAGE_3a (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper attribute) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.StageID attribute) STAGE_3b (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper attribute) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.StageID attribute) STAGE_4 (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper attribute) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.StageID attribute) STAGE_4rot (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper attribute) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio.StageID attribute) STAGE_5 (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper attribute) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio.StageID attribute) stage_complex_namer() (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover static method) stage_for_global_job_id() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) staged_constraints() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) StageID (class in pyrosetta.rosetta.protocols.abinitio) (class in pyrosetta.rosetta.protocols.abinitio.abscript) StagePreparer (class in pyrosetta.rosetta.protocols.abinitio.abscript) stagger() (pyrosetta.rosetta.protocols.dna.DNABasepair method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) standard (pyrosetta.rosetta.utility.sql_database.TransactionMode attribute) (pyrosetta.rosetta.utility.sql_database.TransactionMode.e attribute) standard_bb_stdev() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) standard_packer_task() (in module pyrosetta) standard_RG (class in pyrosetta.rosetta.numeric.random) standard_task_factory() (in module pyrosetta) standard_width() (pyrosetta.rosetta.ObjexxFCL.TypeTraits_double_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_float_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_int_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_long_double_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_long_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_short_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_unsigned_int_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_unsigned_long_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_unsigned_short_t static method) StandardDisulfPairingLibrary (class in pyrosetta.rosetta.protocols.jumping) StandardInnerLarvalJob (class in pyrosetta.rosetta.protocols.jd3.standard) StandardJobQueen (class in pyrosetta.rosetta.protocols.jd3.standard) StandardPairingLibrary (class in pyrosetta.rosetta.protocols.jumping) StandardPivots (class in pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers) StandardPoseJobSummary (class in pyrosetta.rosetta.protocols.jd3.job_summaries) Star (class in pyrosetta.rosetta.ObjexxFCL) star_fold_tree() (in module pyrosetta.rosetta.protocols.protein_interface_design) StarAbinitio (class in pyrosetta.rosetta.protocols.star) StarAbinitio_main() (in module pyrosetta.rosetta.protocols.star) start (pyrosetta.rosetta.core.io.pdb.Field property) (pyrosetta.rosetta.protocols.antibody.FrameWork property) (pyrosetta.rosetta.protocols.denovo_design.movers.RotationRange property) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier attribute) (pyrosetta.rosetta.protocols.loops.SerializedLoop property) (pyrosetta.rosetta.protocols.membrane.SpanInfo property) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptidesSegment property) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentSpec property) start() (pyrosetta.rosetta.core.conformation.membrane.Span method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (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.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.environment.Environment method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelicalFragment 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.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.jumping.Interval method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.noesy_assign.FoldResonance method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo method) start_ (pyrosetta.rosetta.protocols.jumping.Interval property) start_atom() (pyrosetta.rosetta.core.kinematics.Edge method) start_atomid() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) start_atomid1() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) start_atomid2() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) start_atoms1() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) start_atoms2() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) start_cdr_loop (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) start_decoy() (pyrosetta.toolbox.py_jobdistributor.PyJobDistributor method) start_doc() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) start_end() (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) start_evaluation_timer() (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) start_file() (in module pyrosetta.rosetta.basic.options) start_files() (in module pyrosetta.rosetta.basic.options) start_from_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) start_key() (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) start_label() (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) start_list() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) start_local() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) start_loop() (pyrosetta.rosetta.protocols.splice.ResidueBBDofs method) start_map() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) start_new_batch() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) start_new_match() (pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage method) start_overlap_pose (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover.Overlap property) start_overlap_xmlPose (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover.Overlap property) start_pdb() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo method) start_pdb_chain() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo method) start_pose() (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) start_position() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) start_res (pyrosetta.rosetta.core.select.residue_selector.SSElementSelector.SSElement property) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover.Chunk property) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover.SSElement property) start_res() (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.LoopFromFileData method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation method) start_res_ (pyrosetta.rosetta.protocols.hybridization.detailedControlsTagSetting property) start_seq2() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) start_struct (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover.Design property) start_time() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) (pyrosetta.rosetta.protocols.simple_filters.ExpiryFilter method) start_timing() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) start_tree_at_chain() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) start_udp_server() (in module pyrosetta.network.rosetta_udp_to_tcp_bridge) start_udp_to_tcp_bridge_daemon() (in module pyrosetta.network.rosetta_udp_to_tcp_bridge) start_weight() (pyrosetta.rosetta.protocols.moves.RampingMover method) started_jobs() (pyrosetta.rosetta.protocols.jd3.JobTracker method) started_jobs_for_node() (pyrosetta.rosetta.protocols.jd3.JobTracker method) StartFrom (class in pyrosetta.rosetta.protocols.ligand_docking) StartFromCreator (class in pyrosetta.rosetta.protocols.ligand_docking) starting_dofs() (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) starting_node() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) starting_pose() (pyrosetta.rosetta.protocols.dna.PDBOutput method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmtfJobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) StartingNodeMotifScorer (class in pyrosetta.rosetta.protocols.sewing.scoring) StartingNodeMotifScorerCreator (class in pyrosetta.rosetta.protocols.sewing.scoring) startres (pyrosetta.rosetta.protocols.denovo_design.task_operations.LoopInfo property) StartStructClaimer (class in pyrosetta.rosetta.protocols.topology_broker) startswith() (in module pyrosetta.rosetta.utility) startup() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) StartUpError stat_motifs() (pyrosetta.rosetta.core.scoring.motif.MotifHits method) state() (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) state_energies() (pyrosetta.rosetta.protocols.pack_daemon.MPIMultistateFitnessFunction method) (pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction method) state_has_same_backbone_as_current() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) state_in_rh (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct property) state_info() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) state_is_starting_aa_type() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) state_momento() (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) state_name() (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction method) (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunctionDriver method) state_offsets_for_aa_for_bb() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) state_offsets_for_bb() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) state_unassigned() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NodeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) StateAccumulatingMatchFilter (class in pyrosetta.rosetta.protocols.match.output) statement (class in pyrosetta.rosetta.cppdb) (class in pyrosetta.rosetta.cppdb.backend) statements_cache (class in pyrosetta.rosetta.cppdb.backend) states() (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) static_get() (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t static method) static_get_filter() (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects static method) static_get_mover() (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects static method) static_get_residue_selector() (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects static method) static_get_score_function() (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects static method) static_get_simple_metric() (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects static method) static_get_task_operation() (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects static method) static_set() (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t static method) StaticIndexRange (class in pyrosetta.rosetta.ObjexxFCL) statistics_filename() (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) statistics_valid() (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) StatsType (class in pyrosetta.rosetta.protocols.moves) status (pyrosetta.rosetta.protocols.jd3.CompletedJobOutput property) status() (pyrosetta.rosetta.numeric.RocPoint method) (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobResult method) (pyrosetta.rosetta.protocols.jd3.job_results.PoseJobResult method) (pyrosetta.rosetta.protocols.jd3.JobResult method) status_prefix() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) status_suffix() (pyrosetta.rosetta.protocols.jd3.LarvalJob method) stdev() (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) stdRes (pyrosetta.rosetta.core.io.ModifiedResidueInformation property) steal() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.fragment.BBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.DownJumpSRFD method) (pyrosetta.rosetta.core.fragment.FragData method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SecstructSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.UpJumpSRFD method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) steal_alignment() (in module pyrosetta.rosetta.core.sequence) steal_constant_length_frag_set_from_pose() (in module pyrosetta.rosetta.core.fragment) steal_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) steal_def_clone() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) steal_frag_set_from_pose() (in module pyrosetta.rosetta.core.fragment) steal_frags() (pyrosetta.rosetta.protocols.abinitio.Template method) steal_inversion() (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) steal_jumps() (pyrosetta.rosetta.protocols.jumping.JumpSample method) steal_ligands() (in module pyrosetta.rosetta.protocols.comparative_modeling) steal_orientation_and_pleating() (pyrosetta.rosetta.protocols.jumping.JumpSample method) StealLigandMover (class in pyrosetta.rosetta.protocols.comparative_modeling) StealSideChainsMover (class in pyrosetta.rosetta.protocols.comparative_modeling) steepness() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) stem_pairing_sets() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) StemFinder (class in pyrosetta.rosetta.protocols.simple_filters) StemFinderFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) stems() (pyrosetta.rosetta.core.pose.rna.RNA_SecStruct method) stems_are_neighbors() (pyrosetta.rosetta.protocols.simple_filters.StemFinder method) stems_on_sse() (pyrosetta.rosetta.protocols.simple_filters.StemFinder method) step (pyrosetta.rosetta.protocols.make_rot_lib.TorsionRange property) step() (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceBounds method) (pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler method) step_count() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) step_data() (pyrosetta.rosetta.core.optimization.NumDerivCheckData method) (pyrosetta.rosetta.core.optimization.SimpleDerivCheckResult method) step_size (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData property) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData property) step_size() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.symmetry.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SymmetrySlider method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) stepbound (pyrosetta.rosetta.numeric.nls.lm_control_struct property) stepsize() (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) stepwise_addable_pose_residue() (in module pyrosetta.rosetta.core.pose) stepwise_addable_residue() (in module pyrosetta.rosetta.core.pose) stepwise_move_selector() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) StepWiseBasicModelerOptions (class in pyrosetta.rosetta.protocols.stepwise.modeler.options) StepWiseBasicOptions (class in pyrosetta.rosetta.protocols.stepwise.options) StepWiseBasicWorkingParameters (class in pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters) StepWiseClusterer (class in pyrosetta.rosetta.protocols.stepwise.modeler.align) StepWiseConnectionSampler (class in pyrosetta.rosetta.protocols.stepwise.modeler) StepWiseLegacyClusterer (class in pyrosetta.rosetta.protocols.stepwise.modeler.align) StepWiseLegacyClustererSilentBased (class in pyrosetta.rosetta.protocols.stepwise.modeler.align) StepWiseMasterMover (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) StepWiseMasterPacker (class in pyrosetta.rosetta.protocols.stepwise.modeler.packer) StepWiseMinimizer (class in pyrosetta.rosetta.protocols.stepwise.modeler) StepWiseModeler (class in pyrosetta.rosetta.protocols.stepwise.modeler) StepWiseModelerOptions (class in pyrosetta.rosetta.protocols.stepwise.modeler.options) StepWiseMonteCarlo (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo) StepWiseMonteCarloOptions (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.options) StepWiseMove (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) StepWiseMoveSelector (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) StepWiseMoveSelectorOptions (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options) StepWisePacker (class in pyrosetta.rosetta.protocols.stepwise.modeler.packer) StepWisePoseAligner (class in pyrosetta.rosetta.protocols.stepwise.modeler.align) StepWiseProteinBackboneSampler (class in pyrosetta.rosetta.protocols.stepwise.modeler.protein) StepWiseProteinCCD_Closer (class in pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close) StepWiseProteinCCD_MultiPoseCloser (class in pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close) StepWiseProteinKIC_LoopBridger (class in pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close) StepWiseProteinMinimizer (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) StepWiseProteinModelerOptions (class in pyrosetta.rosetta.protocols.stepwise.modeler.options) StepWiseProteinPoseSetup (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) StepWiseResiduePairScreener (class in pyrosetta.rosetta.protocols.stepwise.screener) StepWiseRNA_Clusterer (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) StepWiseRNA_CombineLongLoopFilterer (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna) StepWiseRNA_CountStruct (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna) StepWiseRNA_ModelerOptions (class in pyrosetta.rosetta.protocols.stepwise.modeler.options) StepWiseRNA_PoseSelection (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) StepWiseRNA_PoseSetup (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) StepWiseSampleAndScreen (class in pyrosetta.rosetta.protocols.stepwise) StepWiseSampler (class in pyrosetta.rosetta.protocols.stepwise.sampler) StepWiseSamplerComb (class in pyrosetta.rosetta.protocols.stepwise.sampler) StepWiseSamplerOneDOF (class in pyrosetta.rosetta.protocols.stepwise.sampler) StepWiseSamplerOneTorsion (class in pyrosetta.rosetta.protocols.stepwise.sampler) StepWiseSamplerOneValue (class in pyrosetta.rosetta.protocols.stepwise.sampler) StepWiseSamplerOneValueComb (class in pyrosetta.rosetta.protocols.stepwise.sampler) StepWiseSamplerRingConformer (class in pyrosetta.rosetta.protocols.stepwise.sampler) StepWiseSamplerSized (class in pyrosetta.rosetta.protocols.stepwise.sampler) StepWiseSamplerSizedAny (class in pyrosetta.rosetta.protocols.stepwise.sampler) StepWiseSamplerSizedComb (class in pyrosetta.rosetta.protocols.stepwise.sampler) StepWiseScreener (class in pyrosetta.rosetta.protocols.stepwise.screener) StepWiseScreenerType (class in pyrosetta.rosetta.protocols.stepwise.screener) StepWiseWorkingParameters (class in pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters) StepWiseWorkingParametersSetup (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) stereochem() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) stich_motif_in_scaffold_by_indexes_rotation_and_translation() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) still_interested() (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) STM_STORED_TASKS (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) STMStoredTask (class in pyrosetta.rosetta.protocols.task_operations) StochasticFilter (class in pyrosetta.rosetta.protocols.filters) StochasticFilterCreator (class in pyrosetta.rosetta.protocols.filters) stop (pyrosetta.rosetta.protocols.antibody.FrameWork property) (pyrosetta.rosetta.protocols.denovo_design.movers.RotationRange property) (pyrosetta.rosetta.protocols.loops.ResidueIdentifier attribute) (pyrosetta.rosetta.protocols.loops.SerializedLoop property) (pyrosetta.rosetta.protocols.membrane.SpanInfo property) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptidesSegment property) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentSpec property) stop() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRange method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) (pyrosetta.rosetta.protocols.jd2.DebugOut_MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd2.MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd2.WriteOut_MpiFileBuffer method) (pyrosetta.rosetta.protocols.jumping.Interval method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo method) stop_at_closure() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) stop_atom() (pyrosetta.rosetta.core.kinematics.Edge method) stop_before_condition() (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) stop_early() (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) stop_local() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) stop_loop() (pyrosetta.rosetta.protocols.splice.ResidueBBDofs method) stop_pdb() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo method) stop_pdb_chain() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo method) stop_res() (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) stop_res_ (pyrosetta.rosetta.protocols.hybridization.detailedControlsTagSetting property) stop_sampling() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) stopped_early() (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) stopping_condition() (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) store() (pyrosetta.rosetta.core.fragment.CacheWrapper_protocols_simple_moves_GunnTuple_core_fragment_MapCacheUnit_protocols_simple_moves_GunnTuple_t method) (pyrosetta.rosetta.core.fragment.FragCache_protocols_simple_moves_GunnTuple_t method) (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookup method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) (pyrosetta.rosetta.protocols.wum.SilentStructStore method) store_active_energies() (pyrosetta.rosetta.core.scoring.EnergyEdge method) store_argv_in_file() (pyrosetta.rosetta.core.io.silent.SilentFileData method) store_authors() (pyrosetta.rosetta.core.io.HeaderInformation method) store_base_residue_type_name_in_sfr() (in module pyrosetta.rosetta.core.io.pdb) store_by_atmpairno() (pyrosetta.rosetta.core.scoring.ResidueExclParams method) store_by_bondno() (pyrosetta.rosetta.core.scoring.ResidueExclParams method) store_classification() (pyrosetta.rosetta.core.io.HeaderInformation method) store_compound() (pyrosetta.rosetta.core.io.HeaderInformation method) store_connection_architect() (in module pyrosetta.rosetta.protocols.denovo_design.connection) store_constraints() (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) store_coordinates() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) store_CSA_in_pose() (in module pyrosetta.rosetta.core.scoring) store_current_derivatives() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) store_DC_in_pose() (in module pyrosetta.rosetta.core.scoring) store_denovo_architect() (in module pyrosetta.rosetta.protocols.denovo_design.architects) store_deposition_date() (pyrosetta.rosetta.core.io.HeaderInformation method) store_experimental_technique() (pyrosetta.rosetta.core.io.HeaderInformation method) store_experimental_techniques() (pyrosetta.rosetta.core.io.HeaderInformation method) store_filteronly_solutions() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) store_H3_cter_fragment() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) store_idCode() (pyrosetta.rosetta.core.io.HeaderInformation method) store_induced_dipoles() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) store_interaction_energy_first_node() (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge static method) store_interaction_energy_second_node() (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge static method) store_keywords() (pyrosetta.rosetta.core.io.HeaderInformation method) store_line() (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.WriteFileSFB method) store_new_sphere() (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) store_path() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) store_pose() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector method) store_RDC_in_pose() (in module pyrosetta.rosetta.core.scoring) store_RDC_ROHL_in_pose() (in module pyrosetta.rosetta.core.scoring) store_RDC_segments_in_pose() (in module pyrosetta.rosetta.protocols.scoring) store_reference_pdb() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) store_remark() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) store_sheetpositions() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) store_sheets() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) store_source_pose_for_segment() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) store_string_pair() (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputSource method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputSource method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputSource method) store_title() (pyrosetta.rosetta.core.io.HeaderInformation method) store_trie() (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) store_trj() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) store_unknown_records_in_sfr() (in module pyrosetta.rosetta.core.io.pdb) store_xyz() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) StoreCombinedStoredTasksMover (class in pyrosetta.rosetta.protocols.task_operations) StoreCombinedStoredTasksMoverCreator (class in pyrosetta.rosetta.protocols.task_operations) StoreCompoundTaskMover (class in pyrosetta.rosetta.protocols.task_operations) StoreCompoundTaskMoverCreator (class in pyrosetta.rosetta.protocols.task_operations) stored_angle() (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) stored_data() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) stored_edge_reweights (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ReweightData property) stored_induced_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) stored_induced_rf_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) stored_jump() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) STORED_RESIDUE_SUBSET (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) stored_subset_name() (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) stored_task_names() (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) StoredResidueSubsetSelector (class in pyrosetta.rosetta.protocols.residue_selectors) StoredResidueSubsetSelectorCreator (class in pyrosetta.rosetta.protocols.residue_selectors) StoredRotamerLibraryCreator (class in pyrosetta.rosetta.core.pack.rotamers) StoredRotamerLibrarySpecification (class in pyrosetta.rosetta.core.chemical.rotamers) StoredRotamerLibrarySpecificationCreator (class in pyrosetta.rosetta.core.chemical.rotamers) StorePoseSnapshot (class in pyrosetta.rosetta.protocols.simple_moves) StorePoseSnapshotCreator (class in pyrosetta.rosetta.protocols.simple_moves) StoreResidueSubsetMover (class in pyrosetta.rosetta.protocols.residue_selectors) StoreResidueSubsetMoverCreator (class in pyrosetta.rosetta.protocols.residue_selectors) stores_residue_map() (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) StoreTaskMover (class in pyrosetta.rosetta.protocols.task_operations) StoreTaskMoverCreator (class in pyrosetta.rosetta.protocols.task_operations) stossc() (pyrosetta.rosetta.std.filebuf method) (pyrosetta.rosetta.std.streambuf method) (pyrosetta.rosetta.std.stringbuf method) (pyrosetta.rosetta.std.wstreambuf method) (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) str (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfo property) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfo property) str() (pyrosetta.rosetta.basic.datacache.CacheableString method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.scoring.packstat.CavityBall method) (pyrosetta.rosetta.protocols.frag_picker.QuotaDebug method) (pyrosetta.rosetta.std.istringstream method) (pyrosetta.rosetta.std.ostringstream method) (pyrosetta.rosetta.std.stringbuf method) (pyrosetta.rosetta.std.stringstream method) str_dn() (in module pyrosetta.rosetta.ObjexxFCL) str_dncase() (in module pyrosetta.rosetta.ObjexxFCL) str_type (pyrosetta.rosetta.utility.json_spirit.Value_type attribute) str_type() (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) str_up() (in module pyrosetta.rosetta.ObjexxFCL) str_upcase() (in module pyrosetta.rosetta.ObjexxFCL) Strand (class in pyrosetta.rosetta.protocols.fldsgn.topology) STRAND (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing.PairingType attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing.PairingType attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentCounts attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentCounts.SegmentType attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing.PairingType attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing.PairingType attribute) strand (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SecondaryStructureType attribute) strand() (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) strand1 (pyrosetta.rosetta.protocols.fldsgn.topology.TripletID property) strand1() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif method) (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet method) strand2 (pyrosetta.rosetta.protocols.fldsgn.topology.TripletID property) strand2() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif method) (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet method) strand_fraction() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) strand_id() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) strand_id1() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) strand_id2() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) strand_length() (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) strand_num (pyrosetta.rosetta.core.io.SHEETInformation property) strand_order() (pyrosetta.rosetta.protocols.fldsgn.topology.Sheet method) strand_pairing() (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) strand_pairing_set() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) strand_pairing_stats() (pyrosetta.rosetta.protocols.abinitio.Templates method) strand_pairings() (pyrosetta.rosetta.protocols.abinitio.Template method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.parser.BluePrint method) strand_weight() (pyrosetta.rosetta.protocols.abinitio.PairingStatistics method) StrandArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) StrandArchitectCreator (class in pyrosetta.rosetta.protocols.denovo_design.architects) StrandBundleFeatures (class in pyrosetta.rosetta.protocols.features.strand_assembly) StrandBundleFeaturesCreator (class in pyrosetta.rosetta.protocols.features.strand_assembly) strandClass (pyrosetta.rosetta.core.io.SHEETInformation property) StrandConstraints (class in pyrosetta.rosetta.protocols.abinitio) StrandCurvatureByLevels (class in pyrosetta.rosetta.protocols.fldsgn.filters) StrandCurvatureByLevelsCreator (class in pyrosetta.rosetta.protocols.fldsgn.filters) StrandFragment (class in pyrosetta.rosetta.protocols.features.strand_assembly) StrandHelixGeometryFilter (class in pyrosetta.rosetta.protocols.fldsgn.filters) StrandHelixGeometryFilterCreator (class in pyrosetta.rosetta.protocols.fldsgn.filters) StrandOrientation (class in pyrosetta.rosetta.protocols.denovo_design.components) StrandPairing (class in pyrosetta.rosetta.core.scoring.dssp) (class in pyrosetta.rosetta.protocols.denovo_design.components) (class in pyrosetta.rosetta.protocols.fldsgn.topology) StrandPairing.PairingType (class in pyrosetta.rosetta.protocols.denovo_design.components) StrandPairingSet (class in pyrosetta.rosetta.core.scoring.dssp) (class in pyrosetta.rosetta.protocols.fldsgn.topology) Strands (class in pyrosetta.rosetta.core.scoring) strands() (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) StrandTwistingMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) Strategy (class in pyrosetta.rosetta.core.conformation) strategy() (pyrosetta.rosetta.protocols.match.upstream.SampleStrategyData method) stream() (pyrosetta.rosetta.basic.resource_manager.locator.FileStream method) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream method) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream method) (pyrosetta.rosetta.basic.resource_manager.ResourceStream method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) streambuf (class in pyrosetta.rosetta.std) streams_from_cmd_line() (in module pyrosetta.rosetta.core.import_pose.pose_stream) strength() (pyrosetta.rosetta.protocols.environment.claims.JumpClaim method) (pyrosetta.rosetta.protocols.environment.claims.TorsionClaim method) (pyrosetta.rosetta.protocols.environment.claims.VirtResClaim method) (pyrosetta.rosetta.protocols.environment.claims.XYZClaim method) stretch() (pyrosetta.rosetta.protocols.dna.DNABasepair method) strict() (pyrosetta.rosetta.utility.Bound_bool_t method) Strict() (pyrosetta.rosetta.utility.Bound_bool_t static method) strict() (pyrosetta.rosetta.utility.Bound_double_t method) Strict() (pyrosetta.rosetta.utility.Bound_double_t static method) strict() (pyrosetta.rosetta.utility.Bound_int_t method) Strict() (pyrosetta.rosetta.utility.Bound_int_t static method) strict() (pyrosetta.rosetta.utility.Bound_std_string_t method) Strict() (pyrosetta.rosetta.utility.Bound_std_string_t static method) strict() (pyrosetta.rosetta.utility.Bound_utility_file_FileName_t method) Strict() (pyrosetta.rosetta.utility.Bound_utility_file_FileName_t static method) strict() (pyrosetta.rosetta.utility.Bound_utility_file_PathName_t method) Strict() (pyrosetta.rosetta.utility.Bound_utility_file_PathName_t static method) strict_base_pairing_count (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) strict_column_mode() (pyrosetta.rosetta.core.io.silent.SilentFileData method) strict_looprelax_checks() (pyrosetta.rosetta.protocols.loops.Loops method) strict_lower() (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.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_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_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) strict_upper() (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.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_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_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) STRICT_WC_STACKED_PAIR (pyrosetta.rosetta.core.scoring.rna.RNA_MotifType attribute) stride() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) string2float() (in module pyrosetta.rosetta.utility) string2int() (in module pyrosetta.rosetta.utility) string2Real() (in module pyrosetta.rosetta.utility) string2Size() (in module pyrosetta.rosetta.utility) string2uint() (in module pyrosetta.rosetta.utility) string_being_added (pyrosetta.rosetta.protocols.relax.VariableSubstitutionPair property) string_being_replaced (pyrosetta.rosetta.protocols.relax.VariableSubstitutionPair property) string_blosum() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) string_contains_gt_lt_or_ampersand() (in module pyrosetta.rosetta.utility.tag) string_data_ (pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct property) string_from_cycpep_rigid_body_permutation_mover_mode() (in module pyrosetta.rosetta.protocols.cyclic_peptide) string_from_property() (pyrosetta.rosetta.core.chemical.AtomPropertiesManager static method) string_from_type_set_mode() (in module pyrosetta.rosetta.core.chemical) string_groups (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore property) STRING_MAP (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) string_msg() (pyrosetta.rosetta.utility.SimulateMPIMessage method) string_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) STRING_OPTION (pyrosetta.rosetta.utility.options.OptionTypes attribute) string_path() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) string_properties() (pyrosetta.rosetta.core.chemical.ResidueProperties method) string_refine() (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) string_rep() (pyrosetta.rosetta.protocols.contact_map.Contact method) (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) string_split() (in module pyrosetta.rosetta.utility) string_split_multi_delim() (in module pyrosetta.rosetta.utility) string_split_simple() (in module pyrosetta.rosetta.utility) string_string_map() (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputSource method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputSource method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputSource method) string_string_pair_msg (pyrosetta.rosetta.protocols.jd3.deallocation.deallocation_msg_type attribute) string_to_CDRbounds() (in module pyrosetta.rosetta.protocols.tcr) string_to_compound_token() (pyrosetta.rosetta.core.io.HeaderInformation static method) string_to_enum() (pyrosetta.rosetta.core.io.mmtf.ExtraDataEnumManager method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric static method) string_to_experimental_technique() (in module pyrosetta.rosetta.core.io.rcsb) string_to_hb_eval_type() (in module pyrosetta.rosetta.core.scoring.hbonds) string_to_icoord_type() (in module pyrosetta.rosetta.core.chemical) string_to_int() (in module pyrosetta.rosetta.core.pose.rna) (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) string_to_real() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) string_to_sha1() (in module pyrosetta.rosetta.utility) string_value (pyrosetta.rosetta.protocols.features.MetricData property) string_value() (pyrosetta.rosetta.core.io.silent.SilentEnergy method) string_value_ (pyrosetta.rosetta.utility.py.Base property) string_vector_from_char_vector() (in module pyrosetta.rosetta.utility) STRING_VECTOR_OPTION (pyrosetta.rosetta.utility.options.OptionTypes attribute) stringafteroption() (in module pyrosetta.rosetta.basic.options) stringbuf (class in pyrosetta.rosetta.std) Stringifier (class in pyrosetta.rosetta.utility_exit_detail) StringMetric (class in pyrosetta.rosetta.core.simple_metrics) StringOption (class in pyrosetta.rosetta.utility.options) StringOptionKey (class in pyrosetta.rosetta.utility.options) StringResourceStream (class in pyrosetta.rosetta.basic.resource_manager.locator) stringstream (class in pyrosetta.rosetta.std) stringstream.sentry (class in pyrosetta.rosetta.std) StringVectorOption (class in pyrosetta.rosetta.utility.options) StringVectorOptionKey (class in pyrosetta.rosetta.utility.options) Stringy (class in pyrosetta.rosetta.utility_exit_detail) strip() (in module pyrosetta.rosetta.ObjexxFCL) (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) strip_atoms() (pyrosetta.rosetta.protocols.constel.SingResCnlCrea static method) strip_brackets() (in module pyrosetta.rosetta.core.io.nmr) strip_out_magnesiums() (in module pyrosetta.rosetta.protocols.magnesium) strip_rotamer_library_specification() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) strip_spacers() (in module pyrosetta.rosetta.core.sequence) STRIP_VIRTUAL_SIDE_CHAIN (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) strip_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) STRIPEHASH (pyrosetta.rosetta.core.conformation.Strategy attribute) stripped() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.protocols.constel.SingResCnlCrea static method) stripped_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) StrongT_unsigned_long_core_scoring_hbonds_graph_MResIDSize_t (class in pyrosetta.rosetta.utility) StrongT_unsigned_long_core_scoring_hbonds_graph_NodeIDSize_t (class in pyrosetta.rosetta.utility) StrongT_unsigned_long_core_scoring_hbonds_graph_RotamerIDSize_t (class in pyrosetta.rosetta.utility) StrongT_unsigned_long_protocols_jd3_GlobalJobID_t (class in pyrosetta.rosetta.utility) StrongT_unsigned_long_protocols_jd3_JobDAGNodeID_t (class in pyrosetta.rosetta.utility) StrongT_unsigned_long_protocols_jd3_NStructIndex_t (class in pyrosetta.rosetta.utility) StrongT_unsigned_long_protocols_jd3_PrelimJobNodeID_t (class in pyrosetta.rosetta.utility) StrongT_unsigned_long_protocols_jd3_ResultIndex_t (class in pyrosetta.rosetta.utility) StrongWolfe() (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) StrongWolfeLineMinimization (class in pyrosetta.rosetta.core.optimization) Stru (class in pyrosetta.rosetta.protocols.cluster.calibur) struct_file_rep() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) struct_from_job() (pyrosetta.rosetta.protocols.jd2.LazySilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) struct_id (pyrosetta.rosetta.protocols.antibody.CDRDBPose property) struct_ids_from_tag() (in module pyrosetta.rosetta.protocols.features) struct_source (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) StructAvrgMover (class in pyrosetta.rosetta.protocols.mpi_refinement) StructFileReaderOptions (class in pyrosetta.rosetta.core.io) StructFileRep (class in pyrosetta.rosetta.core.io) StructFileRepOptions (class in pyrosetta.rosetta.core.io) StructFragmentMover (class in pyrosetta.rosetta.protocols.struct_fragment) StructFragmentMoverCreator (class in pyrosetta.rosetta.protocols.struct_fragment) StructInfo (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) StructInfoComp (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) StructInfoCompdH (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) StructPerturberCM (class in pyrosetta.rosetta.protocols.abinitio.abscript) StructPerturberCMCreator (class in pyrosetta.rosetta.protocols.abinitio.abscript) StructProfileMover (class in pyrosetta.rosetta.protocols.simple_moves) StructProfileMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) StructuralSimilarityEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) structure() (pyrosetta.rosetta.core.io.rna.RDAT method) structure_database() (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) structure_has_moved() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) structure_id (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueEntry property) structure_id_ (pyrosetta.rosetta.protocols.legacy_sewing.Model property) structure_length (pyrosetta.rosetta.protocols.antibody.CDRDBPose property) structure_list() (pyrosetta.rosetta.core.io.silent.SilentFileData method) 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) structure_store() (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) structure_store_path() (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) StructureArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) StructureData (class in pyrosetta.rosetta.protocols.denovo_design.components) STRUCTUREDATA_OBSERVER (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType attribute) StructureDataCreator (class in pyrosetta.rosetta.protocols.denovo_design.components) StructureDataFactory (class in pyrosetta.rosetta.protocols.denovo_design.components) StructureDataObserver (class in pyrosetta.rosetta.protocols.denovo_design.components) StructureDataPerturber (class in pyrosetta.rosetta.protocols.denovo_design.components) StructureDependentCalculator (class in pyrosetta.rosetta.core.pose.metrics) StructureDependentPeakCalibrator (class in pyrosetta.rosetta.protocols.noesy_assign) StructureEntry (class in pyrosetta.rosetta.protocols.indexed_structure_store) StructureFeatures (class in pyrosetta.rosetta.protocols.features) StructureFeaturesCreator (class in pyrosetta.rosetta.protocols.features) StructureFileNames (class in pyrosetta.rosetta.protocols.pack_daemon) StructureIndependentPeakCalibrator (class in pyrosetta.rosetta.protocols.noesy_assign) StructureRestrictor (class in pyrosetta.rosetta.protocols.moves) structures() (pyrosetta.rosetta.core.io.rna.RDAT method) StructureScoresFeatures (class in pyrosetta.rosetta.protocols.features) StructureScoresFeaturesCreator (class in pyrosetta.rosetta.protocols.features) StructureSimilarityEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) StructureSlice (class in pyrosetta.rosetta.protocols.denovo_design.components) StructureStoreManager (class in pyrosetta.rosetta.protocols.indexed_structure_store) StructureStoreProvider (class in pyrosetta.rosetta.protocols.indexed_structure_store) Stub (class in pyrosetta.rosetta.core.kinematics) STUB_APPLIER (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) stub_atom() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.MutableICoorRecord method) stub_atom1() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.MutableICoorRecord method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) stub_atom1_id() (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) stub_atom2() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.MutableICoorRecord method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) stub_atom2_id() (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) stub_atom3() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.MutableICoorRecord method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) stub_atom3_id() (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) stub_defined() (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) STUB_DISTANCE (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) stub_from_id() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) stub_from_points() (in module pyrosetta.rosetta.protocols.hotspot_hashing) stub_id_to_named_stub_id() (in module pyrosetta.rosetta.core.conformation) (in module pyrosetta.rosetta.core.pose) stub_minimize_movers() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) stub_sets() (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreFilter 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.PlaceSimultaneouslyMover method) stub_tgt_angle() (in module pyrosetta.rosetta.protocols.hotspot_hashing) stub_to_points() (in module pyrosetta.rosetta.protocols.hotspot_hashing) stub_type() (pyrosetta.rosetta.core.chemical.MutableICoorRecord method) stub_type1() (pyrosetta.rosetta.core.chemical.MutableICoorRecord method) stub_type2() (pyrosetta.rosetta.core.chemical.MutableICoorRecord method) stub_type3() (pyrosetta.rosetta.core.chemical.MutableICoorRecord method) StubApplier (class in pyrosetta.rosetta.protocols.stepwise.screener) StubDistanceScreener (class in pyrosetta.rosetta.protocols.stepwise.screener) StubGenerator (class in pyrosetta.rosetta.protocols.hotspot_hashing) StubID (class in pyrosetta.rosetta.core.id) stubs_intra_residue() (pyrosetta.rosetta.protocols.environment.claims.JumpClaim method) StubScoreFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) StubScoreFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) StubScoreLoopsFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) StubScoreLoopsFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) StubStatus (class in pyrosetta.rosetta.protocols.hotspot_hashing) StubStubType (class in pyrosetta.rosetta.core.pose.rna) style (pyrosetta.rosetta.protocols.canonical_sampling.TorsionSpec property) sub_rank() (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) sub_to_full() (in module pyrosetta.rosetta.core.pose.full_model_info) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) subbin_cdf_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) subbin_cdf_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) subbin_end_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) subbin_end_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) subbin_start_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) subbin_start_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) subbin_type_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) subbin_type_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) subdir() (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepSequence method) subelement_behavior() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) subelement_ct_namer() (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect static method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover static method) subfilter() (pyrosetta.rosetta.protocols.filters.ReplicateFilter method) (pyrosetta.rosetta.protocols.filters.StochasticFilter method) subgraphs (pyrosetta.rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph property) SUBMOTIF (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AttachmentType attribute) submotif_frequency() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) submotif_info() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) submotif_info_containing_residues() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) submotif_info_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) submotif_library() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) submotif_tag() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) SubMotifInfo (class in pyrosetta.rosetta.core.pose.full_model_info) SubMotifLibrary (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.submotif) submover() (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) subprio() (pyrosetta.rosetta.protocols.environment.claims.ClaimStrength method) SubroutineMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) SubroutineMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) subset() (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) subset_mapping (class in pyrosetta.rosetta.utility) SubsetPartnerMotifScorer (class in pyrosetta.rosetta.protocols.sewing.scoring) SubsetPartnerMotifScorerCreator (class in pyrosetta.rosetta.protocols.sewing.scoring) substate() (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) substituent_full_name (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow property) substitute_residue() (in module pyrosetta.rosetta.protocols.dna) substitute_variables() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) substitute_variables_in_stream() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser static method) substitution_group() (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) substrate_type() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) subsubelement_ct_namer() (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover static method) subTest() (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) SUBTRACT (pyrosetta.rosetta.protocols.calc_taskop_filters.Operation attribute) subtract() (pyrosetta.rosetta.protocols.match.Bool3DGrid method) subtract_chi_angles() (in module pyrosetta.rosetta.core.pack.dunbrack) subtract_degree_angles() (in module pyrosetta.rosetta.basic) subtract_diagonal() (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) subtract_iterations() (pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet method) subtract_neighbors_mass() (pyrosetta.rosetta.core.scoring.TenANeighborNode method) subtract_radian_angles() (in module pyrosetta.rosetta.basic) SUBTRACT_SYMBOL (pyrosetta.rosetta.numeric.expression_parser.TokenType attribute) SubtractExpression (class in pyrosetta.rosetta.numeric.expression_parser) subtype() (pyrosetta.rosetta.protocols.environment.claims.ClaimStrength method) subunit_index() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) subunits() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) subunits_moved_by_jump() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) succeed_substitute_info() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) SUCCESS (pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus attribute) Success (pyrosetta.rosetta.protocols.loops.loop_mover.LoopResult attribute) success() (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) success_message (pyrosetta.rosetta.protocols.pack_daemon.DaemonSetMessage attribute) successful_jobs() (pyrosetta.rosetta.protocols.jd3.JobTracker method) SUCCINYLATION (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes attribute) suck (pyrosetta.rosetta.core.scoring.ScoreType attribute) SuckerEnergy (class in pyrosetta.rosetta.core.energy_methods) SuckerEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) suffix() (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.utility.options.OptionCollection static method) suffix_from_jd_with_sep() (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) suga (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) SUGAR (pyrosetta.rosetta.core.chemical.rna.BaseEdge attribute) (pyrosetta.rosetta.RNAAtomType attribute) sugar_bb (pyrosetta.rosetta.core.scoring.ScoreType attribute) sugar_edge_paired() (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential method) SUGAR_INSTANTIATOR (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) sugar_modifications_from_suffix() (in module pyrosetta.rosetta.core.io.carbohydrates) sugar_modifications_table_file() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager static method) sugar_torsion_atom_names() (in module pyrosetta.rosetta.core.scoring.dna) SugarBackboneEnergy (class in pyrosetta.rosetta.core.energy_methods) SugarBackboneEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) SugarBBSampler (class in pyrosetta.rosetta.protocols.simple_moves.bb_sampler) SugarInstantiateMover (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) SugarInstantiator (class in pyrosetta.rosetta.protocols.stepwise.screener) SugarModeling (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) SugarModificationsNomenclatureTableRow (class in pyrosetta.rosetta.core.chemical.carbohydrates) SugarVirtualizeMover (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) suggest_residue_number() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) suggest_topology() (pyrosetta.rosetta.protocols.abinitio.PairingStatistics method) SuggestValueMessage (class in pyrosetta.rosetta.protocols.topology_broker) suite_rmsd() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) suite_square_deviation() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) suiteness (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment property) suiteness_bonus (pyrosetta.rosetta.core.scoring.ScoreType attribute) suiteness_bonus() (pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions method) SULFATED_SUGAR (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) SULFATION (pyrosetta.rosetta.core.chemical.VariantType attribute) SULFOAMINO_SUGAR (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) SULPH (pyrosetta.rosetta.protocols.match.ProbeRadius attribute) SUM (pyrosetta.rosetta.core.scoring.nmr.NMR_VALUE_AVERAGING_TYPE attribute) sum (pyrosetta.rosetta.core.simple_metrics.metrics.summary_type attribute) SUM (pyrosetta.rosetta.protocols.calc_taskop_filters.Operation attribute) sum (pyrosetta.rosetta.protocols.cluster.DataPoint property) sum() (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.numeric.MathNTensor_bool_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_1_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_2_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_4_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_5_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_6_t method) (pyrosetta.rosetta.numeric.MathVector_double_t method) (pyrosetta.rosetta.protocols.frag_picker.scores.AdaptiveScoreHistogram method) sum_bound() (pyrosetta.rosetta.protocols.simple_ddg.ddG method) sum_constraint_scoreterms() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) sum_ddG() (pyrosetta.rosetta.protocols.simple_ddg.ddG method) sum_deriv_contributions_for_heavyatom_pair() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) sum_deriv_contributions_for_heavyatom_pair_one_way() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) sum_energies() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) sum_Hbond_terms() (pyrosetta.rosetta.protocols.simple_pose_metric_calculators.NumberHBondsCalculator static method) sum_of_neighbors_masses() (pyrosetta.rosetta.core.scoring.TenANeighborNode method) sum_of_square_differences() (in module pyrosetta.rosetta.numeric.linear_algebra) sum_of_squares() (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDecayData method) sum_total_residue_energy() (in module pyrosetta.rosetta.protocols.protein_interface_design) sum_unbound() (pyrosetta.rosetta.protocols.simple_ddg.ddG method) SumFunc (class in pyrosetta.rosetta.core.scoring.func) summarize_data() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) summarize_stored_data() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculator method) summary_lines() (pyrosetta.rosetta.protocols.residue_optimization.MetapatchEnumeration method) summary_type (class in pyrosetta.rosetta.core.simple_metrics.metrics) summary_type_total (pyrosetta.rosetta.core.simple_metrics.metrics.summary_type attribute) sumName (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) SUMOYLATION (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes attribute) sungetc() (pyrosetta.rosetta.std.filebuf method) (pyrosetta.rosetta.std.streambuf method) (pyrosetta.rosetta.std.stringbuf method) (pyrosetta.rosetta.std.wstreambuf method) (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) super_mute() (pyrosetta.rosetta.basic.MemTracer static method) (pyrosetta.rosetta.basic.MemTracerImpl static method) (pyrosetta.rosetta.basic.Tracer static method) (pyrosetta.rosetta.basic.TracerImpl static method) super_twiddles() (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) Supercharge (class in pyrosetta.rosetta.protocols.design_opt) superenv() (pyrosetta.rosetta.core.environment.EnvCore method) (pyrosetta.rosetta.protocols.environment.Environment method) superimpose() (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilter method) (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) superimpose_all() (in module pyrosetta.rosetta.protocols.mpi_refinement) superimpose_atom_id_map() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner method) superimpose_comb() (pyrosetta.rosetta.protocols.fldsgn.MatchResidues method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) superimpose_on_all() (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilter method) superimpose_over_all() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions 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.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) superimpose_over_all_instantiated() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner method) superimpose_overhangs_heavy() (in module pyrosetta.rosetta.protocols.grafting) superimpose_polymer_heavyatoms() (in module pyrosetta.rosetta.core.scoring) superimpose_pose() (in module pyrosetta.rosetta.core.scoring) superimpose_pose_legacy() (in module pyrosetta.rosetta.protocols.stepwise.modeler.align) superimpose_pose_on_subset_bb() (in module pyrosetta.rosetta.protocols.fibril) superimpose_pose_on_subset_CA() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) superimpose_res_in_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner method) superimpose_rmsd() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner method) superimpose_source_on_pose() (pyrosetta.rosetta.protocols.splice.RBOutMover 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) superimpose_to_ref_pose() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) superimpose_to_single_user_input_chunk() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) superimpose_with_stepwise_aligner() (in module pyrosetta.rosetta.protocols.stepwise.modeler.align) superimposeAndReplace() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) superimposed() (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) SuperimposeMover (class in pyrosetta.rosetta.protocols.simple_moves) SuperimposeMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) superposition_transform() (in module pyrosetta.rosetta.protocols.seeded_abinitio) (in module pyrosetta.rosetta.protocols.toolbox) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) supports_trRosetta_constraints() (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) suppress_bp_constraint() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) suppress_CSI_codes() (pyrosetta.rosetta.utility.CSI_Sequence static method) suppress_sampler_display() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) suppress_zero_occ_pdb_output() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) surf (pyrosetta.rosetta.core.scoring.packing.SurfVol property) (pyrosetta.rosetta.core.scoring.packing.SurfVolDeriv property) surf() (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) surf_vol_available() (in module pyrosetta.rosetta.core.scoring.packing) SURFACE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) surface (pyrosetta.rosetta.core.scoring.ScoreType attribute) SURFACE (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid attribute) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid.PtType attribute) surface_accessibility (pyrosetta.rosetta.core.scoring.packstat.CavityBallCluster property) surface_area (pyrosetta.rosetta.core.scoring.packstat.CavityBallCluster property) surface_atom_cutoff() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) surface_exposed_nb_cutoff() (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation method) SURFACE_EXPOSURE (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) surface_residue_cutoff() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) surface_vectors() (pyrosetta.rosetta.protocols.hotspot_hashing.SurfaceSearchPattern method) SurfaceCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) SurfaceDockingProtocol (class in pyrosetta.rosetta.protocols.surface_docking) SurfaceEnergies (class in pyrosetta.rosetta.core.scoring.solid_surface) SurfaceEnergy (class in pyrosetta.rosetta.core.pack.interaction_graph) SurfaceEnergyCreator (class in pyrosetta.rosetta.core.pack.interaction_graph) SurfaceOrientMover (class in pyrosetta.rosetta.protocols.surface_docking) SurfaceParameters (class in pyrosetta.rosetta.protocols.surface_docking) SurfacePotential (class in pyrosetta.rosetta.core.pack.interaction_graph) SurfaceSearchPattern (class in pyrosetta.rosetta.protocols.hotspot_hashing) SurfaceVectorLoader (class in pyrosetta.rosetta.protocols.surface_docking) SurfaceVectorLoaderCreator (class in pyrosetta.rosetta.protocols.surface_docking) SurfEnergy (class in pyrosetta.rosetta.core.energy_methods) SurfEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) SurfPrec (pyrosetta.rosetta.protocols.sparta.PDB property) SurfVol (class in pyrosetta.rosetta.core.scoring.packing) SurfVolDeriv (class in pyrosetta.rosetta.core.scoring.packing) SurfVolEnergy (class in pyrosetta.rosetta.core.energy_methods) SurfVolEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) surname() (pyrosetta.rosetta.basic.citation_manager.AuthorNames method) SurrogateVariableExpression (class in pyrosetta.rosetta.protocols.pack_daemon) surrounding_sasa_smoothing_window (pyrosetta.rosetta.core.scoring.packstat.SasaOptions property) SurroundingSS (class in pyrosetta.rosetta.protocols.denovo_design.task_operations) SVD (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet attribute) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet.COMPUTATION_TYPE attribute) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet attribute) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet.COMPUTATION_TYPE attribute) SVD_Solver (class in pyrosetta.rosetta.basic.svd) svdcmp() (in module pyrosetta.rosetta.numeric.linear_algebra) Svm_node_rosetta (class in pyrosetta.rosetta.utility.libsvm) Svm_rosetta (class in pyrosetta.rosetta.utility.libsvm) SW() (in module pyrosetta.rosetta.ObjexxFCL.format) swa_moves() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) SWAligner (class in pyrosetta.rosetta.core.sequence) swap() (in module pyrosetta.rosetta.ObjexxFCL) (in module pyrosetta.rosetta.std) (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.io.Remarks method) (pyrosetta.rosetta.numeric.Quaternion_double_t method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) 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(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.pointer.DeepCopyOP_const_core_kinematics_MoveMap_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_core_pose_Pose_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_core_scoring_bin_transitions_BinTransitionCalculator_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_protocols_antibody_AntibodyInfo_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_protocols_loops_Loops_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_chemical_AtomProperties_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_chemical_ResidueProperties_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_chemical_rotamers_RotamerLibrarySpecification_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_kinematics_MoveMap_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_pose_Pose_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_scoring_ScoreFunction_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_interpolation_spline_BicubicSpline_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_interpolation_spline_CubicSpline_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_interpolation_spline_PolycubicSplineBase_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_MathNTensorBase_double_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_protocols_loops_Loops_t method) swap4_aligned() (in module pyrosetta.rosetta.utility) swap_chain() (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) swap_chain_number() (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) swap_cols() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) swap_coordinates_in_pose() (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) swap_edge_energies() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) swap_file() (pyrosetta.rosetta.protocols.wum.WorkUnitQueue_Swapped method) swap_in() (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) swap_in_movemap() (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) swap_no_notify() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) swap_replicas() (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy method) swap_rows() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) swap_transform() (in module pyrosetta.rosetta.core.pose) SwapSegment (class in pyrosetta.rosetta.protocols.seeded_abinitio) SwapSegmentCreator (class in pyrosetta.rosetta.protocols.seeded_abinitio) sweep_incomplete() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) swin (pyrosetta.rosetta.core.scoring.APBSConfig.R_PARAM property) switch_chain_order() (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) switch_conformer() (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) SWITCH_EDGE (pyrosetta.rosetta.protocols.legacy_sewing.move_type attribute) switch_focus_among_poses_randomly() (in module pyrosetta.rosetta.protocols.stepwise.modeler) switch_focus_frequency() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) switch_focus_to_other_pose() (in module pyrosetta.rosetta.protocols.stepwise.modeler) switch_movemap() (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.Loops method) switch_residue_type_set() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) switch_segment() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) switch_to_centroid_rot_set() (in module pyrosetta.rosetta.core.util) SWITCH_TO_FULLATOM (pyrosetta.rosetta.protocols.abinitio.StageID attribute) switch_to_fullatom() (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.TopologyBroker method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) switch_to_residue_type_set() (in module pyrosetta.rosetta.core.util) SwitchChainOrderMover (class in pyrosetta.rosetta.protocols.simple_moves) SwitchChainOrderMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) SwitchMover (class in pyrosetta.rosetta.protocols.moves) SwitchMoverCreator (class in pyrosetta.rosetta.protocols.moves) SwitchResidueTypeSetMover (class in pyrosetta.rosetta.protocols.simple_moves) SwitchResidueTypeSetMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) sym (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet property) sym1 (pyrosetta.rosetta.core.io.SSBondInformation property) sym2 (pyrosetta.rosetta.core.io.SSBondInformation property) sym_bonus_lr (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) sym_dof_jump_num() (in module pyrosetta.rosetta.core.pose.symmetry) sym_dof_name() (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) sym_dof_names() (in module pyrosetta.rosetta.core.pose.symmetry) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilter method) (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceSasaFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter method) sym_lig (pyrosetta.rosetta.core.scoring.ScoreType attribute) SymAtomTreeMinimizer (class in pyrosetta.rosetta.core.optimization.symmetry) SymAtomTreeMultifunc (class in pyrosetta.rosetta.core.optimization.symmetry) symbol2index() (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.core.sequence.SSManager method) symbolString2base5index() (pyrosetta.rosetta.core.sequence.ABEGOManager method) symbolString2index() (pyrosetta.rosetta.core.sequence.SSManager method) SymDock_main() (in module pyrosetta.rosetta.protocols.symmetric_docking) SymDockBaseProtocol (class in pyrosetta.rosetta.protocols.symmetric_docking) SymDockingHiRes (class in pyrosetta.rosetta.protocols.symmetric_docking) SymDockingInitialPerturbation (class in pyrosetta.rosetta.protocols.symmetry) SymDockingLowRes (class in pyrosetta.rosetta.protocols.symmetric_docking) SymDockingSlideIntoContact (class in pyrosetta.rosetta.protocols.symmetry) SymDockProtocol (class in pyrosetta.rosetta.protocols.symmetric_docking) SymDockProtocolCreator (class in pyrosetta.rosetta.protocols.symmetric_docking) SymDof (class in pyrosetta.rosetta.core.conformation.symmetry) SymDofMover (class in pyrosetta.rosetta.protocols.matdes) SymDofMoverCreator (class in pyrosetta.rosetta.protocols.matdes) SymDofMoverSampler (class in pyrosetta.rosetta.protocols.matdes) symE_bonus (pyrosetta.rosetta.core.scoring.ScoreType attribute) symECreator (class in pyrosetta.rosetta.core.scoring.sym_e) symEnergy (class in pyrosetta.rosetta.core.scoring.sym_e) SymEnergyCutRotamerTrialsMover (class in pyrosetta.rosetta.protocols.minimization_packing.symmetry) SymFoldandDockMoveRbJumpMover (class in pyrosetta.rosetta.protocols.symmetric_docking) SymFoldandDockMoveRbJumpMoverCreator (class in pyrosetta.rosetta.protocols.symmetric_docking) SymFoldandDockRbTrialMover (class in pyrosetta.rosetta.protocols.symmetric_docking) SymFoldandDockRbTrialMoverCreator (class in pyrosetta.rosetta.protocols.symmetric_docking) SymFoldandDockSlideTrialMover (class in pyrosetta.rosetta.protocols.symmetric_docking) SymFoldandDockSlideTrialMoverCreator (class in pyrosetta.rosetta.protocols.symmetric_docking) symhash64() (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.xyzTransform_double_t method) (pyrosetta.rosetta.numeric.xyzTransform_float_t method) SymInterfaceSidechainMinMover (class in pyrosetta.rosetta.protocols.symmetric_docking) symm_count() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) symm_debug() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapDatabase method) symm_debug_force_map() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapDatabase method) symm_hack_arity() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) symm_info() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) symm_repeats() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) symm_subunits_expected() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper method) symm_type() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) SymmData (class in pyrosetta.rosetta.core.conformation.symmetry) SymmDataLoader (class in pyrosetta.rosetta.core.conformation.symmetry) SymmDataLoaderCreator (class in pyrosetta.rosetta.core.conformation.symmetry) symmetric() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) symmetric_components() (in module pyrosetta.rosetta.core.pose.symmetry) symmetric_fold_tree() (in module pyrosetta.rosetta.protocols.denovo_design) symmetric_gly_tables() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) symmetric_pcs_calc() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) symmetric_pre_calc() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) symmetric_rdc_calc() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) symmetric_residue_subset() (in module pyrosetta.rosetta.protocols.denovo_design) symmetric_rotamer_trials() (in module pyrosetta.rosetta.core.pack) symmetric_secstruct() (in module pyrosetta.rosetta.protocols.denovo_design) symmetric_sequence() (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) symmetric_task() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterface method) symmetric_transform() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) SymmetricAddMembraneMover (class in pyrosetta.rosetta.protocols.membrane.symmetry) SymmetricAddMembraneMoverCreator (class in pyrosetta.rosetta.protocols.membrane.symmetry) SymmetricalResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) SymmetricalResidueSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) SymmetricConformation (class in pyrosetta.rosetta.core.conformation.symmetry) SymmetricCycpepAlign (class in pyrosetta.rosetta.protocols.cyclic_peptide) SymmetricCycpepAlignCreator (class in pyrosetta.rosetta.protocols.cyclic_peptide) SymmetricEnergies (class in pyrosetta.rosetta.core.scoring.symmetry) SymmetricFragmentMover (class in pyrosetta.rosetta.protocols.simple_moves) SymmetricLigandEnergy (class in pyrosetta.rosetta.core.energy_methods) SymmetricLigandEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) SymmetricMotifFilter (class in pyrosetta.rosetta.protocols.simple_filters) SymmetricMotifFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) SymmetricRmsdEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) SymmetricRMSMover (class in pyrosetta.rosetta.protocols.symmetry) SymmetricRotamerSet_ (class in pyrosetta.rosetta.core.pack.rotamer_set.symmetry) SymmetricRotamerSets (class in pyrosetta.rosetta.core.pack.rotamer_set.symmetry) SymmetricScoreFunction (class in pyrosetta.rosetta.core.scoring.symmetry) symmetrize_by_intersection() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) symmetrize_by_union() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) symmetrize_fold_tree() (in module pyrosetta.rosetta.core.conformation.symmetry) (in module pyrosetta.rosetta.core.pose.symmetry) symmetrize_gly() (pyrosetta.rosetta.core.chemical.mainchain_potential.MainchainScoreTable method) symmetrize_output() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) symmetrize_spans() (in module pyrosetta.rosetta.protocols.membrane.symmetry) symmetry() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) symmetry_compliance() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) symmetry_compliance_weight_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) symmetry_copies() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) symmetry_definition() (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) symmetry_duplicate() (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) symmetry_info() (in module pyrosetta.rosetta.core.pose.symmetry) Symmetry_Info() (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) symmetry_info() (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) symmetry_repeats() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) SymmetryClaim (class in pyrosetta.rosetta.protocols.topology_broker.claims) SymmetryClaim.ClaimRight (class in pyrosetta.rosetta.protocols.topology_broker.claims) SymmetryClaimer (class in pyrosetta.rosetta.protocols.topology_broker) SymmetryInfo (class in pyrosetta.rosetta.core.conformation.symmetry) SymmetrySlider (class in pyrosetta.rosetta.protocols.symmetry) SymmetryTransform (class in pyrosetta.rosetta.core.conformation.symmetry) symminfo_ (pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions property) (pyrosetta.rosetta.protocols.electron_density.SelectDensityPointsOptions property) SymMinimizeInterface() (in module pyrosetta.rosetta.protocols.protein_interface_design) SymMinimizerMap (class in pyrosetta.rosetta.core.optimization.symmetry) SymMinMover (class in pyrosetta.rosetta.protocols.minimization_packing.symmetry) SymMinMoverCreator (class in pyrosetta.rosetta.protocols.minimization_packing.symmetry) SymmLinearMemEdge (class in pyrosetta.rosetta.core.pack.interaction_graph) SymmLinearMemNode (class in pyrosetta.rosetta.core.pack.interaction_graph) SymmLinearMemoryInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) SymmMinimalistEdge (class in pyrosetta.rosetta.core.pack.interaction_graph) SymmMinimalistInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) SymmMinimalistNode (class in pyrosetta.rosetta.core.pack.interaction_graph) SymmOnTheFlyEdge (class in pyrosetta.rosetta.core.pack.interaction_graph) SymmOnTheFlyInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) SymmOnTheFlyNode (class in pyrosetta.rosetta.core.pack.interaction_graph) symmop() (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) symmops() (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) SymPackRotamersMover (class in pyrosetta.rosetta.protocols.minimization_packing.symmetry) SymPackRotamersMoverCreator (class in pyrosetta.rosetta.protocols.minimization_packing.symmetry) SymRestrictTaskForDocking (class in pyrosetta.rosetta.protocols.symmetric_docking) SymRotamerTrialsMover (class in pyrosetta.rosetta.protocols.minimization_packing.symmetry) SymRotamerTrialsMoverCreator (class in pyrosetta.rosetta.protocols.minimization_packing.symmetry) SymShakeStructureMover (class in pyrosetta.rosetta.protocols.symmetry) SymSidechainMinMover (class in pyrosetta.rosetta.protocols.symmetric_docking) SymSlideInfo (class in pyrosetta.rosetta.core.conformation.symmetry) SymUnsatHbondFilter (class in pyrosetta.rosetta.protocols.matdes) SymUnsatHbondFilterCreator (class in pyrosetta.rosetta.protocols.matdes) SYN (pyrosetta.rosetta.core.chemical.rna.ChiState attribute) (pyrosetta.rosetta.core.fragment.rna.SYN_ANTI_RESTRICTION attribute) SYN_ANTI_RESTRICTION (class in pyrosetta.rosetta.core.fragment.rna) syn_G_potential_bonus() (pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions method) sync() (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.mpi_stream.basic_mpi_streambuf_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) sync_magnitudes_with_flags() (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) sync_objects_with_flags() (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) sync_with_stdio() (pyrosetta.rosetta.std.ios_base static method) SYNONYM (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation.CompoundToken attribute) sys_sleep() (in module pyrosetta.rosetta.utility)