Index – C

c (pyrosetta.rosetta.basic.sampling.orientations.Triple property) C (pyrosetta.rosetta.core.chemical.element.Elements attribute) (pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme.Enum attribute) (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueOrientEntry property) c (pyrosetta.rosetta.protocols.sic_dock.Vec3 property) C() (pyrosetta.rosetta.core.io.CrystInfo method) (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering method) (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) c0 (pyrosetta.rosetta.numeric.CubicPolynomial property) c0() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) c1 (pyrosetta.rosetta.numeric.CubicPolynomial property) c1() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) C1_ACETYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C1_AMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C1_BRANCH_POINT (pyrosetta.rosetta.core.chemical.VariantType attribute) C1_DEOXY_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C1_FLUORO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C1_GLYCOLYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C1_METHYLATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C1_MODIFIED (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) C1_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) C1_PHOSPHORYLATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C1_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C1_SULFATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C1_SULFOAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C1_THIO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) c1prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) c1prime_index_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) c2 (pyrosetta.rosetta.numeric.CubicPolynomial property) c2() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) c21 (pyrosetta.rosetta.protocols.normalmode.ContactStruct property) C2_ACETYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C2_AMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C2_BRANCH_POINT (pyrosetta.rosetta.core.chemical.VariantType attribute) C2_DEOXY_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C2_FLUORO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C2_GLYCOLYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C2_KETOALDONIC_ACID (pyrosetta.rosetta.core.chemical.VariantType attribute) C2_METHYLATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C2_MODIFIED (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) C2_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) C2_PHOSPHORYLATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C2_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C2_SULFATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C2_SULFOAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C2_THIO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) c2f() (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) c2n (pyrosetta.rosetta.protocols.rigid.Direction attribute) c2prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) c2prime_index_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) c3 (pyrosetta.rosetta.numeric.CubicPolynomial property) c3() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) C3_ACETYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C3_AMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C3_BRANCH_POINT (pyrosetta.rosetta.core.chemical.VariantType attribute) C3_DEOXY_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C3_FLUORO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C3_GLYCOLYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C3_KETOALDONIC_ACID (pyrosetta.rosetta.core.chemical.VariantType attribute) C3_METHYLATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C3_MODIFIED (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) C3_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) C3_PHOSPHORYLATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C3_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C3_SULFATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C3_SULFOAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C3_THIO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) c3prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) c3prime_index_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) C4_ACETYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C4_AMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C4_BRANCH_POINT (pyrosetta.rosetta.core.chemical.VariantType attribute) C4_DEOXY_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C4_FLUORO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C4_GLYCOLYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C4_KETOALDONIC_ACID (pyrosetta.rosetta.core.chemical.VariantType attribute) C4_METHYLATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C4_MODIFIED (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) C4_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) C4_PHOSPHORYLATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C4_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C4_SULFATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C4_SULFOAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C4_THIO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) c4prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) c4prime_index_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) C5_ACETYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C5_AMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C5_BRANCH_POINT (pyrosetta.rosetta.core.chemical.VariantType attribute) C5_DEOXY_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C5_FLUORO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C5_GLYCOLYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C5_KETOALDONIC_ACID (pyrosetta.rosetta.core.chemical.VariantType attribute) C5_METHYLATED_NA (pyrosetta.rosetta.core.chemical.VariantType attribute) C5_METHYLATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C5_MODIFIED (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) C5_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) C5_PHOSPHORYLATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C5_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C5_SULFATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C5_SULFOAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C5_THIO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) c5prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) c5prime_index_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) C6_ACETYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C6_AMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C6_BRANCH_POINT (pyrosetta.rosetta.core.chemical.VariantType attribute) C6_DEOXY_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C6_FLUORO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C6_GLYCOLYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C6_KETOALDONIC_ACID (pyrosetta.rosetta.core.chemical.VariantType attribute) C6_METHYLATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C6_MODIFIED (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) C6_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) C6_PHOSPHORYLATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C6_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C6_SULFATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C6_SULFOAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C6_THIO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C7_ACETYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C7_AMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C7_BRANCH_POINT (pyrosetta.rosetta.core.chemical.VariantType attribute) C7_DEOXY_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C7_FLUORO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C7_GLYCOLYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C7_KETOALDONIC_ACID (pyrosetta.rosetta.core.chemical.VariantType attribute) C7_METHYLATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C7_MODIFIED (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) C7_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) C7_PHOSPHORYLATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C7_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C7_SULFATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C7_SULFOAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C7_THIO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C8_ACETYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C8_AMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C8_BRANCH_POINT (pyrosetta.rosetta.core.chemical.VariantType attribute) C8_DEOXY_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C8_FLUORO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C8_GLYCOLYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C8_KETOALDONIC_ACID (pyrosetta.rosetta.core.chemical.VariantType attribute) C8_METHYLATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C8_MODIFIED (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) C8_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) C8_PHOSPHORYLATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C8_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C8_SULFATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C8_SULFOAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C8_THIO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C9_ACETYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C9_AMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C9_BRANCH_POINT (pyrosetta.rosetta.core.chemical.VariantType attribute) C9_DEOXY_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C9_FLUORO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C9_GLYCOLYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C9_METHYLATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C9_MODIFIED (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) C9_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) C9_PHOSPHORYLATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C9_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C9_SULFATED_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C9_SULFOAMINO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C9_THIO_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) C_ALA (pyrosetta.rosetta.protocols.match.ProbeRadius attribute) c_alpha_index() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) c_anchor() (pyrosetta.rosetta.protocols.sic_dock.Rose method) c_array_mult() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) C_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) c_beta_index() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) C_CAR (pyrosetta.rosetta.protocols.match.ProbeRadius attribute) C_D_dist_Ang (pyrosetta.rosetta.core.kinematics.inverse.InternalCoordGeometry property) C_D_E_bond_angle_rad (pyrosetta.rosetta.core.kinematics.inverse.InternalCoordGeometry property) C_D_E_F_torsion_angle_rad (pyrosetta.rosetta.core.kinematics.inverse.InternalCoordGeometry property) c_flex (pyrosetta.rosetta.protocols.fold_from_loops.utils.NubSegment property) c_linked_NxC (pyrosetta.rosetta.protocols.carbohydrates.GlycanSequon attribute) c_linked_WSTxC (pyrosetta.rosetta.protocols.carbohydrates.GlycanSequon attribute) c_linked_WxxW (pyrosetta.rosetta.protocols.carbohydrates.GlycanSequon attribute) C_METHYLAMIDATION (pyrosetta.rosetta.core.chemical.VariantType attribute) C_METHYLATED_SUGAR (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) c_mult_ip() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) c_n() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) c_n_bond() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) c_n_ca() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) c_n_ca_angle() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) C_pi_sp2 (pyrosetta.rosetta.core.chemical.orbitals.orbital_type_enum attribute) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics attribute) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics.orbital_type_name attribute) C_pos() (pyrosetta.rosetta.protocols.match.upstream.OriginalBackboneBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.ProteinBackboneBuildPoint method) c_segment() (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) c_str (pyrosetta.rosetta.protocols.environment.claims.DOFElement property) c_str() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) c_term_pose (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover.Design property) c_term_stack (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover.Design property) c_terminal_constraint_strength() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) c_terminus_size() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) c_xyz() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) Ca (pyrosetta.rosetta.core.chemical.element.Elements attribute) CA (pyrosetta.rosetta.protocols.frag_picker.ContactType attribute) (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueOrientEntry property) CA() (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) CA2_COORDINATION (pyrosetta.rosetta.core.chemical.VariantType attribute) CA_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) ca_c() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) ca_c_bond() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) ca_c_n() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) ca_c_n_angle() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) ca_cb_orient() (pyrosetta.rosetta.protocols.fldsgn.topology.Sheet method) ca_cb_orients() (pyrosetta.rosetta.protocols.fldsgn.topology.Sheet method) CA_CONNECT (pyrosetta.rosetta.core.chemical.VariantType attribute) CA_CONNECT2 (pyrosetta.rosetta.core.chemical.VariantType attribute) CA_CONNECT3 (pyrosetta.rosetta.core.chemical.VariantType attribute) CA_CONNECT4 (pyrosetta.rosetta.core.chemical.VariantType attribute) CA_CONNECT5 (pyrosetta.rosetta.core.chemical.VariantType attribute) CA_CONNECT6 (pyrosetta.rosetta.core.chemical.VariantType attribute) CA_CONNECT7 (pyrosetta.rosetta.core.chemical.VariantType attribute) Ca_coords() (in module pyrosetta.rosetta.protocols.protein_interface_design.filters) ca_cprev_n_h_interres_improper_params() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) CA_DME_EVALUATION (pyrosetta.rosetta.basic.ProfTag attribute) CA_gdtmm() (in module pyrosetta.rosetta.core.scoring) CA_gdttm() (in module pyrosetta.rosetta.core.scoring) CA_maxsub() (in module pyrosetta.rosetta.core.scoring) ca_nnext_c_o_interres_improper_params() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) CA_ONLY (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover.AtomSelector attribute) ca_only (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.ConstraintConditions property) CA_only() (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilter method) CA_or_equiv_rmsd() (in module pyrosetta.rosetta.core.scoring) CA_pos() (pyrosetta.rosetta.protocols.match.upstream.OriginalBackboneBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.ProteinBackboneBuildPoint method) CA_rmsd() (in module pyrosetta.rosetta.core.scoring) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) CA_RMSD_EVALUATION (pyrosetta.rosetta.basic.ProfTag attribute) CA_rmsd_symmetric() (in module pyrosetta.rosetta.core.scoring) CA_Sscore() (in module pyrosetta.rosetta.protocols.mpi_refinement) CA_superimpose() (in module pyrosetta.rosetta.protocols.toolbox) ca_xyz() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) CaCbCb_Angle_Func (class in pyrosetta.rosetta.core.scoring.disulfides) CaCbCbCa_Dihedral_Func (class in pyrosetta.rosetta.core.scoring.disulfides) cache() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.cppdb.backend.statement method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) cache_all_types_with_variants_aa() (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) cache_all_types_with_variants_residuetypecops() (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) cache_fragments() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) cache_limit() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) cache_pose() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) cache_prefix_ (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric property) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric property) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric property) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric property) cache_profile() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) cache_resfile() (pyrosetta.rosetta.core.pack.task.operation.ReadResfile method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) cache_suffix_ (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric property) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric property) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric property) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric property) cache_tag() (pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) cache_task() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) CacheableAtomID_MapVector (class in pyrosetta.rosetta.core.id) CacheableData (class in pyrosetta.rosetta.basic.datacache) CacheableDataType (class in pyrosetta.rosetta.core.pose.datacache) CacheableDataType.Enum (class in pyrosetta.rosetta.core.pose.datacache) CacheableObserver (class in pyrosetta.rosetta.core.pose.datacache) CacheableObserverType (class in pyrosetta.rosetta.core.pose.datacache) CacheablePoseRawPtr (class in pyrosetta.rosetta.core.pose.datacache) CacheableResidueTypeSets (class in pyrosetta.rosetta.core.chemical) CacheableResRotPairFloatMap (class in pyrosetta.rosetta.basic.datacache) CacheableString (class in pyrosetta.rosetta.basic.datacache) CacheableStringFloatMap (class in pyrosetta.rosetta.basic.datacache) CacheableStringIntegerMap (class in pyrosetta.rosetta.basic.datacache) CacheableStringMap (class in pyrosetta.rosetta.basic.datacache) CacheableUint64MathMatrixFloatMap (class in pyrosetta.rosetta.basic.datacache) cached_calculate() (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.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) cached_data (pyrosetta.rosetta.protocols.environment.EnvClaimBroker.BrokerResult property) cached_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.CachingScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.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.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.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) CachedResidueSubset (class in pyrosetta.rosetta.core.select.residue_selector) CacheWrapper_protocols_simple_moves_GunnTuple_core_fragment_MapCacheUnit_protocols_simple_moves_GunnTuple_t (class in pyrosetta.rosetta.core.fragment) CachingScoringMethod (class in pyrosetta.rosetta.protocols.frag_picker.scores) CAcrd (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData property) CAcstGenerator (class in pyrosetta.rosetta.protocols.seeded_abinitio) CAcstGeneratorCreator (class in pyrosetta.rosetta.protocols.seeded_abinitio) cal_delta_internal_coordinates() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) cal_delta_internal_coordinates_squared() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) cal_dis_angle_to_find_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) cal_distance() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.protocols.pockets.SmallMol method) cal_distance_squared() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) cal_min_avg_dis_between_sheets_by_cen_res() (in module pyrosetta.rosetta.protocols.features.strand_assembly) cal_min_avg_dis_between_two_sheets_by_cen_res() (in module pyrosetta.rosetta.protocols.features.strand_assembly) cal_min_dis_between_sheets_by_all_res() (in module pyrosetta.rosetta.protocols.features.strand_assembly) cal_min_dis_between_two_sheets_by_all_res() (in module pyrosetta.rosetta.protocols.features.strand_assembly) cal_min_dist() (pyrosetta.rosetta.protocols.pockets.SmallMol method) cal_num_of_sheets_that_surround_this_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) cal_shortest_dis_between_facing_aro_in_sw() (in module pyrosetta.rosetta.protocols.features.strand_assembly) Calc() (pyrosetta.rosetta.core.scoring.sc.ContactMolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ElectrostaticComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ElectrostaticSimilarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeSimilarityCalculator method) calc_accept_rate() (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) calc_all_averages() (in module pyrosetta.rosetta.protocols.unfolded_state_energy_calculator) calc_all_dist() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) calc_ang_score() (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergy method) calc_angle_rmsd() (in module pyrosetta.rosetta.protocols.membrane) calc_avg_nbrhood_bfac() (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) calc_avg_residue_bfac() (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) calc_bb_boltz_probs() (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) calc_boltz_score() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) calc_CA_Irmsd() (in module pyrosetta.rosetta.protocols.docking) calc_CAPRI_rank() (in module pyrosetta.rosetta.protocols.docking) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) calc_cenlist() (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) calc_centroids() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) calc_curr_hbond_weights() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) calc_delta_sasa() (in module pyrosetta.rosetta.protocols.fldsgn.topology) calc_dihedral() (in module pyrosetta.rosetta.protocols.denovo_design.movers) (in module pyrosetta.toolbox.numpy_utils) calc_dist() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) calc_ElectricField() (pyrosetta.rosetta.protocols.sparta.PDB method) calc_energy() (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) calc_ensemble_accept_rate_() (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) calc_exp_value_aa_matrix() (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) calc_exp_value_rot_matrix() (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) calc_final_rotamer_probs() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) calc_final_rotamers() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) calc_Fnat() (in module pyrosetta.rosetta.protocols.docking) calc_fnat() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) calc_Fnonnat() (in module pyrosetta.rosetta.protocols.docking) calc_frac_native_contacts() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics method) calc_gamma_I() (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingleSet method) calc_gdt() (pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator method) calc_geometry() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Sheet method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) calc_gJ() (pyrosetta.rosetta.core.io.nmr.ParaIon method) calc_GlycanDock_intf_metrics() (in module pyrosetta.rosetta.protocols.glycan_docking) calc_helix_axis() (in module pyrosetta.rosetta.protocols.membrane) calc_helix_tilt_angle() (in module pyrosetta.rosetta.protocols.membrane) calc_HN_S2() (pyrosetta.rosetta.protocols.sparta.PDB method) calc_IMMS_score() (pyrosetta.rosetta.core.energy_methods.CCS_IMMSEnergy method) calc_inout() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif method) calc_interacting_vector() (in module pyrosetta.rosetta.core.select.util) calc_interaction_energy() (in module pyrosetta.rosetta.protocols.docking) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) calc_interface_metrics() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics method) calc_interface_vector() (in module pyrosetta.rosetta.core.select.util) calc_intf_score() (in module pyrosetta.rosetta.protocols.docking) calc_Irms() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) calc_Irmsd() (in module pyrosetta.rosetta.protocols.docking) calc_Irmsd_legacy() (in module pyrosetta.rosetta.protocols.docking) calc_kl_divergence() (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) calc_long_range() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge method) calc_Lrmsd() (in module pyrosetta.rosetta.protocols.docking) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) calc_mean_field() (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) calc_medoids() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) calc_new_atom_location() (in module pyrosetta.rosetta.core.kinematics.inverse) calc_omega_I() (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingleSet method) calc_P1rmsd() (in module pyrosetta.rosetta.protocols.docking) calc_P2rmsd() (in module pyrosetta.rosetta.protocols.docking) calc_penalty_vec() (pyrosetta.rosetta.core.scoring.constraints.FabConstraint method) calc_pep_scores() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics method) calc_per_atom_sasa() (in module pyrosetta.rosetta.core.scoring) calc_per_atom_sasa_sc() (in module pyrosetta.rosetta.core.scoring) calc_per_res_hydrophobic_sasa() (in module pyrosetta.rosetta.core.scoring) calc_per_rsd_score() (in module pyrosetta.rosetta.core.scoring.electron_density) calc_pfront_poses_filter_ranks() (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) calc_phipsi_RMSD() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics method) calc_point_mut_filters() (pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator method) (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) calc_product() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser method) calc_quadratic() (in module pyrosetta.rosetta.basic) calc_res_contact() (in module pyrosetta.rosetta.protocols.docking) (in module pyrosetta.rosetta.protocols.glycan_docking) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) calc_residue_burial() (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) CALC_RMS (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) calc_rms() (in module pyrosetta.rosetta.numeric.model_quality) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) calc_rms_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) calc_rmsd_Theobald_method() (pyrosetta.rosetta.numeric.alignment.QCPKernel_double_t static method) calc_rnp_pair_dist_score() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPairDistPotential method) calc_rotamer_clusters() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) calc_rsd_sasa() (in module pyrosetta.rosetta.protocols.forge.methods) calc_running_avg() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) calc_sasa_bothsides() (pyrosetta.rosetta.protocols.fldsgn.topology.Sheet method) calc_sc_neighbors() (in module pyrosetta.rosetta.core.select.util) calc_score() (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) calc_short_range() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge method) calc_shortest_dist_by_atoms() (pyrosetta.rosetta.protocols.simple_filters.HelixHelixAngleFilter method) calc_sl_for_res() (pyrosetta.rosetta.core.scoring.epr_deer.EPRSpinLabel method) calc_span_score() (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) calc_standard_deviations() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) calc_strand_helix_angle() (in module pyrosetta.rosetta.protocols.fldsgn.topology) calc_strand_pairing_set() (in module pyrosetta.rosetta.protocols.fldsgn.topology) calc_time() (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) calc_total_sasa() (in module pyrosetta.rosetta.core.scoring) calc_vector_boltzmann() (in module pyrosetta.rosetta.protocols.unfolded_state_energy_calculator) calc_vector_mean() (in module pyrosetta.rosetta.protocols.unfolded_state_energy_calculator) calc_vector_median() (in module pyrosetta.rosetta.protocols.unfolded_state_energy_calculator) calc_vector_mode() (in module pyrosetta.rosetta.protocols.unfolded_state_energy_calculator) calc_xyzs() (pyrosetta.rosetta.core.scoring.constraints.AtomToAxisConstraint method) calc_zscore() (in module pyrosetta.rosetta.numeric) CalcContactArea() (pyrosetta.rosetta.core.scoring.sc.ContactMolecularSurfaceCalculator method) calcdepth() (pyrosetta.rosetta.core.scoring.atomic_depth.AtomicDepth method) calcenergy (pyrosetta.rosetta.core.scoring.APBSConfig property) (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) calcExplicitValence() (pyrosetta.rosetta.RDKit.Atom method) calcforce (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) calcImplicitValence() (pyrosetta.rosetta.RDKit.Atom method) CalcInterNeighborGroup (class in pyrosetta.rosetta.protocols.toolbox) calcLevel1() (pyrosetta.rosetta.protocols.sparta.ANN method) calcLevel2() (pyrosetta.rosetta.protocols.sparta.ANN method) calcPlane() (pyrosetta.rosetta.protocols.sparta.PDB method) CalcSc() (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator static method) CalcSs() (pyrosetta.rosetta.core.scoring.sc.ShapeSimilarityCalculator method) calcSurface() (pyrosetta.rosetta.protocols.sparta.PDB method) calcualate_total_score_and_tensors() (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergy method) calculate() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric method) (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa method) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod 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.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.dna.DNAParameters 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.filters.StochasticFilter method) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportPSSMDifferences method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric method) (pyrosetta.rosetta.protocols.scoring.Interface method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDistSasaCalculator method) calculate_additional_glycosylation_metrics() (in module pyrosetta.rosetta.protocols.glycopeptide_docking) calculate_and_store_all_derivs() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) calculate_angles() (pyrosetta.rosetta.protocols.features.SmotifFeatures method) calculate_atom_id_domain_map() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) calculate_atom_id_map() (pyrosetta.rosetta.core.pose.toolbox.AtomID_Mapper method) calculate_auc() (pyrosetta.rosetta.numeric.RocCurve method) calculate_axes() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) calculate_blocks() (in module pyrosetta.rosetta.protocols.pose_sewing) calculate_blocks_from_subset() (in module pyrosetta.rosetta.protocols.pose_sewing) calculate_center_xyz() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) calculate_contact_order() (pyrosetta.rosetta.core.energy_methods.ContactOrderEnergy method) calculate_cost_only_with_svd() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide method) calculate_current_temperature() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_SigmoidalTemperatureScheduleGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator method) calculate_density_nbr() (in module pyrosetta.rosetta.core.scoring.electron_density) calculate_dihedral_distance() (in module pyrosetta.rosetta.numeric.model_quality) (in module pyrosetta.rosetta.protocols.antibody.clusters) calculate_dihedral_w_4_resnums() (in module pyrosetta.rosetta.protocols.features.strand_assembly) calculate_distance_matrix() (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) calculate_distance_score_bt_residues() (in module pyrosetta.rosetta.protocols.pose_sewing) calculate_energy() (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_ChemicalMappingEnergy 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_DomeHelper 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.sap.SapConstraintHelper method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.scoring.annealing.ResidueArrayAnnealableEnergy method) calculate_error_twist() (in module pyrosetta.rosetta.core.kinematics.jacobian) calculate_fitness() (pyrosetta.rosetta.protocols.recon_design.FitnessFilter method) calculate_fitness_mpi() (pyrosetta.rosetta.protocols.recon_design.FitnessFilter method) calculate_fixed_fields_for_polarization() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) calculate_frh_frl() (in module pyrosetta.rosetta.protocols.antibody.grafting) calculate_geometry() (in module pyrosetta.rosetta.core.scoring.electron_density) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) calculate_grid() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) calculate_helical_parameters() (pyrosetta.rosetta.protocols.simple_filters.RepeatParameterFilter method) calculate_helical_parameters_helper() (pyrosetta.rosetta.protocols.simple_filters.RepeatParameterFilter method) calculate_helices() (in module pyrosetta.rosetta.protocols.pose_sewing) calculate_highres_ref_energy() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) calculate_identity_score() (in module pyrosetta.rosetta.protocols.tcr) calculate_induced_fields_for_polarization() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) calculate_interface_score() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) calculate_interres() (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) calculate_intra_res_hbonds() (in module pyrosetta.rosetta.core.scoring.hbonds) calculate_intrares() (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) calculate_inverting_virtuals() (in module pyrosetta.rosetta.core.conformation.symmetry) calculate_jacobians() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) calculate_ligand_CoM() (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) calculate_ligand_density_correlation() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) calculate_lk_ball_atom_energies() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) calculate_lk_ball_atom_energies_cp() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) calculate_lk_desolvation_of_single_atom_by_residue() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) calculate_lowres_ref_energy() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) calculate_motif_score_bt_residues() (in module pyrosetta.rosetta.protocols.pose_sewing) calculate_neighbor_table() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver method) calculate_new_jump() (in module pyrosetta.rosetta.core.kinematics.inverse) calculate_orbital_icoor() (pyrosetta.rosetta.core.chemical.orbitals.AssignOrbitals method) calculate_pcs_score() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy 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) calculate_pcs_score_on_PCS_data_center_CA() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) calculate_penalty_once_almost_from_scratch_using_reference_graph() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) calculate_penalty_once_from_scratch() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) calculate_per_atom_sap() (in module pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) calculate_per_position_scores() (pyrosetta.rosetta.core.sequence.SequenceAlignment method) calculate_per_res_sap() (in module pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) calculate_per_residue_interface_score() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) calculate_plane_axes() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) calculate_pocket_density_correlation() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) calculate_point_in_cone() (in module pyrosetta.rosetta.core.select.util) calculate_pool_diversity() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) calculate_pose_density_correlation() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) calculate_protein_CoM() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) calculate_rama() (in module pyrosetta.rosetta.core.scoring.electron_density) calculate_res_res_fixed_fields_for_polarization() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) calculate_res_res_induced_fields_for_polarization() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) calculate_rg_score() (pyrosetta.rosetta.core.energy_methods.RG_Energy_Fast method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergy method) calculate_rho_fast2() (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyDens method) calculate_rigid_matrix() (in module pyrosetta.rosetta.core.chemical) calculate_rmsd() (in module pyrosetta.rosetta.protocols.splice) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) calculate_rotamer_set_design_targets_partition_sum() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) calculate_rt() (pyrosetta.rosetta.core.scoring.constraints.RTConstraint method) calculate_sampled_distance() (in module pyrosetta.rosetta.protocols.glycopeptide_docking) calculate_sap() (in module pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) calculate_score() (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) calculate_score_sum_of_pairs() (pyrosetta.rosetta.core.sequence.SequenceAlignment method) calculate_slow_approx_sap() (in module pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) calculate_stability_metric() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) calculate_statistics() (in module pyrosetta.rosetta.protocols.ncbb) calculate_tensor_and_cost_with_svd() (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) calculate_tensor_only_with_svd() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide method) calculate_total_cst_score() (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) (pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint method) calculate_total_score() (pyrosetta.rosetta.protocols.nmr.pre.PREEnergy method) calculate_visibility() (pyrosetta.rosetta.basic.MemTracerImpl.TracerProxyImpl method) (pyrosetta.rosetta.basic.TracerImpl.TracerProxyImpl method) calculate_water_overcoordinated_hb_correction() (in module pyrosetta.rosetta.protocols.hydrate) calculated() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) calculateDensityMap() (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) Calculator (class in pyrosetta.rosetta.numeric) calculator() (pyrosetta.rosetta.protocols.pose_metric_calculators.MetricValueGetter method) calculator_cop() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) calculator_id() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) calculator_name() (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculatorCreator method) calculator_op() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) CalculatorFactory (class in pyrosetta.rosetta.core.pose.metrics) CalculatorFilter (class in pyrosetta.rosetta.protocols.filters) CalculatorFilterCreator (class in pyrosetta.rosetta.protocols.filters) CalculatorMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) CalculatorMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.metrics) CALCULATORMODE (class in pyrosetta.rosetta.protocols.buns) CALIBRATION_ATOM_TYPE (class in pyrosetta.rosetta.protocols.noesy_assign) calibration_atom_type() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) calibration_constant() (pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator method) calibration_convergence_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) calibration_cycles_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) calibration_eliminate_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) calibration_ignore_eliminated_peaks_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) calibration_max_noe_dist_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) calibration_max_nudging_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) calibration_start_nudging_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) calibration_stop_nudging_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) calibration_target_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) calibration_use_median_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) call_order() (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) call_output_observers() (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.Job method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmtfJobOutputter method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob 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.make_rot_lib.MakeRotLibJob method) call_setup() (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) Calpha_restraints_ (pyrosetta.rosetta.protocols.ligand_docking.LigandArea property) calpha_superimpose_pose() (in module pyrosetta.rosetta.core.scoring) calpha_superimpose_with_mapping() (in module pyrosetta.rosetta.core.sequence) calpha_vector_ (pyrosetta.rosetta.protocols.cluster.calibur.SimPDB property) (pyrosetta.rosetta.protocols.cluster.calibur.Stru property) calRMSD() (pyrosetta.rosetta.protocols.pockets.SmallMol static method) came_from() (pyrosetta.rosetta.core.sequence.Cell method) camelid_last_loop (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) CamShiftEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) CamShiftEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) can_be_added_to() (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.LegacyRequirementSet method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyResidueRetentionRequirement method) can_be_copied (pyrosetta.rosetta.core.conformation.parametric.ParameterizationCalculatorProperties property) can_be_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) can_be_deleted() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) can_be_perturbed (pyrosetta.rosetta.core.conformation.parametric.ParameterizationCalculatorProperties property) can_be_perturbed() (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) can_be_sampled (pyrosetta.rosetta.core.conformation.parametric.ParameterizationCalculatorProperties property) can_be_sampled() (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) can_be_set (pyrosetta.rosetta.core.conformation.parametric.ParameterizationCalculatorProperties property) can_be_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) CAN_CONTROL (pyrosetta.rosetta.protocols.environment.claims.ClaimStrength attribute) (pyrosetta.rosetta.protocols.environment.claims.ClaimStrength.PrioSubtype attribute) (pyrosetta.rosetta.protocols.environment.claims.ControlStrength attribute) can_delete() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) can_hash() (pyrosetta.rosetta.protocols.sewing.hashing.Hasher method) can_hold_another() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.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) CAN_INIT (pyrosetta.rosetta.protocols.topology_broker.claims.BBClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.BBClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.CutClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.CutClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.LegacyRootClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.LegacyRootClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.SequenceClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.SequenceClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.SymmetryClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.SymmetryClaim.ClaimRight attribute) can_load() (pyrosetta.protocols.h5_structure_store_provider.H5StructureStoreProvider method) (pyrosetta.rosetta.protocols.indexed_structure_store.DirStructureStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.JSONStructureStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.SilentStructureStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreProvider method) can_write() (pyrosetta.protocols.h5_structure_store_provider.H5StructureStoreProvider method) (pyrosetta.rosetta.protocols.indexed_structure_store.DirStructureStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.JSONStructureStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.SilentStructureStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreProvider method) cancel_batches_previous_to() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) candidate_address_ (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.DataBuffer property) candidate_best_rmsd_ (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.DataBuffer property) candidate_coords_ (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.DataBuffer property) candidate_for (pyrosetta.rosetta.protocols.cluster.DataPoint property) candidate_nbr_index_ (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.DataBuffer property) candidate_res_atoms_reqd_near_target_atom() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.ScoringSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) candidates (pyrosetta.rosetta.protocols.cluster.DataPoint property) CandidatesCollector (class in pyrosetta.rosetta.protocols.frag_picker) canonical() (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepLibrary method) CANONICAL_AA (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) canonical_atom_alias() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) canonical_atom_aliases() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) canonical_atom_count() (in module pyrosetta.rosetta.core.pose) canonical_base_pair_step_library() (pyrosetta.rosetta.core.import_pose.libraries.RNA_LibraryManager method) CANONICAL_NUCLEIC (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) canonical_residue_count() (in module pyrosetta.rosetta.core.pose) canonical_sampling_main() (in module pyrosetta.rosetta.protocols.canonical_sampling) canonicalize() (in module pyrosetta.rosetta.protocols.denovo_design.components) Canonicalize() (pyrosetta.rosetta.basic.sampling.orientations.Quaternion method) CANONICALMOVER_WRITE_TO_FILE (pyrosetta.rosetta.basic.ProfTag attribute) CanonicalSamplingMover (class in pyrosetta.rosetta.protocols.canonical_sampling) cap (pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi property) cap_ends() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) cap_espGrid() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) capacity() (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.heap method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyOptionKey_utility_options_VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyVectorOptionKey_utility_options_VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanOptionKey_utility_options_BooleanOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanVectorOptionKey_utility_options_BooleanVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_FileOptionKey_utility_options_FileOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_FileVectorOptionKey_utility_options_FileVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerOptionKey_utility_options_IntegerOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerVectorOptionKey_utility_options_IntegerVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_OptionKey_utility_options_OptionTypes_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathOptionKey_utility_options_PathOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathVectorOptionKey_utility_options_PathVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealOptionKey_utility_options_RealOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealVectorOptionKey_utility_options_RealVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_ResidueChainVectorOptionKey_utility_options_ResidueChainVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringOptionKey_utility_options_StringOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringVectorOptionKey_utility_options_StringVectorOption_t method) (pyrosetta.rosetta.utility.vector0_core_conformation_ppo_torsion_bin method) (pyrosetta.rosetta.utility.vector0_core_id_AtomID_Map_bool_t method) (pyrosetta.rosetta.utility.vector0_core_io_AtomInformation method) (pyrosetta.rosetta.utility.vector0_double method) (pyrosetta.rosetta.utility.vector0_float method) (pyrosetta.rosetta.utility.vector0_int method) (pyrosetta.rosetta.utility.vector0_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector0_protocols_flexpack_interaction_graph_FlexbbSparseMatrixIndex method) (pyrosetta.rosetta.utility.vector0_std_list_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.utility.vector0_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector0_std_pair_float_float_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_moves_Mover_t method) (pyrosetta.rosetta.utility.vector0_std_string method) (pyrosetta.rosetta.utility.vector0_unsigned_char method) (pyrosetta.rosetta.utility.vector0_unsigned_long method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_double_3_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_double_5_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_utility_fixedsizearray0_double_3_3_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_utility_fixedsizearray0_double_5_5_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray1_double_16_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_core_io_AtomInformation_std_allocator_core_io_AtomInformation_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_int_std_allocator_int_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_std_list_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_list_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_std_allocator_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_std_pair_int_int_std_allocator_std_pair_int_int_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_basic_citation_manager_AuthorNames method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_Column method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_ForeignKey method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_Index method) (pyrosetta.rosetta.utility.vector1_basic_sampling_orientations_QuatDBMetadata method) (pyrosetta.rosetta.utility.vector1_bool method) (pyrosetta.rosetta.utility.vector1_char method) (pyrosetta.rosetta.utility.vector1_const_utility_vector1_int_std_allocator_int__star_t method) (pyrosetta.rosetta.utility.vector1_core_chemical_AA method) (pyrosetta.rosetta.utility.vector1_core_chemical_Adduct method) (pyrosetta.rosetta.utility.vector1_core_chemical_AtomICoor method) (pyrosetta.rosetta.utility.vector1_core_chemical_AtomType method) (pyrosetta.rosetta.utility.vector1_core_chemical_BondName method) (pyrosetta.rosetta.utility.vector1_core_chemical_io_merge_residue_behavior method) (pyrosetta.rosetta.utility.vector1_core_chemical_MutableResidueConnection method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResConnID method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResidueConnection method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty method) (pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingConformer method) (pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingSaturationType method) (pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter method) (pyrosetta.rosetta.utility.vector1_core_chemical_rna_PuckerState method) (pyrosetta.rosetta.utility.vector1_core_chemical_VariantType method) (pyrosetta.rosetta.utility.vector1_core_conformation_Atom method) (pyrosetta.rosetta.utility.vector1_core_conformation_PseudoBond method) (pyrosetta.rosetta.utility.vector1_core_conformation_signals_LengthEvent method) (pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue method) (pyrosetta.rosetta.utility.vector1_core_fragment_FragData method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_scores_VallFragmentScore method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection method) (pyrosetta.rosetta.utility.vector1_core_fragment_rna_SYN_ANTI_RESTRICTION method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_bool_t method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.utility.vector1_core_id_DOF_ID method) (pyrosetta.rosetta.utility.vector1_core_id_NamedAtomID method) (pyrosetta.rosetta.utility.vector1_core_id_TorsionID method) (pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range method) (pyrosetta.rosetta.utility.vector1_core_io_AtomInformation method) (pyrosetta.rosetta.utility.vector1_core_io_HELIXInformation method) (pyrosetta.rosetta.utility.vector1_core_io_LinkInformation method) (pyrosetta.rosetta.utility.vector1_core_io_ResidueInformation method) (pyrosetta.rosetta.utility.vector1_core_io_SHEETInformation method) (pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy method) (pyrosetta.rosetta.utility.vector1_core_io_SSBondInformation method) (pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Edge method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Jump method) (pyrosetta.rosetta.utility.vector1_core_kinematics_RT method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Stub method) (pyrosetta.rosetta.utility.vector1_core_optimization_DerivCheckDataPoint method) (pyrosetta.rosetta.utility.vector1_core_optimization_DOF_DataPoint method) (pyrosetta.rosetta.utility.vector1_core_pack_annealer_PointDwell method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbond method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_sap_BlockParam method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_DotSphere method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_exposed_hydrophobic_data method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_RotamerDots method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_SparseMatrixIndex method) (pyrosetta.rosetta.utility.vector1_core_pack_rotamer_set_ContinuousRotamerSet method) (pyrosetta.rosetta.utility.vector1_core_pack_scmin_ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.utility.vector1_core_pack_task_operation_ResiduePDBIndexIs_ChainPos method) (pyrosetta.rosetta.utility.vector1_core_pack_task_ResidueLevelTask_ method) (pyrosetta.rosetta.utility.vector1_core_pose_PDBInfo_AtomRecord method) (pyrosetta.rosetta.utility.vector1_core_pose_PDBInfo_ResidueRecord method) (pyrosetta.rosetta.utility.vector1_core_pose_Pose method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_Atom_Bin method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_BaseStack method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_Datum method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_Reactivity method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_SuiteInfo method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_VDW_RepScreenInfo method) (pyrosetta.rosetta.utility.vector1_core_pose_UnrecognizedAtomRecord method) (pyrosetta.rosetta.utility.vector1_core_scoring_bin_transitions_BT_PROPERTIES method) (pyrosetta.rosetta.utility.vector1_core_scoring_CSA method) (pyrosetta.rosetta.utility.vector1_core_scoring_DC method) (pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair method) (pyrosetta.rosetta.utility.vector1_core_scoring_disulfides_DisulfideDerivativeAtom method) (pyrosetta.rosetta.utility.vector1_core_scoring_dssp_Pairing method) (pyrosetta.rosetta.utility.vector1_core_scoring_dssp_StrandPairing method) (pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector method) (pyrosetta.rosetta.utility.vector1_core_scoring_epr_deer_EPRSpinLabel method) (pyrosetta.rosetta.utility.vector1_core_scoring_etable_EtableParamsOnePair method) (pyrosetta.rosetta.utility.vector1_core_scoring_etable_etrie_GenericResidueConnectionData method) (pyrosetta.rosetta.utility.vector1_core_scoring_fiber_diffraction_OneGaussianScattering method) (pyrosetta.rosetta.utility.vector1_core_scoring_GenTorsionParams method) (pyrosetta.rosetta.utility.vector1_core_scoring_Hairpin method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_HBondEdge method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_HBondNode method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_HBEvalTuple method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_HBondWeightType method) (pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_Loop method) (pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_LoopCycle method) (pyrosetta.rosetta.utility.vector1_core_scoring_mhc_epitope_energy_AlleleMatrix method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_MotifHit method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_ResPairMotif method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_Xfres method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_pcs_PCSSingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_pre_PRESingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_rdc_RDCSingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_packing_Ball method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBall method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBallCluster method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_LR_AtomData method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_LR_MP_AtomData method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_SimplePDB_Atom method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_Sphere method) (pyrosetta.rosetta.utility.vector1_core_scoring_power_diagram_SAnode method) (pyrosetta.rosetta.utility.vector1_core_scoring_RDC method) (pyrosetta.rosetta.utility.vector1_core_scoring_RDC_Rohl method) (pyrosetta.rosetta.utility.vector1_core_scoring_rna_RNA_Motif method) (pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType method) (pyrosetta.rosetta.utility.vector1_core_scoring_SmallAtNb method) (pyrosetta.rosetta.utility.vector1_core_scoring_SmoothScoreTermCoeffs method) (pyrosetta.rosetta.utility.vector1_core_scoring_SpringParams method) (pyrosetta.rosetta.utility.vector1_core_scoring_tableID method) (pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange method) (pyrosetta.rosetta.utility.vector1_core_sequence_Line method) (pyrosetta.rosetta.utility.vector1_core_sequence_SequenceAlignment method) (pyrosetta.rosetta.utility.vector1_double method) (pyrosetta.rosetta.utility.vector1_float method) (pyrosetta.rosetta.utility.vector1_int method) (pyrosetta.rosetta.utility.vector1_long method) (pyrosetta.rosetta.utility.vector1_numeric_CubicPolynomial method) (pyrosetta.rosetta.utility.vector1_numeric_geometry_hashing_Ball method) (pyrosetta.rosetta.utility.vector1_numeric_histograms_TwoDHistogram_unsigned_long_long_t method) (pyrosetta.rosetta.utility.vector1_numeric_HomogeneousTransform_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_BicubicSpline method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_CubicSpline method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_interp_range method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_Point method) (pyrosetta.rosetta.utility.vector1_numeric_MultiDimensionalHistogram method) (pyrosetta.rosetta.utility.vector1_numeric_random_WeightedSampler method) (pyrosetta.rosetta.utility.vector1_numeric_RocPoint method) (pyrosetta.rosetta.utility.vector1_numeric_urs_Quat method) (pyrosetta.rosetta.utility.vector1_numeric_xyzMatrix_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzTransform_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzVector_float_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray1D_double_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray2D_double_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_AlternativePairings method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_ClassicAbinitio_StageID method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_PairingStatEntry method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_StageID method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_AntibodyNumberingSchemeEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRDefinitionEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRNameEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_clusters_CDRClusterEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_clusters_ClusterData method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_design_PDBNumbering method) (pyrosetta.rosetta.utility.vector1_protocols_backbone_moves_local_backbone_mover_Residue method) (pyrosetta.rosetta.utility.vector1_protocols_backrub_BackrubSegment method) (pyrosetta.rosetta.utility.vector1_protocols_branch_angle_BranchCoef1 method) (pyrosetta.rosetta.utility.vector1_protocols_branch_angle_BranchCoef2 method) (pyrosetta.rosetta.utility.vector1_protocols_canonical_sampling_DbTrajectoryRecorder_Frame method) (pyrosetta.rosetta.utility.vector1_protocols_canonical_sampling_TorsionSpec method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_CartesianAtom method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_Angle method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_Bond method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_HarmonicDihedral method) (pyrosetta.rosetta.utility.vector1_protocols_cluster_DataPoint method) (pyrosetta.rosetta.utility.vector1_protocols_cluster_Exemplar method) (pyrosetta.rosetta.utility.vector1_protocols_constraints_additional_ConstraintEvaluator method) (pyrosetta.rosetta.utility.vector1_protocols_contact_map_Contact method) (pyrosetta.rosetta.utility.vector1_protocols_cyclic_peptide_PSM_StubMode method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_BondInfo method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_StructureSlice method) (pyrosetta.rosetta.utility.vector1_protocols_features_TaskOperationFeatures_Taskop_id_name_factory_ method) (pyrosetta.rosetta.utility.vector1_protocols_fold_from_loops_utils_NubSegment method) (pyrosetta.rosetta.utility.vector1_protocols_forge_build_Interval method) (pyrosetta.rosetta.utility.vector1_protocols_frag_picker_LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareTotalScore_t method) (pyrosetta.rosetta.utility.vector1_protocols_helical_bundle_BPC_Parameters method) (pyrosetta.rosetta.utility.vector1_protocols_hotspot_hashing_VectorPair method) (pyrosetta.rosetta.utility.vector1_protocols_hybridization_detailedControlsTagSetting method) (pyrosetta.rosetta.utility.vector1_protocols_indexed_structure_store_BackboneStub method) (pyrosetta.rosetta.utility.vector1_protocols_jd2_archive_Batch method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_chunk_library_ChunkLibraryPreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_dag_node_managers_ResultElements method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_full_model_FullModelPreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_standard_PreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_DisulfPairing method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_JumpSelector_JumpWeightDef method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_JumpSetup_JumpDef method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_ResiduePairJumpSetup_JumpDef method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewAtom method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewResidue method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_AtomProperties method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_GADockStageParams method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_Pharmacophore method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_ReweightableRepEnergy method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionDistrParams method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionType method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ligand_options_InterfaceInfo method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ProtLigPair_info method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolution method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolutionStore method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_ResTorsions method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_SheetPositions method) (pyrosetta.rosetta.utility.vector1_protocols_loops_Loop method) (pyrosetta.rosetta.utility.vector1_protocols_loops_LoopFromFileData method) (pyrosetta.rosetta.utility.vector1_protocols_loops_Loops method) (pyrosetta.rosetta.utility.vector1_protocols_loops_SerializedLoop method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_CentroidRotNum method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_RotData method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_TorsionRange method) (pyrosetta.rosetta.utility.vector1_protocols_match_Hit method) (pyrosetta.rosetta.utility.vector1_protocols_match_match_dspos1 method) (pyrosetta.rosetta.utility.vector1_protocols_match_ProbeRadius method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_BuildSet method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_hit method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_SampleStrategyData method) (pyrosetta.rosetta.utility.vector1_protocols_md_Constraint method) (pyrosetta.rosetta.utility.vector1_protocols_md_MDscheduleData method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_AAMatrix method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_RotMatrix method) (pyrosetta.rosetta.utility.vector1_protocols_membrane_SpanInfo method) (pyrosetta.rosetta.utility.vector1_protocols_monte_carlo_AcceptedScores method) (pyrosetta.rosetta.utility.vector1_protocols_motif_grafting_movers_motif2scaffold_indexes method) (pyrosetta.rosetta.utility.vector1_protocols_moves_TrialCounter method) (pyrosetta.rosetta.utility.vector1_protocols_mpi_refinement_MethodParams method) (pyrosetta.rosetta.utility.vector1_protocols_multistate_design_SingleStateEntityData method) (pyrosetta.rosetta.utility.vector1_protocols_nonlocal_Chunk method) (pyrosetta.rosetta.utility.vector1_protocols_optimize_weights_WeightRangeConstraint method) (pyrosetta.rosetta.utility.vector1_protocols_pack_daemon_StructureFileNames method) (pyrosetta.rosetta.utility.vector1_protocols_pdbinfo_manipulations_SequenceSpecification method) (pyrosetta.rosetta.utility.vector1_protocols_pmut_scan_Mutant method) (pyrosetta.rosetta.utility.vector1_protocols_pmut_scan_MutationData method) (pyrosetta.rosetta.utility.vector1_protocols_pose_creation_MergePDBMover_Overlap method) (pyrosetta.rosetta.utility.vector1_protocols_pose_creation_SliceToMiniProteinMover_Chunk method) (pyrosetta.rosetta.utility.vector1_protocols_pose_metric_calculators_EnergiesData method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_mutt method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_tm_region method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_VLBInstruction method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_Transformation method) (pyrosetta.rosetta.utility.vector1_protocols_qsar_ColorGradient method) (pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBResidueRange method) (pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment method) (pyrosetta.rosetta.utility.vector1_protocols_recces_Histogram method) (pyrosetta.rosetta.utility.vector1_protocols_relax_DatabaseRelaxScript method) (pyrosetta.rosetta.utility.vector1_protocols_rigid_Partner method) (pyrosetta.rosetta.utility.vector1_protocols_rosetta_scripts_ParsedProtocol_ParsedProtocolStep method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataCenter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataLanthanide method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsEnergyParameter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsGridSearchParameter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsInputLine method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs_PCS_data_per_lanthanides method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs_PCS_line_data method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs1_PCS_data_per_lanthanides_Ts1 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs1_PCS_line_data_Ts1 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_data_per_lanthanides_Ts2 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_line_data_Ts2 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs3_PCS_data_per_lanthanides_Ts3 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs3_PCS_line_data_Ts3 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs4_PCS_data_per_lanthanides_Ts4 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs4_PCS_line_data_Ts4 method) (pyrosetta.rosetta.utility.vector1_protocols_seeded_abinitio_SegmentSpec method) (pyrosetta.rosetta.utility.vector1_protocols_sewing_data_storage_ContactDescription method) (pyrosetta.rosetta.utility.vector1_protocols_sewing_data_storage_LigandDescription method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_Quat method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_RegionalConnections method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_ResidueDepthFrag method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_IonizableResidue method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_LoggedFragmentMover_Item method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_TorsionPerturbType method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_WaterRot method) (pyrosetta.rosetta.utility.vector1_protocols_splice_BBDofs method) (pyrosetta.rosetta.utility.vector1_protocols_splice_ResidueBBDofs method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_protein_MainChainTorsionSet method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_rna_Combine_Tags_Info method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_rna_phosphate_PhosphateMove method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_monte_carlo_mover_Attachment method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_monte_carlo_mover_StepWiseMove method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_sampler_copy_dofs_ResidueAlternativeSet method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_CstResInteractions method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ExternalGeomSampler method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ResInteractions method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_SingleConstraint method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint method) (pyrosetta.rosetta.utility.vector1_protocols_trajectory_DbTrajectoryWriter_Frame method) (pyrosetta.rosetta.utility.vector1_short method) (pyrosetta.rosetta.utility.vector1_signed_char method) (pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_downstream_hit_t method) (pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_upstream_hit_t method) (pyrosetta.rosetta.utility.vector1_std_array_int_3_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_std_shared_ptr_const_protocols_match_downstream_SecMatchResiduePairEvaluator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_shared_ptr_const_numeric_expression_parser_Expression_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_shared_ptr_protocols_pack_daemon_NPDPropCalculator_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_list_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_core_chemical_AA_utility_vector1_double_std_allocator_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_protocols_jumping_cstType_unsigned_long_std_less_protocols_jumping_cstType_std_allocator_std_pair_const_protocols_jumping_cstType_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_protocols_jumping_dofType_unsigned_long_std_less_protocols_jumping_dofType_std_allocator_std_pair_const_protocols_jumping_dofType_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_shared_ptr_const_core_conformation_Residue_double_std_less_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_pair_const_std_shared_ptr_const_core_conformation_Residue_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_core_id_NamedAtomID_std_less_std_string_std_allocator_std_pair_const_std_string_core_id_NamedAtomID_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_numeric_xyzVector_double_std_less_std_string_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_unsigned_long_std_less_std_string_std_allocator_std_pair_const_std_string_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_core_chemical_AA_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_core_chemical_AA_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_shared_ptr_protocols_frag_picker_CandidatesCollector_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_frag_picker_CandidatesCollector_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_unsigned_long_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_utility_keys_Key2Tuple_unsigned_long_unsigned_long_unsigned_long_std_less_utility_keys_Key2Tuple_unsigned_long_unsigned_long_std_allocator_std_pair_const_utility_keys_Key2Tuple_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_unsigned_long_std_less_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_std_allocator_std_pair_const_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_bool_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_core_id_AtomID_t method) 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(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) CARBOHYDRATE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) carbohydrate_info() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) CarbohydrateInfo (class in pyrosetta.rosetta.core.chemical.carbohydrates) CarbohydrateInfoManager (class in pyrosetta.rosetta.core.chemical.carbohydrates) CarbonHBondEnergy (class in pyrosetta.rosetta.core.scoring.carbon_hbonds) CarbonHBondEnergyCreator (class in pyrosetta.rosetta.core.scoring.carbon_hbonds) CarbonHBondPotential (class in pyrosetta.rosetta.core.scoring.carbon_hbonds) carboxyl_wants_2 (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.UnsatCorrectionOptions property) CARBOXYLATION (pyrosetta.rosetta.core.chemical.VariantType attribute) careful_base_pair_classifier() (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential method) carry_out_filtering() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) cart2idx() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) (pyrosetta.rosetta.core.scoring.PoissonBoltzmannPotential method) cart_bonded (pyrosetta.rosetta.core.scoring.ScoreType attribute) cart_bonded_angle (pyrosetta.rosetta.core.scoring.ScoreType attribute) cart_bonded_improper (pyrosetta.rosetta.core.scoring.ScoreType attribute) cart_bonded_length (pyrosetta.rosetta.core.scoring.ScoreType attribute) cart_bonded_lr (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) cart_bonded_proper (pyrosetta.rosetta.core.scoring.ScoreType attribute) cart_bonded_ring (pyrosetta.rosetta.core.scoring.ScoreType attribute) cart_bonded_torsion (pyrosetta.rosetta.core.scoring.ScoreType attribute) cart_min() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) cart_numerical_derivative_check() (in module pyrosetta.rosetta.core.optimization) cart_resl_ (pyrosetta.rosetta.core.scoring.motif.MotifHash property) (pyrosetta.rosetta.core.scoring.motif.XformScore property) cart_size() (pyrosetta.rosetta.core.scoring.motif.MotifHash method) (pyrosetta.rosetta.core.scoring.motif.XformScore method) cart_size_ (pyrosetta.rosetta.core.scoring.motif.MotifHash property) (pyrosetta.rosetta.core.scoring.motif.XformScore property) CartBondedParameters (class in pyrosetta.rosetta.core.scoring.methods) cartesian() (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover 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) cartesian_collect_atompairE_deriv() (in module pyrosetta.rosetta.core.optimization) cartesian_collect_torsional_deriv() (in module pyrosetta.rosetta.core.optimization) cartesian_dfunc() (in module pyrosetta.rosetta.core.optimization) CartesianAtom (class in pyrosetta.rosetta.protocols.cartesian) CartesianBondedEnergy (class in pyrosetta.rosetta.core.energy_methods) CartesianBondedEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) CartesianHybridize (class in pyrosetta.rosetta.protocols.hybridization) CartesianMD (class in pyrosetta.rosetta.protocols.md) CartesianMDCreator (class in pyrosetta.rosetta.protocols.md) CartesianMinimizer (class in pyrosetta.rosetta.core.optimization) CartesianMinimizerMap (class in pyrosetta.rosetta.core.optimization) CartesianMultifunc (class in pyrosetta.rosetta.core.optimization) CartesianSampler (class in pyrosetta.rosetta.protocols.hybridization) CartesianSamplerCreator (class in pyrosetta.rosetta.protocols.hybridization) CartesianSearchPattern (class in pyrosetta.rosetta.protocols.hotspot_hashing) CartGrid_double_t (class in pyrosetta.rosetta.core.grid) CartGrid_int_t (class in pyrosetta.rosetta.core.grid) CartSCMinMinimizerMap (class in pyrosetta.rosetta.core.pack.scmin) CartSCMinMultifunc (class in pyrosetta.rosetta.core.pack.scmin) case_from_lines() (in module pyrosetta.rosetta.core.chemical) catalog() (pyrosetta.rosetta.core.fragment.picking_old.concepts.Librarian_core_fragment_picking_old_vall_scores_VallFragmentScore_core_fragment_picking_old_vall_eval_VallFragmentEval_core_fragment_picking_old_vall_gen_VallFragmentGen_core_fragment_picking_old_vall_VallLibrary_t method) (pyrosetta.rosetta.core.fragment.picking_old.concepts.Librarian_VallFragmentScore_VallFragmentEval_VallFragmentGen_VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) catalytic_res() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) catch_fragment() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ShortLoopClosure method) CatmullRomSplineBoundaryType (class in pyrosetta.rosetta.numeric.interpolation) CatPiCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) cavballs (pyrosetta.rosetta.core.scoring.packstat.CavityBallCluster property) (pyrosetta.rosetta.core.scoring.packstat.SasaResult property) CAVEAT (pyrosetta.rosetta.core.io.pdb.RecordType attribute) CavityBall (class in pyrosetta.rosetta.core.scoring.packstat) CavityBallCluster (class in pyrosetta.rosetta.core.scoring.packstat) CavityCalculator (class in pyrosetta.rosetta.protocols.denovo_design.calculators) CavityVolumeFilter (class in pyrosetta.rosetta.protocols.denovo_design.filters) CavityVolumeFilterCreator (class in pyrosetta.rosetta.protocols.denovo_design.filters) CB (pyrosetta.rosetta.protocols.frag_picker.ContactType attribute) CB() (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) CB_Angle_Func (class in pyrosetta.rosetta.core.scoring.disulfides) CB_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) cb_dist_cut() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.protocols.simple_filters.DomainInterfaceFilter method) CB_dist_cutoff() (pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) Cb_Distance_Func (class in pyrosetta.rosetta.core.scoring.disulfides) cb_force() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) cb_weight() (in module pyrosetta.rosetta.protocols.sic_dock) cb_weight_map_from_pose() (in module pyrosetta.rosetta.protocols.sic_dock) cb_weights_from_map() (in module pyrosetta.rosetta.protocols.sic_dock) cb_weights_from_pose() (in module pyrosetta.rosetta.protocols.sic_dock) cbegin() (pyrosetta.rosetta.std.array_core_kinematics_inverse_AlignmentAtom_3_t method) cbeta (pyrosetta.rosetta.core.scoring.ScoreType attribute) cbeta_smooth (pyrosetta.rosetta.core.scoring.ScoreType attribute) CBScore (class in pyrosetta.rosetta.protocols.sic_dock) CBSG_Dihedral_Func (class in pyrosetta.rosetta.core.scoring.disulfides) cbx() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) cby() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) cbz() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) ccd() (pyrosetta.rosetta.protocols.splice.Splice method) ccd_angle() (in module pyrosetta.rosetta.numeric) CCD_CLOSE (pyrosetta.rosetta.basic.ProfTag attribute) ccd_close() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) ccd_close_loops() (in module pyrosetta.rosetta.protocols.loops) ccd_mover() (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) CCDEndsGraftMover (class in pyrosetta.rosetta.protocols.grafting) CCDEndsGraftMoverCreator (class in pyrosetta.rosetta.protocols.grafting) CCDLoopClosureMover (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) CCDLoopClosureMoverCreator (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) CCluster (class in pyrosetta.rosetta.protocols.pockets) CCluster.Cxyz (class in pyrosetta.rosetta.protocols.pockets) CClusterSet (class in pyrosetta.rosetta.protocols.pockets) ccs_imms (pyrosetta.rosetta.core.scoring.ScoreType attribute) CCS_IMMSEnergy (class in pyrosetta.rosetta.core.energy_methods) CCS_IMMSEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) ccw (pyrosetta.rosetta.core.scoring.packstat.trace property) ccw_angle (pyrosetta.rosetta.core.scoring.packstat.Event property) CD (class in pyrosetta) Cd (pyrosetta.rosetta.core.chemical.element.Elements attribute) cd_1b (pyrosetta.rosetta.core.scoring.methods.EnergyMethodType attribute) cd_1b_types() (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) cd_2b (pyrosetta.rosetta.core.scoring.methods.EnergyMethodType attribute) cd_2b_types() (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) cd_lr_2b (pyrosetta.rosetta.core.scoring.methods.EnergyMethodType attribute) cd_lr_2b_types() (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) cdf_for_aa() (pyrosetta.rosetta.core.scoring.Ramachandran method) cdf_for_aa_for_torsion_bin() (pyrosetta.rosetta.core.scoring.Ramachandran method) CDFr (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) cdr (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData property) (pyrosetta.rosetta.protocols.antibody.ParatopeMetric_double_t property) (pyrosetta.rosetta.protocols.antibody.ParatopeMetric_long_t property) cdr() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.antibody.design.CDRSeqDesignOptions method) cdr1 (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain property) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChainNumbering property) (pyrosetta.rosetta.protocols.tcr.TCRmodel.tcrtmplts property) (pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi property) (pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs property) cdr1_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) cdr2 (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain property) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChainNumbering property) (pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs property) cdr2_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) cdr2hv4 (pyrosetta.rosetta.protocols.tcr.TCRmodel.tcrtmplts property) (pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi property) cdr3 (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain property) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChainNumbering property) (pyrosetta.rosetta.protocols.tcr.TCRmodel.tcrtmplts property) (pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi property) (pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs property) cdr3_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) cdr_backbone_rmsds() (in module pyrosetta.rosetta.protocols.antibody) CDR_Bounds (class in pyrosetta.rosetta.protocols.antibody.grafting) cdr_cluster_enum_to_string() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) CDR_CLUSTER_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) cdr_cluster_is_present() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) cdr_cluster_string_to_enum() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnumManager method) cdr_CN_anchor_distance() (in module pyrosetta.rosetta.protocols.antibody) cdr_definition (pyrosetta.rosetta.protocols.antibody.AntibodyNumbering property) cdr_definition_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_definition_is_present() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_definition_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_definition_transform (pyrosetta.rosetta.protocols.antibody.AntibodyNumbering property) CDR_Detector (class in pyrosetta.rosetta.protocols.antibody.grafting) cdr_end (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum attribute) cdr_energy() (in module pyrosetta.rosetta.protocols.antibody) CDR_H3_cter_filter() (in module pyrosetta.rosetta.protocols.antibody) CDR_H3_filter() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) CDR_H3_filter_legacy_code_with_old_rule() (in module pyrosetta.rosetta.protocols.antibody) cdr_has_res_constraints() (in module pyrosetta.rosetta.protocols.antibody.constraints) cdr_landmark_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_landmark_is_present() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_landmark_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_name_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_name_is_present() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_name_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) cdr_numbering (pyrosetta.rosetta.protocols.antibody.AntibodyNumbering property) cdr_overhang() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) cdr_region (pyrosetta.rosetta.protocols.antibody.AntibodyRegionEnum attribute) cdr_start (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum attribute) CDRCluster (class in pyrosetta.rosetta.protocols.antibody.clusters) CDRClusterEnum (class in pyrosetta.rosetta.protocols.antibody.clusters) CDRClusterEnum_start (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) CDRClusterEnum_stop (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) CDRClusterEnum_total (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) CDRClusterEnumManager (class in pyrosetta.rosetta.protocols.antibody.clusters) CDRClusterFeatures (class in pyrosetta.rosetta.protocols.antibody.clusters) CDRClusterFeaturesCreator (class in pyrosetta.rosetta.protocols.antibody.clusters) CDRClusterMatcher (class in pyrosetta.rosetta.protocols.antibody.clusters) CDRClusterSet (class in pyrosetta.rosetta.protocols.antibody.clusters) CDRDBPose (class in pyrosetta.rosetta.protocols.antibody) CDRDBSequence (class in pyrosetta.rosetta.protocols.antibody) CDRDefinitionEnum (class in pyrosetta.rosetta.protocols.antibody) CDRDefinitionEnum_start (pyrosetta.rosetta.protocols.antibody.CDRDefinitionEnum attribute) CDRDefinitionEnum_total (pyrosetta.rosetta.protocols.antibody.CDRDefinitionEnum attribute) CDRDihedralConstraintMover (class in pyrosetta.rosetta.protocols.antibody.constraints) CDRDihedralConstraintMoverCreator (class in pyrosetta.rosetta.protocols.antibody.constraints) CDRGraftDesignOptions (class in pyrosetta.rosetta.protocols.antibody.design) CDRGraftDesignOptionsParser (class in pyrosetta.rosetta.protocols.antibody.design) CDRH3Modeler (class in pyrosetta.rosetta.protocols.antibody_legacy) CDRLandmarkEnum (class in pyrosetta.rosetta.protocols.antibody) CDRLandmarkEnum_total (pyrosetta.rosetta.protocols.antibody.CDRLandmarkEnum attribute) CDRNameEnum (class in pyrosetta.rosetta.protocols.antibody) CDRNameEnum_proto_start (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) CDRNameEnum_proto_total (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) CDRNameEnum_start (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) CDRNameEnum_total (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) CDRResidueSelector (class in pyrosetta.rosetta.protocols.antibody.residue_selector) CDRResidueSelectorCreator (class in pyrosetta.rosetta.protocols.antibody.residue_selector) CDRSeqDesignOptions (class in pyrosetta.rosetta.protocols.antibody.design) CDRSeqDesignOptionsParser (class in pyrosetta.rosetta.protocols.antibody.design) CDRSetOptions (class in pyrosetta.rosetta.protocols.antibody) CDRSetOptionsParser (class in pyrosetta.rosetta.protocols.antibody) CDRsMinPackMin (class in pyrosetta.rosetta.protocols.antibody) Ce (pyrosetta.rosetta.core.chemical.element.Elements attribute) Cell (class in pyrosetta.rosetta.core.sequence) CEN (pyrosetta.rosetta.protocols.frag_picker.ContactType attribute) cen (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueEntry property) (pyrosetta.rosetta.protocols.kinmatch.KRSQuery property) CEN (pyrosetta.rosetta.protocols.kinmatch.KRSQueryType attribute) CEN2FULLATOM (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) CEN_ANG (pyrosetta.rosetta.protocols.kinmatch.KRSQueryType attribute) CEN_AXS (pyrosetta.rosetta.protocols.kinmatch.KRSQueryType attribute) CEN_AXS_ORI (pyrosetta.rosetta.protocols.kinmatch.KRSQueryType attribute) cen_dist10_pad() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist10_pad_hinv() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist10_pad_minus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist10_pad_plus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist12_pad() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist12_pad_hinv() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist12_pad_minus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist12_pad_plus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist5_pad() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist5_pad_hinv() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist5_pad_minus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist5_pad_plus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist6_pad() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist6_pad_hinv() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist6_pad_plus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist7_pad() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist7_pad_hinv() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist7_pad_minus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) cen_dist7_pad_plus() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) Cen_Distance_Func (class in pyrosetta.rosetta.core.scoring.disulfides) CEN_DOCK_SCORE (pyrosetta.rosetta.core.conformation.symmetry.SlideCriteriaType attribute) cen_env_smooth (pyrosetta.rosetta.core.scoring.ScoreType attribute) cen_hb (pyrosetta.rosetta.core.scoring.ScoreType attribute) CEN_LIST_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) cen_pair_motif_degree (pyrosetta.rosetta.core.scoring.ScoreType attribute) cen_pair_motifs (pyrosetta.rosetta.core.scoring.ScoreType attribute) cen_pair_smooth (pyrosetta.rosetta.core.scoring.ScoreType attribute) cen_rot_cbeta (pyrosetta.rosetta.core.scoring.ScoreType attribute) cen_rot_dun (pyrosetta.rosetta.core.scoring.ScoreType attribute) cen_rot_env (pyrosetta.rosetta.core.scoring.ScoreType attribute) cen_rot_pair (pyrosetta.rosetta.core.scoring.ScoreType attribute) cen_rot_pair_ang (pyrosetta.rosetta.core.scoring.ScoreType attribute) cen_rot_pair_dih (pyrosetta.rosetta.core.scoring.ScoreType attribute) cen_scorefxn() (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) CENcrd (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData property) cend() (pyrosetta.rosetta.std.array_core_kinematics_inverse_AlignmentAtom_3_t method) Cend_orient() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) Cend_pos() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) cenfilter() (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) CenHBEnergy (class in pyrosetta.rosetta.core.energy_methods) CenHBEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) CenHBPotential (class in pyrosetta.rosetta.core.scoring) cenlist_from_pose() (pyrosetta.rosetta.core.scoring.EnvPairPotential static method) (pyrosetta.rosetta.core.scoring.membrane.MembraneData static method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential static method) (pyrosetta.rosetta.core.scoring.MembranePotential static method) CenListInfo (class in pyrosetta.rosetta.core.scoring) cenpack (pyrosetta.rosetta.core.scoring.ScoreType attribute) cenpack_smooth (pyrosetta.rosetta.core.scoring.ScoreType attribute) CenPairEnergy (class in pyrosetta.rosetta.core.energy_methods) CenPairEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) CenPairMotifDegreeEnergy (class in pyrosetta.rosetta.core.energy_methods) CenPairMotifDegreeEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) CenPairMotifEnergy (class in pyrosetta.rosetta.core.energy_methods) CenPairMotifEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) CenRotDunEnergy (class in pyrosetta.rosetta.core.pack.dunbrack.cenrot) CenRotDunEnergyCreator (class in pyrosetta.rosetta.core.pack.dunbrack.cenrot) CenRotEnvEnergy (class in pyrosetta.rosetta.core.energy_methods) CenRotEnvEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) CenRotEnvPairPotential (class in pyrosetta.rosetta.core.scoring) CenrotLibrary (class in pyrosetta.rosetta.core.pack.dunbrack.cenrot) CenRotPairEnergy (class in pyrosetta.rosetta.core.energy_methods) CenRotPairEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) CenrotRotamerLibrarySpecification (class in pyrosetta.rosetta.core.chemical.rotamers) CenrotRotamerLibrarySpecificationCreator (class in pyrosetta.rosetta.core.chemical.rotamers) censorFragByBurial() (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) center (pyrosetta.rosetta.core.chemical.rna.GaussianParameter property) (pyrosetta.rosetta.core.conformation.membrane.MEM attribute) (pyrosetta.rosetta.core.scoring.packstat.CavityBallCluster property) center() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.core.conformation.membrane.Span method) (pyrosetta.rosetta.core.conformation.UltraLightResidue method) (pyrosetta.rosetta.core.id.NamedStubID method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.kinematics.Stub method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.packstat.PackingScore method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.protocols.electron_density.RefinementResult method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) (pyrosetta.rosetta.protocols.scoring.Interface method) center_ (pyrosetta.rosetta.core.id.NamedStubID property) (pyrosetta.rosetta.core.id.StubID property) (pyrosetta.rosetta.protocols.viewer.triangle property) center_all() (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) center_h() (pyrosetta.rosetta.numeric.linear_algebra.EllipseParameters method) center_jumps_in_single_stranded() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) center_k() (pyrosetta.rosetta.numeric.linear_algebra.EllipseParameters method) center_of_geom() (in module pyrosetta.rosetta.protocols.sic_dock) center_of_mass() (in module pyrosetta.rosetta.core.pose) (in module pyrosetta.rosetta.protocols.geometry) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) center_on_middle_ca_ (pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions property) (pyrosetta.rosetta.protocols.electron_density.PoseSphericalSamplesOptions property) (pyrosetta.rosetta.protocols.electron_density.SelectDensityPointsOptions property) center_residues() (in module pyrosetta.rosetta.protocols.cluster.calibur) center_structure() (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) centered() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) centers (pyrosetta.rosetta.core.scoring.packstat.PosePackData property) central_atoms_to_score() (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet method) central_residue() (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborsByDistanceCalculator method) central_residue_group_selector() (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) central_residues() (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborhoodByDistanceCalculator method) centralE (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData property) centroid() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) centroid_bin_max() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) centroid_bin_min() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) centroid_bin_size() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) centroid_by_chain() (in module pyrosetta.rosetta.protocols.geometry) centroid_by_chains() (in module pyrosetta.rosetta.protocols.geometry) centroid_by_residues() (in module pyrosetta.rosetta.protocols.geometry) centroid_dG (pyrosetta.rosetta.protocols.analysis.InterfaceData property) centroid_dist() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) CENTROID_DISTANCE (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) centroid_disulfide_energy (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) centroid_filter() (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) centroid_loop_mover_str() (pyrosetta.rosetta.protocols.forge.components.BDR method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) centroid_mapping_distance_padding_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) centroid_max_temperature() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) centroid_min_temperature() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) centroid_mode_perturbation() (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) centroid_neighbor_graph (pyrosetta.rosetta.core.scoring.ContextGraphType attribute) centroid_neighbors() (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) centroid_output() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) centroid_pair_by_jump() (in module pyrosetta.rosetta.protocols.geometry) centroid_pose_from_pdb() (in module pyrosetta.rosetta.core.import_pose) centroid_relax (pyrosetta.rosetta.protocols.antibody.design.MinTypeEnum attribute) CENTROID_ROT_t (pyrosetta.rosetta.core.chemical.TypeSetMode attribute) centroid_scatter() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) centroid_score_diff_cut() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) centroid_scorefunction() (pyrosetta.rosetta.protocols.forge.components.BDR method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) 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.fold_from_loops.movers.NubInitioLoopClosureMover method) centroid_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) centroid_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) CENTROID_t (pyrosetta.rosetta.core.chemical.TypeSetMode attribute) centroid_weights() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) CENTROID_WITH_HA (pyrosetta.rosetta.core.chemical.VariantType attribute) centroid_x (pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body.BaseBin property) centroid_xyz() (pyrosetta.rosetta.core.scoring.dna.DNA_EnvPairPotential method) centroid_y (pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body.BaseBin property) centroid_z (pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body.BaseBin property) CentroidDistanceScreener (class in pyrosetta.rosetta.protocols.stepwise.screener) CentroidDisulfideEnergy (class in pyrosetta.rosetta.core.energy_methods) CentroidDisulfideEnergyComponents (class in pyrosetta.rosetta.core.scoring.disulfides) CentroidDisulfideEnergyContainer (class in pyrosetta.rosetta.core.scoring.disulfides) CentroidDisulfideEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) CentroidDisulfideNeighborConstIterator (class in pyrosetta.rosetta.core.scoring.disulfides) CentroidDisulfideNeighborIterator (class in pyrosetta.rosetta.core.scoring.disulfides) CentroidDisulfidePotential (class in pyrosetta.rosetta.core.scoring.disulfides) CentroidRelax (class in pyrosetta.rosetta.protocols.relax) CentroidRelaxMover (class in pyrosetta.rosetta.protocols.surface_docking) CentroidRotamerSampleData (class in pyrosetta.rosetta.core.pack.dunbrack.cenrot) CentroidRotNum (class in pyrosetta.rosetta.protocols.make_rot_lib) centroids_by_jump() (in module pyrosetta.rosetta.protocols.geometry) centroids_by_jump_int() (in module pyrosetta.rosetta.protocols.geometry) CentroidScatter (class in pyrosetta.rosetta.core.scoring.fiber_diffraction) cenx() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) ceny() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) cenz() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) Cf (pyrosetta.rosetta.core.chemical.element.Elements attribute) cfac (pyrosetta.rosetta.core.scoring.APBSConfig property) cfg_nd() (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) cfg_r() (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) CFr (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) ch_bond (pyrosetta.rosetta.core.scoring.ScoreType attribute) ch_bond_bb_bb (pyrosetta.rosetta.core.scoring.ScoreType attribute) ch_bond_bb_sc (pyrosetta.rosetta.core.scoring.ScoreType attribute) ch_bond_sc_sc (pyrosetta.rosetta.core.scoring.ScoreType attribute) Chain (class in pyrosetta.rosetta.protocols.pose_length_moves) CHAIN (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation.CompoundToken attribute) chain (pyrosetta.rosetta.core.io.raw_data.DisulfideFile.ResNum property) (pyrosetta.rosetta.core.scoring.packstat.SimplePDB_Atom property) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering property) (pyrosetta.rosetta.protocols.dna.DnaDesignDef property) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo property) (pyrosetta.rosetta.protocols.ligand_docking.Transform_info property) chain() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.FragData method) (pyrosetta.rosetta.core.pack.task.operation.ChainIs method) (pyrosetta.rosetta.core.pack.task.operation.ChainIsnt method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPDB method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.simple_filters.AngleToVector method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) chain1() (pyrosetta.rosetta.protocols.simple_ddg.AlaScan method) chain2() (pyrosetta.rosetta.protocols.simple_ddg.AlaScan method) chain_ (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIs.ChainPos property) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsnt.ChainPos property) (pyrosetta.rosetta.protocols.ligand_docking.LigandArea property) (pyrosetta.rosetta.protocols.simple_filters.PackStatFilter property) chain_begin() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) chain_boundaries() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) chain_break_grid_index_screening (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) chain_break_screening_count (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) chain_break_screening_general() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) chain_closable_geometry_count (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) chain_closable_geometry_count2 (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) chain_closable_geometry_count3 (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) chain_closable_geometry_screen (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Filterer_Count property) CHAIN_COLOR (pyrosetta.rosetta.protocols.viewer.graphics_states_param.ColorMode attribute) chain_com() (in module pyrosetta.rosetta.protocols.membrane) chain_connections() (pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler method) (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) chain_cut() (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) chain_end() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) chain_end_res() (in module pyrosetta.rosetta.core.pose) chain_ending (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueEntry property) chain_endings() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) chain_endings_str() (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) chain_gws_string() (in module pyrosetta.rosetta.core.io.carbohydrates) chain_id (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo property) chain_id() (pyrosetta.rosetta.protocols.ligand_docking.Rotate_info method) (pyrosetta.rosetta.protocols.ligand_docking.Translate_info method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) chain_ids() (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble_info method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) chain_index (pyrosetta.rosetta.core.io.mmtf.sd_index property) chain_letter() (pyrosetta.rosetta.protocols.ligand_docking.Rotate_info method) (pyrosetta.rosetta.protocols.ligand_docking.Translate_info method) chain_letters() (pyrosetta.rosetta.protocols.pose_metric_calculators.ResidueDecompositionByChainCalculator method) chain_lt (class in pyrosetta.rosetta.protocols.pose_length_moves) chain_name (pyrosetta.rosetta.protocols.antibody.FrameWork property) chain_num() (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation method) chain_numbers() (pyrosetta.rosetta.protocols.pose_metric_calculators.ResidueDecompositionByChainCalculator method) chain_order() (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) chain_pair_pose_prepared() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) chain_sequence() (pyrosetta.rosetta.core.pose.Pose method) chain_sequences() (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.pose.PDBInfo method) chain_strings() (pyrosetta.rosetta.core.select.residue_selector.ChainSelector method) chain_tm_com() (in module pyrosetta.rosetta.protocols.membrane) chain_type() (pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo method) ChainBreak (class in pyrosetta.rosetta.protocols.simple_filters) CHAINBREAK (pyrosetta.rosetta.core.pose.rna.StubStubType attribute) chainbreak (pyrosetta.rosetta.core.scoring.ScoreType attribute) chainbreak() (pyrosetta.rosetta.protocols.hybridization.FragmentBiasAssigner method) chainbreak_bias() (pyrosetta.rosetta.protocols.rigid.RigidBodyMotionMover method) CHAINBREAK_BOGUS_ATOM_ID() (pyrosetta.rosetta.core.id.AtomID static method) CHAINBREAK_BOGUS_NAMED_ATOM_ID() (pyrosetta.rosetta.core.id.NamedAtomID static method) CHAINBREAK_BOGUS_PARTIAL_ATOM_ID() (pyrosetta.rosetta.core.id.PartialAtomID static method) chainbreak_check() (pyrosetta.rosetta.protocols.splice.SpliceManager method) chainbreak_weight() (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) ChainbreakDistFunc (class in pyrosetta.rosetta.protocols.jumping) ChainbreakEnergy (class in pyrosetta.rosetta.core.energy_methods) ChainbreakEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) ChainBreakFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) chainbreaks() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) ChainbreakUtil (class in pyrosetta.rosetta.core.util) ChainCountFilter (class in pyrosetta.rosetta.protocols.simple_filters) ChainCountFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) ChainDirection (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) ChainedSolutionList (class in pyrosetta.rosetta.protocols.kinematic_closure) ChainedSolutionList.Iterator (class in pyrosetta.rosetta.protocols.kinematic_closure) ChainExistsFilter (class in pyrosetta.rosetta.protocols.ligand_docking) ChainExistsFilterCreator (class in pyrosetta.rosetta.protocols.ligand_docking) ChainGroupDiscriminator (class in pyrosetta.rosetta.protocols.minimization_packing) chainID (pyrosetta.rosetta.core.io.AtomInformation property) (pyrosetta.rosetta.core.io.ModifiedResidueInformation property) (pyrosetta.rosetta.core.pose.PDBInfo.ResidueRecord property) chainid (pyrosetta.rosetta.protocols.hbnet.HBondResStruct property) chainID (pyrosetta.rosetta.protocols.loops.LoopConfiguration attribute) chainID() (pyrosetta.rosetta.core.io.ResidueInformation method) chainID1 (pyrosetta.rosetta.core.io.CisPeptideInformation property) (pyrosetta.rosetta.core.io.HELIXInformation property) (pyrosetta.rosetta.core.io.LinkInformation property) (pyrosetta.rosetta.core.io.SHEETInformation property) (pyrosetta.rosetta.core.io.SSBondInformation property) chainID2 (pyrosetta.rosetta.core.io.CisPeptideInformation property) (pyrosetta.rosetta.core.io.HELIXInformation property) (pyrosetta.rosetta.core.io.LinkInformation property) (pyrosetta.rosetta.core.io.SHEETInformation property) (pyrosetta.rosetta.core.io.SSBondInformation property) ChainIs (class in pyrosetta.rosetta.core.pack.task.operation) ChainIsCreator (class in pyrosetta.rosetta.core.pack.task.operation) ChainIsnt (class in pyrosetta.rosetta.core.pack.task.operation) ChainIsntCreator (class in pyrosetta.rosetta.core.pack.task.operation) chainName (pyrosetta.rosetta.protocols.sparta.PDB_Entry property) chains (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble_info property) chains() (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) chains_ (pyrosetta.rosetta.protocols.pdbinfo_manipulations.SequenceSpecification property) chains_from_termini() (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) chains_in_full_model() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) chains_to_ignore_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) 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) ChainSelector (class in pyrosetta.rosetta.core.select.residue_selector) ChainSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) ChainSplitMover (class in pyrosetta.rosetta.protocols.simple_moves) ChainTerm (class in pyrosetta.rosetta.protocols.constel) chainXYZ() (in module pyrosetta.rosetta.numeric.kinematic_closure) (in module pyrosetta.rosetta.numeric.kinematic_closure.radians) change_bond_type() (pyrosetta.rosetta.core.chemical.MutableResidueType method) change_chi_without_replacing_residue() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) change_CoM_to_ligandCoM() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) change_conformation() (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) change_conformer() (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) change_conformers() (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) change_cys_state() (in module pyrosetta.rosetta.core.conformation) change_espGrid_for_darc() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) change_foldtree() (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) change_sheet_id_if_possible() (in module pyrosetta.rosetta.protocols.features.strand_assembly) change_volume_move() (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) change_weight() (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) change_working_directory() (in module pyrosetta.rosetta.utility.file) ChangeAncestory (class in pyrosetta.rosetta.core.chemical) ChangeAndResetFoldTreeMover (class in pyrosetta.rosetta.protocols.simple_moves) ChangeAndResetFoldTreeMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) ChangeBondType (class in pyrosetta.rosetta.core.chemical) changed() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) changed_ (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo property) ChangeFoldTreeMover (class in pyrosetta.rosetta.protocols.moves) changes_connections_on() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AddProtonChi method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeAncestory method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.RenameAtom method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.Set_AA method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetBaseName method) (pyrosetta.rosetta.core.chemical.SetDisulfideAtomName method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) changing_baseline() (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter method) channel() (pyrosetta.rosetta.basic.MemTracer method) (pyrosetta.rosetta.basic.MemTracerImpl method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerImpl method) channel_color() (pyrosetta.rosetta.basic.MemTracerImpl method) (pyrosetta.rosetta.basic.TracerImpl method) channel_name_color() (pyrosetta.rosetta.basic.MemTracerImpl method) (pyrosetta.rosetta.basic.TracerImpl method) CHAR() (in module pyrosetta.rosetta.ObjexxFCL.Fortran) char2ss_type() (pyrosetta.rosetta.protocols.comparative_modeling.features.SSFeature static method) char_msg() (pyrosetta.rosetta.utility.SimulateMPIMessage method) char_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) char_to_int() (in module pyrosetta.rosetta.core.io.carbohydrates) char_type() (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) char_valid_as_torsion_bin() (in module pyrosetta.rosetta.core.conformation) charge (pyrosetta.rosetta.core.scoring.PQR property) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeAtom property) charge() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.scoring.elec.electrie.ElecAtom method) ChargeAtom (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) ChargeCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) ChargeChargeFeatures (class in pyrosetta.rosetta.protocols.features) ChargeChargeFeaturesCreator (class in pyrosetta.rosetta.protocols.features) CHARGED (class in pyrosetta.rosetta.core.pack.task) (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) charged() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) ChargeGrid (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) ChargeGridCreator (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) charges() (pyrosetta.rosetta.core.scoring.elec.electrie.ElecAtom method) CharmmPeriodicFunc (class in pyrosetta.rosetta.core.scoring.func) CharPairHash (class in pyrosetta.rosetta.core.sequence) chco (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) CHEAT_CoM() (pyrosetta.rosetta.protocols.pockets.FingerprintBase method) (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) check() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) check2bsc() (pyrosetta.rosetta.protocols.match.downstream.ScoringSecMatchRPE method) check_all_junctions_good() (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) check_all_ligand_atoms() (in module pyrosetta.rosetta.protocols.ligand_docking.ligand_options) check_all_residues_sampled() (in module pyrosetta.rosetta.core.pose.full_model_info) check_and_correct_sister_atom_based_on_chirality() (in module pyrosetta.rosetta.core.io.pose_from_sfr) check_and_correct_sister_atom_based_on_outgroup() (in module pyrosetta.rosetta.core.io.pose_from_sfr) check_and_correct_sister_atoms() (in module pyrosetta.rosetta.core.io.pose_from_sfr) check_and_create_fragments() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) check_auto_stop() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) check_base_pair() (in module pyrosetta.rosetta.protocols.rna.denovo) check_base_pairs() (pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler method) check_binary_chars() (in module pyrosetta.rosetta.core.io.serialization) check_binary_unsigned_int() (in module pyrosetta.rosetta.core.io.serialization) check_boltzmann() (pyrosetta.rosetta.protocols.moves.SimulatedTempering method) check_bounds() (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.motif.MotifHash method) check_buns1 (pyrosetta.rosetta.protocols.buns.CALCULATORMODE attribute) check_calculator_exists() (pyrosetta.rosetta.core.pose.metrics.CalculatorFactory method) check_can_append() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) check_can_prepend() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) check_canonicalness_of_LR() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_canonicalness_of_PA() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_canonicalness_of_parallel_EE() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_cb() (in module pyrosetta.rosetta.protocols.antibody.design) check_centroid_interaction() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker method) check_chain_closable_geometry() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker method) check_chainbreak_variants() (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) check_chbonded() (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_Potential method) check_clear_for_stacking() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) check_closure() (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) CHECK_COMM_SIZE (pyrosetta.rosetta.basic.ProfTag attribute) check_compatibility() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarModeling method) check_compatible_with_sequence() (pyrosetta.rosetta.core.pose.rna.RNA_SecStruct method) check_conformers() (pyrosetta.rosetta.protocols.ligand_docking.Transform method) check_consistency() (pyrosetta.rosetta.core.conformation.signals.LengthEvent method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) check_coordinates() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) check_data_consistency() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo method) check_deprecated_flags() (in module pyrosetta.rosetta.core.init) check_disulfide_cb_distance() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) check_disulfide_match_rt() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) check_disulfide_score() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) check_disulfide_seqpos() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) check_domain_map() (pyrosetta.rosetta.core.scoring.NeighborList method) check_duplicate() (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) check_edges_for_atom_info() (pyrosetta.rosetta.core.kinematics.FoldTree method) check_ensemble_member_compatibility() (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) check_equation() (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric method) check_extra_minimize_res_are_input() (in module pyrosetta.rosetta.core.import_pose) check_fa_dun() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) check_fa_dun_ (pyrosetta.rosetta.protocols.match.upstream.BuildSet property) check_features_reporter_dependencies() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) check_file_size() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded static method) check_filters() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) check_fix_aho_cdr_numbering() (in module pyrosetta.rosetta.protocols.antibody) check_fold_tree() (pyrosetta.rosetta.core.kinematics.FoldTree method) check_fold_tree_OK() (pyrosetta.rosetta.core.import_pose.libraries.ChunkSet method) (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) check_for_base_neighbor() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) check_for_existing_output_file() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) check_for_input_domain() (in module pyrosetta.rosetta.protocols.stepwise.modeler) check_for_messed_up_structure() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) check_for_parse_error() (pyrosetta.rosetta.protocols.metal_interface.ZincSiteFinder method) check_for_symmetric_peaks() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) check_forming_base_pair() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) check_forward_backward() (pyrosetta.rosetta.core.import_pose.libraries.RNA_JumpLibrary method) check_frequency() (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) check_full_model_info_OK() (in module pyrosetta.rosetta.core.pose.full_model_info) check_gaps() (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) check_good_cutpoint_neighbour() (in module pyrosetta.rosetta.core.conformation) check_grid() (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) check_hairpin() (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) check_hbonded() (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_Potential method) check_heading_direction() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_helix_existence() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_if_connected_residues_belong_to_regions() (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) check_if_pose_renumbered_for_clusters() (in module pyrosetta.rosetta.protocols.antibody.clusters) check_if_proton_chi_atom() (in module pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens) check_if_residues_are_Ctermini() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) check_if_residues_are_Ntermini() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) check_in_base_pair_list() (in module pyrosetta.rosetta.core.pose.rna) check_in_pairing_sets() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) check_instantiated_O2Prime_hydrogen() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) check_invariants() (pyrosetta.rosetta.core.scoring.hbonds.Polynomial_1d method) (pyrosetta.rosetta.numeric.Polynomial_1d method) check_is_working_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) check_jump_to_next_residue_in_chain() (in module pyrosetta.rosetta.protocols.stepwise.modeler) check_jump_to_previous_residue_in_chain() (in module pyrosetta.rosetta.protocols.stepwise.modeler) check_key() (pyrosetta.rosetta.utility.options.OptionCollection static method) check_kink_helix() (in module pyrosetta.rosetta.protocols.fldsgn.topology) check_lig_code() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) check_load_fconfig() (in module pyrosetta.rosetta.core.init) check_loop_closed() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) check_loop_cycles_are_disjoint() (pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph method) check_loop_residues_sensible() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) check_loops() (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) check_LR() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_matching_atom_names() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner method) check_membrane_fold_tree() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) check_methods_in_right_order() (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) check_mmt() (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) check_moved() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) check_mutants_ok() (in module pyrosetta.rosetta.protocols.relax.membrane) check_neighbor_ligand_atom() (in module pyrosetta.rosetta.protocols.ligand_docking.ligand_options) check_nucleic_acid_virtual_phosphates() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) check_or_create_fragments() (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) check_orientation() (in module pyrosetta.rosetta.protocols.membrane) check_overlap() (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) check_PA() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_pdb_code() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) check_pdb_for_mem() (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover method) check_phosphate_contacts_donor() (in module pyrosetta.rosetta.core.pose.rna) check_pleat() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) check_pose() (pyrosetta.rosetta.protocols.sparta.Sparta method) check_pose_consistency() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) check_pose_tree_compatibility() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) check_property_overlap() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) check_rama() (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) check_rama2() (pyrosetta.rosetta.core.sequence.ABEGO method) check_rama_scores() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) check_range() (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) check_rdat() (pyrosetta.rosetta.core.io.rna.RDAT method) check_relevant_residues() (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) check_relevant_residues_range() (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) check_residentity_overlap() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) check_residue_type() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) check_restricted_access() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.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) check_rmsd() (pyrosetta.rosetta.protocols.ligand_docking.Transform method) check_rna_loop() (in module pyrosetta.rosetta.core.scoring.rna) check_sample_sugar_in_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) check_score() (in module pyrosetta.rosetta.protocols.ligand_docking) check_score_function_sanity() (in module pyrosetta.rosetta.core.scoring) check_scorefxn_has_constraint_terms_if_pose_has_constraints() (in module pyrosetta.rosetta.protocols.stepwise.modeler) check_screen() (pyrosetta.rosetta.protocols.stepwise.legacy.screener.ProteinAtrRepScreener method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.RNA_AtrRepScreener method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.SimplePoseSelection method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.SimpleRMSD_Screener method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.checker.ProteinAtrRepChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker 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) check_seq_match() (in module pyrosetta.rosetta.protocols.tcr) check_seq_match_from_multiple_input_db() (in module pyrosetta.rosetta.protocols.tcr) check_sequence() (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist method) check_sequence_profile() (pyrosetta.rosetta.protocols.splice.SpliceManager method) check_setup() (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) check_single_format() (pyrosetta.rosetta.protocols.pdbinfo_manipulations.SequenceSpecification method) check_source_segment() (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) check_specs() (pyrosetta.rosetta.utility.options.OptionCollection method) 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) check_ss_lengths() (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) check_stack() (in module pyrosetta.rosetta.core.scoring.rna) check_state() (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) check_statement_sanity() (in module pyrosetta.rosetta.basic.database) check_status() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) check_strand_too_closeness() (in module pyrosetta.rosetta.protocols.features.strand_assembly) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) check_sugar_atom() (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) check_surface_area_leerichards_deriv() (in module pyrosetta.rosetta.core.scoring.packstat) check_sw_by_dis() (in module pyrosetta.rosetta.protocols.features.strand_assembly) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) check_tag() (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) check_tail_residues_sensible() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) check_that_terminal_res_are_unstacked() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker method) check_threads() (pyrosetta.rosetta.core.pack.task.PackerTask_ method) check_valid_membrane() (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) check_validity_and_get_working_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) check_value() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) check_values() (pyrosetta.rosetta.utility.options.OptionCollection method) check_vector() (in module pyrosetta.rosetta.protocols.membrane) check_watson_crick_sequence() (in module pyrosetta.rosetta.core.scoring.rna) check_whether_hairpin_connects_short_strand() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_same_direction_strands_connect_two_sheets_or_a_loop() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_sheets_are_connected_with_near_bb_atoms() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_strand_i_is_in_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_sw_by_sh_id_still_alive() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_sw_is_not_connected_with_continuous_atoms() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_this_pdb_should_be_excluded() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_whether_this_sheet_is_too_short() (in module pyrosetta.rosetta.protocols.features.strand_assembly) check_working_res() (in module pyrosetta.rosetta.core.import_pose) checkFormat() (pyrosetta.rosetta.protocols.sparta.GDB method) checkpoint() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.checkpoint.CheckPointer method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) checkpoint_cleanup() (in module pyrosetta.rosetta.protocols.dna) checkpoint_clear() (pyrosetta.rosetta.protocols.jd2.BOINCJobDistributor method) checkpoint_exists() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) checkpoint_file() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) checkpoint_file_exists() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) checkpoint_read() (pyrosetta.rosetta.protocols.jd2.BOINCJobDistributor method) checkpoint_with_interval() (in module pyrosetta.rosetta.protocols.checkpoint) checkpoint_write() (pyrosetta.rosetta.protocols.jd2.BOINCJobDistributor method) CheckPointer (class in pyrosetta.rosetta.protocols.checkpoint) checkpointing_file() (pyrosetta.rosetta.protocols.simple_filters.ReportFilter method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.Splice method) checkpointing_frequency() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) chem_comp_type (pyrosetta.rosetta.core.io.AtomInformation property) CHEMICAL_MAKE_POSE (pyrosetta.rosetta.basic.ProfTag attribute) CHEMICAL_SHIFT_ANISOTROPY_DATA (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) ChemicalManager (class in pyrosetta.rosetta.core.chemical) ChemicalShiftAnisotropy (class in pyrosetta.rosetta.core.scoring) ChemicalShiftAnisotropyEnergy (class in pyrosetta.rosetta.core.energy_methods) ChemicalShiftAnisotropyEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) ChemicalShiftData (class in pyrosetta.rosetta.core.scoring.rna.chemical_shift) ChemicalShiftEvaluator (class in pyrosetta.rosetta.protocols.sparta) ChemicalShiftEvaluatorCreator (class in pyrosetta.rosetta.protocols.sparta) ChemicalShiftScoringScheme (class in pyrosetta.rosetta.core.sequence) ChemicalShiftSequence (class in pyrosetta.rosetta.core.sequence) ChemicalShiftSequenceCreator (class in pyrosetta.rosetta.core.sequence) chemistries() (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) Chemistry (class in pyrosetta.rosetta.protocols.chemistries) chemistry_loader_ct_namer() (pyrosetta.rosetta.protocols.chemistries.ChemistryLoader static method) chemistry_xml_schema_group_name() (pyrosetta.rosetta.protocols.chemistries.ChemistryFactory static method) ChemistryBase (class in pyrosetta.rosetta.core.chemical.modifications) ChemistryCreator (class in pyrosetta.rosetta.protocols.chemistries) ChemistryFactory (class in pyrosetta.rosetta.protocols.chemistries) ChemistryLoader (class in pyrosetta.rosetta.protocols.chemistries) ChemistryLoaderCreator (class in pyrosetta.rosetta.protocols.chemistries) ChemistryStatus (class in pyrosetta.rosetta.core.chemical.modifications) chemshift_compliance() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) chemshift_overlap_weight_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) cheshire_cell() (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) CheshireCell (class in pyrosetta.rosetta.protocols.cryst) chgm (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) CHI (pyrosetta.rosetta.core.chemical.rna.RNA_Torsion attribute) (pyrosetta.rosetta.core.id.TorsionType attribute) chi (pyrosetta.rosetta.core.pack.dunbrack.ChiSet property) chi() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.io.raw_data.DecoyStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.dna.DNABase method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptERotamerData method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) CHI1 (pyrosetta.rosetta.core.scoring.ProteinTorsion attribute) chi1 (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueSidechainEntry property) chi1() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) (pyrosetta.rosetta.core.scoring.motif.Xfres method) chi11() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) chi12() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) chi13() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) chi14() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) chi1_ (pyrosetta.rosetta.protocols.loop_grower.ResTorsions property) chi1_torsion_atom() (in module pyrosetta.rosetta.core.chemical.rna) chi1_torsion_atom_index() (in module pyrosetta.rosetta.core.chemical.rna) CHI2 (pyrosetta.rosetta.core.scoring.ProteinTorsion attribute) chi2 (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueSidechainEntry property) chi2() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) (pyrosetta.rosetta.core.scoring.motif.Xfres method) chi21() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) chi22() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) chi23() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) chi24() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) chi2_ (pyrosetta.rosetta.protocols.loop_grower.ResTorsions property) CHI2_ANGLES (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) chi2max() (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2_RotamerSetOperation method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation method) chi2min() (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2_RotamerSetOperation method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation method) CHI3 (pyrosetta.rosetta.core.scoring.ProteinTorsion attribute) chi3 (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueSidechainEntry property) chi3() (pyrosetta.rosetta.core.scoring.motif.Xfres method) chi3_ (pyrosetta.rosetta.protocols.loop_grower.ResTorsions property) CHI4 (pyrosetta.rosetta.core.scoring.ProteinTorsion attribute) chi4 (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueSidechainEntry property) chi4() (pyrosetta.rosetta.core.scoring.motif.Xfres method) chi4_ (pyrosetta.rosetta.protocols.loop_grower.ResTorsions property) chi_2_proton_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) chi_angles_ (pyrosetta.rosetta.protocols.legacy_sewing.SewResidue property) CHI_ATOM (pyrosetta.rosetta.core.chemical.GreekDistance attribute) chi_atom_vds() (pyrosetta.rosetta.core.chemical.MutableResidueType method) chi_atoms() (pyrosetta.rosetta.core.chemical.MutableChiRecord method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) chi_clones() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) chi_dev() (pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator method) chi_follows() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) chi_is_independent() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) chi_is_nonrotameric() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) chi_mean() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_float_t method) chi_movable_selector() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) chi_north_anti() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) chi_north_syn() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) chi_number_pseudoalpha() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) chi_number_pseudoalpha_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) chi_number_pseudobeta() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) chi_number_pseudobeta_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) chi_number_pseudoepsilon() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) chi_number_pseudoepsilon_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) chi_number_pseudogamma() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) chi_number_pseudogamma_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) chi_number_pseudozeta() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) chi_number_pseudozeta_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) chi_poly_lookup() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) chi_probability() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) chi_rmsd() (pyrosetta.rosetta.core.scoring.motif.MotifHit method) chi_rmsd_ (pyrosetta.rosetta.core.scoring.motif.MotifHit property) chi_rotamers() (pyrosetta.rosetta.core.chemical.MutableChiRecord method) (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) chi_sample() (pyrosetta.rosetta.protocols.match.upstream.FullChiSampleSet method) chi_samples() (pyrosetta.rosetta.protocols.match.upstream.FullChiSampleSet method) chi_sd() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_1_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_2_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_3_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_4_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerMeanSD_5_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_float_t method) chi_south_anti() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) chi_south_syn() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) chi_stdev() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) chi_torsions() (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) chi_valid() (pyrosetta.rosetta.core.chemical.MutableResidueType method) chi_vec (pyrosetta.rosetta.protocols.splice.ROT property) chi_xx() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_tensor method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_tensor_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_tensor_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_tensor_Ts4 method) chi_xy() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_tensor method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_tensor_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_tensor_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_tensor_Ts4 method) chi_xz() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_tensor method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_tensor_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_tensor_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_tensor_Ts4 method) chi_yy() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_tensor method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_tensor_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_tensor_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_tensor_Ts4 method) chi_yz() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_tensor method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_tensor_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_tensor_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_tensor_Ts4 method) ChiAngleNormalization (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) chidev() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) chidevpen() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) CHIDihedralSamplingData (class in pyrosetta.rosetta.core.scoring.carbohydrates) CHIEnergyFunction (class in pyrosetta.rosetta.core.scoring.carbohydrates) CHIEnergyFunctionLinkageType (class in pyrosetta.rosetta.core.scoring.carbohydrates) ChiInfo (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) child (pyrosetta.rosetta.core.kinematics.inverse.InternalCoordAtoms property) child() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTFactor method) child_index() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) children() (pyrosetta.rosetta.protocols.jd3.JGJobNode method) (pyrosetta.rosetta.protocols.jd3.JGResultNode method) chimean() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) chimera_ (pyrosetta.rosetta.protocols.legacy_sewing.SewSegment property) chimerize() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) chinum() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) ChiralFlipAtoms (class in pyrosetta.rosetta.core.chemical) ChiralFlipNaming (class in pyrosetta.rosetta.core.chemical) Chirality (class in pyrosetta.rosetta.protocols.simple_moves.chiral) chirality_sign() (pyrosetta.rosetta.core.scoring.MultipoleParameter method) ChiralMover (class in pyrosetta.rosetta.protocols.simple_moves.chiral) chis (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.PlaceableRotamer property) (pyrosetta.rosetta.protocols.sewing.hashing.LigandCoordInfo property) chis_from_pose() (pyrosetta.rosetta.protocols.pose_metric_calculators.RotamerRecovery method) chisd() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) ChiSet (class in pyrosetta.rosetta.core.pack.dunbrack) ChiState (class in pyrosetta.rosetta.core.chemical.rna) ChiStrategy (class in pyrosetta.rosetta.protocols.match.upstream) chitip_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) chitip_atoms() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) ChiWellRmsdEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) ChiWellRmsdEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) choices() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.Mutate1Randomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) choose_best_metal_coordinator() (pyrosetta.rosetta.protocols.sewing.hashing.LigandBindingResPlacer method) choose_best_solution_based_on_score_function() (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) choose_canonical() (in module pyrosetta.rosetta.protocols.denovo_design.components) choose_cutpoint() (pyrosetta.rosetta.protocols.loops.Loop method) choose_cutpoints() (pyrosetta.rosetta.protocols.loops.Loops method) choose_effective_sequence_separation() (in module pyrosetta.rosetta.core.scoring.constraints) (pyrosetta.rosetta.core.pack.dunbrack.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) choose_fragment() (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) choose_hbond_parameter_set() (in module pyrosetta.rosetta.protocols.simple_pose_metric_calculators) choose_least_perturb_solution() (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) choose_n_best() (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) choose_new_movable_group() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) choose_origin_with_lowest_eggshell_ruggedness() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) 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.monte_carlo.mover.StepWiseMoveSelector method) choose_random_if_unspecified_nucleotide() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) choose_randomly_from_allowed_at_position() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) choose_solution() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) choose_window_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) choose_window_start() (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) chop_fragments() (in module pyrosetta.rosetta.core.fragment) chothia (pyrosetta.rosetta.core.scoring.sasa.SasaRadii attribute) Chothia (pyrosetta.rosetta.protocols.antibody.CDRDefinitionEnum attribute) Chothia_Numberer (class in pyrosetta.rosetta.protocols.antibody.grafting) Chothia_Scheme (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingSchemeEnum attribute) chr_chains_nonrepeated() (in module pyrosetta.rosetta.utility.tag) chrg (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) ChromophoreDataReader (class in pyrosetta.rosetta.protocols.chromophore) chunk (pyrosetta.rosetta.utility.sql_database.TransactionMode attribute) (pyrosetta.rosetta.utility.sql_database.TransactionMode.e attribute) chunk_coverage() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) chunk_initialization_pdb_files() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) chunk_key() (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) chunk_library_from_input_source() (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputter method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.PDBChunkLibraryInputter method) chunk_library_inputter (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryPreliminaryLarvalJob property) chunk_library_inputter_creators() (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputterFactory method) chunk_library_inputter_xml_schema_group_name() (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputterFactory static method) chunk_library_inputter_xsd_type_definition_w_attributes() (in module pyrosetta.rosetta.protocols.jd3.chunk_library_inputters) chunk_pdb_files() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) chunk_probabilities() (in module pyrosetta.rosetta.protocols.medal) chunk_set() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) chunk_sets() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) chunk_silent_files() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) ChunkExponent (class in pyrosetta.rosetta.ObjexxFCL) ChunkLibraryInnerLarvalJob (class in pyrosetta.rosetta.protocols.jd3.chunk_library) ChunkLibraryInputSource (class in pyrosetta.rosetta.protocols.jd3.chunk_library_inputters) ChunkLibraryInputter (class in pyrosetta.rosetta.protocols.jd3.chunk_library_inputters) ChunkLibraryInputterCreator (class in pyrosetta.rosetta.protocols.jd3.chunk_library_inputters) ChunkLibraryInputterFactory (class in pyrosetta.rosetta.protocols.jd3.chunk_library_inputters) ChunkLibraryJobQueen (class in pyrosetta.rosetta.protocols.jd3.chunk_library) ChunkLibraryJobResult (class in pyrosetta.rosetta.protocols.jd3.chunk_library) ChunkLibraryPreliminaryLarvalJob (class in pyrosetta.rosetta.protocols.jd3.chunk_library) ChunkSet (class in pyrosetta.rosetta.core.import_pose.libraries) ChunkTrialMover (class in pyrosetta.rosetta.protocols.hybridization) Ci() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) Ci_ (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo property) ci_1b (pyrosetta.rosetta.core.scoring.methods.EnergyMethodType attribute) ci_1b_types() (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) ci_2b (pyrosetta.rosetta.core.scoring.methods.EnergyMethodType attribute) ci_2b_types() (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) ci_lr_2b (pyrosetta.rosetta.core.scoring.methods.EnergyMethodType attribute) ci_lr_2b_types() (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) cid (pyrosetta.rosetta.protocols.constel.ResMut property) CIF_file (pyrosetta.rosetta.core.import_pose.FileType attribute) Circle (class in pyrosetta.rosetta.core.scoring.packstat) circle() (pyrosetta.rosetta.core.scoring.PDinter method) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) circles_ (pyrosetta.rosetta.core.scoring.packstat.Slice property) CircularGeneral1D_Func (class in pyrosetta.rosetta.core.scoring.func) CircularHarmonicFunc (class in pyrosetta.rosetta.core.scoring.func) CircularPermutation (class in pyrosetta.rosetta.protocols.fldsgn) CircularPermutationCreator (class in pyrosetta.rosetta.protocols.fldsgn) CircularPermuteFreePeptideMover (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers) CircularPowerFunc (class in pyrosetta.rosetta.core.scoring.func) CircularSigmoidalFunc (class in pyrosetta.rosetta.core.scoring.func) CircularSplineFunc (class in pyrosetta.rosetta.core.scoring.func) CIS (pyrosetta.rosetta.core.chemical.rna.LW_BaseDoubletOrientation attribute) cis_omega() (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) cis_omega_torsion_bin() (in module pyrosetta.rosetta.core.conformation) cis_peptide_bonds() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary method) cis_trans_conf (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData property) cis_trans_match() (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) CISPEP (pyrosetta.rosetta.core.io.pdb.RecordType attribute) cispep_map() (pyrosetta.rosetta.core.io.StructFileRep method) CisPeptideInformation (class in pyrosetta.rosetta.core.io) Citation (class in pyrosetta.rosetta.basic.citation_manager) CitationCollection (class in pyrosetta.rosetta.basic.citation_manager) CitationCollectionBase (class in pyrosetta.rosetta.basic.citation_manager) CitationCollectionList (class in pyrosetta.rosetta.basic.citation_manager) CitationFormat (class in pyrosetta.rosetta.basic.citation_manager) CitationManager (class in pyrosetta.rosetta.basic.citation_manager) citations() (pyrosetta.rosetta.basic.citation_manager.CitationCollectionList method) CitedModuleType (class in pyrosetta.rosetta.basic.citation_manager) CITRULLINATION (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes attribute) Cl (pyrosetta.rosetta.core.chemical.element.Elements attribute) 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.VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) claim_accepted() (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) claim_backbone() (pyrosetta.rosetta.protocols.environment.claims.TorsionClaim method) claim_sidechain() (pyrosetta.rosetta.protocols.environment.claims.TorsionClaim method) claimer() (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) claimer_builds_own_fold_tree() (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) ClaimerMessage (class in pyrosetta.rosetta.protocols.topology_broker) ClaimStrength (class in pyrosetta.rosetta.protocols.environment.claims) ClaimStrength.PrioSubtype (class in pyrosetta.rosetta.protocols.environment.claims) clash (pyrosetta.rosetta.protocols.kinmatch.KRSQuery property) clash() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.numeric.geometry.hashing.MinimalClashHash method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) clash_amount() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) clash_ball() (pyrosetta.rosetta.numeric.geometry.hashing.MinimalClashHash method) clash_check() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelEnsemble method) (pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck method) clash_check_ball() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) clash_check_balls() (pyrosetta.rosetta.numeric.geometry.hashing.MinimalClashHash method) clash_check_residue_pairs() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) clash_check_test() (pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck method) clash_check_trimer() (pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck method) clash_count (pyrosetta.rosetta.protocols.legacy_sewing.HashResult property) clash_count() (pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck method) clash_dis_ (pyrosetta.rosetta.protocols.sic_dock.CBScore property) clash_dist() (pyrosetta.rosetta.protocols.matdes.ClashCheckFilter method) clash_not_resid() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) clash_off() (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer method) clash_on() (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer method) clash_raw() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) clash_score (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data property) clash_score() (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer method) ClashBasedRepackShell (class in pyrosetta.rosetta.core.pack.task.operation) ClashBasedRepackShellCreator (class in pyrosetta.rosetta.core.pack.task.operation) ClashBasedShellSelector (class in pyrosetta.rosetta.core.pack.task.residue_selector) ClashBasedShellSelectorCreator (class in pyrosetta.rosetta.core.pack.task.residue_selector) ClashCheckFilter (class in pyrosetta.rosetta.protocols.matdes) ClashCheckFilterCreator (class in pyrosetta.rosetta.protocols.matdes) ClashCountCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) clashes() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.sic_dock.Rose method) clashes_naive() (pyrosetta.rosetta.protocols.sic_dock.Rose method) ClashRequirement (class in pyrosetta.rosetta.protocols.sewing.requirements) ClashRequirementCreator (class in pyrosetta.rosetta.protocols.sewing.requirements) ClashWithTargetFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) ClashWithTargetFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) class_key() (pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter method) class_name() (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector static method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector static method) (pyrosetta.rosetta.core.select.jump_selector.ExclusivelySharedJumpSelector static method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector static method) (pyrosetta.rosetta.core.select.jump_selector.JumpForResidue static method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector static method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector static method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector static method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelector static method) (pyrosetta.rosetta.core.select.residue_selector.BFactorSelector static method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector static method) (pyrosetta.rosetta.core.select.residue_selector.BlockSelector static method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.ChainSelector static method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.ConfluentSelector static method) (pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.FractionSelector static method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector static method) (pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector static method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector static method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector static method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector static method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector static method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector static method) (pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector static method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector static method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector static method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector static method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector static method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector static method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector static method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector static method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector static method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector static method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector static method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector static method) (pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelector static method) (pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector static method) (pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelector static method) (pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelector static method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelector static method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures static method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeatures static method) (pyrosetta.rosetta.protocols.antibody.design.ResnumFromStringsWithRangesSelector static method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector static method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector static method) (pyrosetta.rosetta.protocols.buns.BuriedUnsatHbondFilter2 static method) (pyrosetta.rosetta.protocols.calc_taskop_filters.ConservedPosMutationFilter static method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids static method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator static method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter static method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight static method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 static method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid static method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover static method) (pyrosetta.rosetta.protocols.chemistries.PatchChemistry static method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter static method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter static method) (pyrosetta.rosetta.protocols.constraint_filters.ShowConstraintsFilter static method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator static method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator static method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator static method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator static method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator static method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator static method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator static method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator static method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter static method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter static method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter static method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector static method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber static method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber static method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber static method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder static method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder static method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder static method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData static method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.constraints.FileConstraintGenerator static method) (pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter static method) (pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter static method) (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter static method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter static method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter static method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover static method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector static method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector static method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation static method) (pyrosetta.rosetta.protocols.environment.claims.CutBiasClaim static method) (pyrosetta.rosetta.protocols.environment.claims.EnvLabelSelector static method) (pyrosetta.rosetta.protocols.environment.claims.JumpClaim static method) (pyrosetta.rosetta.protocols.environment.claims.TorsionClaim static method) (pyrosetta.rosetta.protocols.environment.claims.VirtResClaim static method) (pyrosetta.rosetta.protocols.environment.claims.XYZClaim static method) (pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilter static method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter static method) (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter static method) (pyrosetta.rosetta.protocols.enzdes.LigBurialFilter static method) (pyrosetta.rosetta.protocols.enzdes.LigDSasaFilter static method) (pyrosetta.rosetta.protocols.enzdes.LigInterfaceEnergyFilter static method) (pyrosetta.rosetta.protocols.enzdes.RemoveLigandFilter static method) (pyrosetta.rosetta.protocols.enzdes.RepackWithoutLigandFilter static method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter static method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost static method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder static method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter static method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures static method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures static method) (pyrosetta.rosetta.protocols.features.AtomTypesFeatures static method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures static method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeatures static method) (pyrosetta.rosetta.protocols.features.DdGFeatures static method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeatures static method) (pyrosetta.rosetta.protocols.features.HBondFeatures static method) (pyrosetta.rosetta.protocols.features.HBondParameterFeatures static method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTest static method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeatures static method) (pyrosetta.rosetta.protocols.features.HelixCapFeatures static method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures static method) (pyrosetta.rosetta.protocols.features.JobDataFeatures static method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeatures static method) (pyrosetta.rosetta.protocols.features.ModelFeatures static method) (pyrosetta.rosetta.protocols.features.OrbitalsFeatures static method) (pyrosetta.rosetta.protocols.features.PairFeatures static method) (pyrosetta.rosetta.protocols.features.PdbDataFeatures static method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeatures static method) (pyrosetta.rosetta.protocols.features.PoseConformationFeatures static method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures static method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures static method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures static method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures static method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures static method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures static method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeatures static method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeatures static method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeatures static method) (pyrosetta.rosetta.protocols.features.ResidueFeatures static method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeatures static method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeatures static method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeatures static method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeatures static method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeatures static method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeatures static method) (pyrosetta.rosetta.protocols.features.RotamerFeatures static method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeatures static method) (pyrosetta.rosetta.protocols.features.RuntimeFeatures static method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeatures static method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeatures static method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeatures static method) (pyrosetta.rosetta.protocols.features.ScreeningFeatures static method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeatures static method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeatures static method) (pyrosetta.rosetta.protocols.features.SmotifFeatures static method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeatures static method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures static method) (pyrosetta.rosetta.protocols.features.StructureFeatures static method) (pyrosetta.rosetta.protocols.features.StructureScoresFeatures static method) (pyrosetta.rosetta.protocols.features.TaskOperationFeatures static method) (pyrosetta.rosetta.protocols.features.TotalScoreFeatures static method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeatures static method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeatures static method) (pyrosetta.rosetta.protocols.features.WaterFeatures static method) (pyrosetta.rosetta.protocols.filters.CalculatorFilter static method) (pyrosetta.rosetta.protocols.filters.CombinedFilter static method) (pyrosetta.rosetta.protocols.filters.CompoundFilter static method) (pyrosetta.rosetta.protocols.filters.ContingentFilter static method) (pyrosetta.rosetta.protocols.filters.FalseFilter static method) (pyrosetta.rosetta.protocols.filters.IfThenFilter static method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter static method) (pyrosetta.rosetta.protocols.filters.ReplicateFilter static method) (pyrosetta.rosetta.protocols.filters.StochasticFilter static method) (pyrosetta.rosetta.protocols.filters.TimeFilter static method) (pyrosetta.rosetta.protocols.filters.TrueFalseFilter static method) (pyrosetta.rosetta.protocols.filters.TrueFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.CoreDunbrackFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.FragQualFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.InterlockingAromaFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.NcontactsFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.ParallelBetaPairingPreferenceFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureCountFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureHasResidueFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels static method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter static method) (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator static method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator static method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator static method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ConstraintFulfilmentFilter static method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilter static method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ScorePoseSegmentFromResidueSelectorFilter static method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ConstraintResidueSelector static method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.CutpointResidueSelector static method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ProteinResidueSelector static method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter static method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelector static method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter static method) (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilter static method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalLengthRequirement static method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyResidueRetentionRequirement static method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentDsspRequirement static method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentLengthRequirement static method) (pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilter static method) (pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilter static method) (pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilter static method) (pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilter static method) (pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilter static method) (pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilter static method) (pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilter static method) (pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilter static method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction static method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction static method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction static method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction static method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction static method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction static method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction static method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter static method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner static method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefiner static method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefiner static method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsStringDefiner static method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilter static method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues static method) (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter static method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter static method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter static method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter static method) (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorer static method) (pyrosetta.rosetta.protocols.pose_sewing.filters.HasDisulfideFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AtomicContactCountFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AverageDegreeFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.ClashWithTargetFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FNatFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.InterfaceHolesFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.IRmsdFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.LRmsdFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdSimpleFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SpecificResiduesNearInterfaceFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SSamountFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreLoopsFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.Torsion static method) (pyrosetta.rosetta.protocols.residue_selectors.HBondSelector static method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector static method) (pyrosetta.rosetta.protocols.residue_selectors.NativeSelector static method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector static method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector static method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover static method) (pyrosetta.rosetta.protocols.score_filters.GeometryFilter static method) (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilter static method) (pyrosetta.rosetta.protocols.score_filters.ScoreTypeFilter static method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover static method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover static method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMoverCreator static method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover static method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMoverCreator static method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover static method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMoverCreator static method) (pyrosetta.rosetta.protocols.simple_ddg.AlaScan static method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter static method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScan static method) (pyrosetta.rosetta.protocols.simple_ddg.InterfaceBindingEnergyDensityFilter static method) (pyrosetta.rosetta.protocols.simple_ddg.SSElementBisectddGFilter static method) (pyrosetta.rosetta.protocols.simple_filters.AngleToVector static method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter static method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter static method) (pyrosetta.rosetta.protocols.simple_filters.AveragePathLengthFilter static method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter static method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak static method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilter static method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter static method) (pyrosetta.rosetta.protocols.simple_filters.DisulfideEntropyFilter static method) (pyrosetta.rosetta.protocols.simple_filters.EnergyPerResidueFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ExpiryFilter static method) (pyrosetta.rosetta.protocols.simple_filters.FileExistFilter static method) (pyrosetta.rosetta.protocols.simple_filters.FileRemoveFilter static method) (pyrosetta.rosetta.protocols.simple_filters.HelixHelixAngleFilter static method) (pyrosetta.rosetta.protocols.simple_filters.HolesFilter static method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilter static method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHydrophobicResidueContactsFilter static method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceSasaFilter static method) (pyrosetta.rosetta.protocols.simple_filters.InterRepeatContactFilter static method) (pyrosetta.rosetta.protocols.simple_filters.IntraRepeatContactFilter static method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter static method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter static method) (pyrosetta.rosetta.protocols.simple_filters.MembAccesResidueLipophilicityFilter static method) (pyrosetta.rosetta.protocols.simple_filters.MotifScoreFilter static method) (pyrosetta.rosetta.protocols.simple_filters.MPSpanAngleFilter static method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilter static method) (pyrosetta.rosetta.protocols.simple_filters.NeighborTypeFilter static method) (pyrosetta.rosetta.protocols.simple_filters.NetChargeFilter static method) (pyrosetta.rosetta.protocols.simple_filters.NMerPSSMEnergyFilter static method) (pyrosetta.rosetta.protocols.simple_filters.NMerSVMEnergyFilter static method) (pyrosetta.rosetta.protocols.simple_filters.NonSequentialNeighborsFilter static method) (pyrosetta.rosetta.protocols.simple_filters.PackStatFilter static method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment static method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter static method) (pyrosetta.rosetta.protocols.simple_filters.RangeFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ReadPoseExtraScoreFilter static method) (pyrosetta.rosetta.protocols.simple_filters.RepeatParameterFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ReportFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ResidueBurialFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ResidueChiralityFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDistanceFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ResidueIEFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ResidueLipophilicityFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSelectionDistanceFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSetChainEnergyFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ResiduesInInterfaceFilter static method) (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter static method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter static method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance static method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter static method) (pyrosetta.rosetta.protocols.simple_filters.SidechainRmsdFilter static method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter static method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter static method) (pyrosetta.rosetta.protocols.simple_filters.SpanTopologyMatchPoseFilter static method) (pyrosetta.rosetta.protocols.simple_filters.SSElementLengthFilter static method) (pyrosetta.rosetta.protocols.simple_filters.SSElementMotifContactFilter static method) (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinder static method) (pyrosetta.rosetta.protocols.simple_filters.StemFinder static method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilter static method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareSASAFilter static method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter static method) (pyrosetta.rosetta.protocols.simple_filters.TerminusDistanceFilter static method) (pyrosetta.rosetta.protocols.simple_filters.TMsAACompFilter static method) (pyrosetta.rosetta.protocols.simple_filters.TMsSpanMembraneFilter static method) (pyrosetta.rosetta.protocols.simple_filters.TotalSasaFilter static method) (pyrosetta.rosetta.protocols.simple_filters.Worst9merFilter static method) (pyrosetta.rosetta.protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGenerator static method) classic (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolBackboneRandomizationMode attribute) classic() (pyrosetta.rosetta.std.locale static method) classic0 (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolBackboneMinimizationMode attribute) classic1 (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolBackboneMinimizationMode attribute) classic2 (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolBackboneMinimizationMode attribute) ClassicAbinitio (class in pyrosetta.rosetta.protocols.abinitio) ClassicAbinitio.StageID (class in pyrosetta.rosetta.protocols.abinitio) ClassicFragmentMover (class in pyrosetta.rosetta.protocols.simple_moves) ClassicGrid (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) ClassicGridCreator (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) ClassicMatchAlgorithm (class in pyrosetta.rosetta.protocols.match.downstream) ClassicRelax (class in pyrosetta.rosetta.protocols.relax) ClassicRelaxCreator (class in pyrosetta.rosetta.protocols.relax) classification() (pyrosetta.rosetta.core.io.HeaderInformation method) classifier (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo property) classify_base_pairs() (in module pyrosetta.rosetta.core.pose.rna) classify_base_pairs_lores() (in module pyrosetta.rosetta.protocols.rna.denovo) classname() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator static method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator static method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator static method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator static method) (pyrosetta.rosetta.core.conformation.symmetry.SymmDataLoader static method) (pyrosetta.rosetta.core.fragment.FragmentSetLoader static method) (pyrosetta.rosetta.core.import_pose.PoseResourceLoader static method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader static method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader static method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader static method) clean_for_storage() (in module pyrosetta.rosetta.protocols.denovo_design.components) clean_frag_cache() (pyrosetta.rosetta.core.fragment.FragmentIO method) clean_from_storage() (in module pyrosetta.rosetta.protocols.denovo_design.components) clean_jumps() (pyrosetta.rosetta.protocols.abinitio.FixTemplateJumpSetup method) (pyrosetta.rosetta.protocols.abinitio.TemplateJumpSetup method) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) clean_pose() (pyrosetta.rosetta.protocols.simple_ddg.ddG method) clean_pose_store() (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) clean_residue_task() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) clean_up() (pyrosetta.rosetta.protocols.frag_picker.scores.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.CachingScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.HydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.JCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.LAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.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.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager 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.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) clean_up_after_packing() (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) clean_up_dangling_connect() (in module pyrosetta.rosetta.core.chemical) clean_up_residuearrayannealableenergy_after_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) cleanATOM() (in module pyrosetta.toolbox.cleaning) cleanCRYS() (in module pyrosetta.toolbox.cleaning) cleaned() (pyrosetta.rosetta.utility.options.OptionCollection static method) cleaned_alignment_file() (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) cleanup() (in module pyrosetta.rosetta.core.import_pose) cleanup_files() (pyrosetta.rosetta.core.scoring.PoissonBoltzmannPotential method) cleanup_rdvalue() (pyrosetta.rosetta.RDKit.RDValue static method) clear() (pyrosetta.bindings.pose.PoseScoreAccessor method) (pyrosetta.bindings.pose.ResidueLabelAccessor method) (pyrosetta.io.silent_file_map.SilentFileMap method) (pyrosetta.rosetta.basic.citation_manager.Citation method) (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.basic.resource_manager.ResourceManager method) Clear() (pyrosetta.rosetta.basic.sampling.orientations.QuatSet method) clear() (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.CacheableResidueTypeSets method) (pyrosetta.rosetta.core.chemical.mainchain_potential.MainchainScoreTable method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.FrameList method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame 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.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.id.AtomID_Map_AtomID method) (pyrosetta.rosetta.core.id.AtomID_Map_bool method) (pyrosetta.rosetta.core.id.AtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_MP_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_Real method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_NamedAtomID method) (pyrosetta.rosetta.core.id.SequenceMapping method) (pyrosetta.rosetta.core.io.Remarks method) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) (pyrosetta.rosetta.core.pack.rotamer_set.WaterPackingInfo method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLT method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pose.copydofs.CopyDofsInfo method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.CenHBPotential method) (pyrosetta.rosetta.core.scoring.constraints.Constraints method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.Hairpins method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.motif.MotifHits method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotifs method) (pyrosetta.rosetta.core.scoring.motif.XformScore method) (pyrosetta.rosetta.core.scoring.NeighborList method) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.core.scoring.SmoothScoreTermCoeffs method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.Strands method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) (pyrosetta.rosetta.core.scoring.TMscoreStore method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRanges method) (pyrosetta.rosetta.core.select.residue_selector.ResidueVector method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.core.sequence.DP_Matrix method) (pyrosetta.rosetta.core.sequence.SequenceAlignment method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricData method) (pyrosetta.rosetta.cppdb.backend.statements_cache method) (pyrosetta.rosetta.cppdb.pool method) (pyrosetta.rosetta.cppdb.result method) (pyrosetta.rosetta.cppdb.statement method) 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(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.FArrayInitializer_bool_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_bool_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_char_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepNRChiSample_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_1_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_1_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_2_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_2_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_3_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_3_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_4_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_4_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_5_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_5_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBIndNRChiSample_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray4D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray5D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_float_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_float_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_float_ObjexxFCL_FArray5D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray4D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray5D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_numeric_xyzVector_double_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_ObjexxFCL_FArray1D_int_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_ObjexxFCL_FArray2D_float__star__ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_ObjexxFCL_ubyte_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_std_complex_double_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_std_string_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_std_string_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_std_vector_unsigned_long_std_allocator_unsigned_long_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_char_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_char_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_char_ObjexxFCL_FArray4D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_long_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_long_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_long_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_double_std_allocator_double_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_double_std_allocator_double_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_unsigned_int_std_allocator_unsigned_int_ObjexxFCL_FArray3D_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.AbrelaxMover method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultVector 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.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) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.Cluster 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.IgnoreSubsetConstraintSet 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.MaxSeqSepConstraintSet 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.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.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.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.DnaChains 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.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion 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.evaluation.MetaPoseEvaluator method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.filters.CalculatorFilter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.ContingentFilter method) (pyrosetta.rosetta.protocols.filters.FalseFilter method) (pyrosetta.rosetta.protocols.filters.Filter method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.filters.ReplicateFilter method) (pyrosetta.rosetta.protocols.filters.StochasticFilter method) (pyrosetta.rosetta.protocols.filters.TimeFilter method) (pyrosetta.rosetta.protocols.filters.TrueFalseFilter method) (pyrosetta.rosetta.protocols.filters.TrueFilter method) (pyrosetta.rosetta.protocols.filters.VectorPoseFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.CoreDunbrackFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.FragQualFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.InterlockingAromaFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.NcontactsFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.ParallelBetaPairingPreferenceFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureCountFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureHasResidueFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairings 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.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.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_CompareTotalScore method) (pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareByScoreCombination_t method) (pyrosetta.rosetta.protocols.frag_picker.LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareTotalScore_t method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frag_picker.scores.AdaptiveScoreHistogram method) (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.hbnet.HBNetScore method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments method) (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilter method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.EvenlyPartitionedNodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManagerStorageMatrix method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph 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.OutputStructureStore method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.RotamerPairEnergies 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.ligand_options.Interface method) (pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilter method) (pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilter method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.match.Bool3DGrid method) (pyrosetta.rosetta.protocols.match.downstream.ActiveSiteGrid 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.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.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverStatistics method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) (pyrosetta.rosetta.protocols.pack_daemon.TopEntitySet method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorer method) (pyrosetta.rosetta.protocols.pose_sewing.filters.HasDisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AtomicContactCountFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AverageDegreeFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.ClashWithTargetFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FNatFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.InterfaceHolesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.IRmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.LRmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdSimpleFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SpecificResiduesNearInterfaceFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SSamountFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreLoopsFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.Torsion method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.qsar.qsarMap method) (pyrosetta.rosetta.protocols.recces.Histogram method) (pyrosetta.rosetta.protocols.recon_design.FitnessFilter method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol 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.hashing.SegmentVector 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.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.splice.ResidueBBDofs method) (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) (pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoints method) (pyrosetta.rosetta.protocols.wum.SilentStructStore method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue_Swapped method) (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) (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.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.std.vector_core_io_AtomInformation method) (pyrosetta.rosetta.std.vector_core_io_RemarkInfo method) (pyrosetta.rosetta.std.vector_core_pose_Pose method) 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(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.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) 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(pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) (pyrosetta.rosetta.utility.recent_history_queue method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_chemical_RestypeDestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_ConnectionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_IdentityEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_LengthEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_XYZEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_ConformationEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_DestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_EnergyEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.PausableSignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_chemical_RestypeDestructionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_ConnectionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_IdentityEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_LengthEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_XYZEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_ConformationEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_DestructionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_EnergyEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.tag.Tag 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 method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_core_id_NamedAtomID_std_less_std_string_std_allocator_std_pair_const_std_string_core_id_NamedAtomID_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_numeric_xyzVector_double_std_less_std_string_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_unsigned_long_std_less_std_string_std_allocator_std_pair_const_std_string_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_core_chemical_AA_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_core_chemical_AA_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_shared_ptr_protocols_frag_picker_CandidatesCollector_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_frag_picker_CandidatesCollector_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_unsigned_long_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_utility_keys_Key2Tuple_unsigned_long_unsigned_long_unsigned_long_std_less_utility_keys_Key2Tuple_unsigned_long_unsigned_long_std_allocator_std_pair_const_utility_keys_Key2Tuple_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_unsigned_long_std_less_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_std_allocator_std_pair_const_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_bool_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_core_id_AtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_core_kinematics_Jump_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_std_pair_core_id_AtomID_core_id_AtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_DOF_ID_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_NamedAtomID_core_id_NamedAtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_TorsionID_core_id_TorsionID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_TorsionID_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_io_HeaderInformation_CompoundToken_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_io_raw_data_DisulfideFile_ResNum_core_io_raw_data_DisulfideFile_ResNum_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_aa_composition_energy_TailFunction_core_scoring_aa_composition_energy_TailFunction_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_disulfides_CentroidDisulfideEnergyComponents_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_disulfides_DisulfideMatchingEnergyComponents_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_disulfides_FullatomDisulfideEnergyComponents_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_int_int_t method) (pyrosetta.rosetta.utility.vector1_std_pair_int_std_shared_ptr_const_core_conformation_ResidueMatcher_t method) (pyrosetta.rosetta.utility.vector1_std_pair_int_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_long_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_numeric_xyzVector_double_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_numeric_xyzVector_double_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_numeric_xyzVector_float_int_t method) (pyrosetta.rosetta.utility.vector1_std_pair_protocols_forge_build_Interval_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_protocols_loophash_BackboneSegment_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_protocols_sewing_data_storage_Basis_protocols_sewing_data_storage_Basis_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_list_std_shared_ptr_const_core_conformation_Residue_utility_vector1_std_shared_ptr_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_std_allocator_std_shared_ptr_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_pair_unsigned_long_unsigned_long_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_set_unsigned_long_std_set_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_const_core_pose_ResidueIndexDescription_std_shared_ptr_const_core_pose_ResidueIndexDescription_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_const_numeric_expression_parser_Expression_std_shared_ptr_protocols_pack_daemon_SurrogateVariableExpression_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_core_io_silent_SilentStruct_utility_file_FileName_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_calc_taskop_movers_DesignRepackMover_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_calc_taskop_movers_DesignRepackMover_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_filters_Filter_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_genetic_algorithm_Entity_std_pair_utility_vector1_double_std_allocator_double_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_hotspot_hashing_HotspotStubSet_std_pair_std_shared_ptr_protocols_hotspot_hashing_HotspotStub_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_jd3_InnerLarvalJob_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_protocols_jd3_JobSummary_std_shared_ptr_protocols_jd3_JobResult_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_string_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_string_core_kinematics_Jump_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_string_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_string_protocols_ligand_docking_Translate_info_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_string_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_string_std_shared_ptr_const_protocols_qsar_scoring_grid_GridSet_t method) 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(pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_AtomPairConstraintsData_std_allocator_std_shared_ptr_protocols_frag_picker_scores_AtomPairConstraintsData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_FourAtomsConstraintData_std_allocator_std_shared_ptr_protocols_frag_picker_scores_FourAtomsConstraintData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_Entity_std_allocator_std_shared_ptr_protocols_genetic_algorithm_Entity_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_std_allocator_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_jd3_JGJobNode_std_allocator_std_shared_ptr_protocols_jd3_JGJobNode_t method) 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(pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_void__star__std_allocator_void__star__t method) clear_() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) clear_active_dofs() (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) clear_active_pose_constraints() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache method) clear_active_pose_constraints_for_block() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) clear_all() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) clear_all_strand_data() (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) clear_all_vectors() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector method) clear_atoms() (pyrosetta.rosetta.core.optimization.DOF_Node method) clear_authors() (pyrosetta.rosetta.core.io.HeaderInformation method) clear_blacklist() (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) clear_buffer() (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_chemical_RestypeDestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_ConnectionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_IdentityEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_LengthEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_XYZEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_ConformationEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_DestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_EnergyEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.PausableSignalHub_void_core_conformation_signals_GeneralEvent_t method) clear_cache() (pyrosetta.rosetta.cppdb.backend.connection method) (pyrosetta.rosetta.cppdb.session method) (pyrosetta.rosetta.utility.sql_database.session method) clear_cached_data() (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) clear_cached_maps() (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) clear_calculators() (pyrosetta.rosetta.core.pose.metrics.CalculatorFactory method) clear_checkpoints() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.checkpoint.CheckPointer method) clear_chi_rotamers() (pyrosetta.rosetta.core.chemical.MutableChiRecord method) (pyrosetta.rosetta.core.chemical.MutableResidueType method) clear_citations() (pyrosetta.rosetta.basic.citation_manager.CitationManager method) clear_combine_history() (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) clear_comments() (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) clear_compounds() (pyrosetta.rosetta.core.io.HeaderInformation method) clear_conformation_viewers() (in module pyrosetta.rosetta.protocols.viewer) clear_connected_resonances() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) clear_connections() (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) clear_constraint_generators() (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) clear_data() (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.motifs.BuildPosition method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) clear_dCCdx_res_cache() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) clear_dependencies() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) clear_design_taskset() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) clear_downstream_orientation_atoms() (pyrosetta.rosetta.protocols.match.MatcherTask method) clear_edges() (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) clear_energies() (pyrosetta.rosetta.core.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.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) clear_evaluators() (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) clear_events() (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) clear_experimental_techniques() (pyrosetta.rosetta.core.io.HeaderInformation method) clear_extent_eval() (pyrosetta.rosetta.core.fragment.picking_old.concepts.Librarian_core_fragment_picking_old_vall_scores_VallFragmentScore_core_fragment_picking_old_vall_eval_VallFragmentEval_core_fragment_picking_old_vall_gen_VallFragmentGen_core_fragment_picking_old_vall_VallLibrary_t method) (pyrosetta.rosetta.core.fragment.picking_old.concepts.Librarian_VallFragmentScore_VallFragmentEval_VallFragmentGen_VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) clear_extent_gen() (pyrosetta.rosetta.core.fragment.picking_old.concepts.Librarian_core_fragment_picking_old_vall_scores_VallFragmentScore_core_fragment_picking_old_vall_eval_VallFragmentEval_core_fragment_picking_old_vall_gen_VallFragmentGen_core_fragment_picking_old_vall_VallLibrary_t method) (pyrosetta.rosetta.core.fragment.picking_old.concepts.Librarian_VallFragmentScore_VallFragmentEval_VallFragmentGen_VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) clear_external_geom_samplers() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) clear_filters() (pyrosetta.rosetta.protocols.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.match.output.MatchConsolidator method) (pyrosetta.rosetta.protocols.match.output.MatchOutputter method) (pyrosetta.rosetta.protocols.match.output.MatchProcessor method) clear_focus() (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector method) clear_fragment_eval() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) clear_fragment_gen() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) clear_fragments() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.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) clear_free_peptide_movers() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) clear_from_pose() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) clear_glycan_trees() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) clear_hash_map() (pyrosetta.rosetta.protocols.match.HitHasher method) clear_hbond_counts() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) clear_history() (pyrosetta.rosetta.protocols.pack_daemon.MPIMultistateFitnessFunction method) (pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction method) clear_icoor() (pyrosetta.rosetta.core.chemical.MutableResidueType method) CLEAR_IF_CACHING_FRAGMENTS (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum attribute) clear_imporated_data() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser method) clear_induced_fields() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) clear_info() (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) clear_initialization() (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) clear_input_files() (pyrosetta.rosetta.utility.Inline_File_Provider method) clear_input_sources() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.standard.StandardInnerLarvalJob method) clear_internals() (pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader method) clear_inverse_rotamers() (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) clear_jumps() (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) clear_keywords() (pyrosetta.rosetta.core.io.HeaderInformation method) clear_lib() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HPool_RMSD method) clear_loop_residues() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) clear_motif_cst() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) clear_movers() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) clear_movers_and_refiners() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) clear_movesets() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) clear_mutation_sets() (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) clear_no_notify() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) clear_observers() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) clear_occlusions() (pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo method) clear_orbitals() (pyrosetta.rosetta.core.chemical.MutableResidueType method) clear_other_pose_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) clear_output() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) clear_overall_prob_set() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) clear_pairings() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) clear_parameters_list() (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) clear_parameters_set_list() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) clear_parents() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) clear_perturber_residue_list() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) clear_perturber_residue_lists() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) clear_perturbers() (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) clear_pool() (pyrosetta.rosetta.cppdb.session method) (pyrosetta.rosetta.utility.sql_database.session method) clear_poses() (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) clear_positions() (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) clear_postfold_movers() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) clear_prefold_movers() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) clear_prob_set() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) clear_properties() (pyrosetta.rosetta.core.chemical.AtomType method) clear_rcgs() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) clear_refiners() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) clear_res_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) clear_reset_filters() (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) clear_residue_connections() (pyrosetta.rosetta.core.conformation.Residue method) clear_residues() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) clear_reslabel() (pyrosetta.rosetta.core.pose.PDBInfo method) clear_rms() (pyrosetta.rosetta.numeric.model_quality.RmsData method) clear_rna_scoring_info() (in module pyrosetta.rosetta.core.scoring.rna) clear_rna_secstruct_legacy_info() (in module pyrosetta.rosetta.core.pose.rna.secstruct_legacy) clear_rnl_pose() (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) clear_rotamer() (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb 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_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) clear_rotamer_bb_torsion_indices() (pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification method) clear_rots() (pyrosetta.rosetta.protocols.motifs.BuildPosition method) clear_rv_infos() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) clear_score() (pyrosetta.rosetta.protocols.moves.MoverStatistics method) clear_segment_envelopes() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector method) clear_segments() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) clear_sequence_constraints() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) clear_serial_data() (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) clear_setup_movers() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) clear_shared_silent_data() (pyrosetta.rosetta.core.io.silent.SilentFileData method) clear_sm_data() (in module pyrosetta.rosetta.core.simple_metrics) clear_stored_solutions() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) clear_structure_map() (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) clear_suckers() (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) clear_sym_def() (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) clear_target_selectors() (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) clear_task() (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) clear_task_factory() (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) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) clear_template_selectors() (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) clear_terminal_vectors() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector method) clear_title() (pyrosetta.rosetta.core.io.HeaderInformation method) clear_torsion_string_stack() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) clear_torsions_using() (pyrosetta.rosetta.protocols.normalmode.NormalMode method) clear_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) clear_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) clear_user_provided_movers() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) clear_Vall() (pyrosetta.rosetta.core.fragment.picking_old.FragmentLibraryManager method) clearAllAtomBookmarks() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) clearAllBondBookmarks() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) clearAtomBookmark() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) clearBondBookmark() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) ClearChiRotamers (class in pyrosetta.rosetta.core.chemical) ClearCompositionConstraintsMover (class in pyrosetta.rosetta.protocols.aa_composition) ClearCompositionConstraintsMoverCreator (class in pyrosetta.rosetta.protocols.aa_composition) clearComputedProps() (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) clearConformers() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) ClearConstraintsMover (class in pyrosetta.rosetta.protocols.constraint_movers) ClearConstraintsMoverCreator (class in pyrosetta.rosetta.protocols.constraint_movers) clearMask() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) clearPoseExtraScore() (in module pyrosetta.rosetta.core.pose) clearPoseExtraScores() (in module pyrosetta.rosetta.core.pose) clearProp() (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) clearVal() (pyrosetta.rosetta.RDKit.Dict method) ClientMover (class in pyrosetta.rosetta.protocols.environment) clique_saver (class in pyrosetta.rosetta.protocols.features) clockwise() (in module pyrosetta.rosetta.core.membrane) clone() (pyrosetta.rosetta.basic.citation_manager.AuthorNames method) (pyrosetta.rosetta.basic.citation_manager.Citation method) (pyrosetta.rosetta.basic.citation_manager.CitationCollection method) (pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleAuthor method) (pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleInfo method) (pyrosetta.rosetta.basic.datacache.CacheableData method) (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.basic.MetricValueBase method) (pyrosetta.rosetta.basic.tensorflow_manager.RosettaTensorflowProtocolBase method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) Clone() (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) clone() (pyrosetta.rosetta.core.chemical.mainchain_potential.MainchainScoreTable method) (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) (pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters 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.orbitals.OrbitalXYZCoords method) (pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.Parameter method) (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator 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.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetryTransform method) (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.FAElecContextData 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.PBLifetimeCache 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.PoseSequence 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_Local_MinData method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergy method) (pyrosetta.rosetta.core.energy_methods.RG_MinData 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.ScoreCache 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.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.BaseCacheUnit method) (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.fragment.BBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.DownJumpSRFD method) (pyrosetta.rosetta.core.fragment.FragData method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragSetCollection method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD 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.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.LengthGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.SecStructGen method) (pyrosetta.rosetta.core.fragment.picking_old.vall.gen.VallFragmentGen method) (pyrosetta.rosetta.core.fragment.SecstructSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.UpJumpSRFD method) (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) (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.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.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.jacobian.JacobianStructure method) (pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1 method) (pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobians 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.optimization.MinimizerOptions 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.dunbrack.RotamericSingleResidueDunbrackLibraryParser 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.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphContainer method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData 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.PerResidueSapScoreMetric 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.SapConstraintOptions method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.pack.palette.CustomBaseTypePackerPalette method) (pyrosetta.rosetta.core.pack.palette.DefaultPackerPalette method) (pyrosetta.rosetta.core.pack.palette.NCAADefaultPackerPalette method) (pyrosetta.rosetta.core.pack.palette.NoDesignPackerPalette method) (pyrosetta.rosetta.core.pack.palette.PackerPalette method) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminator method) (pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminatorTaskOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetsOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.WaterPackingInfo method) (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AROMATIC method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.CHARGED method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLT method) (pyrosetta.rosetta.core.pack.task.operation.AllResFilter method) (pyrosetta.rosetta.core.pack.task.operation.AnyResFilter method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.ChainIs method) (pyrosetta.rosetta.core.pack.task.operation.ChainIsnt method) (pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShell method) (pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLT method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLT method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrent method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLT method) (pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandline method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandline method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.NoResFilter method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBeta method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLT method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLT method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfile method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ReplicateTask method) (pyrosetta.rosetta.core.pack.task.operation.ResFilter method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterComposition method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIs method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsnt method) (pyrosetta.rosetta.core.pack.task.operation.ResidueLacksProperty method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3Is method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3Isnt method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIs method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsnt method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoHasLabel method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoLacksLabel method) (pyrosetta.rosetta.core.pack.task.operation.ResidueTypeFilter method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAAS method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASExceptNativeRLT method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASRLT method) (pyrosetta.rosetta.core.pack.task.operation.RestrictInteractionGraphThreadsOperation method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepackingRLT method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToResidueProperties method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToSpecifiedBaseResidueTypes method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerCouplings method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerLinks method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.UseMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PROPERTY method) (pyrosetta.rosetta.core.pack.task.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) (pyrosetta.rosetta.core.pose.full_model_info.SubMotifInfo method) (pyrosetta.rosetta.core.pose.metrics.EnergyDependentCalculator method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.InterfaceDefinitionCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.InterfaceDeltaEnergeticsCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.InterfaceNeighborDefinitionCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.InterfaceSasaDefinitionCalculator method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.SasaCalculator2 method) (pyrosetta.rosetta.core.pose.metrics.simple_calculators.SasaCalculatorLegacy method) (pyrosetta.rosetta.core.pose.metrics.StructureDependentCalculator method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.core.pose.toolbox.AtomID_Mapper method) (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint method) (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculator method) (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.CenListInfo 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.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.CstEnergyContainer method) (pyrosetta.rosetta.core.scoring.constraints.CstMinimizationData 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.ContextGraph method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.DistanceFunc method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer 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.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer 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.dna.BasePartner method) (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator 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.coulomb.Coulomb method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) (pyrosetta.rosetta.core.scoring.facts.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.facts.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.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.GenBondedExclInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBondsTrieVsTrieCachedDataContainer method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet 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.lkball.LKB_ResidueInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo method) (pyrosetta.rosetta.core.scoring.LREnergyContainer 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.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.MembraneTopology 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.EnergyMethodOptions 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.NeighborListData 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.mhc_epitope_energy.MHCEpitopeEnergySetup method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.MultipoleParameter method) (pyrosetta.rosetta.core.scoring.NeighborList method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSData method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREData method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCData method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer 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.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling_Rohl method) (pyrosetta.rosetta.core.scoring.ResidueNblistData method) (pyrosetta.rosetta.core.scoring.ResiduePairNeighborList method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.trie.TrieCollection method) (pyrosetta.rosetta.core.scoring.trie.TrieVsTrieCachedDataContainerBase method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (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) (pyrosetta.rosetta.core.select.movemap.MoveMapFactory 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.CachedResidueSubset 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.core.select.util.SelectResiduesByLayer method) (pyrosetta.rosetta.core.sequence.ChemicalShiftScoringScheme method) (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.CompassScoringScheme method) (pyrosetta.rosetta.core.sequence.CompositeScoringScheme method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.DPScoringScheme method) (pyrosetta.rosetta.core.sequence.L1ScoringScheme method) (pyrosetta.rosetta.core.sequence.MatrixScoringScheme method) (pyrosetta.rosetta.core.sequence.PairScoringScheme method) (pyrosetta.rosetta.core.sequence.ProfSimScoringScheme method) (pyrosetta.rosetta.core.sequence.ScoringScheme method) (pyrosetta.rosetta.core.sequence.Sequence method) (pyrosetta.rosetta.core.sequence.SequenceAlignment method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) (pyrosetta.rosetta.core.sequence.SimpleScoringScheme method) (pyrosetta.rosetta.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.SimpleMetricData 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) Clone() (pyrosetta.rosetta.numeric.interpolation.spline.BicubicSpline method) clone() (pyrosetta.rosetta.numeric.interpolation.spline.BicubicSpline method) (pyrosetta.rosetta.numeric.interpolation.spline.CompoundInterpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.CubicSpline method) (pyrosetta.rosetta.numeric.interpolation.spline.Interpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_1_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_2_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_3_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_4_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_5_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_6_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSplineBase method) (pyrosetta.rosetta.numeric.interpolation.spline.SimpleInterpolator method) Clone() (pyrosetta.rosetta.numeric.interpolation.spline.TricubicSpline method) clone() (pyrosetta.rosetta.numeric.linear_algebra.EllipseParameters method) Clone() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) clone() (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.numeric.MathVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.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.JumpSampleData 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.burial_metrics.PolarGroupBurialPyMolStringMetric 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.ConstraintsMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.clusters.BasicCDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodySeqDesignTFCreator method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptionsParser method) (pyrosetta.rosetta.protocols.antibody.design.CDRSeqDesignOptions method) (pyrosetta.rosetta.protocols.antibody.design.CDRSeqDesignOptionsParser method) (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.antibody.design.ResnumFromStringsWithRangesSelector 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.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol 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.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.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.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.buns.BuriedUnsatHbondFilter2 method) (pyrosetta.rosetta.protocols.buns.BuriedUnsatisfiedPolarsCalculator2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.ConservedPosMutationFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover 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.BiasedMonteCarlo 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.chromophore.ChromophoreDataReader method) (pyrosetta.rosetta.protocols.chromophore.ReadResidueCoordinatesFromPDB 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.features.ResidueFeature method) (pyrosetta.rosetta.protocols.comparative_modeling.features.SSFeature method) (pyrosetta.rosetta.protocols.comparative_modeling.features.TorsionFeature 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_filters.ConstraintScoreCutoffFilter method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.constraint_filters.ShowConstraintsFilter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.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.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator 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.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector 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.cyclic_peptide_predict.HierarchicalHybridJD_PNearToArbitraryStateSummary 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) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.PNearCalculator method) (pyrosetta.rosetta.protocols.ddg.ddGMover 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.calculators.CavityCalculator method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror method) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.constraints.FileConstraintGenerator method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) (pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover 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.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaChains method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceFinder method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterface method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.dna.WatsonCrickRotamerCouplings method) (pyrosetta.rosetta.protocols.dna_dock.DNAClashCheckFilter method) (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilter method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter 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.DockingLowResFilter 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.RDKitMetric 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.energy_based_clustering.EnergyBasedClusteringOptions method) (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringProtocol method) (pyrosetta.rosetta.protocols.environment.AutoCutData method) (pyrosetta.rosetta.protocols.environment.claims.CutBiasClaim method) (pyrosetta.rosetta.protocols.environment.claims.EnvClaim method) (pyrosetta.rosetta.protocols.environment.claims.EnvLabelSelector 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.ProtectedConformation method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamers method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfs method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilter 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.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.LigBurialFilter method) (pyrosetta.rosetta.protocols.enzdes.LigDSasaFilter method) (pyrosetta.rosetta.protocols.enzdes.LigInterfaceEnergyFilter 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.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.RemoveLigandFilter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.RepackWithoutLigandFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior 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.esm_perplexity.EsmPerplexityTensorflowProtocol method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost 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.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.filters.CalculatorFilter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.ContingentFilter method) (pyrosetta.rosetta.protocols.filters.FalseFilter method) (pyrosetta.rosetta.protocols.filters.Filter method) (pyrosetta.rosetta.protocols.filters.FilterValueMetric method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.filters.ReplicateFilter method) (pyrosetta.rosetta.protocols.filters.StochasticFilter method) (pyrosetta.rosetta.protocols.filters.TimeFilter method) (pyrosetta.rosetta.protocols.filters.TrueFalseFilter method) (pyrosetta.rosetta.protocols.filters.TrueFilter method) (pyrosetta.rosetta.protocols.filters.VectorPoseFilter method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.filters.CoreDunbrackFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.FragQualFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.InterlockingAromaFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.NcontactsFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.ParallelBetaPairingPreferenceFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureCountFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureHasResidueFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.NcontactsCalculator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Sheet method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags 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.CombinedTaskOperation method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ConstraintFulfilmentFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ScorePoseSegmentFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover 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.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.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeSequencePosition method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) (pyrosetta.rosetta.protocols.forge.components.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.RemodelRotamerLinks method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (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) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.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.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetScore method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelector method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter 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.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (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) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) (pyrosetta.rosetta.protocols.hotspot_hashing.AddSearchPatternRotSetOp method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hotspot_hashing.SearchPatternRotSetOp 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.TemplateHistory 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.filters.FragmentLookupFilter method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover 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.JobTracker method) (pyrosetta.rosetta.protocols.jumping.ChainbreakDistFunc method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.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.LegacyReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFile 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.AtomCountFilter method) (pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilter method) (pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilter 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.HBondAcceptorFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilter 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.MolarMassFilter method) (pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilter 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.loophash.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter 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.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.loops.Loops method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsStringDefiner 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.mainchain_potential.GenerateMainchainPotential method) (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (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.MatcherMover method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) (pyrosetta.rosetta.protocols.match.upstream.ProteinUpstreamBuilder method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamBuilder method) (pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperation method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilter method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) (pyrosetta.rosetta.protocols.matdes.MotifHitsRotamersOperation method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.EnergiesByTaskCalculator 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.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams 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.ChainGroupDiscriminator 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.GroupDiscriminator 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.minimization_packing.UserDefinedGroupDiscriminator method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.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.BuildPosition method) (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.motifs.MotifHit method) (pyrosetta.rosetta.protocols.motifs.SingleMotif 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.MonteCarlo 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.ReplicaExchangeMC 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.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.multistate_design.MultiStateEntity method) (pyrosetta.rosetta.protocols.multistate_design.PosType 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.PCSEnergy method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergy method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergy method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.pack_interface.ProteinProteinInterfaceUpweighter method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter 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.CatPiCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.ChargeCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.ClashCountCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.FragQualCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.HPatchCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.InterGroupNeighborsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborhoodByDistanceCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborsByDistanceCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.NonlocalContactsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.PackstatCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.PiPiCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.ResidueDecompositionByChainCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.ResidueDecompositionCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.RotamerBoltzCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SaltBridgeCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SemiExplicitWaterUnsatisfiedPolarsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SHOBuriedUnsatisfiedPolarsCalculator method) (pyrosetta.rosetta.protocols.pose_metric_calculators.SurfaceCalculator method) (pyrosetta.rosetta.protocols.pose_sewing.data_storage.DsspShiftArray method) (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseSegment method) (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) (pyrosetta.rosetta.protocols.pose_sewing.data_storage.SegmentEnvelope method) (pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector method) (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorer method) (pyrosetta.rosetta.protocols.pose_sewing.filters.HasDisulfideFilter 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.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AtomicContactCountFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AverageDegreeFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.ClashWithTargetFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FNatFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.InterfaceHolesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.IRmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.LRmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdSimpleFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SpecificResiduesNearInterfaceFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SSamountFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreLoopsFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.Torsion method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak 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.protein_mpnn.ProteinMPNNProbabilitiesMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionTensorflowProtocol method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionTensorflowProtocolBase method) (pyrosetta.rosetta.protocols.qsar.qsarMover 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.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.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric 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.options.RECCES_Options 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.FitnessFilter 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.RelaxScriptFileContents 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.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.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector 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.AlignmentEnergy 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.score_filters.GeometryFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreTypeFilter method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo 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_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManager method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_Ts4 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.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy 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.Basis method) (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue 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) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSewingResidue method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (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) (pyrosetta.rosetta.protocols.sewing.hashing.ModelFileReader 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.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.LigandClashRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.NonTerminalStartingSegmentRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.SizeInSegmentsRequirement method) (pyrosetta.rosetta.protocols.simple_ddg.AlaScan method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScan method) (pyrosetta.rosetta.protocols.simple_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.EvaluatedTrialMover 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.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.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) (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.simple_pose_metric_calculators.BuriedUnsatisfiedPolarsCalculator method) (pyrosetta.rosetta.protocols.simple_pose_metric_calculators.NumberHBondsCalculator method) (pyrosetta.rosetta.protocols.simple_task_operations.DockingNoRepack1 method) (pyrosetta.rosetta.protocols.simple_task_operations.DockingNoRepack2 method) (pyrosetta.rosetta.protocols.simple_task_operations.InterfaceTaskOperation method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterface method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoops method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation method) (pyrosetta.rosetta.protocols.splice.FindEndpointsOperation method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB method) (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation 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.StepWiseBasicModelerOptions 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.options.StepWiseMoveSelectorOptions 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.StepWiseMove method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector 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.options.StepWiseBasicOptions 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.surface_docking.SurfaceParameters 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.SymRestrictTaskForDocking 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.NCSResMapping 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.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperation method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperation method) (pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2_RotamerSetOperation method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.task_operations.ModifyAnnealer method) (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.ProteinCore method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsats_RotamerSetsOperation method) (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation method) (pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities method) (pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3Loop method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperation method) (pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperation method) (pyrosetta.rosetta.protocols.task_operations.STMStoredTask 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.task_operations.ThreadSequenceOperation method) (pyrosetta.rosetta.protocols.tcr.TCRloopRefine method) (pyrosetta.rosetta.protocols.tcr.TCRmodel method) (pyrosetta.rosetta.protocols.tcr.TCRseqInfo method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.DummyClass method) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.SpecialRotamerRSO method) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.toolbox.SF_Replica method) (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer 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.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.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) (pyrosetta.rosetta.protocols.trRosetta.trRosettaOutputs_v1 method) (pyrosetta.rosetta.protocols.trRosetta.trRosettaOutputsBase method) (pyrosetta.rosetta.protocols.trRosetta.trRosettaProtocol_v1 method) (pyrosetta.rosetta.protocols.trRosetta.trRosettaProtocolBase method) (pyrosetta.rosetta.protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGenerator 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.protocols.vardist_solaccess.VarSolDistSasaCalculator method) (pyrosetta.rosetta.protocols.wum.DatabaseEntryWorkUnit method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.WorkUnit_Wait method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.utility.io.GeneralFileContents method) (pyrosetta.rosetta.utility.io.GeneralFileContentsVector method) (pyrosetta.rosetta.utility.keys.AutoKey_utility_options_Option_utility_keys_Key_utility_keys_NoClient_t method) (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionCollection method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.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.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) (pyrosetta.rosetta.utility.tag.Tag method) clone_as_base_class() (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) clone_cache_data() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) clone_flipping_chirality() (pyrosetta.rosetta.core.conformation.Residue method) clone_info() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) clone_modeler() (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) clone_sampler() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) clone_scorefxn() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) clone_shifted() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragSetCollection method) (pyrosetta.rosetta.core.fragment.MinimalFragSet method) (pyrosetta.rosetta.core.fragment.OrderedFragSet method) clone_with_frags() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) clone_with_new_sequence_numbering() (pyrosetta.rosetta.core.conformation.PseudoBondCollection method) clone_with_template() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) closable() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) close() (pyrosetta.rosetta.cppdb.session method) (pyrosetta.rosetta.protocols.dna.DnaNeighbor method) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.WriteFileSFB method) (pyrosetta.rosetta.std.filebuf method) (pyrosetta.rosetta.std.ifstream method) (pyrosetta.rosetta.std.ofstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_ostream_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) (pyrosetta.rosetta.utility.io.ozstream method) (pyrosetta.rosetta.utility.sql_database.session method) close_bond() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) close_chainbreaks() (in module pyrosetta.rosetta.protocols.jumping) close_file() (pyrosetta.rosetta.protocols.jd2.DebugOut_MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd2.MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd2.WriteOut_MpiFileBuffer method) close_gaps() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) close_loop() (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) close_loops() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) close_loops_after_each_move() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) close_one_loop_stem() (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) close_one_loop_stem_helper() (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) close_to_dna() (in module pyrosetta.rosetta.protocols.dna) CloseContactResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) CloseContactResidueSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) closed_loop() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) CloseFold (class in pyrosetta.rosetta.protocols.seeded_abinitio) CloseFoldCreator (class in pyrosetta.rosetta.protocols.seeded_abinitio) CloseOneCDRLoop (class in pyrosetta.rosetta.protocols.antibody) CloseOneMover (class in pyrosetta.rosetta.protocols.antibody_legacy) closer_ft (pyrosetta.rosetta.protocols.environment.EnvClaimBroker.BrokerResult property) Closest (pyrosetta.rosetta.protocols.indexed_structure_store.filters.LookupMode attribute) closest_by_dist4() (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) closest_interface_residue() (pyrosetta.rosetta.protocols.scoring.Interface method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) closest_larger_peptide_vertex() (in module pyrosetta.rosetta.protocols.forge.methods) closest_non_overlap_residue() (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) closest_orient_atoms_msd() (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method)

closest_smaller_peptide_vertex() (in module pyrosetta.rosetta.protocols.forge.methods) closest_state_on_alt_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) closest_suite() (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) closure_fragments() (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) closure_protocol() (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) ClosureProblem (class in pyrosetta.rosetta.protocols.kinematic_closure) ClosureProblem.Memento (class in pyrosetta.rosetta.protocols.kinematic_closure) ClosureSolution (class in pyrosetta.rosetta.protocols.kinematic_closure) CloudPDBWriter (class in pyrosetta.rosetta.protocols.match.output) CLU_RADIUS (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) Cluster (class in pyrosetta.rosetta.protocols.cluster) cluster (pyrosetta.rosetta.protocols.antibody.CDRDBPose property) (pyrosetta.rosetta.protocols.antibody.CDRDBSequence property) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData property) cluster() (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.cluster.APCluster method) (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) (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.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) cluster_ (pyrosetta.rosetta.core.scoring.packstat.CavityBall property) cluster_by_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) cluster_by_all_atom_rmsd() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) cluster_center_ (pyrosetta.rosetta.protocols.cluster.Cluster property) cluster_check() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) cluster_cyclic_permutations_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) cluster_fragments() (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) cluster_KeyFeatures() (pyrosetta.rosetta.protocols.pockets.GenPharmacophore method) cluster_loop() (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) Cluster_Member (class in pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) cluster_metric() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobSummary method) cluster_metric_xml_schema_group_name() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricFactory static method) cluster_min_volume (pyrosetta.rosetta.core.scoring.packstat.SasaOptions property) cluster_pose() (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) cluster_pose_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection method) cluster_radius (pyrosetta.rosetta.protocols.toolbox.ClusterOptions property) cluster_radius_ (pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions property) (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) cluster_rmsd() (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.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) cluster_rotset() (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) cluster_sampling_cutoff() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) cluster_silent() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) cluster_switch() (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) ClusterBase (class in pyrosetta.rosetta.protocols.cluster) (class in pyrosetta.rosetta.protocols.toolbox) clusterCPockets() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) ClusterData (class in pyrosetta.rosetta.protocols.antibody.clusters) clustered_best_poses() (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) clustered_pose_list() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) clustered_top_poses() (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) Clusterer (class in pyrosetta.rosetta.protocols.mpi_refinement) Clustering (class in pyrosetta.rosetta.protocols.cluster.calibur) ClusteringTreeNode (class in pyrosetta.rosetta.numeric) ClusterMetric (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster) ClusterMetricCreator (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster) ClusterMetricFactory (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster) ClusterOptions (class in pyrosetta.rosetta.numeric) (class in pyrosetta.rosetta.protocols.toolbox) ClusterPhilStyle (class in pyrosetta.rosetta.protocols.cluster) (class in pyrosetta.rosetta.protocols.toolbox) ClusterPhilStyle_Loop (class in pyrosetta.rosetta.protocols.cluster) ClusterPhilStyle_PoseReporter (class in pyrosetta.rosetta.protocols.cluster) clusterPockets() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) ClusterPoseSelector (class in pyrosetta.rosetta.protocols.pose_selectors) ClusterPoseSelectorCreator (class in pyrosetta.rosetta.protocols.pose_selectors) Cm (pyrosetta.rosetta.core.chemical.element.Elements attribute) cm_main() (in module pyrosetta.rosetta.protocols.comparative_modeling) cmaes_lambda() (pyrosetta.rosetta.core.optimization.MinimizerOptions method) CMAES_Minimizer (class in pyrosetta.rosetta.core.optimization) cmaes_rgsigma() (pyrosetta.rosetta.core.optimization.MinimizerOptions method) CMCT (pyrosetta.rosetta.core.pose.rna.RNA_ReactivityType attribute) cmd() (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) cmd_line_csts() (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) cmdline_options_activated() (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule static method) cmp() (pyrosetta.rosetta.core.scoring.packstat.Event method) Cn (pyrosetta.rosetta.core.chemical.element.Elements attribute) cnl_com() (in module pyrosetta.rosetta.protocols.constel) Co (pyrosetta.rosetta.core.chemical.element.Elements attribute) co (pyrosetta.rosetta.core.scoring.ScoreType attribute) CO2_COORDINATION (pyrosetta.rosetta.core.chemical.VariantType attribute) co_authors() (pyrosetta.rosetta.basic.citation_manager.Citation method) COARSE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) coarse_beadlj (pyrosetta.rosetta.core.scoring.ScoreType attribute) coarse_centering_mode (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) coarse_chainbreak_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) coarse_fa_atr (pyrosetta.rosetta.core.scoring.ScoreType attribute) coarse_fa_rep (pyrosetta.rosetta.core.scoring.ScoreType attribute) coarse_fa_sol (pyrosetta.rosetta.core.scoring.ScoreType attribute) COARSE_RNA_t (pyrosetta.rosetta.core.chemical.TypeSetMode attribute) CoarseRNA_Fragments (class in pyrosetta.rosetta.protocols.rna.denovo.coarse) CoarseRNA_LoopCloser (class in pyrosetta.rosetta.protocols.rna.denovo.coarse) code() (pyrosetta.rosetta.utility.keys.AutoKey_utility_options_Option_utility_keys_Key_utility_keys_NoClient_t method) (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.keys.VariantKey_utility_options_OptionKey_t method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.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.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) code_from_6bit() (in module pyrosetta.rosetta.utility) code_to_6bit() (in module pyrosetta.rosetta.utility) codes_to_root_map_file() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager static method) codon2aa() (in module pyrosetta.rosetta.core.chemical.NucleotideTools) coefficients() (pyrosetta.rosetta.core.scoring.hbonds.Polynomial_1d method) (pyrosetta.rosetta.numeric.Polynomial_1d method) coefLoc() (pyrosetta.rosetta.numeric.fourier.SO3coeffs method) COFilter (class in pyrosetta.rosetta.protocols.simple_filters) coil (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SecondaryStructureType attribute) col() (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) col_x() (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) col_y() (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) col_z() (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) coldspot_label() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub static method) coldspots (pyrosetta.rosetta.protocols.fold_from_loops.utils.NubSegment property) colinear_dDome_dBase() (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder method) colinear_dDome_dOther() (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder method) colinear_dDome_dWater() (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder method) colinear_water (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder property) collapse() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) collect() (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) collect_all_inverse_rotamers() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) collect_HN_S2_and_EF() (pyrosetta.rosetta.protocols.sparta.PDB method) collect_jumps() (pyrosetta.rosetta.core.environment.FoldTreeSketch.Node method) collectInsertionPose() (pyrosetta.rosetta.protocols.forge.remodel.RemodelData method) collision_check_id_2_restype_id() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) colonyE() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) Color_mode (pyrosetta.rosetta.protocols.viewer.GraphicsState property) color_name (pyrosetta.rosetta.protocols.qsar.ColorGradient property) color_value (pyrosetta.rosetta.protocols.qsar.ColorGradient property) ColorGradient (class in pyrosetta.rosetta.protocols.qsar) ColorMode (class in pyrosetta.rosetta.protocols.viewer.graphics_states_param) cols() (pyrosetta.rosetta.core.sequence.DP_Matrix method) (pyrosetta.rosetta.cppdb.backend.result method) (pyrosetta.rosetta.cppdb.result method) (pyrosetta.rosetta.numeric.xyzMatrix_double_t static method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t static method) Column (class in pyrosetta.rosetta.basic.database.schema_generator) column_to_name() (pyrosetta.rosetta.cppdb.backend.result method) columns() (pyrosetta.rosetta.basic.database.schema_generator.ForeignKey method) (pyrosetta.rosetta.basic.database.schema_generator.Index method) (pyrosetta.rosetta.basic.database.schema_generator.PrimaryKey method) com (pyrosetta.rosetta.core.energy_methods.RG_Local_MinData property) (pyrosetta.rosetta.core.energy_methods.RG_MinData property) com() (in module pyrosetta.rosetta.protocols.membrane) (pyrosetta.rosetta.protocols.features.helixAssembly.HelicalFragment method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore method) CoM() (pyrosetta.rosetta.protocols.pockets.FingerprintBase method) (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) comatms (pyrosetta.rosetta.core.scoring.elec.ElecGroup property) COMB (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) combine_chains() (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) combine_constraints() (in module pyrosetta.rosetta.core.scoring.constraints) combine_exclude_file() (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) combine_exclude_res() (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) combine_long_loop_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) combine_movemaps_post_insertion() (in module pyrosetta.rosetta.protocols.grafting) combine_names() (in module pyrosetta.rosetta.utility.file) combine_ratio() (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) combine_residue_selections() (pyrosetta.rosetta.core.select.residue_selector.SSElementSelector method) combine_rot_dbs() (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB method) combine_score (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Combine_Tags_Info property) combine_sequence_mappings() (in module pyrosetta.rosetta.core.id) Combine_Tags_Info (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna) combine_two_poses() (in module pyrosetta.rosetta.protocols.seeded_abinitio) combine_xyz_lists() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) CombineChainsMover (class in pyrosetta.rosetta.protocols.domain_assembly) CombinedConstraintEvaluator (class in pyrosetta.rosetta.protocols.constraints_additional) CombinedConstraintEvaluatorCreator (class in pyrosetta.rosetta.protocols.constraints_additional) CombinedFilter (class in pyrosetta.rosetta.protocols.filters) CombinedFilterCreator (class in pyrosetta.rosetta.protocols.filters) CombinedTaskOperation (class in pyrosetta.rosetta.protocols.flxbb) CombinePoseMover (class in pyrosetta.rosetta.protocols.simple_moves) COMCoordinateConstraint (class in pyrosetta.rosetta.protocols.constraints_additional) COMM_REDUCE_SIZE (pyrosetta.rosetta.basic.ProfTag attribute) COMMA (pyrosetta.rosetta.numeric.expression_parser.TokenType attribute) comma_separated_partner_chains() (in module pyrosetta.rosetta.protocols.docking) command (pyrosetta.rosetta.protocols.denovo_design.movers.RelaxScriptCommand property) (pyrosetta.rosetta.protocols.relax.RelaxScriptCommand property) command_string() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) commands_for_residue() (pyrosetta.rosetta.core.pack.task.ResfileContents method) comment (pyrosetta.rosetta.core.io.HELIXInformation property) (pyrosetta.rosetta.core.io.ModifiedResidueInformation property) comment() (pyrosetta.rosetta.core.sequence.SequenceAlignment method) comment_begin() (in module pyrosetta.rosetta.core.pack.task) comment_exists() (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) comment_from_line() (pyrosetta.rosetta.core.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) comment_line() (pyrosetta.rosetta.core.io.silent.SilentFileData method) comment_lines() (pyrosetta.rosetta.core.io.silent.SilentFileData method) comment_name() (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) comment_value() (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) comments() (pyrosetta.rosetta.core.io.rna.RDAT method) (pyrosetta.rosetta.core.sequence.SequenceAlignment method) commit() (pyrosetta.rosetta.cppdb.backend.connection method) (pyrosetta.rosetta.cppdb.session method) (pyrosetta.rosetta.cppdb.transaction method) (pyrosetta.rosetta.utility.sql_database.session method) (pyrosetta.rosetta.utility.sql_database.transaction method) (pyrosetta.rosetta.utility.Version static method) commit_alt_bb_substitution() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) commit_change() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) commit_change_no_res_pointer_update() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) commit_change_npd() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) commit_considered_backbone_move() (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) commit_considered_substitution() (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_DomeHelper 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.sap.SapConstraintHelper method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (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.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode 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.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode 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.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.scoring.annealing.ResidueArrayAnnealableEnergy method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) commit_relaxation() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) commit_transaction() (pyrosetta.rosetta.utility.sql_database.session method) commitBatchEdit() (pyrosetta.rosetta.RDKit.RWMol method) common_res_types (pyrosetta.rosetta.core.pack.annealer.SeqSymmAnnealerSetup property) common_setup() (in module pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) common_type() (pyrosetta.rosetta.utility.tag.XMLSchemaType method) comp_id() (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueEntry static method) (pyrosetta.rosetta.protocols.indexed_structure_store.StructureEntry static method) comparable() (in module pyrosetta.rosetta.utility.keys) comparator() (pyrosetta.rosetta.numeric.AgglomerativeHierarchicalClusterer method) (pyrosetta.rosetta.numeric.AverageLinkClusterer method) (pyrosetta.rosetta.numeric.CompleteLinkClusterer method) (pyrosetta.rosetta.numeric.SingleLinkClusterer method) compare() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastComparator method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastComparator_BitScore_Resolution method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Comparator method) (pyrosetta.rosetta.protocols.hbnet.NetworkStateScoreComparator static method) (pyrosetta.rosetta.protocols.loophash.BackboneSegment method) compare_and_align_poses() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) compare_atom_coordinates() (in module pyrosetta.rosetta.core.pose) compare_atom_icoor() (in module pyrosetta.rosetta.core.chemical) compare_base_bin (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body) compare_binary_protein_silent_struct() (in module pyrosetta.rosetta.core.pose) compare_by_x (class in pyrosetta.rosetta.protocols.hbnet) compare_hbond_residues (class in pyrosetta.rosetta.protocols.hbnet) compare_hbond_resnums (class in pyrosetta.rosetta.protocols.hbnet) compare_int_pair (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body) compare_job_nodes (class in pyrosetta.rosetta.protocols.jd3) compare_motif2scaffold_data_by_scaffold_low2high() (in module pyrosetta.rosetta.protocols.motif_grafting.movers) compare_net_vec (class in pyrosetta.rosetta.protocols.hbnet) compare_residue_connection() (in module pyrosetta.rosetta.core.chemical) compare_residue_energies_all() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) compare_residue_energies_mut() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) compare_RNA_char() (in module pyrosetta.rosetta.core.import_pose) compare_RNA_secstruct() (in module pyrosetta.rosetta.core.import_pose) compare_SizeRealPairs() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion static method) compare_to_native() (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison method) compare_to_ref() (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) CompareByScoreCombination (class in pyrosetta.rosetta.protocols.frag_picker) compareCoverage() (pyrosetta.rosetta.protocols.pockets.ComparisonGrid method) CompareKDPoints (class in pyrosetta.rosetta.numeric.kdtree) CompareQueryPosition (class in pyrosetta.rosetta.protocols.frag_picker) CompareScoreComponent (class in pyrosetta.rosetta.protocols.frag_picker) CompareTags (class in pyrosetta.rosetta.protocols.jd2) CompareTotalScore (class in pyrosetta.rosetta.protocols.frag_picker) ComparingTracer (class in pyrosetta.rosetta.basic) ComparingTracer.sentry (class in pyrosetta.rosetta.basic) comparison_type (class in pyrosetta.rosetta.protocols.simple_filters) comparison_type_total (pyrosetta.rosetta.protocols.simple_filters.comparison_type attribute) ComparisonGrid (class in pyrosetta.rosetta.protocols.pockets) CompassScoringScheme (class in pyrosetta.rosetta.core.sequence) compatibility_check() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) compatible() (pyrosetta.rosetta.protocols.abinitio.AlternativePairings method) (pyrosetta.rosetta.protocols.abinitio.PairingStatEntry 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.upstream.OriginalBackboneBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.ProteinBackboneBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.ProteinUpstreamBuilder method) (pyrosetta.rosetta.protocols.match.upstream.ScaffoldBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamBuilder method) compatible_restype() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) compatible_with() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) compatible_with_current_format() (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) complete() (pyrosetta.rosetta.core.id.PartialAtomID method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) (pyrosetta.rosetta.protocols.jd3.job_distributors.JobExtractor method) complete_partial_state_assignment() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) complete_state_assignment() (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.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) CompleteConnectionsFilter (class in pyrosetta.rosetta.protocols.ligand_docking) CompleteConnectionsFilterCreator (class in pyrosetta.rosetta.protocols.ligand_docking) completed() (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) completed_job_summary() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobQueen method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen method) (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) completed_jobs() (pyrosetta.rosetta.protocols.jd3.JobTracker method) completed_jobs_for_node() (pyrosetta.rosetta.protocols.jd3.JobTracker method) CompletedJobOutput (class in pyrosetta.rosetta.protocols.jd3) CompleteLinkClusterer (class in pyrosetta.rosetta.numeric) complex_object_name() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub static method) complex_ring_detection() (in module pyrosetta.rosetta.core.chemical) complex_total_energy (pyrosetta.rosetta.protocols.analysis.InterfaceData property) complex_type_gen() (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover static method) complex_type_generator_for_anchored_graft_mover() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover static method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover static method) complex_type_generator_for_backbone_mover() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover static method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover static method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover static method) complex_type_generator_for_backrub_mover() (pyrosetta.rosetta.protocols.backrub.BackrubMover static method) complex_type_generator_for_balancedKIC_mover() (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover static method) complex_type_generator_for_fast_relax() (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign static method) (pyrosetta.rosetta.protocols.relax.FastRelax static method) complex_type_generator_for_logical_selector() (pyrosetta.rosetta.protocols.pose_selectors.AndSelector static method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector static method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector static method) complex_type_generator_for_loop_protocol() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol static method) complex_type_generator_for_min_mover() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover static method) complex_type_generator_for_pack_rotamers_mover() (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA static method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign static method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker static method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack static method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover static method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy static method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover static method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover static method) complex_type_generator_for_rotamer_trials_mover() (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover static method) complex_type_generator_for_simple_metric() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric static method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric static method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric static method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric static method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric static method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric static method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric static method) (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric static method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric static method) (pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric static method) (pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric static method) (pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric static method) (pyrosetta.rosetta.core.simple_metrics.RealMetric static method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric static method) (pyrosetta.rosetta.core.simple_metrics.StringMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric static method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric static method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric static method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric static method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric static method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetric static method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric static method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric static method) (pyrosetta.rosetta.protocols.filters.FilterValueMetric static method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric static method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric static method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric static method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric static method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric static method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric static method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric static method) complex_type_name_for_architect() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory static method) complex_type_name_for_chemistry() (in module pyrosetta.rosetta.protocols.chemistries) complex_type_name_for_chunk_library_inputter() (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputterFactory static method) complex_type_name_for_cluster_metric() (in module pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster) complex_type_name_for_constraint_generator() (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorFactory static method) complex_type_name_for_features_reporter() (in module pyrosetta.rosetta.protocols.features) complex_type_name_for_filter() (in module pyrosetta.rosetta.protocols.filters) complex_type_name_for_full_model_inputter() (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputterFactory static method) complex_type_name_for_jump_selector() (in module pyrosetta.rosetta.core.select.jump_selector) complex_type_name_for_loader() (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory static method) complex_type_name_for_locator() (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory static method) complex_type_name_for_loop_definer() (in module pyrosetta.rosetta.protocols.loops.loops_definers) complex_type_name_for_mover() (in module pyrosetta.rosetta.protocols.moves) complex_type_name_for_packer_palette() (in module pyrosetta.rosetta.core.pack.palette) complex_type_name_for_pairing() (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing static method) complex_type_name_for_pose_inputter() (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterFactory static method) complex_type_name_for_pose_outputter() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory static method) complex_type_name_for_pose_reporter() (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterFactory static method) complex_type_name_for_pose_selector() (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorFactory static method) complex_type_name_for_res_filter() (in module pyrosetta.rosetta.core.pack.task.operation) complex_type_name_for_res_lvl_task_op() (in module pyrosetta.rosetta.core.pack.task.operation) complex_type_name_for_residue_selector() (in module pyrosetta.rosetta.core.select.residue_selector) complex_type_name_for_resource_def() (pyrosetta.rosetta.basic.resource_manager.ResourceManager static method) complex_type_name_for_scoring_grid() (in module pyrosetta.rosetta.protocols.qsar.scoring_grid) complex_type_name_for_secondary_pose_outputter() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory static method) complex_type_name_for_simple_metric() (in module pyrosetta.rosetta.core.simple_metrics) complex_type_name_for_task_op() (in module pyrosetta.rosetta.core.pack.task.operation) complex_type_naming_func() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) complex_typename_for_element() (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) complexed_energy (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData property) complexed_interface_score (pyrosetta.rosetta.protocols.analysis.InterfaceData property) complexed_SASA (pyrosetta.rosetta.protocols.analysis.InterfaceData property) complexed_sasa (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData property) complexscore (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfo property) COMPND (pyrosetta.rosetta.core.io.pdb.RecordType attribute) component() (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) components_moved_by_jump() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) ComposeSearchPatterns (class in pyrosetta.rosetta.protocols.hotspot_hashing) composite_real_data_ (pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct property) composite_string_data_ (pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct property) CompositeEnergyMetric (class in pyrosetta.rosetta.core.simple_metrics.composite_metrics) CompositeEnergyMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.composite_metrics) CompositeFragmentSelector (class in pyrosetta.rosetta.protocols.frag_picker) CompositeRealMetric (class in pyrosetta.rosetta.core.simple_metrics) CompositeScoringScheme (class in pyrosetta.rosetta.core.sequence) CompositeSequence (class in pyrosetta.rosetta.core.sequence) CompositeSequenceCreator (class in pyrosetta.rosetta.core.sequence) CompositeStringMetric (class in pyrosetta.rosetta.core.simple_metrics) CompositionMover (class in pyrosetta.rosetta.protocols.moves) compound_in_progress() (pyrosetta.rosetta.core.io.HeaderInformation method) compound_token_to_string() (pyrosetta.rosetta.core.io.HeaderInformation static method) CompoundArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) CompoundArchitectCreator (class in pyrosetta.rosetta.protocols.denovo_design.architects) CompoundDesignableTask() (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) CompoundFilter (class in pyrosetta.rosetta.protocols.filters) CompoundFilterCreator (class in pyrosetta.rosetta.protocols.filters) CompoundInterpolator (class in pyrosetta.rosetta.numeric.interpolation.spline) CompoundPackableTask() (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) CompoundPerturber (class in pyrosetta.rosetta.protocols.denovo_design.components) compounds() (pyrosetta.rosetta.core.io.HeaderInformation method) CompoundToken_max (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation.CompoundToken attribute) CompoundTranslate (class in pyrosetta.rosetta.protocols.ligand_docking) CompoundTranslateCreator (class in pyrosetta.rosetta.protocols.ligand_docking) compprob() (pyrosetta.rosetta.core.scoring.packstat.PackingScore method) compress() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) compressed() (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) compute() (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) (pyrosetta.rosetta.core.scoring.dna.TorsionFourierComponent method) (pyrosetta.rosetta.core.scoring.packstat.Slice method) (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) (pyrosetta.rosetta.numeric.Calculator method) (pyrosetta.rosetta.protocols.buns.BuriedUnsatHbondFilter2 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.Sigmoid method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.constraint_filters.ShowConstraintsFilter method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover 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.enzdes.DiffAtomSasaFilter 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.RepackWithoutLigandFilter method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.filters.CalculatorFilter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.ReplicateFilter method) (pyrosetta.rosetta.protocols.filters.TimeFilter 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.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.SecondaryStructureHasResidueFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.MatchResidues method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover 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.helical_bundle.BundleReporterFilter method) (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilter 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.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.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.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.Torsion method) (pyrosetta.rosetta.protocols.score_filters.GeometryFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreTypeFilter method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) (pyrosetta.rosetta.protocols.simple_ddg.InterfaceBindingEnergyDensityFilter method) (pyrosetta.rosetta.protocols.simple_ddg.SSElementBisectddGFilter 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.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter 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.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.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.PackStatFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.ReadPoseExtraScoreFilter 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.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.SecretionPredictionFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) (pyrosetta.rosetta.protocols.simple_filters.SidechainRmsdFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter 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.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.toolbox.CalcInterNeighborGroup method) (pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator method) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator method) (pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator method) compute_acceptor_atom_energy() (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) compute_alt_weights_for_hbonds() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) compute_alt_weights_for_npd_hbonds() (in module pyrosetta.rosetta.core.pack.interaction_graph) compute_altbbconf_alternate_state_energy() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) compute_atom_packing_scores() (in module pyrosetta.rosetta.core.scoring.packstat) compute_average_structure() (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) compute_avge_scores() (in module pyrosetta.rosetta.protocols.sasa_scores) compute_bb_centroid() (in module pyrosetta.rosetta.core.scoring) compute_bb_radius() (in module pyrosetta.rosetta.core.scoring) compute_best_solution() (pyrosetta.rosetta.protocols.denovo_design.components.FoldGraph method) compute_Boltzmann_weight() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) compute_cav_ball_clusters() (in module pyrosetta.rosetta.core.scoring.packstat) compute_cav_ball_neighbor_count() (in module pyrosetta.rosetta.core.scoring.packstat) compute_cav_ball_volumes() (in module pyrosetta.rosetta.core.scoring.packstat) compute_center_of_mass() (in module pyrosetta.rosetta.protocols.forge.remodel) compute_centroid_environment() (pyrosetta.rosetta.core.scoring.CenRotEnvPairPotential method) (pyrosetta.rosetta.core.scoring.EnvPairPotential method) (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) compute_chi() (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) compute_comb() (pyrosetta.rosetta.protocols.fldsgn.MatchResidues method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) compute_conservation() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) compute_csascore() (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy method) compute_d2() (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilter method) compute_dcentroid_environment() (pyrosetta.rosetta.core.scoring.CenRotEnvPairPotential method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) compute_dcscore() (pyrosetta.rosetta.core.scoring.DipolarCoupling method) compute_dec15_score() (in module pyrosetta.rosetta.core.scoring.packing) compute_deltas() (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric method) compute_designable_neighbors() (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) compute_dipscore() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) compute_dipscore_nls() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) compute_dipscore_nlsDa() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) compute_dipscore_nlsDaR() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) compute_dipscore_nlsR() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) compute_distance_matrix() (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) compute_donor_atom_energy() (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) compute_embeddings_by_chain() (in module pyrosetta.rosetta.protocols.membrane) compute_energies() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.protocols.features.StructureScoresFeatures method) compute_energy() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge method) compute_energy_for_assignment() (pyrosetta.rosetta.protocols.pack_daemon.DaemonSet method) (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) compute_entropy_reduction() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) compute_exact_geosol() (in module pyrosetta.rosetta.core.energy_methods) compute_fa_projection() (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) compute_folding_energies() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) compute_frag_bias() (pyrosetta.rosetta.protocols.hybridization.FragmentBiasAssigner method) compute_func() (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) compute_gunn() (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCost method) (pyrosetta.rosetta.protocols.simple_moves.GunnCost method) compute_holes_deriv() (in module pyrosetta.rosetta.core.scoring.packing) compute_holes_deriv_res() (in module pyrosetta.rosetta.core.scoring.packing) compute_holes_score() (in module pyrosetta.rosetta.core.scoring.packing) compute_holes_score_res() (in module pyrosetta.rosetta.core.scoring.packing) compute_interface() (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) compute_jump() (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinder method) compute_L1() (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) compute_lb_function_solution() (pyrosetta.rosetta.numeric.interpolation.spline.CompoundInterpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.Interpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.SimpleInterpolator method) compute_ligand_natoms() (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) compute_ligand_natoms_with_hydrogens() (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) compute_ligand_nconformers() (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) compute_ligand_resnum() (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) compute_ligand_score_bonus() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) compute_matching_energy() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential method) compute_membrane_embedding() (pyrosetta.rosetta.core.scoring.MembranePotential method) compute_metrics() (pyrosetta.rosetta.core.scoring.motif.MotifHits method) compute_model_weights() (pyrosetta.rosetta.protocols.abinitio.PairingStatistics method) compute_modified_ddG() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) compute_mpair_score() (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) compute_mpcbeta_score() (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) compute_mpenv_score() (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) compute_nhbonds() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) compute_nonhelix_penalty() (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) compute_normalization() (pyrosetta.rosetta.core.scoring.electron_density_atomwise.ElectronDensityAtomwise method) compute_nres_in_asymmetric_unit() (in module pyrosetta.rosetta.protocols.constraint_generator) compute_number_cavities() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) compute_one_and_two_body_energies() (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) compute_one_body_energies() (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) compute_one_body_energies_for_otf_ig() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) compute_one_body_energy_maps() (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) compute_packing_score() (in module pyrosetta.rosetta.core.scoring.packstat) compute_packing_score_leerichards() (in module pyrosetta.rosetta.core.scoring.packstat) compute_pair_energy_for_alternate_state() (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) compute_pair_energy_for_current_state() (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.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) compute_pairwise_score() (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) compute_pcs_values_and_score_from_tensor() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) compute_pddf() (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) compute_pddf_without_ff() (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) compute_penalty() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) compute_per_residue_coverage() (in module pyrosetta.rosetta.core.fragment) compute_perplexity() (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric static method) compute_pnear_and_dgfolding() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.PNearCalculator method) compute_polar_group_sol_energy() (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) compute_pose_hpatch_score() (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) compute_pose_surface_energy() (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) compute_pre_score_from_point_vector() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) compute_pre_score_from_single_point() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) compute_proposal_density() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) compute_proton_chi_samplings() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) compute_rama_score() (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) compute_rdc_values_and_score_from_tensor() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) compute_residual() (pyrosetta.rosetta.protocols.simple_filters.DisulfideEntropyFilter method) compute_residue() (pyrosetta.rosetta.protocols.simple_filters.NMerPSSMEnergyFilter method) compute_residue_packing_score() (in module pyrosetta.rosetta.core.scoring.packstat) compute_residue_packing_scores() (in module pyrosetta.rosetta.core.scoring.packstat) compute_residue_sasas_for_sasa_scores() (in module pyrosetta.rosetta.protocols.sasa_scores) compute_residue_surface_energy() (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) compute_rmsd() (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) compute_rmsd_with_super() (pyrosetta.rosetta.protocols.simple_ddg.ddG method) compute_rosettaholes_score() (in module pyrosetta.rosetta.core.scoring.packing) compute_rotamer_pair_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) compute_rotdensities() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) compute_samebbconf_alternate_state_energy_first_node() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) compute_samebbconf_alternate_state_energy_second_node() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) compute_sasa() (in module pyrosetta.rosetta.core.scoring.packstat) compute_sasapack_scores() (in module pyrosetta.rosetta.protocols.sasa_scores) compute_sc_centroid() (in module pyrosetta.rosetta.core.scoring) compute_sc_radius() (in module pyrosetta.rosetta.core.scoring) compute_score_all_spinlabel() (pyrosetta.rosetta.core.scoring.nmr.pre.PREData method) compute_sho_acceptor_atom_energy() (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) compute_sho_donor_atom_energy() (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) compute_simple() (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter method) compute_size() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) compute_smooth_nb() (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) compute_spline() (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter method) compute_ss_regions() (in module pyrosetta.rosetta.protocols.loops) compute_structure_based_embedding() (in module pyrosetta.rosetta.protocols.membrane) compute_surface_area_leerichards() (in module pyrosetta.rosetta.core.scoring.packstat) compute_surface_area_leerichards_deriv() (in module pyrosetta.rosetta.core.scoring.packstat) compute_surrounding_sasa() (in module pyrosetta.rosetta.core.scoring.packstat) (pyrosetta.rosetta.core.scoring.packstat.MultiProbePerSphereAccumulator method) compute_symm_rotations() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) compute_tensor_stats() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) compute_termini_penalty() (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) compute_tmproj_penalty() (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) compute_total_score() (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) compute_total_volume_of_current_residues() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) compute_ub_function_solution() (pyrosetta.rosetta.numeric.interpolation.spline.CompoundInterpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.Interpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.SimpleInterpolator method) compute_unique_chains() (in module pyrosetta.rosetta.core.pose) compute_unsats_all_nodes() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) compute_unsats_changed_nodes() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) compute_unsats_for_node() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) compute_volume_of_this_buried_rotamer() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) compute_volumes_of_buried_rotamers() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) compute_zero_intensity() (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) computeAllBoltz() (pyrosetta.rosetta.protocols.pose_metric_calculators.RotamerBoltzCalculator method) computeBoltzWeight() (pyrosetta.rosetta.protocols.pose_metric_calculators.RotamerBoltzCalculator method) ComputeLigandRDF (class in pyrosetta.rosetta.protocols.ligand_docking) ComputeLigandRDFCreator (class in pyrosetta.rosetta.protocols.ligand_docking) computeStats() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) CoMTrackerCM (class in pyrosetta.rosetta.protocols.environment) CoMTrackerCMCreator (class in pyrosetta.rosetta.protocols.environment) concatenate_poses() (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) concatenate_rot_matrix() (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB method) concatenate_topology() (pyrosetta.rosetta.core.conformation.membrane.SpanningTopology method) ConcatenatePosesMover (class in pyrosetta.rosetta.protocols.simple_moves) ConcatenatePosesMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) concave_hull() (in module pyrosetta.rosetta.core.membrane) concave_shell() (in module pyrosetta.rosetta.core.membrane) concavity_direction() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) concavity_reference_residue() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) ConcurrencyTest (class in pyrosetta.rosetta.protocols.features.helixAssembly) ConcurrencyTestCreator (class in pyrosetta.rosetta.protocols.features.helixAssembly) cond_exit() (in module pyrosetta.rosetta.utility) condition() (pyrosetta.rosetta.numeric.expression_parser.ITEExpression method) conditional_erase() (pyrosetta.rosetta.core.pose.PDBPoseMap method) conditionally_add_edge() (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) CONECT (pyrosetta.rosetta.core.io.pdb.RecordType attribute) conf2pdb_chain() (in module pyrosetta.rosetta.core.pose) conf_size() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) ConfChangeMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) ConfChangeMoverCreator (class in pyrosetta.rosetta.protocols.rbsegment_relax) confidence() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.protocols.filters.StochasticFilter method) config (pyrosetta.rosetta.protocols.indexed_structure_store.DirectSegmentLookup property) (pyrosetta.rosetta.protocols.indexed_structure_store.SegmentSequenceProfile property) Config_map_std_basic_string_wchar_t_t (class in pyrosetta.rosetta.utility.json_spirit) Config_map_std_string_t (class in pyrosetta.rosetta.utility.json_spirit) Config_vector_std_basic_string_wchar_t_t (class in pyrosetta.rosetta.utility.json_spirit) Config_vector_std_string_t (class in pyrosetta.rosetta.utility.json_spirit) configure_from_filter_tag() (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) configure_from_options_system() (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) configure_hbond_options() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph static method) configure_rotameric_single_residue_dunbrack_library() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser method) configure_score_fxn() (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) confine_to_user_defined_helices() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments method) confirm_sequence() (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) ConfluentSelector (class in pyrosetta.rosetta.core.select.residue_selector) ConfluentSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) Conformation (class in pyrosetta.rosetta.core.conformation) conformation (pyrosetta.rosetta.protocols.network.UIObserver.ObserverType attribute) conformation() (pyrosetta.rosetta.core.pose.Pose method) CONFORMATION_COPY (pyrosetta.rosetta.basic.ProfTag attribute) CONFORMATION_DETECT_DISULF (pyrosetta.rosetta.basic.ProfTag attribute) conformation_energy() (pyrosetta.rosetta.core.scoring.constraints.Constraints method) CONFORMATION_FIX_DISULF (pyrosetta.rosetta.basic.ProfTag attribute) conformation_observer (pyrosetta.rosetta.protocols.moves.PyMOLObserver attribute) (pyrosetta.rosetta.protocols.moves.PyMOLObserver.ObserverType attribute) conformation_ptr() (pyrosetta.rosetta.core.pose.Pose method) conformation_size (pyrosetta.rosetta.core.conformation.signals.LengthEvent property) ConformationEvent (class in pyrosetta.rosetta.core.pose.signals) conformationEvent() (pyrosetta.rosetta.protocols.moves.PyMOLObserver method) (pyrosetta.rosetta.protocols.network.UIObserver method) ConformationKinWriter (class in pyrosetta.rosetta.core.conformation) ConformationSelectionToRDMol (class in pyrosetta.rosetta.protocols.drug_design) ConformationXYZ (class in pyrosetta.rosetta.core.scoring.func) Conformer (class in pyrosetta.rosetta.RDKit) conformer() (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelAtom method) conformer_bins (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData property) conformer_found() (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) Conformers (pyrosetta.rosetta.protocols.sparta.PDB property) conformers_for_ring_size_and_type() (pyrosetta.rosetta.core.chemical.rings.RingConformerManager static method) ConformerSwitchMover (class in pyrosetta.rosetta.protocols.docking) ConformerSwitchMoverCreator (class in pyrosetta.rosetta.protocols.docking) conj_map_times() (in module pyrosetta.rosetta.core.scoring.electron_density) conjugability() (pyrosetta.rosetta.core.chemical.Bond method) ConjugableBond (pyrosetta.rosetta.core.chemical.BondConjugability attribute) conjugate() (pyrosetta.rosetta.numeric.Quaternion_double_t method) conjugated() (pyrosetta.rosetta.numeric.Quaternion_double_t method) conn_dat() (pyrosetta.rosetta.core.scoring.etable.etrie.CountPairDataGeneric method) conn_dist() (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) CONNECT (pyrosetta.rosetta.core.chemical.ICoordAtomIDType attribute) connect() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorExternal method) (pyrosetta.rosetta.cppdb.backend.driver method) (pyrosetta.rosetta.cppdb.backend.loadable_driver method) (pyrosetta.rosetta.protocols.pockets.SmallMol method) connect_atom() (pyrosetta.rosetta.core.conformation.Residue method) connect_atoms() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) connect_info_cutoff() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) connect_map() (pyrosetta.rosetta.core.conformation.Residue method) connect_map_size() (pyrosetta.rosetta.core.conformation.Residue method) connect_segments() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) ConnectChainsMover (class in pyrosetta.rosetta.protocols.pose_length_moves) ConnectChainsMoverCreator (class in pyrosetta.rosetta.protocols.pose_length_moves) connected() (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.protocols.pockets.SmallMol method) connected_by_twobonds() (pyrosetta.rosetta.core.energy_methods.GoapRsdType method) connected_indices (pyrosetta.rosetta.core.io.AtomInformation property) connected_orders (pyrosetta.rosetta.core.io.AtomInformation property) connected_residue_at_lower() (pyrosetta.rosetta.core.conformation.Residue method) connected_residue_at_resconn() (pyrosetta.rosetta.core.conformation.Residue method) connected_residue_at_upper() (pyrosetta.rosetta.core.conformation.Residue method) connected_resonance_ids() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) connected_resonances() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) connected_segments() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) connection (class in pyrosetta.rosetta.cppdb.backend) connection_distance() (pyrosetta.rosetta.core.conformation.Residue method) connection_exists_to_residue() (pyrosetta.rosetta.core.scoring.trie.RotamerTrieBase method) connection_id_for_residue() (pyrosetta.rosetta.core.scoring.trie.RotamerTrieBase method) connection_incomplete() (pyrosetta.rosetta.core.conformation.Residue method) connection_index() (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParam method) connection_info (class in pyrosetta.rosetta.cppdb) connection_pair() (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParam method) connection_specific_data (class in pyrosetta.rosetta.cppdb) connection_specific_get() (pyrosetta.rosetta.cppdb.backend.connection method) connection_specific_release() (pyrosetta.rosetta.cppdb.backend.connection method) connection_specific_reset() (pyrosetta.rosetta.cppdb.backend.connection method) connection_string (pyrosetta.rosetta.cppdb.connection_info property) connection_theta0() (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParam method) connection_use_theta0() (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParam method) ConnectionArchitect (class in pyrosetta.rosetta.protocols.denovo_design.connection) ConnectionEvent (class in pyrosetta.rosetta.core.conformation.signals) ConnectionEvent.Tag (class in pyrosetta.rosetta.core.conformation.signals) ConnectionPerturber (class in pyrosetta.rosetta.protocols.denovo_design.components) connections() (pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler method) connections_match() (pyrosetta.rosetta.core.conformation.Residue method) connections_to_residue() (pyrosetta.rosetta.core.conformation.Residue method) connectivity_index() (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) ConnectRight (class in pyrosetta.rosetta.protocols.forge.build) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBInstructionType attribute) ConnectSulfurAndMakeVirtualProton (class in pyrosetta.rosetta.core.chemical) connid() (pyrosetta.rosetta.core.chemical.ResConnID method) connid_for_entry_connpoint() (pyrosetta.rosetta.core.scoring.trie.CPDataCorrespondence method) consensus_residues (pyrosetta.rosetta.core.enzymes.EnzymeData property) consensus_sequence (pyrosetta.rosetta.core.enzymes.EnzymeData property) ConsensusDesignMover (class in pyrosetta.rosetta.protocols.calc_taskop_movers) ConsensusDesignMoverCreator (class in pyrosetta.rosetta.protocols.calc_taskop_movers) ConsensusLoopDatabase (class in pyrosetta.rosetta.protocols.denovo_design.task_operations) ConsensusLoopDesignOperation (class in pyrosetta.rosetta.protocols.denovo_design.task_operations) ConsensusLoopDesignOperationCreator (class in pyrosetta.rosetta.protocols.denovo_design.task_operations) ConsensusSequenceType (class in pyrosetta.rosetta.core.enzymes) conservation_cutoff_aligned_segments() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation method) conservation_cutoff_protein_interface_design() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation method) ConservativeDesignOperation (class in pyrosetta.rosetta.protocols.task_operations) ConservativeDesignOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) ConservedPosMutationFilter (class in pyrosetta.rosetta.protocols.calc_taskop_filters) ConservedPosMutationFilterCreator (class in pyrosetta.rosetta.protocols.calc_taskop_filters) consider_already_bonded() (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) consider_alt_states() (pyrosetta.rosetta.core.scoring.lDDT_Calculator method) consider_backbone_move() (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) consider_bbmove_w_state_substitution() (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) consider_mainchain_only() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelector method) consider_substitution() (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.NPDHBSimpleInteractionGraph 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.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) (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) considered_scores_ (pyrosetta.rosetta.core.energy_methods.ScoreCache property) considered_start_ (pyrosetta.rosetta.core.energy_methods.ScoreCache property) considered_stop_ (pyrosetta.rosetta.core.energy_methods.ScoreCache property) consolidate_matches() (pyrosetta.rosetta.protocols.match.MatcherTask method) CONST (pyrosetta.rosetta.core.scoring.nmr.SINGLE_NMR_VALUE_WEIGHTING attribute) const_access_Real_MathNTensor() (in module pyrosetta.rosetta.numeric) const_begin() (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) const_data_cache() (pyrosetta.rosetta.core.pose.Pose method) const_data_map() (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) const_edge() (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) const_edge_list_begin() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintGraph method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.protocols.jd3.JobDigraph method) (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.DirectedNode method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t method) (pyrosetta.rosetta.utility.graph.LowMemNode method) (pyrosetta.rosetta.utility.graph.Node method) const_edge_list_end() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintGraph method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.protocols.jd3.JobDigraph method) (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.DirectedNode method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t method) (pyrosetta.rosetta.utility.graph.LowMemNode method) (pyrosetta.rosetta.utility.graph.Node method) const_end() (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) const_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) const_full_to_sub() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) const_incoming_edge_list_begin() (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.utility.graph.DirectedNode method) const_incoming_edge_list_end() (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.utility.graph.DirectedNode method) const_last() (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) const_location() (pyrosetta.rosetta.numeric.kdtree.KDPoint method) const_lower_edge_list_begin() (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) const_lower_edge_list_end() (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) const_my_group() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) const_neighbor_iterator_begin() (pyrosetta.rosetta.core.scoring.constraints.CstEnergyContainer method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.LREnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) const_neighbor_iterator_end() (pyrosetta.rosetta.core.scoring.constraints.CstEnergyContainer method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.LREnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) const_next() (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) const_outgoing_edge_list_begin() (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.utility.graph.DirectedNode method) const_outgoing_edge_list_end() (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.utility.graph.DirectedNode method) const_pdb_segments() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) (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) const_pose_apply() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) const_previous() (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) const_residues() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) const_seed() (pyrosetta.rosetta.basic.random.RandomGeneratorSettings method) const_sub_to_full() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) const_upper_edge_list_begin() (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) const_upper_edge_list_end() (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) const_upper_neighbor_iterator_begin() (pyrosetta.rosetta.core.scoring.constraints.CstEnergyContainer method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.LREnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) const_upper_neighbor_iterator_end() (pyrosetta.rosetta.core.scoring.constraints.CstEnergyContainer method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.LREnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) const_vdw_cached_rep_screen_info_from_pose() (in module pyrosetta.rosetta.protocols.scoring) ConstAbinitioMoverWeight (class in pyrosetta.rosetta.protocols.topology_broker.weights) constant() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) constant_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) ConstantConstraint (class in pyrosetta.rosetta.core.scoring.constraints) ConstantFunc (class in pyrosetta.rosetta.core.scoring.func) ConstantLengthFragSet (class in pyrosetta.rosetta.core.fragment) ConstantLengthFragSetIterator_ (class in pyrosetta.rosetta.core.fragment) ConstantScoreBase (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) ConstDataMap (class in pyrosetta.rosetta.basic.datacache) ConstFrameIterator (class in pyrosetta.rosetta.core.fragment) ConstPattern (class in pyrosetta.rosetta.protocols.hotspot_hashing) constrain_coords() (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) constrain_ligand_torsions() (in module pyrosetta.rosetta.protocols.ligand_docking) constrain_linker() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) constrain_phosphate() (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) constrain_pose_res_to_invrots() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) constrain_relax_segments() (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) constrain_relax_to_native_coords() (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) constrain_relax_to_start_coords() (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) constrain_residue() (in module pyrosetta.rosetta.protocols.mpi_refinement) constrain_ring_atoms() (in module pyrosetta.rosetta.core.pose.ncbb) constrain_to_antigen_chains() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) constrain_to_epitope_residues() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) constrain_to_paratope_cdrs() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) constrain_to_paratope_residues() (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) constrain_vlvh_qq() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) constrained_lig_atoms() (pyrosetta.rosetta.protocols.enzdes.EnzdesConstraintReporter method) constrained_nonligand_atoms() (pyrosetta.rosetta.protocols.enzdes.EnzdesConstraintReporter method) constrained_optimization_weight_func (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType attribute) ConstrainHBondNetwork (class in pyrosetta.rosetta.protocols.hbnet) ConstrainHBondNetworkCreator (class in pyrosetta.rosetta.protocols.hbnet) Constraint (class in pyrosetta.rosetta.basic.database.schema_generator) (class in pyrosetta.rosetta.core.scoring.constraints) (class in pyrosetta.rosetta.protocols.md) constraint() (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) constraint_definition (pyrosetta.rosetta.protocols.forge.remodel.LineObject property) constraint_energy() (pyrosetta.rosetta.protocols.enzdes.LigInterfaceEnergyFilter method) constraint_file() (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) CONSTRAINT_GENERATOR (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) constraint_generator_name() (pyrosetta.rosetta.protocols.denovo_design.constraints.FileConstraintGeneratorCreator static method) (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGeneratorCreator static method) constraint_generator_xml_schema_group_name() (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorFactory static method) constraint_relax() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) CONSTRAINT_SCORE (pyrosetta.rosetta.basic.ProfTag attribute) constraint_set() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) CONSTRAINT_SET_COPY (pyrosetta.rosetta.basic.ProfTag attribute) constraint_set_slice() (in module pyrosetta.rosetta.protocols.stepwise.modeler) ConstraintClaimer (class in pyrosetta.rosetta.protocols.topology_broker) ConstraintConditions (class in pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator) ConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) ConstraintEdge (class in pyrosetta.rosetta.core.scoring.constraints) ConstraintedOptimizationWeightFunc (class in pyrosetta.rosetta.protocols.optimize_weights) ConstraintEvaluator (class in pyrosetta.rosetta.protocols.constraints_additional) ConstraintEvaluatorCreator (class in pyrosetta.rosetta.protocols.constraints_additional) ConstraintEvaluatorWrapper (class in pyrosetta.rosetta.protocols.topology_broker) ConstraintEvaluatorWrapperCreator (class in pyrosetta.rosetta.protocols.topology_broker) ConstraintFactory (class in pyrosetta.rosetta.core.scoring.constraints) ConstraintFragmentSampler (class in pyrosetta.rosetta.protocols.abinitio) ConstraintFulfilmentFilter (class in pyrosetta.rosetta.protocols.fold_from_loops.filters) ConstraintFulfilmentFilterCreator (class in pyrosetta.rosetta.protocols.fold_from_loops.filters) ConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) (pyrosetta.rosetta.basic.citation_manager.CitedModuleType attribute) ConstraintGeneratorCreator (class in pyrosetta.rosetta.protocols.constraint_generator) ConstraintGeneratorFactory (class in pyrosetta.rosetta.protocols.constraint_generator) ConstraintGeneratorLoader (class in pyrosetta.rosetta.protocols.parser) ConstraintGeneratorLoaderCreator (class in pyrosetta.rosetta.protocols.parser) ConstraintGraph (class in pyrosetta.rosetta.core.scoring.constraints) ConstraintInfo (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) ConstraintIO (class in pyrosetta.rosetta.core.scoring.constraints) ConstraintNode (class in pyrosetta.rosetta.core.scoring.constraints) ConstrainToIdealMover (class in pyrosetta.rosetta.protocols.simple_moves) ConstraintPreparer (class in pyrosetta.rosetta.protocols.abinitio.abscript) ConstraintPreparerCreator (class in pyrosetta.rosetta.protocols.abinitio.abscript) ConstraintResidueSelector (class in pyrosetta.rosetta.protocols.fold_from_loops.selectors) ConstraintResidueSelectorCreator (class in pyrosetta.rosetta.protocols.fold_from_loops.selectors) Constraints (class in pyrosetta.rosetta.core.scoring.constraints) constraints() (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraints method) (pyrosetta.rosetta.core.scoring.constraints.CstMinimizationData method) (pyrosetta.rosetta.protocols.abinitio.Template method) (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) (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo method) constraints_from_link_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) constraints_lr (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) constraints_NtoC() (in module pyrosetta.rosetta.protocols.flxbb) constraints_only() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) constraints_sheet() (in module pyrosetta.rosetta.protocols.flxbb) ConstraintScoreCutoffFilter (class in pyrosetta.rosetta.protocols.constraint_filters) ConstraintScoreCutoffFilterCreator (class in pyrosetta.rosetta.protocols.constraint_filters) ConstraintScoreFilter (class in pyrosetta.rosetta.protocols.constraint_filters) ConstraintScoreFilterCreator (class in pyrosetta.rosetta.protocols.constraint_filters) ConstraintsEnergy (class in pyrosetta.rosetta.core.scoring.constraints) ConstraintsEnergyCreator (class in pyrosetta.rosetta.core.scoring.constraints) ConstraintSet (class in pyrosetta.rosetta.core.scoring.constraints) ConstraintSetMover (class in pyrosetta.rosetta.protocols.constraint_movers) ConstraintSetMoverCreator (class in pyrosetta.rosetta.protocols.constraint_movers) ConstraintSetScore (class in pyrosetta.rosetta.protocols.sic_dock) ConstraintsManager (class in pyrosetta.rosetta.protocols.constraint_generator) ConstraintsMap (class in pyrosetta.rosetta.protocols.constraint_generator) ConstraintsMetric (class in pyrosetta.rosetta.protocols.analysis.simple_metrics) ConstraintsMetricCreator (class in pyrosetta.rosetta.protocols.analysis.simple_metrics) construct_and_dump_outpose() (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination method) CONSTRUCT_DISTANCE_MATRIX (pyrosetta.rosetta.basic.ProfTag attribute) construct_dummy_pose() (in module pyrosetta.rosetta.protocols.denovo_design) construct_from_pose() (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) construct_kd_tree() (in module pyrosetta.rosetta.numeric.kdtree) construct_poly_ala_pose() (in module pyrosetta.rosetta.protocols.denovo_design) (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) construct_poly_beta_ala_pose() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) construct_poly_d_ala_pose() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) construct_poly_d_beta_ala_pose() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) construct_poly_uniq_restype_pose() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) construct_poly_XXX_pose() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) ConstScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) Contact (class in pyrosetta.rosetta.protocols.contact_map) (class in pyrosetta.rosetta.protocols.frag_picker) contact() (pyrosetta.rosetta.protocols.dna.DnaNeighbor method) contact_atom_name (pyrosetta.rosetta.protocols.sewing.data_storage.ContactDescription property) contact_atom_num (pyrosetta.rosetta.protocols.sewing.data_storage.ContactDescription property) contact_buried_problematic_res() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo method) contact_dis_ (pyrosetta.rosetta.protocols.sic_dock.CBScore property) contact_dist() (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter method) contact_distance() (pyrosetta.rosetta.protocols.fldsgn.filters.InterlockingAromaFilter method) (pyrosetta.rosetta.protocols.fldsgn.NcontactsCalculator method) contact_label() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub static method) contact_list() (pyrosetta.rosetta.protocols.scoring.Interface method) contact_name() (in module pyrosetta.rosetta.protocols.frag_picker) contact_order() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.protocols.abinitio.PairingStatEntry method) contact_order_score() (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorer method) contact_resnum (pyrosetta.rosetta.protocols.sewing.data_storage.ContactDescription property) contact_resnum_string (pyrosetta.rosetta.protocols.sewing.data_storage.ContactDescription property) contact_type() (in module pyrosetta.rosetta.protocols.frag_picker) ContactCounts (class in pyrosetta.rosetta.protocols.frag_picker) ContactDescription (class in pyrosetta.rosetta.protocols.sewing.data_storage) ContactMap (class in pyrosetta.rosetta.protocols.contact_map) ContactMapCreator (class in pyrosetta.rosetta.protocols.contact_map) ContactMapEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) ContactMapEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) ContactMolecularSurfaceCalculator (class in pyrosetta.rosetta.core.scoring.sc) ContactMolecularSurfaceFilter (class in pyrosetta.rosetta.protocols.simple_filters) ContactMolecularSurfaceFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) ContactOrderEnergy (class in pyrosetta.rosetta.core.energy_methods) ContactOrderEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) ContactPartner (class in pyrosetta.rosetta.protocols.contact_map) CONTACTS (pyrosetta.rosetta.core.conformation.symmetry.SlideCriteriaType attribute) contacts() (pyrosetta.rosetta.protocols.sic_dock.Rose method) contacts_naive() (pyrosetta.rosetta.protocols.sic_dock.Rose method) contacts_remaining() (pyrosetta.rosetta.protocols.sewing.hashing.LigandBindingResPlacer method) ContactStruct (class in pyrosetta.rosetta.protocols.normalmode) ContactType (class in pyrosetta.rosetta.protocols.frag_picker) contain() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) contain_nic() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) contains() (in module pyrosetta.rosetta.protocols.sparta) Contains() (in module pyrosetta.rosetta.protocols.toolbox) contains() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfoSet method) (pyrosetta.rosetta.core.scoring.packstat.Circle method) (pyrosetta.rosetta.core.scoring.packstat.Octree2D method) (pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.FArray1_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_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) (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.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.dna.DnaChains method) (pyrosetta.rosetta.protocols.forge.build.Interval method) contains_atom_type() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) contains_bond_length() (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) contains_carbohydrate_residues() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) contains_catalytic_res() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) contains_element_type() (pyrosetta.rosetta.core.chemical.ElementSet method) contains_position() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache method) contains_protein() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) contains_seqpos() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) contents_in_pose_store() (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) context_chain_selector() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) context_derivative_empty() (pyrosetta.rosetta.core.scoring.facts.FACTSPoseInfo method) context_derivative_empty_ (pyrosetta.rosetta.core.scoring.facts.FACTSPoseInfo property) context_graph() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) context_label() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub static method) context_update_step() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) ContextDependentGeometricSolEnergy (class in pyrosetta.rosetta.core.energy_methods) ContextDependentGeometricSolEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) ContextDependentLRTwoBodyEnergy (class in pyrosetta.rosetta.core.scoring.methods) ContextDependentOneBodyEnergy (class in pyrosetta.rosetta.core.scoring.methods) ContextDependentTwoBodyEnergy (class in pyrosetta.rosetta.core.scoring.methods) ContextGraph (class in pyrosetta.rosetta.core.scoring) ContextGraphFactory (class in pyrosetta.rosetta.core.scoring) ContextGraphType (class in pyrosetta.rosetta.core.scoring) ContextIndependentGeometricSolEnergy (class in pyrosetta.rosetta.core.energy_methods) ContextIndependentGeometricSolEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) ContextIndependentLRTwoBodyEnergy (class in pyrosetta.rosetta.core.scoring.methods) ContextIndependentOneBodyEnergy (class in pyrosetta.rosetta.core.scoring.methods) ContextIndependentTwoBodyEnergy (class in pyrosetta.rosetta.core.scoring.methods) CONTIGUOUS (pyrosetta.rosetta.core.select.residue_selector.slice_enums.SliceMode attribute) contiguous_monomers() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) ContingentAcceptMover (class in pyrosetta.rosetta.protocols.simple_moves) ContingentAcceptMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) ContingentFilter (class in pyrosetta.rosetta.protocols.filters) ContingentFilterCreator (class in pyrosetta.rosetta.protocols.filters) continue_at_dimension() (pyrosetta.rosetta.utility.LexicographicalIterator method) continue_if_silent() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) continue_slide() (pyrosetta.rosetta.protocols.symmetry.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SymmetrySlider method) continue_until_none_missing() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) continuous() (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) ContinuousAssembly (class in pyrosetta.rosetta.protocols.legacy_sewing) ContinuousRotamerSet (class in pyrosetta.rosetta.core.pack.rotamer_set) ContinuousRotamerSets (class in pyrosetta.rosetta.core.pack.rotamer_set) control_grid_param() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter method) controlling_chi_for_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) ControlStrength (class in pyrosetta.rosetta.protocols.environment.claims) conventional_chains() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) conventional_numbering() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) conventional_segids() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) conventional_to_full() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) converge() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) ConvergenceTest (class in pyrosetta.rosetta.core.optimization) convert() (pyrosetta.rosetta.core.chemical.RefConvert_std_string_t static method) (pyrosetta.rosetta.core.chemical.RefConvert_unsigned_long_t static method) (pyrosetta.rosetta.core.chemical.RefConvert_void__star__t static method) convert_aa_to_index() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPairDistPotential method) convert_acgu_to_1234() (in module pyrosetta.rosetta.core.chemical.rna) convert_atom_name() (in module pyrosetta.rosetta.core.io.pose_from_sfr) convert_based_on_match_type() (in module pyrosetta.rosetta.core.import_pose) convert_binary_checkpoint() (in module pyrosetta.rosetta.protocols.frag_picker) convert_cart_to_spherical_and_round() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) convert_cartesian_to_grid() (in module pyrosetta.rosetta.protocols.pockets) convert_cartesian_to_spherical_coor_triplet() (in module pyrosetta.rosetta.protocols.pockets) convert_from_rdkit_bondtype() (in module pyrosetta.rosetta.core.chemical.rdkit) convert_from_std_map() (in module pyrosetta.rosetta.core.pose) convert_GeomSampleInfo_to_FuncOP() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters static method) convert_grid_to_cartesian() (in module pyrosetta.rosetta.protocols.pockets) convert_inorder_table_to_original_order() (in module pyrosetta.rosetta.core.scoring.trie) convert_inorder_vector_to_original_order() (in module pyrosetta.rosetta.core.scoring.trie) convert_matrix_to_xyz() (pyrosetta.rosetta.protocols.hybridization.TMalign method) convert_pose_into_segment_vector() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector method) convert_pre_spin_type_to_string() (in module pyrosetta.rosetta.core.scoring.nmr) convert_probabilities_to_logits() (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover static method) convert_profile_to_probs() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) convert_protein_centroid() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) convert_rdc_type_to_string() (in module pyrosetta.rosetta.core.scoring.nmr) convert_res_name() (in module pyrosetta.rosetta.core.io.pose_from_sfr) convert_residue_names_into_linkage_map_key() (in module pyrosetta.rosetta.core.chemical.carbohydrates) convert_scores_to_probabilities() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation method) convert_spherical_coor_triplet_to_cartesian() (in module pyrosetta.rosetta.protocols.pockets) convert_spherical_list_to_cartesian_list() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) convert_string_to_averaging_type() (in module pyrosetta.rosetta.core.scoring.nmr) convert_string_to_normalization_type() (in module pyrosetta.rosetta.core.scoring.nmr) convert_string_to_rate_type() (in module pyrosetta.rosetta.core.scoring.nmr) convert_string_to_weighting_scheme() (in module pyrosetta.rosetta.core.scoring.nmr) convert_sugar_modeling_to_residue_alternative_set() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) convert_to_BondName() (in module pyrosetta.rosetta.core.chemical) convert_to_fasta() (in module pyrosetta.rosetta.core.sequence) convert_to_full_pose() (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) convert_to_rdkit_bondtype() (in module pyrosetta.rosetta.core.chemical.rdkit) convert_to_ResidueType() (in module pyrosetta.rosetta.core.chemical.sdf) (pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule method) convert_to_ResidueTypes() (in module pyrosetta.rosetta.core.chemical.sdf) convert_to_rotation_matrix() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.EulerAngles method) convert_to_working_res() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) convert_vector_to_xyz() (pyrosetta.rosetta.protocols.hybridization.TMalign method) convert_xyz_to_matrix() (pyrosetta.rosetta.protocols.hybridization.TMalign method) convert_xyz_to_vector() (pyrosetta.rosetta.protocols.hybridization.TMalign method) convert_xyz_v_to_vectors() (pyrosetta.rosetta.protocols.hybridization.TMalign method) ConvertRealToVirtualMover (class in pyrosetta.rosetta.protocols.simple_moves) ConvertRealToVirtualMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) ConvertVirtualToRealMover (class in pyrosetta.rosetta.protocols.simple_moves) ConvertVirtualToRealMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) convex_hull() (in module pyrosetta.rosetta.core.membrane) convolute() (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) convolute_maps() (in module pyrosetta.rosetta.core.scoring.electron_density) convolute_single_residue_ (pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions property) (pyrosetta.rosetta.protocols.electron_density.SelectDensityPointsOptions property) coor (pyrosetta.rosetta.core.scoring.sc._DOT property) coor_const() (pyrosetta.rosetta.protocols.splice.Splice method) coord() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo method) (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) coord_atom_index (pyrosetta.rosetta.protocols.sewing.hashing.LigandCoordInfo property) coord_constrain_sidechains() (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) coord_csts() (pyrosetta.rosetta.protocols.protein_interface_design.movers.CoordinateConstraintStack method) coord_dev() (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) coord_equal_to (class in pyrosetta.rosetta.protocols.legacy_sewing) (class in pyrosetta.rosetta.protocols.sewing.hashing) coord_frame_ref() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) coord_hash (class in pyrosetta.rosetta.protocols.legacy_sewing) (class in pyrosetta.rosetta.protocols.sewing.hashing) coord_res_name (pyrosetta.rosetta.protocols.sewing.hashing.LigandCoordInfo property) coord_sdev() (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) coord_type() (pyrosetta.rosetta.core.scoring.MultipoleParameter method) CoordConstraintClaimer (class in pyrosetta.rosetta.protocols.topology_broker) coordinate_array_broadcast_rmsd() (in module pyrosetta.rosetta.numeric.alignment) coordinate_array_rmsd() (in module pyrosetta.rosetta.numeric.alignment) coordinate_array_superimpose() (in module pyrosetta.rosetta.numeric.alignment) coordinate_constrain_selection() (in module pyrosetta.rosetta.protocols.relax) coordinate_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) coordinate_constraint_energy() (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) coordinate_constraint_weight() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) coordinate_constraints_during_minimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) coordinate_filter() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) coordinate_for_nonchi_atom_in_ideal_frame() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) coordinate_in_D3_frame() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) coordinate_in_global_frame() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) coordinate_transform_onto_target_site() (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelEnsemble method) CoordinateConstraint (class in pyrosetta.rosetta.core.scoring.constraints) CoordinateConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) CoordinateConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) CoordinateConstraintGeneratorCreator (class in pyrosetta.rosetta.protocols.constraint_generator) CoordinateConstraintKC (class in pyrosetta.rosetta.protocols.abinitio) CoordinateConstraintStack (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) CoordinateCst (class in pyrosetta.rosetta.protocols.seeded_abinitio) CoordinateCstCreator (class in pyrosetta.rosetta.protocols.seeded_abinitio) coordinates() (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) coordinates_exist() (pyrosetta.rosetta.protocols.chromophore.ReadResidueCoordinatesFromPDB method) coordinates_from_hit() (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) coordinates_from_orientation() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) coordinates_per_fragment() (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentSpecification method) Coordinates_Tetrahedral_bondedto3atoms_helper() (pyrosetta.rosetta.core.chemical.orbitals.AssignOrbitals method) Coordinates_TriganolPlanar_bondedto1atom_helper() (pyrosetta.rosetta.core.chemical.orbitals.AssignOrbitals method) coords() (in module pyrosetta.rosetta.protocols.splice) (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) (pyrosetta.rosetta.core.io.raw_data.DecoyStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) (pyrosetta.rosetta.protocols.toolbox.KClusterData method) coords_ (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.DataBuffer property) (pyrosetta.rosetta.protocols.legacy_sewing.SewAtom property) (pyrosetta.rosetta.protocols.simple_moves.WaterRot property) coords_vector() (pyrosetta.rosetta.core.conformation.UltraLightResidue method) copies_pitch() (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) copy() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.FragData method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) (pyrosetta.rosetta.RDGeom.Point method) (pyrosetta.rosetta.RDGeom.Point3D method) (pyrosetta.rosetta.RDKit.Atom method) (pyrosetta.rosetta.RDKit.Bond method) copy_all_chi_ (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover property) copy_all_o2prime_torsions() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) copy_array_contents() (pyrosetta.rosetta.utility.graph.ArrayPoolElement_double_t method) copy_backbone_dihedrals (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) copy_bb_donor_acceptor_arrays() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) copy_begin (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) copy_bulge_res_and_sugar_torsion() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) copy_CCD_torsions() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) copy_CCD_torsions_general() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) copy_clone() (pyrosetta.rosetta.core.energy_methods.PoseSequence method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) copy_comments() (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) copy_connectivity() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintGraph method) (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) (pyrosetta.rosetta.protocols.jd3.JobDigraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) COPY_COORDS (pyrosetta.rosetta.basic.ProfTag attribute) copy_coords() (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) copy_data() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) copy_dna_chains() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterface method) COPY_DOF (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) copy_dofs() (in module pyrosetta.rosetta.core.pose.copydofs) copy_dofs_from_pose() (pyrosetta.rosetta.core.optimization.CartesianMinimizerMap method) (pyrosetta.rosetta.core.optimization.MinimizerMap method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) copy_dofs_from_source() (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) copy_dofs_info() (pyrosetta.rosetta.core.pose.copydofs.CopyDofs method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) copy_dofs_match_atom_names() (in module pyrosetta.rosetta.core.pose.copydofs) copy_dofs_rotamer() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) copy_dofs_sort_criterion() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) copy_dofs_to_pose() (pyrosetta.rosetta.core.optimization.CartesianMinimizerMap method) (pyrosetta.rosetta.core.optimization.MinimizerMap method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) copy_end (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) copy_fragments() (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) copy_from() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.TenANeighborEdge method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TwelveANeighborEdge method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.protocols.jd3.JobDirectedEdge method) (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.utility.graph.DirectedEdge method) (pyrosetta.rosetta.utility.graph.DirectedNode method) (pyrosetta.rosetta.utility.graph.Edge method) (pyrosetta.rosetta.utility.graph.Node 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) 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) copy_from_ref() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_tensor method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_tensor_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_tensor_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_tensor_Ts4 method) copy_helix_bondangles() (in module pyrosetta.rosetta.protocols.helical_bundle) copy_helix_bondlengths() (in module pyrosetta.rosetta.protocols.helical_bundle) copy_helix_dihedrals() (in module pyrosetta.rosetta.protocols.helical_bundle) copy_hit() (pyrosetta.rosetta.protocols.match.downstream_hit method) (pyrosetta.rosetta.protocols.match.upstream_hit method) copy_i_bins_to_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) copy_interface() (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterface method) copy_layer_residues() (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) copy_leaf_ids() (pyrosetta.rosetta.numeric.ClusteringTreeNode method) copy_loop_pose_to_original() (in module pyrosetta.rosetta.protocols.generalized_kinematic_closure) copy_member_ids() (pyrosetta.rosetta.numeric.ClusteringTreeNode method) copy_next_pose_segment() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) copy_node_and_connected_edges() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) copy_opts_swapped() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) copy_over_phosphate_variants() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) copy_params_from_previous_helices() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) copy_params_from_previous_helices_makebundlehelix_style() (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) copy_params_from_previous_helices_perturbbundle_style() (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator static method) copy_pdbinfo() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) copy_phosphates() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) copy_pose_crd() (in module pyrosetta.rosetta.protocols.mpi_refinement) copy_residue_connections() (pyrosetta.rosetta.core.conformation.Residue method) copy_residue_connections_from() (pyrosetta.rosetta.core.conformation.Residue method) copy_residue_coordinates_and_rebuild_missing_atoms() (in module pyrosetta.rosetta.core.conformation) copy_rotamer_matrix() (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation method) copy_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) copy_segment() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) copy_sequence() (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) copy_sidechains() (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) copy_stretch() (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) 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) copy_targeted_dna() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterface method) copy_to_cstr_buffer() (in module pyrosetta.rosetta.utility) copy_unset_params_from_globals() (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) copy_value_from_parameter() (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) copy_values() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) copy_without_output() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) CopyDofMover (class in pyrosetta.rosetta.protocols.simple_moves) CopyDofs (class in pyrosetta.rosetta.core.pose.copydofs) CopyDofsInfo (class in pyrosetta.rosetta.core.pose.copydofs) CopyDofStepWiseSampler (class in pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs) copyfmt_event (pyrosetta.rosetta.std.ios_base attribute) (pyrosetta.rosetta.std.ios_base.event attribute) copying_information_was_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) CopyRotamerMover (class in pyrosetta.rosetta.protocols.simple_moves) CopyRotamerMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) copysign() (in module pyrosetta.rosetta.utility) COradius2() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) CORE_GENERIC (pyrosetta.rosetta.basic.thread_manager.RosettaThreadRequestOriginatingLevel attribute) CORE_PACK (pyrosetta.rosetta.basic.thread_manager.RosettaThreadRequestOriginatingLevel attribute) CORE_SCORING (pyrosetta.rosetta.basic.thread_manager.RosettaThreadRequestOriginatingLevel attribute) CoreDunbrackFilter (class in pyrosetta.rosetta.protocols.fldsgn.filters) CoreDunbrackFilterCreator (class in pyrosetta.rosetta.protocols.fldsgn.filters) CoreScorer (class in pyrosetta.rosetta.protocols.pose_sewing.filters) CoreScorerCreator (class in pyrosetta.rosetta.protocols.pose_sewing.filters) corrcoef() (in module pyrosetta.rosetta.numeric.statistics) corrcoef_with_provided_mean_and_std_dev() (in module pyrosetta.rosetta.numeric.statistics) correct() (pyrosetta.rosetta.numeric.DiscreteIntervalEncodingTree_unsigned_long_t method) correct_polymer_dependent_atoms() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) correct_polymer_dependent_atoms_in_pose_segment() (in module pyrosetta.rosetta.protocols.generalized_kinematic_closure) correct_sign() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) correct_thioether_virtuals() (in module pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) corrected_xyz() (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) correction_weights() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) correctly_add_2prime_connection_variants() (in module pyrosetta.rosetta.core.pose) correctly_add_cutpoint_variants() (in module pyrosetta.rosetta.core.pose) correctly_remove_variants_incompatible_with_lower_cutpoint_variant() (in module pyrosetta.rosetta.core.pose) correctly_remove_variants_incompatible_with_upper_cutpoint_variant() (in module pyrosetta.rosetta.core.pose) correspondence() (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) correspondence_file_name_ (pyrosetta.rosetta.protocols.pack_daemon.StructureFileNames property) corresponding_mress_for_mres (pyrosetta.rosetta.core.pack.annealer.SeqSymmAnnealerSetup property) corresponding_res_block() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) corresponding_residue_in_current() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) cos_theta() (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) (pyrosetta.rosetta.core.scoring.SAnode method) cosAHD_fade_lookup() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) cosAHD_long_poly_lookup() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) cosAHD_short_poly_lookup() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) cosBAH2_fade_lookup() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) cosBAH2_poly_lookup() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) cosBAH_fade_lookup() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) cosBAH_long_poly_lookup() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) cosBAH_short_poly_lookup() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) cose (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder property) COSFXN() (in module pyrosetta.rosetta.numeric.crick_equations) cosine_distance() (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) could_be_accepted() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) CouldHaveHybridization() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) Coulomb (class in pyrosetta.rosetta.core.scoring.etable.coulomb) coulomb() (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) count (pyrosetta.rosetta.numeric.geometry.hashing.Counter property) count() (pyrosetta.CD 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.fragment.FrameList method) (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.core.scoring.elec.CountPairRepresentative method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairAll method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover3 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover34 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover3full method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover4 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairGeneric method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairNone method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) (pyrosetta.rosetta.core.select.residue_selector.ResidueVector method) (pyrosetta.rosetta.core.sequence.CompositeScoringScheme method) (pyrosetta.rosetta.numeric.model_quality.RmsData 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.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.fldsgn.topology.DimerPairings method) (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) (pyrosetta.rosetta.protocols.nmr.pre.PREDistanceRecord method) (pyrosetta.rosetta.protocols.sewing.hashing.SegmentVector method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.ProteinAtrRepScreener method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.RNA_AtrRepScreener method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.SimplePoseSelection method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.SimpleRMSD_Screener method) (pyrosetta.rosetta.protocols.stepwise.screener.AlignRMSD_Screener method) (pyrosetta.rosetta.protocols.stepwise.screener.AnchorSugarScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.BaseBinMapUpdater method) (pyrosetta.rosetta.protocols.stepwise.screener.BaseCentroidScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.BulgeApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.CentroidDistanceScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.FastForwardToNextResidueAlternative method) (pyrosetta.rosetta.protocols.stepwise.screener.FastForwardToNextRigidBody method) (pyrosetta.rosetta.protocols.stepwise.screener.IntegrationTestBreaker method) (pyrosetta.rosetta.protocols.stepwise.screener.O2PrimeScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PackScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PartitionContactScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PhosphateScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PoseSelectionScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.ProteinCCD_ClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.ResidueContactScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryResidueBasedScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryStubBasedScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.SampleApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.Scorer method) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseResiduePairScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.StubApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.StubDistanceScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.SugarInstantiator method) (pyrosetta.rosetta.protocols.stepwise.screener.TagDefinition method) (pyrosetta.rosetta.protocols.stepwise.screener.VDW_BinScreener method) (pyrosetta.rosetta.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.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.std.vector_core_scoring_hbonds_graph_HBondInfo method) (pyrosetta.rosetta.std.vector_core_scoring_sc_Atom method) (pyrosetta.rosetta.std.vector_double method) (pyrosetta.rosetta.std.vector_float method) (pyrosetta.rosetta.std.vector_int method) (pyrosetta.rosetta.std.vector_numeric_xyzMatrix_double_t method) (pyrosetta.rosetta.std.vector_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.vector_std_list_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.vector_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t method) (pyrosetta.rosetta.std.vector_std_map_unsigned_long_unsigned_long_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_pair_std_shared_ptr_protocols_filters_Filter_protocols_filters_boolean_operations_t method) (pyrosetta.rosetta.std.vector_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_set_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_chemical_Orbital_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_fragment_FragSet_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_pose_Pose_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_cluster_calibur_Stru_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_hbnet_HBondNetStruct_t method) 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(pyrosetta.rosetta.utility.vector1_utility_vector0_unsigned_short_std_allocator_unsigned_short_t method) (pyrosetta.rosetta.utility.vector1_utility_vector0_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_bool_std_allocator_bool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_char_std_allocator_char_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_chemical_BondName_std_allocator_core_chemical_BondName_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_chemical_BondRingness_std_allocator_core_chemical_BondRingness_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_chemical_VariantType_std_allocator_core_chemical_VariantType_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_id_AtomID_std_allocator_core_id_AtomID_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_id_DOF_ID_std_allocator_core_id_DOF_ID_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_id_NamedAtomID_std_allocator_core_id_NamedAtomID_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_id_TorsionID_std_allocator_core_id_TorsionID_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_scoring_packstat_Circle__star__std_allocator_core_scoring_packstat_Circle__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_scoring_power_diagram_PDsphere__star__std_allocator_core_scoring_power_diagram_PDsphere__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_scoring_ScoreType_std_allocator_core_scoring_ScoreType_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_float_std_allocator_float_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_int_std_allocator_int_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_long_std_allocator_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_interpolation_spline_CubicSpline_std_allocator_numeric_interpolation_spline_CubicSpline_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_xyzVector_float_std_allocator_numeric_xyzVector_float_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_ObjexxFCL_ubyte_std_allocator_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_denovo_design_components_StrandOrientation_std_allocator_protocols_denovo_design_components_StrandOrientation_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_denovo_design_components_StructureSlice_std_allocator_protocols_denovo_design_components_StructureSlice_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_loops_Loops_std_allocator_protocols_loops_Loops_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_std_allocator_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_int_int_std_allocator_std_pair_int_int_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_numeric_xyzVector_double_numeric_xyzVector_double_std_allocator_std_pair_numeric_xyzVector_double_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_std_allocator_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_std_string_std_string_std_allocator_std_pair_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_std_pair_std_pair_double_double_unsigned_long_std_allocator_std_pair_unsigned_long_std_pair_std_pair_double_double_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_unsigned_long_std_allocator_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_core_scoring_dna_TorsionFourierComponent_std_allocator_std_shared_ptr_const_core_scoring_dna_TorsionFourierComponent_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_std_allocator_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_match_upstream_ScaffoldBuildPoint_std_allocator_std_shared_ptr_const_protocols_match_upstream_ScaffoldBuildPoint_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_simple_filters_ResidueDepthData_std_allocator_std_shared_ptr_const_protocols_simple_filters_ResidueDepthData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_conformation_Residue_std_allocator_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_kinematics_tree_Atom_std_allocator_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_optimization_DOF_Node_std_allocator_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_pack_interaction_graph_NPDHBond_std_allocator_std_shared_ptr_core_pack_interaction_graph_NPDHBond_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_pack_task_ResfileCommand_std_allocator_std_shared_ptr_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_scoring_saxs_DistanceHistogram_std_allocator_std_shared_ptr_core_scoring_saxs_DistanceHistogram_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_sequence_Cell_std_allocator_std_shared_ptr_core_sequence_Cell_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_antibody_PDBLandmark_std_allocator_std_shared_ptr_protocols_antibody_PDBLandmark_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_fldsgn_topology_HelixPairing_std_allocator_std_shared_ptr_protocols_fldsgn_topology_HelixPairing_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_std_allocator_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_flexpack_rotamer_set_FlexbbRotamerSet_std_allocator_std_shared_ptr_protocols_flexpack_rotamer_set_FlexbbRotamerSet_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_quota_QuotaPool_std_allocator_std_shared_ptr_protocols_frag_picker_quota_QuotaPool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_AdaptiveScoreHistogram_std_allocator_std_shared_ptr_protocols_frag_picker_scores_AdaptiveScoreHistogram_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_AtomPairConstraintsData_std_allocator_std_shared_ptr_protocols_frag_picker_scores_AtomPairConstraintsData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_FourAtomsConstraintData_std_allocator_std_shared_ptr_protocols_frag_picker_scores_FourAtomsConstraintData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_Entity_std_allocator_std_shared_ptr_protocols_genetic_algorithm_Entity_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_std_allocator_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_jd3_JGJobNode_std_allocator_std_shared_ptr_protocols_jd3_JGJobNode_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_minimization_packing_MinimalRotamer_std_allocator_std_shared_ptr_protocols_minimization_packing_MinimalRotamer_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_pose_sewing_data_storage_SegmentEnvelope_std_allocator_std_shared_ptr_protocols_pose_sewing_data_storage_SegmentEnvelope_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_keys_Key2Tuple_unsigned_long_unsigned_long_std_allocator_utility_keys_Key2Tuple_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_keys_Key3Tuple_unsigned_long_unsigned_long_unsigned_long_std_allocator_utility_keys_Key3Tuple_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_std_allocator_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_std_allocator_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_std_allocator_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_void__star__std_allocator_void__star__t method) count_ (pyrosetta.rosetta.protocols.features.TopCountOfAllInputs property) (pyrosetta.rosetta.protocols.features.TopCountOfEachInput property) count_AA_w_direction() (in module pyrosetta.rosetta.protocols.features.strand_assembly) count_AA_wo_direction() (in module pyrosetta.rosetta.protocols.features.strand_assembly) count_accepted() (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.moves.TrialCounter method) count_assignments() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList method) count_at_path_distance() (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover3 static method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover34 static method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover3full static method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover4 static method) count_bb_atoms() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) count_bb_atoms_in_residue() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) count_bulges() (in module pyrosetta.rosetta.protocols.denovo_design) count_candidates() (pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_CompareTotalScore method) (pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) count_CBs() (in module pyrosetta.rosetta.protocols.sic_dock) count_clashes_between_two_poses() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) count_components() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) count_connected_components_and_initialize_vertex_groups() (pyrosetta.rosetta.core.pack.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) count_cutpoints() (in module pyrosetta.rosetta.protocols.forge.methods) count_data() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker method) count_dynamic_memory() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (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.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode 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.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NodeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode 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.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.TenANeighborEdge method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TwelveANeighborEdge method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.jd3.JobDirectedEdge method) (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.utility.graph.DirectedEdge method) (pyrosetta.rosetta.utility.graph.DirectedNode method) (pyrosetta.rosetta.utility.graph.Edge method) (pyrosetta.rosetta.utility.graph.LowMemEdge method) (pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t method) (pyrosetta.rosetta.utility.graph.LowMemNode method) (pyrosetta.rosetta.utility.graph.Node method) count_energy_drop() (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.moves.TrialCounter method) count_energy_to_node_in_my_fragtotalE() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) count_ff() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) count_fixed_residues() (pyrosetta.rosetta.core.kinematics.FoldTree method) count_gly_as_polar() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) count_inserted() (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) count_linkers() (in module pyrosetta.rosetta.protocols.sic_dock) count_motifs() (pyrosetta.rosetta.core.scoring.motif.MotifHash method) count_n_matches() (pyrosetta.rosetta.protocols.match.MatchCounter method) count_neighbors() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) count_neighbors_on_coord() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) count_num_covered() (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) count_pair_bs() (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) count_pair_full() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) count_pair_hybrid() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) count_pools() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) count_query_ss() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) count_residues() (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilter method) count_rotamer_as_native() (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) count_scoring_atoms() (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) count_segments() (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) count_selected() (in module pyrosetta.rosetta.core.select.residue_selector) count_static_memory() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (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.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode 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.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NodeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode 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.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.TenANeighborEdge method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TwelveANeighborEdge method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) (pyrosetta.rosetta.protocols.jd3.JobDirectedEdge method) (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.utility.graph.DirectedEdge method) (pyrosetta.rosetta.utility.graph.DirectedNode method) (pyrosetta.rosetta.utility.graph.Edge method) (pyrosetta.rosetta.utility.graph.LowMemEdge method) (pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t method) (pyrosetta.rosetta.utility.graph.LowMemNode method) (pyrosetta.rosetta.utility.graph.Node method) count_trial() (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.moves.TrialCounter method) count_uniq_char() (in module pyrosetta.rosetta.protocols.ncbb) count_water() (pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector method) counted_residue_description() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) Counter (class in pyrosetta.rosetta.numeric.geometry.hashing) CountFromLeft (class in pyrosetta.rosetta.protocols.forge.build) CountPairAll (class in pyrosetta.rosetta.core.scoring.etable.count_pair) CountPairCrossover3 (class in pyrosetta.rosetta.core.scoring.etable.count_pair) CountPairCrossover34 (class in pyrosetta.rosetta.core.scoring.etable.count_pair) CountPairCrossover3full (class in pyrosetta.rosetta.core.scoring.etable.count_pair) CountPairCrossover4 (class in pyrosetta.rosetta.core.scoring.etable.count_pair) CountPairData_1_1 (class in pyrosetta.rosetta.core.scoring.etable.etrie) CountPairData_1_2 (class in pyrosetta.rosetta.core.scoring.etable.etrie) CountPairData_1_3 (class in pyrosetta.rosetta.core.scoring.etable.etrie) CountPairDataGeneric (class in pyrosetta.rosetta.core.scoring.etable.etrie) CountPairFactory (class in pyrosetta.rosetta.core.scoring.etable.count_pair) CountPairFunction (class in pyrosetta.rosetta.core.scoring.etable.count_pair) CountPairGeneric (class in pyrosetta.rosetta.core.scoring.etable.count_pair) CountPairNone (class in pyrosetta.rosetta.core.scoring.etable.count_pair) CountPairRepMap (class in pyrosetta.rosetta.core.scoring.elec) CountPairRepresentative (class in pyrosetta.rosetta.core.scoring.elec) counts (pyrosetta.rosetta.protocols.indexed_structure_store.SegmentSequenceProfileResult property) counts() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.protocols.frag_picker.ContactCounts method) countTestCases() (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) CountViolFunc (class in pyrosetta.rosetta.core.scoring.func) CoupledMover (class in pyrosetta.rosetta.protocols.simple_moves) CoupledMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) CoupledMovesProtocol (class in pyrosetta.rosetta.protocols.coupled_moves) CoupledMovesProtocolCreator (class in pyrosetta.rosetta.protocols.coupled_moves) cov() (in module pyrosetta.rosetta.numeric.statistics) cov_with_provided_mean() (in module pyrosetta.rosetta.numeric.statistics) coval() (pyrosetta.rosetta.utility.heap method) coval_for_val() (pyrosetta.rosetta.utility.heap method) covalent_compliance() (in module pyrosetta.rosetta.protocols.noesy_assign) covalent_compliance_weight_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) covalent_connections() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache method) covalent_labeling (pyrosetta.rosetta.core.scoring.ScoreType attribute) covalent_labeling_fa (pyrosetta.rosetta.core.scoring.ScoreType attribute) covalent_labeling_fa_input() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) covalent_labeling_input() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) CovalentCompliance (class in pyrosetta.rosetta.protocols.noesy_assign) CovalentConnectionReplaceInfo (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) CovalentLabelingEnergy (class in pyrosetta.rosetta.core.energy_methods) CovalentLabelingEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) CovalentLabelingFAEnergy (class in pyrosetta.rosetta.core.energy_methods) CovalentLabelingFAEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) CovalentRadius (pyrosetta.rosetta.core.chemical.Element attribute) (pyrosetta.rosetta.core.chemical.Element.Properties attribute) CovalentRadiusAromaticBond (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) CovalentRadiusDoubleBond (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) CovalentRadiusSingleBond (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) CovalentRadiusTripleBond (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) CovalentResidueNetwork (class in pyrosetta.rosetta.protocols.toolbox) cover (pyrosetta.rosetta.basic.sampling.orientations.QuatDBMetadata property) CP_CROSSOVER_3 (pyrosetta.rosetta.core.scoring.etable.count_pair.CPCrossoverBehavior attribute) CP_CROSSOVER_34 (pyrosetta.rosetta.core.scoring.etable.count_pair.CPCrossoverBehavior attribute) CP_CROSSOVER_3FULL (pyrosetta.rosetta.core.scoring.etable.count_pair.CPCrossoverBehavior attribute) CP_CROSSOVER_4 (pyrosetta.rosetta.core.scoring.etable.count_pair.CPCrossoverBehavior attribute) CP_MULTIPLE_BONDS_OR_PSEUDOBONDS (pyrosetta.rosetta.core.scoring.etable.count_pair.CPResidueConnectionType attribute) CP_NO_BONDS (pyrosetta.rosetta.core.scoring.etable.count_pair.CPResidueConnectionType attribute) CP_ONE_BOND (pyrosetta.rosetta.core.scoring.etable.count_pair.CPResidueConnectionType attribute) CP_parameters (pyrosetta.rosetta.core.chemical.rings.RingConformer property) CPCrossoverBehavior (class in pyrosetta.rosetta.core.scoring.etable.count_pair) CPDataCorrespondence (class in pyrosetta.rosetta.core.scoring.trie) CPK_COLOR (pyrosetta.rosetta.protocols.viewer.graphics_states_param.ColorMode attribute) CPParameter (class in pyrosetta.rosetta.core.chemical.rings) CPResidueConnectionType (class in pyrosetta.rosetta.core.scoring.etable.count_pair) cprev_n_bond_length_params() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) Cr (pyrosetta.rosetta.core.chemical.element.Elements attribute) crankshaft_alpha_gamma() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) CrankshaftFlipMover (class in pyrosetta.rosetta.protocols.cyclic_peptide) CrankshaftFlipMoverCreator (class in pyrosetta.rosetta.protocols.cyclic_peptide) cranny_packer() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) crash_log() (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.environment.EXCN_Env_Exception method) (pyrosetta.rosetta.core.environment.EXCN_FTSketchGraph method) (pyrosetta.rosetta.core.id.EXCN_AtomNotFound method) (pyrosetta.rosetta.core.kinematics.EXCN_InvalidFoldTree method) (pyrosetta.rosetta.core.pack.task.ResfileReaderException method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.EXCN_CalcFailed method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.EXCN_InitFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_CalcFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_detection_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_undefined_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_grafting_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_invalid_cdr_region_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_json_cdr_detection_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_numbering_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_scs_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_unexpected_region_length_ method) (pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Heat_Converged method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Pool_Converged method) (pyrosetta.rosetta.protocols.constraint_generator.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.denovo_design.architects.EXCN_PreFilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_PoseInconsistent method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_RemarksNotPresent method) (pyrosetta.rosetta.protocols.denovo_design.connection.EXCN_ConnectionSetupFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_NothingToFold method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Passport method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Security_Exception method) (pyrosetta.rosetta.protocols.forge.remodel.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.jd2.archive.EXCN_Archive method) (pyrosetta.rosetta.protocols.jd2.JD2Failure method) (pyrosetta.rosetta.protocols.loophash.EXCN_bbdb_Merge_Failed method) (pyrosetta.rosetta.protocols.loophash.EXCN_DB_IO_Failed method) (pyrosetta.rosetta.protocols.loophash.EXCN_Invalid_Hashmap method) (pyrosetta.rosetta.protocols.loophash.EXCN_No_Extra_Data_To_Write method) (pyrosetta.rosetta.protocols.loophash.EXCN_Wrong_DB_Format method) (pyrosetta.rosetta.protocols.loops.EXCN_Loop_not_closed method) (pyrosetta.rosetta.protocols.moves.EXCN_Converged method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_AssignmentNotFound method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_FileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_NoesyAssign method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownAtomname method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownResonance method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_FailedBroking method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_Input method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_TopologyBroker method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_Unknown method) (pyrosetta.rosetta.utility.excn.BadInput method) (pyrosetta.rosetta.utility.excn.Exception method) (pyrosetta.rosetta.utility.excn.FileNotFound method) (pyrosetta.rosetta.utility.excn.IOError method) (pyrosetta.rosetta.utility.excn.KeyError method) (pyrosetta.rosetta.utility.excn.NullPointerError method) (pyrosetta.rosetta.utility.excn.RangeError method) (pyrosetta.rosetta.utility.excn.RosettaScriptsOptionError method) (pyrosetta.rosetta.utility.excn.UserCorrectableIssue method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) create() (pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.fragment.BBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.DownJumpSRFD method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.SecstructSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.UpJumpSRFD method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibraryCreator method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibraryCreator method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibraryCreator method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibraryCreator method) (pyrosetta.rosetta.core.pack.rotamers.SingleNCAARotamerLibraryCreator method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryCreator method) (pyrosetta.rosetta.core.pack.rotamers.StoredRotamerLibraryCreator method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.cppdb.pool static 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.CompoundPerturber static method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber static method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber static method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber static method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber static 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.build.BuildManager 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.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.DummyClass static method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver 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) (pyrosetta.rosetta.utility.tag.Tag static method) create_acc_orientation_vector() (in module pyrosetta.rosetta.core.scoring.hbonds) create_alignment_id_map_legacy() (in module pyrosetta.rosetta.protocols.stepwise.modeler.align) create_alpha_beta_models_table() (in module pyrosetta.rosetta.protocols.legacy_sewing) create_and_attach_task_factory() (pyrosetta.rosetta.protocols.docking.DockTaskFactory method) create_and_init_hbond_graph() (in module pyrosetta.rosetta.core.pack.hbonds) create_and_initialize_annealing_graph() (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphFactory static method) create_and_initialize_two_body_interaction_graph() (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphFactory static method) create_and_set_initial_job_dag() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobQueen method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen method) (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) create_and_store_atom_tree_minimization_graph() (in module pyrosetta.rosetta.core.scoring) create_annealer() (pyrosetta.rosetta.core.pack.annealer.AnnealerFactory static method) create_architect() (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.MotifArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitectCreator method) create_assembly() (pyrosetta.rosetta.protocols.legacy_sewing.AssemblyFactory static method) create_assembly_scorer() (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorerCreator method) create_atom_id_map() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) create_atom_tree() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) create_attach_nmr_data_to_pose() (pyrosetta.rosetta.core.scoring.nmr.NMRDataFactory method) create_blank_file() (in module pyrosetta.rosetta.utility.file) create_bond_length() (in module pyrosetta.rosetta.core.chemical) create_bump_grid_for_bb() (pyrosetta.rosetta.protocols.match.BumpGrid method) create_cache() (in module pyrosetta.rosetta.protocols.frag_picker.scores) create_calculator_from_file() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters method) create_centroid_move_generator() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication static method) create_centroid_scorefunction() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication static method) create_chemistry() (pyrosetta.rosetta.protocols.chemistries.ChemistryCreator method) (pyrosetta.rosetta.protocols.chemistries.PatchChemistryCreator method) create_chimera_segment() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) create_command_map() (in module pyrosetta.rosetta.core.pack.task) create_comparer() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSDCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerChiDiffCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerElecDensDiffCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerRotBinsCreator method) create_complex_type_generator() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation static method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation static method) create_compound_statement_from_logic() (in module pyrosetta.rosetta.protocols.filters) create_consensus_design_task() (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) create_constraint() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.NamedAtomPairConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.NamedAtomPairConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator method) create_constraint_from_file() (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) create_constraint_from_file_contents() (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) create_constraint_generator() (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.denovo_design.constraints.FileConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGeneratorCreator method) create_constraints() (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) create_context_graph() (pyrosetta.rosetta.core.scoring.ContextGraphFactory static method) create_coordinate_constraint_atom_id_map() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner method) create_coordinate_constraints() (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner method) create_corresponding_mress_for_mres() (pyrosetta.rosetta.core.pack.annealer.SequenceSymmetricAnnealer method) create_count_pair_function() (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFactory static method) create_count_pair_function_and_invoke() (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFactory static method) create_cpdata_correspondence_for_rotamer() (in module pyrosetta.rosetta.core.scoring.trie) create_cpdata_correspondence_for_rotamerset() (in module pyrosetta.rosetta.core.scoring.trie) create_data() (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.JumpSampleDataCreator method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataCreator method) (pyrosetta.rosetta.protocols.environment.AutoCutDataCreator method) create_db() (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) create_dense_pdig_from_rot_to_pack() (pyrosetta.rosetta.protocols.pack_daemon.DenseIGRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.DoubleDenseIGRepacker method) create_destination_stub() (pyrosetta.rosetta.core.kinematics.inverse.AlignmentAtomArray method) create_directed_dependency() (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.components.BDR method) create_directory() (in module pyrosetta.rosetta.utility.file) create_directory_recursive() (in module pyrosetta.rosetta.utility.file) create_dist_constraints() (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) create_dist_constraints_median() (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) create_docking_high_res_mover() (pyrosetta.rosetta.protocols.docking.DockingHighResFactory method) create_don_orientation_vector() (in module pyrosetta.rosetta.core.scoring.hbonds) create_empty_map() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) create_energy_method() (pyrosetta.rosetta.core.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.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN 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.SAXSEnergyFA 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.PDDFEnergy 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) create_entity_resfile_contents() (in module pyrosetta.rosetta.protocols.pack_daemon) create_enzdes_movemap() (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) create_enzdes_pack_task() (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) create_euler_rotation() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) create_ExactSHOEnergy_from_cmdline() (in module pyrosetta.rosetta.core.energy_methods) create_excl_info() (pyrosetta.rosetta.core.scoring.ResidueExclParams method) create_expression_tree() (pyrosetta.rosetta.numeric.expression_parser.BooleanExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.SimpleExpressionCreator method) (pyrosetta.rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator method) (pyrosetta.rosetta.protocols.pack_daemon.EntityFuncExpressionCreator method) (pyrosetta.rosetta.protocols.pack_daemon.VectorExpressionCreator method) create_extra_output() (in module pyrosetta.rosetta.protocols.chemically_conjugated_docking) (in module pyrosetta.rosetta.protocols.floppy_tail) create_fa_and_cen_constraint() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) create_fasta_file() (in module pyrosetta.rosetta.core.sequence) create_faster_ig_from_rot_to_pack() (pyrosetta.rosetta.protocols.pack_daemon.FASTER_IG_Repacker method) create_features_reporter() (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator method) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator method) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RuntimeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TotalScoreFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator method) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator method) create_filter() (pyrosetta.rosetta.protocols.buns.BuriedUnsatHbondFilter2Creator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.ConservedPosMutationFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoidsFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.OperatorFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2Creator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeightFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.SigmoidFilterCreator method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreCutoffFilterCreator method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilterCreator method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilterCreator method) (pyrosetta.rosetta.protocols.constraint_filters.ShowConstraintsFilterCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilterCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilterCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilterCreator method) (pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilterCreator method) (pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilterCreator method) (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilterCreator method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilterCreator method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilterCreator method) (pyrosetta.rosetta.protocols.dna_dock.DNAClashCheckFilterCreator method) (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.LigBurialFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.LigDSasaFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.LigInterfaceEnergyFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.RemoveLigandFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.RepackWithoutLigandFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilterCreator method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCostFilterCreator method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinderFilterCreator method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserterFilterCreator method) (pyrosetta.rosetta.protocols.filters.CalculatorFilterCreator method) (pyrosetta.rosetta.protocols.filters.CombinedFilterCreator method) (pyrosetta.rosetta.protocols.filters.CompoundFilterCreator method) (pyrosetta.rosetta.protocols.filters.ContingentFilterCreator method) (pyrosetta.rosetta.protocols.filters.FalseFilterCreator method) (pyrosetta.rosetta.protocols.filters.FilterCreator method) (pyrosetta.rosetta.protocols.filters.IfThenFilterCreator method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilterCreator method) (pyrosetta.rosetta.protocols.filters.ReplicateFilterCreator method) (pyrosetta.rosetta.protocols.filters.StochasticFilterCreator method) (pyrosetta.rosetta.protocols.filters.TimeFilterCreator method) (pyrosetta.rosetta.protocols.filters.TrueFalseFilterCreator method) (pyrosetta.rosetta.protocols.filters.TrueFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.CoreDunbrackFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.FragQualFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.InterlockingAromaFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.NcontactsFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.ParallelBetaPairingPreferenceFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureCountFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureHasResidueFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevelsCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilterCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ConstraintFulfilmentFilterCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilterCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ScorePoseSegmentFromResidueSelectorFilterCreator method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilterCreator method) (pyrosetta.rosetta.protocols.hbnet.HBNetScoreFilterCreator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterCreator method) (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilterCreator method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilterCreator method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilterCreator method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValuesCreator method) (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilterCreator method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilterCreator method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilterCreator method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilterCreator method) (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorerCreator method) (pyrosetta.rosetta.protocols.pose_sewing.filters.HasDisulfideFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AtomicContactCountFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AverageDegreeFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.ClashWithTargetFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FNatFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.InterfaceHolesFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.IRmsdFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.LRmsdFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdSimpleFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SpecificResiduesNearInterfaceFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SSamountFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreLoopsFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.TorsionCreator method) (pyrosetta.rosetta.protocols.recon_design.FitnessFilterCreator method) (pyrosetta.rosetta.protocols.score_filters.GeometryFilterCreator method) (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilterCreator method) (pyrosetta.rosetta.protocols.score_filters.ScoreTypeFilterCreator method) (pyrosetta.rosetta.protocols.simple_ddg.AlaScanFilterCreator method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilterCreator method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScanCreator method) (pyrosetta.rosetta.protocols.simple_ddg.InterfaceBindingEnergyDensityFilterCreator method) (pyrosetta.rosetta.protocols.simple_ddg.SSElementBisectddGFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.AngleToVectorFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.AveragePathLengthFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreakFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.DisulfideEntropyFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.EnergyPerResidueFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ExpiryFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.FileExistFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.FileRemoveFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.HelixHelixAngleFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.HolesFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHydrophobicResidueContactsFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceSasaFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.InterRepeatContactFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.IntraRepeatContactFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.MembAccesResidueLipophilicityFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.MotifScoreFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.MPSpanAngleFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.NeighborTypeFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.NetChargeFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.NMerPSSMEnergyFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.NMerSVMEnergyFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.NonSequentialNeighborsFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.PackStatFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoseCommentFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.RangeFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ReadPoseExtraScoreFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.RepeatParameterFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ReportFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueBurialFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueChiralityFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDistanceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueIEFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueLipophilicityFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSelectionDistanceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSetChainEnergyFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResiduesInInterfaceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistanceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SidechainRmsdFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SpanTopologyMatchPoseFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SSElementLengthFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SSElementMotifContactFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinderFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.StemFinderFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareSASAFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TerminusDistanceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TMsAACompFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TMsSpanMembraneFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TotalSasaFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.Worst9merFilterCreator method) create_final_fullatom_refinement_move_generator() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication method) create_flexbb_interaction_graph() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbIGFactory static method) create_fragment_set() (in module pyrosetta.rosetta.protocols.hybridization) create_fragment_set_no_ssbias() (in module pyrosetta.rosetta.protocols.hybridization) create_from_cacheable_data() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) create_from_file() (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects static method) create_from_motifs() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) create_from_pose() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) create_from_remarks() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) create_from_string() (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects static method) create_from_tag() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) create_from_xml() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) create_full_to_input_res_map() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) create_fullatom_scorefunction() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication static method) create_func() (in module pyrosetta.rosetta.protocols.constraint_generator) create_glycan_movemap_from_residue_selector() (in module pyrosetta.rosetta.core.pose.carbohydrates) create_grid() (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScoreCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGridCreator method) create_grid_for_bb() (pyrosetta.rosetta.protocols.match.Bool3DGrid method) create_grid_for_sphere() (pyrosetta.rosetta.protocols.match.Bool3DGrid method) create_ignore_list() (in module pyrosetta.rosetta.protocols.tcr) create_info() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) create_init_and_create_edges_for_hbond_graph() (in module pyrosetta.rosetta.core.pack.hbonds) create_initial_job_dag() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobQueen method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) create_inner_cycle() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleFactory method) create_inputter() (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputterCreator method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.PDBChunkLibraryInputterCreator method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputterCreator method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.PDBFullModelInputterCreator method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.SilentFileFullModelInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputterCreator method) create_instance() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) create_interaction_graph() (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphFactory static method) create_intrares_count_pair_function() (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFactory static method) create_job_distributor() (pyrosetta.rosetta.protocols.jd2.JobDistributorFactory static method) (pyrosetta.rosetta.protocols.jd3.JobDistributorFactory static method) create_job_inputter() (pyrosetta.rosetta.protocols.jd2.JobDistributorFactory static method) create_job_outputter() (pyrosetta.rosetta.protocols.jd2.JobDistributorFactory static method) create_JobInputter() (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputterCreator method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.EmptyPoseJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.LazySilentFileJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.ScreeningJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputterCreator method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputterCreator method) create_JobOutputter() (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputterCreator method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.mmtfJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputterCreator method) create_jump_def() (pyrosetta.rosetta.protocols.abinitio.Templates method) create_jump_fragments() (pyrosetta.rosetta.protocols.jumping.BasePairingLibrary method) (pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.PairingLibrary method) (pyrosetta.rosetta.protocols.jumping.SpecificGeometryLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) create_jump_sample() (pyrosetta.rosetta.protocols.abinitio.FixTemplateJumpSetup method) (pyrosetta.rosetta.protocols.abinitio.TemplateJumpSetup method) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) create_jump_selector() (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.ExclusivelySharedJumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.JumpForResidueCreator method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.JumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelectorCreator method) create_loader() (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) create_long_range_energy_container() (in module pyrosetta.rosetta.core.scoring.methods) create_loop_mover() (pyrosetta.rosetta.protocols.loops.LoopMoverFactory method) create_loops() (pyrosetta.rosetta.protocols.denovo_design.components.FoldGraph method) create_loops_definer() (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsStringDefinerCreator method) create_map_for_Blosum62Map() (in module pyrosetta.rosetta.core.sequence) create_match_position_modifier() (in module pyrosetta.rosetta.protocols.match) create_maximum_length_pose() (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) create_mean_field() (pyrosetta.rosetta.protocols.mean_field.MeanFieldFactory static method) create_membrane_docking_foldtree_from_partners() (in module pyrosetta.rosetta.protocols.membrane) create_membrane_foldtree_anchor_com() (in module pyrosetta.rosetta.protocols.membrane) create_membrane_foldtree_anchor_pose_tmcom() (in module pyrosetta.rosetta.protocols.membrane) create_membrane_foldtree_anchor_tmcom() (in module pyrosetta.rosetta.protocols.membrane) create_membrane_foldtree_from_anchors() (in module pyrosetta.rosetta.protocols.membrane) create_membrane_multi_partner_foldtree_anchor_tmcom() (in module pyrosetta.rosetta.protocols.membrane) create_metric() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricCreator method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetricCreator method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.SequenceMetricCreator method) create_mhc_epitope_energy_setup_instance() (pyrosetta.rosetta.core.scoring.ScoringManager static method) create_model_from_pose() (in module pyrosetta.rosetta.protocols.legacy_sewing) create_movemap_from_pose() (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) create_mover() (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMoverCreator method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMoverCreator method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMoverCreator method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCMCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMoverCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparerCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCMCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCMCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCMCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCMCreator method) (pyrosetta.rosetta.protocols.abinitio.DomainAssemblyCreator method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMoverCreator method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMoverCreator method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMoverCreator method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMoverCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafterCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMoverCreator method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMoverCreator method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMoverCreator method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMoverCreator method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMoverCreator method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForClusterCreator method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockCreator method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMoverCreator method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPreProCreator method) (pyrosetta.rosetta.protocols.backrub.BackrubMoverCreator method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocolCreator method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMoverCreator method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMoverCreator method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMoverCreator method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSamplerCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModelerCreator method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogensCreator method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMoverCreator method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMoverCreator method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraintsCreator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraintsCreator method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMoverCreator method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMoverCreator method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMoverCreator method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMoverCreator method) (pyrosetta.rosetta.protocols.contact_map.ContactMapCreator method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocolCreator method) (pyrosetta.rosetta.protocols.cryst.CrystRMSCreator method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMoverCreator method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMoverCreator method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMoverCreator method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMoverCreator method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMoverCreator method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMoverCreator method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMoverCreator method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMoverCreator method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMoverCreator method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMoverCreator method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfoCreator method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMoverCreator method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomainCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraintCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraintCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraintCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlignCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutationsCreator method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesignCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMoverCreator method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMoverCreator method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNACreator method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMoverCreator method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesignCreator method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePackerCreator method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDnaCreator method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMoverCreator method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacyCreator method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbationCreator method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocolCreator method) (pyrosetta.rosetta.protocols.docking.DockingProtocolCreator method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContactCreator method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocolCreator method) (pyrosetta.rosetta.protocols.docking.DockMinMoverCreator method) (pyrosetta.rosetta.protocols.docking.DockSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.docking.TemperedDockingCreator method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMoverCreator method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMoverCreator method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMoverCreator method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMoverCreator method) (pyrosetta.rosetta.protocols.electron_density.DensityZscoresCreator method) (pyrosetta.rosetta.protocols.electron_density.ReportFSCCreator method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensitiesCreator method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMoverCreator method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMoverCreator method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCMCreator method) (pyrosetta.rosetta.protocols.environment.EnvMoverCreator method) (pyrosetta.rosetta.protocols.environment.ScriptCMCreator method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCstsCreator method) (pyrosetta.rosetta.protocols.enzdes.BackboneSamplerCreator method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimizeCreator method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedyCreator method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMoverCreator method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMoverCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMoverCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMoverCreator method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutationCreator method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMoverCreator method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMoverCreator method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMoverCreator method) (pyrosetta.rosetta.protocols.features.ReportToDBCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDBCreator method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDRCreator method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutationCreator method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMoverCreator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotentialCreator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergiesCreator method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocolCreator method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignCreator method) (pyrosetta.rosetta.protocols.flxbb.InterlockAromaCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMoverCreator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersCstGeneratorCreator method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeCstGeneratorCreator method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCstsCreator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMoverCreator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityCstGeneratorCreator method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKICCreator method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocolCreator method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocolCreator method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMoverCreator method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMoverCreator method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMoverCreator method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMoverCreator method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMoverCreator method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMoverCreator method) (pyrosetta.rosetta.protocols.hbnet.HBNetCreator method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterfaceCreator method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerCreator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerCreator method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixCreator method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleCreator method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelixCreator method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleCreator method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelixCreator method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbeCreator method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbationCreator method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSamplerCreator method) (pyrosetta.rosetta.protocols.hybridization.CartesianSamplerCreator method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocolCreator method) (pyrosetta.rosetta.protocols.idealize.IdealizeMoverCreator method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMoverCreator method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMoverCreator method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMoverCreator method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragmentsCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogensCreator method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslateCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDFCreator method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizerCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDockCreator method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigandCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDockerCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsembleCreator method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculatorCreator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesignCreator method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackboneCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsembleCreator method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformersCreator method) (pyrosetta.rosetta.protocols.ligand_docking.RotateCreator method) (pyrosetta.rosetta.protocols.ligand_docking.RotatesCreator method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogetherCreator method) (pyrosetta.rosetta.protocols.ligand_docking.StartFromCreator method) (pyrosetta.rosetta.protocols.ligand_docking.TransformCreator method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsembleCreator method) (pyrosetta.rosetta.protocols.ligand_docking.TranslateCreator method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFileCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapperCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtensionCreator method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModelerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilderCreator method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocolCreator method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefinerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefinerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefinerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSamplerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroidCreator method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatomCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifierCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapperCreator method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoopsCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCMCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.match.MatcherMoverCreator method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMoverCreator method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMoverCreator method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMoverCreator method) (pyrosetta.rosetta.protocols.matdes.SymDofMoverCreator method) (pyrosetta.rosetta.protocols.md.CartesianMDCreator method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraintCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraintCreator method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinderCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelixCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAnglesCreator method) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequenceCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibilityCreator method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSamplerCreator method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMoverCreator method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.MinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazyCreator method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMoverCreator method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMoverCreator method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealerCreator method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecoverCreator method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloResetCreator method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTestCreator method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMoverCreator method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftCreator method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPackerCreator method) (pyrosetta.rosetta.protocols.moves.DsspMoverCreator method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMoverCreator method) (pyrosetta.rosetta.protocols.moves.IfMoverCreator method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMoverCreator method) (pyrosetta.rosetta.protocols.moves.MoverCreator method) (pyrosetta.rosetta.protocols.moves.PyMOLMoverCreator method) (pyrosetta.rosetta.protocols.moves.RampingMoverCreator method) (pyrosetta.rosetta.protocols.moves.RandomMoverCreator method) (pyrosetta.rosetta.protocols.moves.SequenceMoverCreator method) (pyrosetta.rosetta.protocols.moves.SwitchMoverCreator method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocolCreator method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMoverCreator method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocolCreator method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMoverCreator method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinderCreator method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMoverCreator method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMoverCreator method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMoverCreator method) (pyrosetta.rosetta.protocols.nmr.pre.PREMoverCreator method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizerCreator method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMoverCreator method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotentialCreator method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequencesCreator method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMoverCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModelingCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMoverCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMoverCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMoverCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloserCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreakCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspotsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPoseCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbondsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechainsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycleCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycleCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinderCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChangeCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLineCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodelCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspotCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransformCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoopCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutationCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimizeCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechainsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTreeCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactorCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCstsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TryRotamersCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBCreator method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMoverCreator method) (pyrosetta.rosetta.protocols.qsar.qsarCreator method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemageCreator method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoaderCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMoverCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMoverCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMoverCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMoverCreator method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizerCreator method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMoverCreator method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequenceCreator method) (pyrosetta.rosetta.protocols.recon_design.MSDMoverCreator method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMoverCreator method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMoverCreator method) (pyrosetta.rosetta.protocols.relax.ClassicRelaxCreator method) (pyrosetta.rosetta.protocols.relax.FastRelaxCreator method) (pyrosetta.rosetta.protocols.relax.LocalRelaxCreator method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMoverCreator method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelaxCreator method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMoverCreator method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMoverCreator method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMoverCreator method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMoverCreator method) (pyrosetta.rosetta.protocols.rigid.RollMoverCreator method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCMCreator method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMoverCreator method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMoverCreator method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocolCreator method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2ProtocolCreator method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMoverCreator method) (pyrosetta.rosetta.protocols.rna.movers.RNA_CoarsifyCreator method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DecoarsifyCreator method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMoverCreator method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMoverCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapperCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapperCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMoverCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocolCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMoverCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMoverCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGeneratorCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFoldCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCstCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoopsCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptidesCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTreeCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMoverCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizerCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegmentCreator method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMoverCreator method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMoverCreator method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.simple_ddg.ddGCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairDataCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBinsCreator method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBinsCreator method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBondCreator method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdbCreator method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamersCreator method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfileCreator method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequenceCreator method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotifCreator method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopologyCreator method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidueCreator method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKACreator method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZCreator method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTreeCreator method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilitiesCreator method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsionCreator method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ShearMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SmallMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshotCreator method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.TumbleCreator method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPoseCreator method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMoverCreator method) (pyrosetta.rosetta.protocols.splice.AlignEndsMoverCreator method) (pyrosetta.rosetta.protocols.splice.RBInMoverCreator method) (pyrosetta.rosetta.protocols.splice.RBOutMoverCreator method) (pyrosetta.rosetta.protocols.splice.RotLibOutCreator method) (pyrosetta.rosetta.protocols.splice.SpliceCreator method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibodyCreator method) (pyrosetta.rosetta.protocols.splice.SpliceInCreator method) (pyrosetta.rosetta.protocols.splice.SpliceInTailCreator method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibodyCreator method) (pyrosetta.rosetta.protocols.splice.SpliceOutCreator method) (pyrosetta.rosetta.protocols.splice.SpliceOutTailCreator method) (pyrosetta.rosetta.protocols.splice.TailSegmentMoverCreator method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMoverCreator method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMoverCreator method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.FromScratchMoverCreator method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMoverCreator method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocolCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetryMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMoverCreator method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMoverCreator method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMoverCreator method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMoverCreator method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMoverCreator method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMoverCreator method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMoverCreator method) create_new_bump_grid_for_bb() (pyrosetta.rosetta.protocols.match.BumpGrid method) create_new_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.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) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) create_new_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) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) create_new_parameters_set() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) create_new_submotif() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.submotif.SubMotifLibrary method) create_operation() (pyrosetta.rosetta.core.chemical.PatchOperationCreator method) create_oriented_water_rotamer() (in module pyrosetta.rosetta.core.pack.rotamer_set) create_orthogonal() (pyrosetta.rosetta.core.kinematics.Stub static method) create_output_specification() (pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter method) create_output_upstream_pose() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) create_outputter() (pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputterCreator method) create_packer_data() (pyrosetta.rosetta.protocols.multistate_design.PackingState method) create_packer_graph() (in module pyrosetta.rosetta.core.pack) create_packer_palette() (pyrosetta.rosetta.core.pack.palette.CustomBaseTypePackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.DefaultPackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.NCAADefaultPackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.NoDesignPackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.PackerPaletteCreator method) create_packer_palette_from_global_defaults() (pyrosetta.rosetta.core.pack.palette.PackerPaletteFactory method) create_packer_task() (pyrosetta.rosetta.core.pack.task.TaskFactory static method) create_parser() (pyrosetta.rosetta.protocols.jd2.JobDistributorFactory static method) create_pdb_contents_from_sfr() (in module pyrosetta.rosetta.core.io.pdb) create_pddf() (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) create_position_data() (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataFactory static method) create_potential_loops() (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) create_prepared_statement() (pyrosetta.rosetta.cppdb.session method) (pyrosetta.rosetta.utility.sql_database.session method) create_prepared_uncached_statement() (pyrosetta.rosetta.cppdb.session method) (pyrosetta.rosetta.utility.sql_database.session method) create_processor() (pyrosetta.rosetta.protocols.match.output.ProcessorFactory static method) create_protocol() (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolMinPackCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolMoverCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolPackRotamersCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolReferenceStructureCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRelaxCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRotamerTrialsCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRTMinCreator method) create_ptask() (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) create_rdf_function() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator method) create_records_from_pdb_file_contents() (in module pyrosetta.rosetta.core.io.pdb) create_records_from_pdb_lines() (in module pyrosetta.rosetta.core.io.pdb) create_records_from_sfr() (in module pyrosetta.rosetta.core.io.pdb) create_remark_headers_from_cstcache() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) create_reporter() (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporterCreator method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporterCreator method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporterCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHumanCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSimpleCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSQLiteCreator method) create_requirement() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalLengthRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyIntraSegmentRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyResidueRetentionRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentDsspRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentLengthRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.AssemblyRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.ClashRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.DsspSpecificLengthRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.KeepLigandContactsRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.LengthInResiduesRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandClashRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.NonTerminalStartingSegmentRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.SizeInSegmentsRequirementCreator method) create_res_filter() (pyrosetta.rosetta.core.pack.task.operation.AllResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.AnyResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ChainIsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ChainIsntCreator method) (pyrosetta.rosetta.core.pack.task.operation.NoResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasPropertyCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsntCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueLacksPropertyCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3IsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3IsntCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsntCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoHasLabelCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoLacksLabelCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueTypeFilterCreator method) (pyrosetta.rosetta.protocols.task_operations.ProteinCoreFilterCreator method) create_res_level_task_operation() (pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASExceptNativeRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepackingRLTCreator method) create_residue() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.ResidueFactory static method) create_residue_names_maps() (pyrosetta.rosetta.protocols.chromophore.ChromophoreDataReader method) create_residue_selector() (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.BFactorSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.BinSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.BlockSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ChainSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ConfluentSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.FractionSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelectorCreator method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelectorCreator method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelectorCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelectorCreator method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelectorCreator method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelectorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ConstraintResidueSelectorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.CutpointResidueSelectorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ProteinResidueSelectorCreator method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.HBondSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.NativeSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelectorCreator method) create_resource_loader() (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.core.conformation.symmetry.SymmDataLoaderCreator method) (pyrosetta.rosetta.core.fragment.FragmentSetLoaderCreator method) (pyrosetta.rosetta.core.import_pose.PoseResourceLoaderCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoaderCreator method) create_resource_locator() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) create_resource_manager_from_options_system() (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory method) create_rna_vall_torsions() (in module pyrosetta.rosetta.protocols.rna.denovo) create_rotamer() (pyrosetta.rosetta.core.conformation.Residue method) create_rotamer_set() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetFactory static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot method) create_rotamer_sets() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetsFactory static method) create_rotamer_string() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) create_rotamer_subsets_from_rot_to_pack() (pyrosetta.rosetta.protocols.pack_daemon.DenseIGRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.DoubleDenseIGRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.FASTER_IG_Repacker method) (pyrosetta.rosetta.protocols.pack_daemon.RotamerSubsetRepacker method) create_rotamer_trie() (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) create_sample_vector() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) create_sasa_method() (in module pyrosetta.rosetta.core.scoring.sasa) create_score_function() (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory static method) create_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) create_scorefxn_from_tag() (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader static method) create_scores() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) create_scoring_method() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) create_SecMatchResiduePairEvaluatorOP() (pyrosetta.rosetta.protocols.match.downstream.SecMatchEvaluatorFactory static method) create_segment_file() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector method) create_selector() (pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelectorCreator method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelectorCreator method) (pyrosetta.rosetta.protocols.pose_selectors.FilterCreator method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelectorCreator method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByPropertyCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator method) create_sequence() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequenceCreator method) (pyrosetta.rosetta.core.sequence.CompositeSequenceCreator method) (pyrosetta.rosetta.core.sequence.SequenceCouplingCreator method) (pyrosetta.rosetta.core.sequence.SequenceCreator method) (pyrosetta.rosetta.core.sequence.SequenceProfileCreator method) (pyrosetta.rosetta.core.sequence.SimpleSequenceCreator method) create_sequence_profile_constraints() (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) create_sequons() (in module pyrosetta.rosetta.protocols.carbohydrates) create_sfr_from_cif_file_op() (in module pyrosetta.rosetta.core.io.mmcif) create_sfr_from_mmtf_filename() (in module pyrosetta.rosetta.core.io.mmtf) create_sfr_from_pdb_file_contents() (in module pyrosetta.rosetta.core.io.pdb) create_sfr_from_pdb_records() (in module pyrosetta.rosetta.core.io.pdb) create_shuffle_map_recursive_rms() (in module pyrosetta.rosetta.core.scoring) create_silent_struct() (pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.SilentStructCreator method) create_SilentStructOP() (pyrosetta.rosetta.core.io.silent.SilentFileData method) create_simple_metric() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetricCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetricCreator method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetricCreator method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetricCreator method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetricCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetricCreator method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricCreator method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetricCreator method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetricCreator method) (pyrosetta.rosetta.protocols.filters.FilterValueMetricCreator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetricCreator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetricCreator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetricCreator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetricCreator method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetricCreator method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetricCreator method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetricCreator method) create_sliced_pose() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.SlicedPoseWorkingParameters method) create_source_pose_for_segment() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.PoseWithTerminalSegmentsOfKnownDSSP method) create_specific_membrane_foldtree() (in module pyrosetta.rosetta.protocols.membrane) create_ss_defaults() (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) create_standard_o2prime_pack_task() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) create_statement() (pyrosetta.rosetta.cppdb.backend.connection method) (pyrosetta.rosetta.cppdb.session method) (pyrosetta.rosetta.utility.sql_database.session method) create_stub_from_atom_ids() (pyrosetta.rosetta.core.kinematics.inverse.AlignmentAtomArray method) create_sub_to_full_map() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) create_subpose() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) create_surface_params() (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader static method) create_tag() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) create_tag_from_xml() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) create_tag_from_xml_string() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) create_task_and_apply_taskoperations() (pyrosetta.rosetta.core.pack.task.TaskFactory method) create_task_for_allhotspot_packing() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) create_task_for_hotspot_packing() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) create_task_operation() (pyrosetta.rosetta.core.pack.task.operation.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.EnableMultiCoolAnnealerCreator method) (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealerCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericCreator method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentCreator 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.PreventRepackingCreator 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.RestrictAbsentCanonicalAASCreator 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.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) create_temp_filename() (in module pyrosetta.rosetta.utility.file) create_torsion_value_string() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) create_VDW_screen_bin() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker method) create_vrt_if_necessary() (pyrosetta.rosetta.protocols.environment.claims.JumpClaim method) create_working_data() (in module pyrosetta.rosetta.core.io.pose_from_sfr) create_xyz_constraints_median() (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) CreateAngleConstraint (class in pyrosetta.rosetta.protocols.cyclic_peptide) CreateAngleConstraintCreator (class in pyrosetta.rosetta.protocols.cyclic_peptide) createConstraints() (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) CreateDistanceConstraint (class in pyrosetta.rosetta.protocols.cyclic_peptide) CreateDistanceConstraintCreator (class in pyrosetta.rosetta.protocols.cyclic_peptide) CreateGlycanSequonMover (class in pyrosetta.rosetta.protocols.carbohydrates) CreateGlycanSequonMoverCreator (class in pyrosetta.rosetta.protocols.carbohydrates) createPartialBond() (pyrosetta.rosetta.RDKit.RWMol method) creates_undefined_backbone() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) CreateSequenceMotifMover (class in pyrosetta.rosetta.protocols.calc_taskop_movers) CreateSequenceMotifMoverCreator (class in pyrosetta.rosetta.protocols.calc_taskop_movers) CreateTorsionConstraint (class in pyrosetta.rosetta.protocols.cyclic_peptide) CreateTorsionConstraintCreator (class in pyrosetta.rosetta.protocols.cyclic_peptide) creator_map() (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationFactory method) (pyrosetta.rosetta.core.select.jump_selector.JumpSelectorFactory method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorFactory method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricFactory method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricFactory method) crick_params_filename() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix method) criteria_match_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) criteria_match_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) CriticalFailure (pyrosetta.rosetta.protocols.loops.loop_mover.LoopResult attribute) cross() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.numeric.kinematic_closure) (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) cross_angle() (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilter method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing method) cross_chain_bonus() (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.HBondBonusOptions method) cross_chain_bonus_ (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.HBondBonusOptions property) cross_over() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif method) cross_product() (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) cross_product_helper() (pyrosetta.rosetta.core.chemical.orbitals.AssignOrbitals method) crossing_angle (pyrosetta.rosetta.protocols.features.helixAssembly.FragmentPair property) CrossLinker (class in pyrosetta.rosetta.protocols.cyclic_peptide) CrosslinkerMover (class in pyrosetta.rosetta.protocols.cyclic_peptide) CrosslinkerMoverCreator (class in pyrosetta.rosetta.protocols.cyclic_peptide) CrosslinkerMoverHelper (class in pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) (pyrosetta.rosetta.basic.citation_manager.CitedModuleType attribute) crossover() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) (pyrosetta.rosetta.core.scoring.etable.etrie.TrieCountPairGeneric method) (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) CrossPeak (class in pyrosetta.rosetta.protocols.noesy_assign) crosspeak() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) CrossPeak.EliminationReason (class in pyrosetta.rosetta.protocols.noesy_assign) CrossPeak.QualityClass (class in pyrosetta.rosetta.protocols.noesy_assign) CrossPeak.Spin (class in pyrosetta.rosetta.protocols.noesy_assign) CrossPeak3D (class in pyrosetta.rosetta.protocols.noesy_assign) CrossPeak3D.EliminationReason (class in pyrosetta.rosetta.protocols.noesy_assign) CrossPeak3D.QualityClass (class in pyrosetta.rosetta.protocols.noesy_assign) CrossPeak3D.Spin (class in pyrosetta.rosetta.protocols.noesy_assign) CrossPeak4D (class in pyrosetta.rosetta.protocols.noesy_assign) CrossPeak4D.EliminationReason (class in pyrosetta.rosetta.protocols.noesy_assign) CrossPeak4D.QualityClass (class in pyrosetta.rosetta.protocols.noesy_assign) CrossPeak4D.Spin (class in pyrosetta.rosetta.protocols.noesy_assign) CrossPeakInfo (class in pyrosetta.rosetta.protocols.noesy_assign) CrossPeakList (class in pyrosetta.rosetta.protocols.noesy_assign) crosspeaks() (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) crossProduct() (pyrosetta.rosetta.RDGeom.Point3D method) crossterm_interface_energy (pyrosetta.rosetta.protocols.analysis.InterfaceData property) crossterm_interface_energy_dSASA_ratio (pyrosetta.rosetta.protocols.analysis.InterfaceData property) CROTONYLATION (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes attribute) CRYO_ELECTRON_MICROSCOPY (pyrosetta.rosetta.core.io.rcsb.ExperimentalTechnique attribute) CRYST1 (pyrosetta.rosetta.core.io.pdb.RecordType attribute) CrystalContactsOperation (class in pyrosetta.rosetta.protocols.task_operations) CrystalContactsOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) CrystInfo (class in pyrosetta.rosetta.core.io) crystinfo() (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.pose.PDBInfo method) CrystRMS (class in pyrosetta.rosetta.protocols.cryst) crystRMS() (in module pyrosetta.rosetta.protocols.cryst) CrystRMSCreator (class in pyrosetta.rosetta.protocols.cryst) crystRMSfast() (in module pyrosetta.rosetta.protocols.cryst) Cs (pyrosetta.rosetta.core.chemical.element.Elements attribute) CS2ndShift (class in pyrosetta.rosetta.protocols.frag_picker) cs_resnum (pyrosetta.rosetta.core.enzymes.EnzymeData property) cs_type (pyrosetta.rosetta.core.enzymes.EnzymeData property) CSA (class in pyrosetta.rosetta.core.scoring) csa (pyrosetta.rosetta.core.scoring.ScoreType attribute) CSAcomputed() (pyrosetta.rosetta.core.scoring.CSA method) CSAerr() (pyrosetta.rosetta.core.scoring.CSA method) CSAval() (pyrosetta.rosetta.core.scoring.CSA method) CSAval_computed_ (pyrosetta.rosetta.core.scoring.CSA property) csca (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) CSI_bgBlack() (in module pyrosetta.rosetta.utility) CSI_bgBlue() (in module pyrosetta.rosetta.utility) CSI_bgCyan() (in module pyrosetta.rosetta.utility) CSI_bgDefault() (in module pyrosetta.rosetta.utility) CSI_bgGreen() (in module pyrosetta.rosetta.utility) CSI_bgMagenta() (in module pyrosetta.rosetta.utility) CSI_bgRed() (in module pyrosetta.rosetta.utility) CSI_bgWhite() (in module pyrosetta.rosetta.utility) CSI_bgYellow() (in module pyrosetta.rosetta.utility) CSI_Black() (in module pyrosetta.rosetta.utility) CSI_Blue() (in module pyrosetta.rosetta.utility) CSI_Bold() (in module pyrosetta.rosetta.utility) CSI_Cyan() (in module pyrosetta.rosetta.utility) CSI_Default() (in module pyrosetta.rosetta.utility) CSI_Enum (class in pyrosetta.rosetta.utility.CSI) CSI_Green() (in module pyrosetta.rosetta.utility) CSI_Magenta() (in module pyrosetta.rosetta.utility) CSI_Nothing() (in module pyrosetta.rosetta.utility) CSI_Red() (in module pyrosetta.rosetta.utility) CSI_Reset() (in module pyrosetta.rosetta.utility) CSI_Sequence (class in pyrosetta.rosetta.utility) CSI_Underline() (in module pyrosetta.rosetta.utility) CSI_White() (in module pyrosetta.rosetta.utility) CSI_Yellow() (in module pyrosetta.rosetta.utility) CSP_fraction() (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) CSScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) CSSettings (class in pyrosetta.rosetta.protocols.pose_sewing.filters) cst (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfo property) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfo property) cst_block() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) cst_cache() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver method) cst_file() (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) cst_file_written (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) cst_files_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) cst_gap() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) cst_gen_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader static method) cst_interactions() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo method) cst_io() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.OutputWriter method) (pyrosetta.rosetta.protocols.match.output.PDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter method) cst_max_seq_sep() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) cst_minimize() (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) cst_on_pose_dynamic() (pyrosetta.rosetta.protocols.md.CartesianMD method) cst_on_pose_simple() (pyrosetta.rosetta.protocols.md.CartesianMD method) cst_res_data (pyrosetta.rosetta.core.scoring.min_single_data attribute) cst_residue_in_pose() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) cst_respair_data (pyrosetta.rosetta.core.scoring.min_pair_data attribute) cst_sd() (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) cst_sdev() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) cst_set() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) cst_sidechain() (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) cst_strength_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) cst_string() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) cst_type() (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) cst_weight() (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) cst_width() (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) cst_wtd_ (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy property) CstAction (class in pyrosetta.rosetta.protocols.enzdes) CSTalosIO (class in pyrosetta.rosetta.protocols.frag_picker) cstAtoms() (pyrosetta.rosetta.protocols.jumping.ResiduePairJump method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) cstAtoms_defined() (pyrosetta.rosetta.protocols.jumping.ResiduePairJump method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) CstEnergyContainer (class in pyrosetta.rosetta.core.scoring.constraints) cstfile() (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) cstfile_name() (pyrosetta.rosetta.protocols.match.MatcherTask method) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) cstInfoMap_defined() (pyrosetta.rosetta.protocols.jumping.ResiduePairJump method) CstInfoMover (class in pyrosetta.rosetta.protocols.constraint_movers) CstInfoMoverCreator (class in pyrosetta.rosetta.protocols.constraint_movers) cstJump (pyrosetta.rosetta.protocols.jumping.dofType attribute) CstMinimizationData (class in pyrosetta.rosetta.core.scoring.constraints) CstResInteractions (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) CstResNeighbConstIterator (class in pyrosetta.rosetta.core.scoring.constraints) CstResNeighbIterator (class in pyrosetta.rosetta.core.scoring.constraints) Cstring (class in pyrosetta.rosetta.ObjexxFCL) cstType (class in pyrosetta.rosetta.protocols.jumping) cstw (pyrosetta.rosetta.protocols.mpi_refinement.MethodParams property) ct_group (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList.ElementSummary attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList.ElementSummary.ElementType attribute) ct_name (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList.ElementSummary property) ct_ref (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList.ElementSummary attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList.ElementSummary.ElementType attribute) ct_simple (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList.ElementSummary attribute) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList.ElementSummary.ElementType attribute) CtabParserBase (class in pyrosetta.rosetta.core.chemical.sdf) CtabV2000Parser (class in pyrosetta.rosetta.core.chemical.sdf) CtabV3000Parser (class in pyrosetta.rosetta.core.chemical.sdf) CTERM_AMIDATION (pyrosetta.rosetta.core.chemical.VariantType attribute) CTERM_CONNECT (pyrosetta.rosetta.core.chemical.VariantType attribute) cterm_included() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) Cterm_offset() (pyrosetta.rosetta.protocols.splice.FindEndpointsOperation method) CTGenSubelementBehavior (class in pyrosetta.rosetta.utility.tag) ctrl_strength() (pyrosetta.rosetta.protocols.environment.claims.TorsionClaim method) (pyrosetta.rosetta.protocols.environment.claims.XYZClaim method) Cu (pyrosetta.rosetta.core.chemical.element.Elements attribute) CU2_COORDINATION (pyrosetta.rosetta.core.chemical.VariantType attribute) cube() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.ObjexxFCL) cubes (pyrosetta.rosetta.core.scoring.packstat.Octree2D property) CUBIC (pyrosetta.rosetta.protocols.cryst.SpacegroupSetting attribute) cubic_interpolation() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) cubic_polynomial_deriv() (in module pyrosetta.rosetta.numeric) cubic_polynomial_from_spline() (in module pyrosetta.rosetta.numeric) cubic_roots1() (in module pyrosetta.rosetta.protocols.cluster.calibur) cubic_roots2() (in module pyrosetta.rosetta.protocols.cluster.calibur) CubicPolynomial (class in pyrosetta.rosetta.numeric) CubicSpline (class in pyrosetta.rosetta.numeric.interpolation.spline) cull_mutatable_residues() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) cull_violators() (in module pyrosetta.rosetta.core.scoring.constraints) (pyrosetta.rosetta.protocols.abinitio.Template method) cummulative_time() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) cumulate_jobs() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) cumulate_probability() (pyrosetta.rosetta.protocols.hybridization.FragmentBiasAssigner method) cumulate_replicas() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) cumulative_peak_volume() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) cur_energy() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) curr_aa() (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) curr_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) curr_exemplar (pyrosetta.rosetta.protocols.cluster.DataPoint property) curr_gen_entity() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) curr_id() (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) curr_num_in_recent_history() (pyrosetta.rosetta.utility.recent_history_queue method) curr_rot() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) curr_sc_centroid() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) curr_sc_radius() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) curr_state_energy() (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) curr_state_one_body_energy() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) curr_state_total_energy() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) curr_state_two_body_energies() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) current_acceptance_ratio() (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) current_batch() (in module pyrosetta.rosetta.protocols.jd2) current_batch_id() (in module pyrosetta.rosetta.protocols.jd2) (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) current_closed_as_target() (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) current_cycle_number() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) current_dna_design_string() (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) current_end (pyrosetta.rosetta.protocols.antibody_legacy.Antibody property) current_generation() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) current_generation_complete() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) current_idx_ (pyrosetta.rosetta.protocols.pdbinfo_manipulations.SequenceSpecification property) current_input_tag() (in module pyrosetta.rosetta.protocols.jd2) current_job() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob static method) (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) current_job_finished() (pyrosetta.rosetta.protocols.jd2.BOINCJobDistributor method) (pyrosetta.rosetta.protocols.jd2.FileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.ShuffleFileSystemJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor method) current_job_id() (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) current_job_index() (pyrosetta.rosetta.protocols.jd3.JobTracker method) current_kinematics() (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) current_links() (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_chemical_RestypeDestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_ConnectionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_IdentityEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_LengthEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_XYZEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_ConformationEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_DestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_EnergyEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.PausableSignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_chemical_RestypeDestructionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_ConnectionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_IdentityEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_LengthEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_XYZEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_ConformationEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_DestructionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_EnergyEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_GeneralEvent_t method) current_nstruct_index() (in module pyrosetta.rosetta.protocols.jd2) current_one_body_energy() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) current_output_filename() (in module pyrosetta.rosetta.protocols.jd2) current_output_name() (in module pyrosetta.rosetta.protocols.jd2) (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) current_pose() (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) 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) 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) 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) 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) current_replica() (in module pyrosetta.rosetta.protocols.jd2) current_rotamer() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) current_rotamer_coords() (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet method) 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) current_score (pyrosetta.rosetta.protocols.stepwise.modeler.rna.output_data_struct property) current_score() (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomeHelper method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintHelper method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) current_scorefxn() (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) current_size() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) current_start (pyrosetta.rosetta.protocols.antibody_legacy.Antibody property) current_state() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) current_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) current_trial() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) current_working_sequence() (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) CurrentProbabilityMetric (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) CurrentProbabilityMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) custom_angle() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) custom_atom_pair (pyrosetta.rosetta.core.scoring.ScoreType attribute) custom_rama_table() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) custom_type_name() (pyrosetta.rosetta.utility.tag.XMLSchemaType method) custom_types() (pyrosetta.rosetta.core.chemical.Patch method) custom_variant_types() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) CustomAtomPairEnergy (class in pyrosetta.rosetta.core.energy_methods) CustomAtomPairEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) CustomBaseTypePackerPalette (class in pyrosetta.rosetta.core.pack.palette) CustomBaseTypePackerPaletteCreator (class in pyrosetta.rosetta.core.pack.palette) CustomRealValueMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) CustomRealValueMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.metrics) CustomScoreSelector (class in pyrosetta.rosetta.protocols.frag_picker) CustomStringValueMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) CustomStringValueMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.metrics) CustomType (pyrosetta.rosetta.basic.citation_manager.CitedModuleType attribute) cut (pyrosetta.rosetta.protocols.loops.SerializedLoop property) cut() (pyrosetta.rosetta.protocols.environment.claims.JumpClaim method) (pyrosetta.rosetta.protocols.loops.Loop method) cut_bond() (pyrosetta.rosetta.core.chemical.Bond method) cut_bond_neighbor() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) cut_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) cut_point (pyrosetta.rosetta.protocols.loops.ResidueIdentifier attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Jump_point property) cut_reg_ (pyrosetta.rosetta.protocols.jumping.JumpSetup.JumpDef property) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup.JumpDef property) cut_residue() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) cut_secondarystruc() (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) cut_site() (pyrosetta.rosetta.protocols.splice.ResidueBBDofs method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) CutAndJump (class in pyrosetta.rosetta.protocols.denovo_design.movers) CutBiasClaim (class in pyrosetta.rosetta.protocols.environment.claims) CutBiasClaimer (class in pyrosetta.rosetta.protocols.topology_broker) CutBiasElement (class in pyrosetta.rosetta.protocols.environment.claims) CutChainMover (class in pyrosetta.rosetta.protocols.simple_moves) CutChainMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) CutClaim (class in pyrosetta.rosetta.protocols.topology_broker.claims) CutClaim.ClaimRight (class in pyrosetta.rosetta.protocols.topology_broker.claims) CutElement (class in pyrosetta.rosetta.protocols.environment.claims) cutoff (pyrosetta.rosetta.numeric.interpolation.spline.LinearFunction property) cutoff() (pyrosetta.rosetta.core.scoring.CenHBPotential method) (pyrosetta.rosetta.core.scoring.epr_deer.EPRSpinLabel 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.PDDFScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.SAXSScoreFilter method) (pyrosetta.rosetta.protocols.simple_moves.FragmentCost method) (pyrosetta.rosetta.protocols.simple_moves.GunnCost method) cutoff_ (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator property) (pyrosetta.rosetta.protocols.ligand_docking.LigandArea property) cutoff_buried_surface_area() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) cutoff_distance() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) cutoff_lower() (pyrosetta.rosetta.core.scoring.func.FadeFunc method) cutoff_upper() (pyrosetta.rosetta.core.scoring.func.FadeFunc method) CutOutDomain (class in pyrosetta.rosetta.protocols.cutoutdomain) CutOutDomainCreator (class in pyrosetta.rosetta.protocols.cutoutdomain) cutpoint (pyrosetta.rosetta.protocols.denovo_design.movers.CutAndJump property) cutpoint() (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) cutpoint_by_jump() (pyrosetta.rosetta.core.kinematics.FoldTree method) cutpoint_closed_list() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) CUTPOINT_LOWER (pyrosetta.rosetta.core.chemical.VariantType attribute) cutpoint_map() (pyrosetta.rosetta.core.kinematics.FoldTree method) CUTPOINT_OPEN (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) cutpoint_open_in_full_model() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) cutpoint_open_list() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) cutpoint_probabilities() (in module pyrosetta.rosetta.protocols.medal) cutpoint_res() (pyrosetta.rosetta.protocols.loops.LoopFromFileData method) cutpoint_segment() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) cutpoint_separation() (in module pyrosetta.rosetta.protocols.antibody) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) CUTPOINT_UPPER (pyrosetta.rosetta.core.chemical.VariantType attribute) CutpointResidueSelector (class in pyrosetta.rosetta.protocols.fold_from_loops.selectors) CutpointResidueSelectorCreator (class in pyrosetta.rosetta.protocols.fold_from_loops.selectors) cutpoints() (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.star.Extender method) cutpoints_closed() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) cutpoints_cyclize() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) cutpoints_open() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) cutpoints_separation() (in module pyrosetta.rosetta.protocols.antibody) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) cutpos_list() (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) cuts() (pyrosetta.rosetta.protocols.environment.AutoCutData method) (pyrosetta.rosetta.protocols.jumping.JumpSample method) cw_angle (pyrosetta.rosetta.core.scoring.packstat.Event property) cwd() (in module pyrosetta.rosetta.utility.file) Cyan (pyrosetta.rosetta.utility.CSI.CSI_Enum attribute) cyc_comment (pyrosetta.rosetta.protocols.peptide_deriver.CyclizedPeptideInfo property) cyc_isc (pyrosetta.rosetta.protocols.peptide_deriver.CyclizedPeptideInfo property) cyc_pose (pyrosetta.rosetta.protocols.peptide_deriver.CyclizedPeptideInfo property) cycle() (pyrosetta.rosetta.core.environment.FoldTreeSketch method) CycleMover (class in pyrosetta.rosetta.protocols.moves) cycles (pyrosetta.rosetta.protocols.ligand_docking.Rotate_info property) (pyrosetta.rosetta.protocols.ligand_docking.Transform_info property) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble_info property) (pyrosetta.rosetta.protocols.ligand_docking.Translate_info property) cycles() (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) CYCLIC (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) cyclic_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) cyclic_oxygen() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) cyclic_oxygen_index() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) cyclic_oxygen_name() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) cyclic_permutation_offset_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) cyclic_symmetry_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) cyclic_symmetry_mirroring_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) cyclic_symmetry_threshold_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) cyclic_symmetry_threshold_specified_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) CyclicMover (class in pyrosetta.rosetta.protocols.moves) CYCLIZATION_METHOD_DISULFIDE (pyrosetta.rosetta.protocols.peptide_deriver.CyclizationMethod attribute) CYCLIZATION_METHOD_END_TO_END (pyrosetta.rosetta.protocols.peptide_deriver.CyclizationMethod attribute) CyclizationMethod (class in pyrosetta.rosetta.protocols.peptide_deriver) CyclizationMover (class in pyrosetta.rosetta.protocols.simple_moves) cyclize_pose() (in module pyrosetta.rosetta.protocols.relax) CYCLIZE_RES (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) cyclize_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) CyclizedPeptideInfo (class in pyrosetta.rosetta.protocols.peptide_deriver) cycpep_rigid_body_permutation_mover_mode_from_string() (in module pyrosetta.rosetta.protocols.cyclic_peptide) CycpepRigidBodyPermutationMover (class in pyrosetta.rosetta.protocols.cyclic_peptide) CycpepRigidBodyPermutationMoverCreator (class in pyrosetta.rosetta.protocols.cyclic_peptide) CycpepRigidBodyPermutationMoverMode (class in pyrosetta.rosetta.protocols.cyclic_peptide) CycpepSymmetryFilter (class in pyrosetta.rosetta.protocols.cyclic_peptide) CycpepSymmetryFilterCreator (class in pyrosetta.rosetta.protocols.cyclic_peptide) CYS_C_ALPHA (pyrosetta.rosetta.core.scoring.disulfides.DisulfideDerivativeAtom attribute) CYS_C_BETA (pyrosetta.rosetta.core.scoring.disulfides.DisulfideDerivativeAtom attribute) CYS_CEN (pyrosetta.rosetta.core.scoring.disulfides.DisulfideDerivativeAtom attribute) cys_design_selector() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) CYS_S_GAMMA (pyrosetta.rosetta.core.scoring.disulfides.DisulfideDerivativeAtom attribute)