Index – A

a (pyrosetta.rosetta.basic.sampling.orientations.Triple property) (pyrosetta.rosetta.core.scoring.packstat.PointPair property) A (pyrosetta.rosetta.protocols.comparative_modeling.features.TorsionBin attribute) (pyrosetta.rosetta.protocols.features.RamachandranHash attribute) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.hbAcc property) a (pyrosetta.rosetta.protocols.md.Constraint property) (pyrosetta.rosetta.protocols.sic_dock.Vec3 property) A() (in module pyrosetta.rosetta.ObjexxFCL.format) (pyrosetta.rosetta.core.io.CrystInfo method) a() (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.OneGaussianScattering 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_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_int_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_unsigned_long_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_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_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_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_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_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3A_double_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_unsigned_long_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.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_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) A() (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) a0() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) a1() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) a2() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) a3() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) A3B_HBS_POST (pyrosetta.rosetta.core.chemical.VariantType attribute) A3B_HBS_PRE (pyrosetta.rosetta.core.chemical.VariantType attribute) A3BHbsPatcher (class in pyrosetta.rosetta.protocols.simple_moves.a3b_hbs) A_B_C_D_torsion_angle_rad (pyrosetta.rosetta.core.kinematics.inverse.InternalCoordGeometry property) a_form_range() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) a_ik (pyrosetta.rosetta.protocols.cluster.Exemplar property) a_ind() (pyrosetta.rosetta.core.scoring.hbonds.HBDerivAssigner method) a_kappa (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) a_kk (pyrosetta.rosetta.protocols.cluster.DataPoint property) a_logA (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) A_MINOR (pyrosetta.rosetta.core.scoring.rna.RNA_MotifType attribute) a_mu (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideParams13 property) a_to_i() (pyrosetta.rosetta.protocols.normalmode.NormalMode method) AA (class in pyrosetta.rosetta.core.chemical) (pyrosetta.rosetta.core.enzymes.ConsensusSequenceType attribute) aa (pyrosetta.rosetta.core.fragment.torsions property) (pyrosetta.rosetta.core.scoring.tableID property) (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) (pyrosetta.rosetta.protocols.hbnet.HBondResStruct property) (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueSidechainEntry property) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover.mutt property) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBInstruction property) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData property) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter.mutt property) AA (pyrosetta.rosetta.protocols.splice.ROT property) aa() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) (pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecification method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) (pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.motif.Xfres method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) (pyrosetta.rosetta.core.sequence.AnnotatedSequence method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.minimization_packing.MinimalRotamer method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.MethylNames method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFrag method) aa1 (pyrosetta.rosetta.core.import_pose.libraries.BasePairType property) aa1() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) aa2 (pyrosetta.rosetta.core.import_pose.libraries.BasePairType property) aa2() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) aa2idx() (in module pyrosetta.rosetta.core.energy_methods) aa2randomCodon() (in module pyrosetta.rosetta.core.chemical.NucleotideTools) aa_ (pyrosetta.rosetta.protocols.simple_moves.WaterRot property) aa_ala (pyrosetta.rosetta.core.chemical.AA attribute) aa_arg (pyrosetta.rosetta.core.chemical.AA attribute) aa_asn (pyrosetta.rosetta.core.chemical.AA attribute) aa_asp (pyrosetta.rosetta.core.chemical.AA attribute) aa_b2a (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3a (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3c (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3cisACHC (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3cisACPC (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3d (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3e (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3f (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3g (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3h (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3i (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3k (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3l (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3m (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3n (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3p (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3q (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3r (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3s (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3t (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3transACPC (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3v (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3w (pyrosetta.rosetta.core.chemical.AA attribute) aa_b3y (pyrosetta.rosetta.core.chemical.AA attribute) aa_cmp (pyrosetta.rosetta.core.scoring.ScoreType attribute) aa_composition (pyrosetta.rosetta.core.scoring.ScoreType attribute) aa_composition_energy_setup() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint method) aa_composition_setup_file() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) aa_composition_setup_file_count() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) aa_cys (pyrosetta.rosetta.core.chemical.AA attribute) aa_dal (pyrosetta.rosetta.core.chemical.AA attribute) aa_dan (pyrosetta.rosetta.core.chemical.AA attribute) aa_dar (pyrosetta.rosetta.core.chemical.AA attribute) aa_das (pyrosetta.rosetta.core.chemical.AA attribute) aa_dcs (pyrosetta.rosetta.core.chemical.AA attribute) aa_dgn (pyrosetta.rosetta.core.chemical.AA attribute) aa_dgu (pyrosetta.rosetta.core.chemical.AA attribute) aa_dhi (pyrosetta.rosetta.core.chemical.AA attribute) aa_dil (pyrosetta.rosetta.core.chemical.AA attribute) aa_dle (pyrosetta.rosetta.core.chemical.AA attribute) aa_dly (pyrosetta.rosetta.core.chemical.AA attribute) aa_dme (pyrosetta.rosetta.core.chemical.AA attribute) aa_dph (pyrosetta.rosetta.core.chemical.AA attribute) aa_dpr (pyrosetta.rosetta.core.chemical.AA attribute) aa_dse (pyrosetta.rosetta.core.chemical.AA attribute) aa_dth (pyrosetta.rosetta.core.chemical.AA attribute) aa_dtr (pyrosetta.rosetta.core.chemical.AA attribute) aa_dty (pyrosetta.rosetta.core.chemical.AA attribute) aa_dva (pyrosetta.rosetta.core.chemical.AA attribute) aa_frequencies() (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation method) aa_from_name() (in module pyrosetta.rosetta.core.chemical) aa_from_one_or_three() (in module pyrosetta.rosetta.core.chemical) aa_from_oneletter_code() (in module pyrosetta.rosetta.core.chemical) aa_from_resid() (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) aa_gln (pyrosetta.rosetta.core.chemical.AA attribute) aa_glu (pyrosetta.rosetta.core.chemical.AA attribute) aa_gly (pyrosetta.rosetta.core.chemical.AA attribute) aa_h2o (pyrosetta.rosetta.core.chemical.AA attribute) aa_his (pyrosetta.rosetta.core.chemical.AA attribute) aa_ile (pyrosetta.rosetta.core.chemical.AA attribute) aa_ind() (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) aa_leu (pyrosetta.rosetta.core.chemical.AA attribute) aa_lys (pyrosetta.rosetta.core.chemical.AA attribute) aa_matrices() (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) aa_matrix() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) aa_met (pyrosetta.rosetta.core.chemical.AA attribute) aa_name() (pyrosetta.rosetta.protocols.noesy_assign.MethylNames method) aa_none (pyrosetta.rosetta.core.chemical.AA attribute) aa_occurrence_filter() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation static method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation static method) aa_penalty() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) aa_phe (pyrosetta.rosetta.core.chemical.AA attribute) aa_pro (pyrosetta.rosetta.core.chemical.AA attribute) aa_probability_filter() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation method) aa_repeat (pyrosetta.rosetta.core.scoring.ScoreType attribute) aa_sequence() (pyrosetta.rosetta.protocols.splice.ResidueBBDofs method) aa_ser (pyrosetta.rosetta.core.chemical.AA attribute) aa_str() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) aa_submatrix_energies_retrievable() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) aa_thr (pyrosetta.rosetta.core.chemical.AA attribute) aa_trp (pyrosetta.rosetta.core.chemical.AA attribute) aa_trustworthiness() (in module pyrosetta.rosetta.core.scoring.motif) aa_tyr (pyrosetta.rosetta.core.chemical.AA attribute) aa_unk (pyrosetta.rosetta.core.chemical.AA attribute) aa_unp (pyrosetta.rosetta.core.chemical.AA attribute) aa_val (pyrosetta.rosetta.core.chemical.AA attribute) aa_vrt (pyrosetta.rosetta.core.chemical.AA attribute) AACompositionConstraint (class in pyrosetta.rosetta.core.scoring.aa_composition_energy) AACompositionEnergy (class in pyrosetta.rosetta.core.energy_methods) (class in pyrosetta.rosetta.protocols.fldsgn.potentials) AACompositionEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) (class in pyrosetta.rosetta.protocols.fldsgn.potentials) AACompositionEnergySetup (class in pyrosetta.rosetta.core.scoring.aa_composition_energy) AACompositionPropertiesSet (class in pyrosetta.rosetta.core.scoring.aa_composition_energy) AAFrequencies (class in pyrosetta.rosetta.protocols.denovo_design.task_operations) AAFrequency (class in pyrosetta.rosetta.protocols.denovo_design.task_operations) aaho_posi() (pyrosetta.rosetta.protocols.tcr.TCRseqInfo method) AAlist (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) AAMatrix (class in pyrosetta.rosetta.protocols.mean_field) AAProb (class in pyrosetta.rosetta.protocols.mean_field) AARepeatEnergy (class in pyrosetta.rosetta.core.energy_methods) AARepeatEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) aas_to_keep() (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASExceptNativeRLT method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASRLT method) AASynthesisFitnessCost (class in pyrosetta.rosetta.protocols.evolution) AASynthesisFitnessCostFilterCreator (class in pyrosetta.rosetta.protocols.evolution) aatm_ (pyrosetta.rosetta.protocols.simple_moves.WaterRot property) aatype_for_node_state() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) aatype_for_state() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) ab_dock_chains() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) ab_fold_tree() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) ab_movemap (pyrosetta.rosetta.protocols.antibody_legacy.Antibody property) Ab_TemplateInfo (class in pyrosetta.rosetta.protocols.antibody) abase1_ (pyrosetta.rosetta.protocols.simple_moves.WaterRot property) abase2() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) abase2_ (pyrosetta.rosetta.protocols.simple_moves.WaterRot property) abase2_deriv (pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs property) abase2_ind() (pyrosetta.rosetta.core.scoring.hbonds.HBDerivAssigner method) abase_deriv (pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs property) abase_ind() (pyrosetta.rosetta.core.scoring.hbonds.HBDerivAssigner method) abase_prime_ind() (pyrosetta.rosetta.core.scoring.hbonds.HBDerivAssigner method) Abego (class in pyrosetta.rosetta.core.energy_methods) ABEGO (class in pyrosetta.rosetta.core.sequence) abego (pyrosetta.rosetta.core.scoring.ScoreType attribute) (pyrosetta.rosetta.protocols.denovo_design.architects.SecStructInfo property) (pyrosetta.rosetta.protocols.denovo_design.task_operations.LoopInfo property) (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) abego() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.parser.BluePrint method) abego_char() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map method) abego_index() (in module pyrosetta.rosetta.protocols.frag_picker.quota) ABEGO_SS_Config (class in pyrosetta.rosetta.protocols.frag_picker.quota) ABEGO_SS_Map (class in pyrosetta.rosetta.protocols.frag_picker.quota) ABEGO_SS_Pool (class in pyrosetta.rosetta.protocols.frag_picker.quota) ABEGO_SS_Score (class in pyrosetta.rosetta.protocols.frag_picker.scores) abego_str() (in module pyrosetta.rosetta.protocols.denovo_design) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) abego_vector() (in module pyrosetta.rosetta.protocols.denovo_design) AbegoEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) ABEGOEval (class in pyrosetta.rosetta.core.fragment.picking_old.vall.eval) ABEGOManager (class in pyrosetta.rosetta.core.sequence) ABINITIO (pyrosetta.rosetta.basic.ProfTag attribute) AbinitioBaseFilter (class in pyrosetta.rosetta.protocols.simple_filters) AbinitioMoverWeight (class in pyrosetta.rosetta.protocols.topology_broker.weights) abort_min() (pyrosetta.rosetta.core.optimization.AtomTreeMultifunc method) (pyrosetta.rosetta.core.optimization.CartesianMultifunc method) (pyrosetta.rosetta.core.optimization.Multifunc method) (pyrosetta.rosetta.core.optimization.SingleResidueMultifunc method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMultifunc method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMultifunc method) (pyrosetta.rosetta.core.pack.scmin.SCMinMultifunc method) (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GriddedAtomTreeMultifunc method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSTensorOptimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pockets.FingerprintMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc method) (pyrosetta.rosetta.protocols.qsar.qsarOptFunc method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.TensorsOptimizer method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizer method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerFix method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerSvd method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.TensorsOptimizer_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.TensorsOptimizer_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.TensorsOptimizer_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.TensorsOptimizer_Ts4 method) ABOVE (pyrosetta.rosetta.core.chemical.rna.BaseStackWhichSide attribute) above (pyrosetta.rosetta.core.sequence.AlignMove attribute) AbrelaxApplication (class in pyrosetta.rosetta.protocols.abinitio) AbrelaxMover (class in pyrosetta.rosetta.protocols.abinitio) ABS (pyrosetta.rosetta.protocols.calc_taskop_filters.Operation attribute) abs_deriv_dev() (pyrosetta.rosetta.core.optimization.NumDerivCheckData method) (pyrosetta.rosetta.core.optimization.SimpleDerivCheckResult method) abs_score_convergence_threshold() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) abs_score_diff_after_minimization() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) AbscriptLoopCloserCM (class in pyrosetta.rosetta.protocols.abinitio.abscript) AbscriptLoopCloserCMCreator (class in pyrosetta.rosetta.protocols.abinitio.abscript) AbscriptMover (class in pyrosetta.rosetta.protocols.abinitio.abscript) AbscriptMoverCreator (class in pyrosetta.rosetta.protocols.abinitio.abscript) AbscriptStageMover (class in pyrosetta.rosetta.protocols.abinitio.abscript) absfpart() (in module pyrosetta.rosetta.protocols.cryst) absolute() (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) absolute_stereochemistry() (pyrosetta.rosetta.core.chemical.Atom method) absolute_vec() (in module pyrosetta.rosetta.protocols.features.strand_assembly) AbsoluteValueExpression (class in pyrosetta.rosetta.numeric.expression_parser) abstract_parse_tag() (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) AbstractArchiveBase (class in pyrosetta.rosetta.protocols.jd2.archive) AbstractRotamerTrie (class in pyrosetta.rosetta.core.conformation) absX (pyrosetta.rosetta.protocols.pockets.CCluster.Cxyz property) absY (pyrosetta.rosetta.protocols.pockets.CCluster.Cxyz property) absZ (pyrosetta.rosetta.protocols.pockets.CCluster.Cxyz property) Ac (pyrosetta.rosetta.core.chemical.element.Elements attribute) acc() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) acc_atm() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) acc_atm_ (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBond property) acc_atm_is_backbone() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) acc_atm_is_protein_backbone() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) acc_bbg_in_bb_bb_hbond() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) acc_chem_type_from_name() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) acc_deriv (pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs property) acc_dist_cutoff() (pyrosetta.rosetta.protocols.features.WaterFeatures method) acc_index() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) acc_npd_weight() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) acc_occ_type_has_data() (pyrosetta.rosetta.core.scoring.geometric_solvation.DatabaseOccSolEne method) acc_occ_type_mapping() (pyrosetta.rosetta.core.scoring.geometric_solvation.DatabaseOccSolEne method) acc_res() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) acc_res_is_dna() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) acc_res_is_protein() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) acc_rsd_ (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBond property) acc_strength() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) acc_type() (pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple method) acc_type_has_data() (pyrosetta.rosetta.core.scoring.geometric_solvation.DatabaseOccSolEne method) acc_type_mapping() (pyrosetta.rosetta.core.scoring.geometric_solvation.DatabaseOccSolEne method) acc_wt_ (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBond property) acc_wt_alt_ (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBond property) accept (pyrosetta.rosetta.core.pack.annealer.RotSub property) (pyrosetta.rosetta.protocols.hotspot_hashing.StubStatus attribute) accept() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) accept_counter() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) accept_declined_claim() (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) accept_new_conformation() (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) accept_no_op_moves() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) accept_reject (pyrosetta.rosetta.protocols.moves.StatsType attribute) acceptance_rate() (pyrosetta.rosetta.protocols.moves.MoverStatistics method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) AcceptanceCheck (class in pyrosetta.rosetta.protocols.loop_modeling.utilities) ACCEPTED (pyrosetta.rosetta.protocols.monte_carlo.TrialResult attribute) accepted() (pyrosetta.rosetta.protocols.moves.MoverStatistics method) (pyrosetta.rosetta.protocols.moves.TrialCounter method) accepted_scores() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) AcceptedScores (class in pyrosetta.rosetta.protocols.monte_carlo) acceptor() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties method) acceptor_group() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond method) acceptor_selector() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) acceptor_symmetry_copy_index() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond method) AcceptorAtomFilter (class in pyrosetta.rosetta.core.chemical) acceptorList (pyrosetta.rosetta.protocols.sparta.PDB property) accepts() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) accepts_since_last_batch() (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) AcceptToBestMover (class in pyrosetta.rosetta.protocols.relax) AcceptToBestMoverCreator (class in pyrosetta.rosetta.protocols.relax) access (pyrosetta.rosetta.core.scoring.sc.Atom property) access_Real_MathNTensor() (in module pyrosetta.rosetta.numeric) accomodate_length_change() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) accpt_pos() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) accpt_pos_sc() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) acctype (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.hbAcc property) accum_ (pyrosetta.rosetta.core.scoring.packstat.Slice property) (pyrosetta.rosetta.core.scoring.packstat.trace property) accumulate() (pyrosetta.rosetta.core.scoring.EMapVector method) accumulate_area() (pyrosetta.rosetta.core.scoring.packstat.Accumulator method) (pyrosetta.rosetta.core.scoring.packstat.AreaAccumulator method) (pyrosetta.rosetta.core.scoring.packstat.MultiProbePerSphereAccumulator method) (pyrosetta.rosetta.core.scoring.packstat.MultiProbePoseAccumulator method) (pyrosetta.rosetta.core.scoring.packstat.PerSphereAccumulator method) accumulate_dxdy() (pyrosetta.rosetta.core.scoring.packstat.Accumulator method) (pyrosetta.rosetta.core.scoring.packstat.AreaAccumulator method) (pyrosetta.rosetta.core.scoring.packstat.MultiProbePerSphereAccumulator method) (pyrosetta.rosetta.core.scoring.packstat.MultiProbePoseAccumulator method) (pyrosetta.rosetta.core.scoring.packstat.PerSphereAccumulator method) accumulate_energy() (pyrosetta.rosetta.core.scoring.constraints.CstResNeighbConstIterator method) (pyrosetta.rosetta.core.scoring.constraints.CstResNeighbIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbIterator method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.ResidueNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.ResidueNeighborIterator method) accumulate_single_atom_contributions() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) Accumulator (class in pyrosetta.rosetta.core.scoring.packstat) accuracy_weight (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData property) ACETYL_SUGAR (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) ACETYLAMINO_SUGAR (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) ACETYLATED_NTERMINUS (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) ACETYLATED_NTERMINUS_CONNECTION_VARIANT (pyrosetta.rosetta.core.chemical.VariantType attribute) ACETYLATED_NTERMINUS_VARIANT (pyrosetta.rosetta.core.chemical.VariantType attribute) ACETYLATION (pyrosetta.rosetta.core.chemical.VariantType attribute) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes attribute) ACHAR() (in module pyrosetta.rosetta.ObjexxFCL.Fortran) ACHIRAL_BACKBONE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) ACHIRAL_SIDECHAIN (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) acid_base_coefficient() (pyrosetta.rosetta.protocols.simple_moves.IonizableResidue method) acknowledge_last_substititon_not_committed() (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) acknowledge_neighbors_partial_state_assignment() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) acknowledge_neighbors_partial_state_substitution() (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) acknowledge_neighbors_perturbed_state() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) acknowledge_neighbors_state_substitution() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) acknowledge_neighbors_substitution() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) acknowledge_partial_state_assignment() (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) acknowledge_partial_state_change() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) acknowledge_participation_in_perturbation() (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) acknowledge_perturbed_state() (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) acknowledge_state_change() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) acknowledge_state_zeroed() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) acknowledge_substitution() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) actcoord() (pyrosetta.rosetta.core.conformation.Residue method) actcoord_atoms() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) activate() (pyrosetta.rosetta.utility.Bound_bool_t method) (pyrosetta.rosetta.utility.Bound_double_t method) (pyrosetta.rosetta.utility.Bound_int_t method) (pyrosetta.rosetta.utility.Bound_std_string_t method) (pyrosetta.rosetta.utility.Bound_utility_file_FileName_t method) (pyrosetta.rosetta.utility.Bound_utility_file_PathName_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) (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) activate_daemon_mode() (pyrosetta.rosetta.protocols.pack_daemon.DaemonSet method) activate_dof_deriv_one_body_method() (pyrosetta.rosetta.core.scoring.MinimizationNode method) activate_dof_deriv_terms_for_cart_min() (in module pyrosetta.rosetta.core.optimization) activate_dof_deriv_two_body_method() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) activate_residue_dofs() (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) active() (pyrosetta.rosetta.cppdb.backend.statements_cache 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.FArray_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.utility.Bound_bool_t method) (pyrosetta.rosetta.utility.Bound_double_t method) (pyrosetta.rosetta.utility.Bound_int_t method) (pyrosetta.rosetta.utility.Bound_std_string_t method) (pyrosetta.rosetta.utility.Bound_utility_file_FileName_t method) (pyrosetta.rosetta.utility.Bound_utility_file_PathName_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyOptionKey_utility_options_VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyVectorOptionKey_utility_options_VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanOptionKey_utility_options_BooleanOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanVectorOptionKey_utility_options_BooleanVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_FileOptionKey_utility_options_FileOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_FileVectorOptionKey_utility_options_FileVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerOptionKey_utility_options_IntegerOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerVectorOptionKey_utility_options_IntegerVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_OptionKey_utility_options_OptionTypes_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathOptionKey_utility_options_PathOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathVectorOptionKey_utility_options_PathVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealOptionKey_utility_options_RealOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealVectorOptionKey_utility_options_RealVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_ResidueChainVectorOptionKey_utility_options_ResidueChainVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringOptionKey_utility_options_StringOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringVectorOptionKey_utility_options_StringVectorOption_t method) (pyrosetta.rosetta.utility.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) active_ (pyrosetta.rosetta.protocols.optimize_weights.WeightRangeConstraint property) active_2b_score_types() (pyrosetta.rosetta.core.scoring.EnergyGraph method) active_angle() (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) active_atom_tree() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) active_constraint() (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) (pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint method) active_constraints() (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) active_dofs() (pyrosetta.rosetta.core.environment.DofPassport method) active_jump() (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) active_jumps() (pyrosetta.rosetta.core.environment.DofPassport method) active_pose_constraints() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache method) active_residue() (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) active_residue_cop() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) active_residue_data() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) active_restype() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) active_restype_index() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) active_score_types() (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.core.scoring.EnergyGraph method) active_total_energies() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) active_variables() (pyrosetta.rosetta.numeric.expression_parser.AbsoluteValueExpression method) (pyrosetta.rosetta.numeric.expression_parser.AddExpression method) (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.BinaryExpression method) (pyrosetta.rosetta.numeric.expression_parser.DivideExpression method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.ITEExpression method) (pyrosetta.rosetta.numeric.expression_parser.LiteralExpression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.MaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression method) (pyrosetta.rosetta.numeric.expression_parser.MinExpression method) (pyrosetta.rosetta.numeric.expression_parser.MultiplyExpression method) (pyrosetta.rosetta.numeric.expression_parser.NaryExpression method) (pyrosetta.rosetta.numeric.expression_parser.NotExpression method) (pyrosetta.rosetta.numeric.expression_parser.OrExpression method) (pyrosetta.rosetta.numeric.expression_parser.SquarerootExpression method) (pyrosetta.rosetta.numeric.expression_parser.SubtractExpression method) (pyrosetta.rosetta.numeric.expression_parser.UnaryExpression method) (pyrosetta.rosetta.numeric.expression_parser.VariableExpression method) (pyrosetta.rosetta.protocols.optimize_weights.OptEVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.ExpExpression method) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) (pyrosetta.rosetta.protocols.pack_daemon.IterativeVectorExpression method) (pyrosetta.rosetta.protocols.pack_daemon.LnExpression method) (pyrosetta.rosetta.protocols.pack_daemon.Mean method) (pyrosetta.rosetta.protocols.pack_daemon.PowExpression method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VariableVectorExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VectorExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VectorFunction method) (pyrosetta.rosetta.protocols.pack_daemon.VectorFunction2 method) (pyrosetta.rosetta.protocols.pack_daemon.VMax method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMin method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) active_variables_vector() (pyrosetta.rosetta.protocols.pack_daemon.IterativeVectorExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VariableVectorExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VectorExpression method) ActiveSiteGrid (class in pyrosetta.rosetta.protocols.match.downstream) activity (pyrosetta.rosetta.protocols.qsar.qsarOptData property) actual_bb() (pyrosetta.rosetta.protocols.match.Bool3DGrid method) actual_cycles() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) actual_residue_connection() (pyrosetta.rosetta.core.conformation.Residue method) actual_twobody_memory_use() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) actually_moving_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) acyclic() (in module pyrosetta.rosetta.ObjexxFCL.internal.ObserverMediator) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) adaptation_period() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) adaptive() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) adaptive_inner_cycle() (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) adaptive_movers() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) AdaptiveScoreHistogram (class in pyrosetta.rosetta.protocols.frag_picker.scores) ADD (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.MoveType attribute) add() (pyrosetta.bindings.pose.ResidueLabelAccessor method) (pyrosetta.rosetta.basic.citation_manager.CitationCollectionList method) Add() (pyrosetta.rosetta.basic.sampling.orientations.QuatSet method) add() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragSetCollection method) (pyrosetta.rosetta.core.fragment.MinimalFragSet method) (pyrosetta.rosetta.core.fragment.OrderedFragSet method) (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t method) (pyrosetta.rosetta.core.pack.palette.BaseTypeList method) (pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t 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.calibur.AdjacentList method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairSet method) (pyrosetta.rosetta.protocols.forge.build.BuildManager 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.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.PCluster method) (pyrosetta.rosetta.protocols.recces.Histogram method) (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) (pyrosetta.rosetta.protocols.wum.SilentStructStore method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue_Swapped 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.utility.json_spirit.Config_map_std_string_t static method) (pyrosetta.rosetta.utility.json_spirit.Config_vector_std_string_t static method) (pyrosetta.rosetta.utility.keys.KeyLookup_utility_options_OptionKey_t static method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyOptionKey_utility_options_VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyVectorOptionKey_utility_options_VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanOptionKey_utility_options_BooleanOption_t method) (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.options.OptionCollection method) add_a3b_hbs_constraint() (in module pyrosetta.rosetta.core.pose.ncbb) add_acceptance_check() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) add_actcoord_atom() (pyrosetta.rosetta.core.chemical.MutableResidueType method) add_additional_low_resolution_step() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) add_additional_task_operaration() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockTaskFactory method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) add_adduct() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) add_alanine_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) add_all_atoms() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) add_all_evaluators() (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory method) add_all_model_edges_from_binary() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) add_all_rosetta_options() (in module pyrosetta.rosetta) add_aln() (pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster method) add_already_defined_subelement() (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) add_already_defined_subelement_w_alt_element_name() (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) add_and_average() (pyrosetta.rosetta.protocols.nmr.pre.PREDistanceRecord method) add_and_initialize_reference_pose() (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) add_angle_parameter() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) add_anonymous_option() (in module pyrosetta.rosetta.basic.options) add_another_virtual_res() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) add_anti_chi_constraints() (in module pyrosetta.rosetta.core.pose.rna) add_apply_mover() (pyrosetta.rosetta.protocols.environment.EnvMover method) add_arbitrary_score_data_from_pose() (pyrosetta.rosetta.core.io.raw_data.ScoreMap static method) add_arbitrary_string_data_from_pose() (pyrosetta.rosetta.core.io.raw_data.ScoreMap static method) add_architect() (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) add_as_other_struct_if_relevant() (pyrosetta.rosetta.core.io.silent.SilentFileData method) add_assignment() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D.Spin method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D.Spin method) add_at_ind() (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) add_atmname_using() (pyrosetta.rosetta.core.energy_methods.GoapRsdType method) add_atom() (in module pyrosetta.rosetta.core.kinematics) (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule method) (pyrosetta.rosetta.core.kinematics.MinimizerMapBase method) (pyrosetta.rosetta.core.optimization.CartesianMinimizerMap method) (pyrosetta.rosetta.core.optimization.DOF_Node method) (pyrosetta.rosetta.core.optimization.MinimizerMap method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) (pyrosetta.rosetta.core.scoring.PDinter method) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) (pyrosetta.rosetta.protocols.pockets.SmallMol method) add_atom_alias() (pyrosetta.rosetta.core.chemical.MutableResidueType method) add_atom_set() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) add_atom_type_set_parameters_from_command_line() (in module pyrosetta.rosetta.core.chemical) add_atom_types_from_command_line() (in module pyrosetta.rosetta.core.chemical) add_atomgeom_evaluator() (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) add_atomset_to_perturber_atomset_list() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) add_attribute() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) add_attributes() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) add_attributes_for_common_options() (in module pyrosetta.rosetta.protocols.ncbb) add_attributes_for_helix_params() (in module pyrosetta.rosetta.protocols.helical_bundle) add_attributes_for_make_bundle_minorhelix_defaults() (in module pyrosetta.rosetta.protocols.helical_bundle) add_attributes_for_make_bundle_other_defaults() (in module pyrosetta.rosetta.protocols.helical_bundle) add_attributes_for_make_bundle_symmetry() (in module pyrosetta.rosetta.protocols.helical_bundle) add_attributes_for_minor_helix_params() (in module pyrosetta.rosetta.protocols.helical_bundle) add_attributes_for_other_helix_params() (in module pyrosetta.rosetta.protocols.helical_bundle) add_author() (pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleInfo method) (pyrosetta.rosetta.core.io.HeaderInformation method) add_backrub_mover() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) add_base_name_to_exclude() (pyrosetta.rosetta.core.pack.task.NOTAA method) add_base_name_to_keep() (pyrosetta.rosetta.core.pack.task.PIKAA method) add_base_residue_type() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) add_batch() (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) add_bb_action() (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) add_bb_clone() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) add_bb_csts_to_loop() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) add_bb_index_action() (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) add_bbdep_angle_parameter() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) add_bbdep_length_parameter() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) add_bckg() (in module pyrosetta.rosetta.core.scoring.epr_deer) add_behavior() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) add_big_fragments() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) add_black_listed_file() (pyrosetta.rosetta.utility.Inline_File_Provider method) add_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) add_bond() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule method) add_bondangles_action() (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) add_bonded_orbital() (pyrosetta.rosetta.core.chemical.Atom method) add_bondlengths_action() (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) add_bonus_map_entry() (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) add_boundary_function() (pyrosetta.rosetta.numeric.interpolation.spline.SplineGenerator method) add_branches_action() (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) add_buffer() (pyrosetta.rosetta.numeric.linear_algebra.EllipseParameters method) add_build_set() (pyrosetta.rosetta.protocols.match.upstream.ProteinUpstreamBuilder method) add_built_in_options() (pyrosetta.rosetta.utility.options.OptionCollection method) add_c_terminal_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) add_canonical_atom_alias() (pyrosetta.rosetta.core.chemical.MutableResidueType method) add_case() (pyrosetta.rosetta.core.chemical.Patch method) add_CDR_to_MoveMap() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) add_chain_ending() (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) add_chain_from_pose() (in module pyrosetta.rosetta.protocols.denovo_design) add_chain_id() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) add_chain_name() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) add_chainbreak_variants() (pyrosetta.rosetta.protocols.abinitio.CoordinateConstraintKC method) (pyrosetta.rosetta.protocols.abinitio.KinematicControl method) (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) add_chainbreaks() (pyrosetta.rosetta.protocols.jumping.JumpSample method) add_chainbreaks_according_to_jumps() (in module pyrosetta.rosetta.protocols.toolbox.pose_manipulation) add_chainbreaks_as_distance_constraint() (pyrosetta.rosetta.protocols.jumping.JumpSample method) add_chemistry() (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) add_chi() (pyrosetta.rosetta.core.chemical.MutableResidueType method) add_chi_action() (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) add_chi_clone() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) add_chi_constraints() (in module pyrosetta.rosetta.core.pose.rna) add_chi_rotamer() (pyrosetta.rosetta.core.chemical.MutableChiRecord method) (pyrosetta.rosetta.core.chemical.MutableResidueType method) add_chi_rotamer_to_last_chi() (pyrosetta.rosetta.core.chemical.MutableResidueType method) add_child() (pyrosetta.rosetta.protocols.jd3.JGResultNode method) (pyrosetta.rosetta.utility.tag.XMLSchemaRepeatableCTNode method) add_choice() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) add_chunk_filter() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) add_chunk_set() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) add_circle() (pyrosetta.rosetta.core.scoring.packstat.Slice method) add_citation() (pyrosetta.rosetta.basic.citation_manager.CitationCollection method) (pyrosetta.rosetta.basic.citation_manager.CitationManager method) add_citations() (pyrosetta.rosetta.basic.citation_manager.CitationManager method) add_clashes_to_shell() (in module pyrosetta.rosetta.core.pack.task.residue_selector) add_cluster_comments_to_pose() (in module pyrosetta.rosetta.protocols.antibody.clusters) add_cmdline_claims() (in module pyrosetta.rosetta.protocols.topology_broker) add_co_author() (pyrosetta.rosetta.basic.citation_manager.Citation method) add_column() (pyrosetta.rosetta.basic.database.insert_statement_generator.InsertGenerator method) (pyrosetta.rosetta.basic.database.schema_generator.PrimaryKey method) (pyrosetta.rosetta.basic.database.schema_generator.Schema method) add_comment() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) add_common_denovo_architect_attributes() (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.DeNovoArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.MotifArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect static method) add_components_to_pose_if_necessary() (pyrosetta.rosetta.protocols.matdes.SymDofMover method) add_compositeSegmentMover() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) add_condition() (pyrosetta.rosetta.protocols.filters.IfThenFilter method) add_conformation_viewer() (in module pyrosetta.rosetta.protocols.viewer) add_connected_resonance() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) add_connection() (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) add_constant() (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric method) (pyrosetta.rosetta.protocols.filters.CalculatorFilter method) add_constraint() (pyrosetta.rosetta.basic.database.schema_generator.Schema method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.constraints.Constraints method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) add_constraint_generator() (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) add_constraints() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) add_constraints_from_cmdline() (in module pyrosetta.rosetta.core.scoring.constraints) add_constraints_from_cmdline_to_pose() (in module pyrosetta.rosetta.core.scoring.constraints) add_constraints_from_cmdline_to_scorefxn() (in module pyrosetta.rosetta.core.scoring.constraints) add_constraints_from_file() (in module pyrosetta.rosetta.protocols.dna) add_constraints_to_metal() (in module pyrosetta.rosetta.core.util) add_constraints_to_pose() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) add_constraints_to_pose_for_block_without_clearing_and_header_processing() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) add_contact() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) add_coordinate_constraint_func_atoms() (in module pyrosetta.rosetta.protocols.relax) add_coordinate_constraints() (in module pyrosetta.rosetta.core.scoring.constraints) (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) add_coordinate_constraints_to_pose() (in module pyrosetta.rosetta.protocols.loops) (in module pyrosetta.rosetta.protocols.relax) add_coordinate_from_string() (pyrosetta.rosetta.core.conformation.symmetry.VirtualCoordinate method) add_coordinatecst_for_hotspot_packing() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) add_coords() (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) add_coords_hash() (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) add_covalent_bond() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) add_covalent_linkage() (in module pyrosetta.rosetta.core.util) add_covalent_linkages_to_metal() (in module pyrosetta.rosetta.core.util) add_creator() (pyrosetta.rosetta.core.pack.palette.PackerPaletteFactory method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterFactory method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationFactory method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory method) add_ct_name() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover static method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover static method) add_current_job_data_to_ss() (in module pyrosetta.rosetta.protocols.jd2) add_custom_type() (pyrosetta.rosetta.core.chemical.Patch method) add_custom_variant_type_to_pose_residue() (in module pyrosetta.rosetta.core.pose) add_cut_bond() (pyrosetta.rosetta.core.chemical.MutableResidueType method) add_cutpoint_closed() (in module pyrosetta.rosetta.core.import_pose) add_cutpoint_open() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) add_cutpoint_variants() (in module pyrosetta.rosetta.protocols.forge.methods) (in module pyrosetta.rosetta.protocols.loops) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) add_cutpoint_variants_for_ccd() (in module pyrosetta.rosetta.protocols.grafting) add_cutpoints() (in module pyrosetta.rosetta.protocols.denovo_design) add_daemon (pyrosetta.rosetta.protocols.pack_daemon.DaemonSetMessage attribute) add_data_point() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.PNearCalculator method) add_datum() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) add_decoy() (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData method) add_delete_frequency() (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) add_dens_scores_from_cmdline_to_scorefxn() (in module pyrosetta.rosetta.core.scoring.electron_density) add_dependency_to() (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) add_deriv_data() (pyrosetta.rosetta.core.optimization.NumericalDerivCheckResult method) add_design_task() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) add_diagonal() (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) add_dihedral_constraints() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) add_dihedral_constraints_to_pose() (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) add_dihedral_csts() (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) add_dihedral_csts_to_rb() (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) add_dist_viol_to_assignments() (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) add_distance() (pyrosetta.rosetta.protocols.contact_map.Contact method) add_disulfide_bond() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) add_DoF() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) add_dof_access() (pyrosetta.rosetta.core.environment.DofPassport method) add_dof_constraint() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) add_dof_from_string() (pyrosetta.rosetta.core.conformation.symmetry.SymDof method) ADD_EDGE (pyrosetta.rosetta.protocols.legacy_sewing.move_type attribute) add_edge() (pyrosetta.rosetta.core.conformation.PointGraphPy method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (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.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.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode 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.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode 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.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.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.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.hbnet.NetworkState method) (pyrosetta.rosetta.protocols.jd3.JobDigraph 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.Graph method) (pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t method) (pyrosetta.rosetta.utility.graph.Node method) (pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) add_edge_to_new_node() (pyrosetta.rosetta.protocols.jd3.JobDigraphUpdater method) add_edges_from_binary() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) add_edits() (pyrosetta.rosetta.utility.options.OptionCollection static method) add_encoded_termini() (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) add_energies_data_from_scored_pose() (pyrosetta.rosetta.core.io.raw_data.ScoreMap static method) add_energy() (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) add_energy_edge() (pyrosetta.rosetta.core.scoring.EnergyGraph method) add_entity() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) add_entry() (pyrosetta.rosetta.protocols.abinitio.PairingStatistics method) add_entry_to_octahedral_metal_positions() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) add_entry_to_square_planar_metal_positions() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) add_entry_to_square_pyramidal_metal_positions() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) add_entry_to_tetrahedral_metal_positions() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) add_entry_to_trigonal_planar_metal_positions() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) add_entry_to_trigonal_pyramidal_metal_positions() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) add_error() (pyrosetta.rosetta.utility.tag.XMLValidationOutput method) add_errors() (pyrosetta.rosetta.utility.tag.XMLValidationOutput method) add_evaluated_structure() (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) add_evaluation() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.abinitio.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.dna.PDBOutput method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmtfJobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) add_evaluator() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) add_evaluator_for_target_restype() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) add_evaluators() (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.NativeEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator method) add_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) add_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) add_external_geom_sampler() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) add_external_geometry_samples_for_constraint() (pyrosetta.rosetta.protocols.match.Matcher method) add_external_loop_rotamer() (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) add_extra_bodies() (in module pyrosetta.rosetta.protocols.chemically_conjugated_docking) add_extra_data() (pyrosetta.rosetta.protocols.loophash.BackboneDB method) add_extra_method() (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) add_fa_constraints_from_cmdline() (in module pyrosetta.rosetta.core.scoring.constraints) add_fa_constraints_from_cmdline_to_pose() (in module pyrosetta.rosetta.core.scoring.constraints) add_fa_constraints_from_cmdline_to_scorefxn() (in module pyrosetta.rosetta.core.scoring.constraints) add_fade_chain_break_constraint_across_gap() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) add_features_reporter() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) add_file_contents() (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction method) (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunctionDriver method) add_file_provider_hook() (pyrosetta.rosetta.utility.Inline_File_Provider method) add_filename() (pyrosetta.rosetta.protocols.simple_filters.StemFinder method) add_filter() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastPlus method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_LoopOverSCs method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrix method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.filters.CalculatorFilter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.match.MatcherTask method) (pyrosetta.rosetta.protocols.match.output.MatchConsolidator method) (pyrosetta.rosetta.protocols.match.output.MatchOutputter method) (pyrosetta.rosetta.protocols.match.output.MatchProcessor method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.FilterMover method) add_filter_param() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) add_filter_parameter() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) add_fixed_res_constraints() (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) add_flanking_virtual_residues() (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) add_flexible_region() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) add_foreign_key() (pyrosetta.rosetta.basic.database.schema_generator.Schema method) add_frag_type() (pyrosetta.rosetta.core.fragment.FragFactory method) add_fragment() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) add_fragment_csts() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) add_fragment_eval() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) add_fragment_gen() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) add_fragments() (pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet 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) add_fragset() (pyrosetta.rosetta.core.fragment.FragSetCollection method) add_frame_type() (pyrosetta.rosetta.core.fragment.FragFactory method) add_free_peptide_mover() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) add_from_file() (pyrosetta.rosetta.protocols.motifs.MotifLibrary method) add_func() (pyrosetta.rosetta.core.scoring.func.SumFunc method) add_function() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticScanner method) (pyrosetta.rosetta.numeric.expression_parser.BooleanExpressionScanner method) add_function_name() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) add_gaussian() (pyrosetta.rosetta.core.scoring.SmoothScoreTermCoeffs method) add_generator() (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) add_genericRBMover() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) add_GlyCorrection_values() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) add_GlyCorrection_values_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) add_grid() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) add_group() (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.task_operations.LinkResidues method) add_group_subelement() (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) add_groupD() (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) add_groupE() (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) add_harmonic_chain_break_constraint() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) add_harmonic_dihedral_cst_general() (in module pyrosetta.rosetta.protocols.antibody.constraints) add_hbond() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdgeData method) add_hbs_constraint() (in module pyrosetta.rosetta.core.pose.ncbb) add_helix() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) add_helixMover() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) add_histogram_file() (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) add_hits() (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) add_hotspot_constraints_to_pose() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) add_hotspot_constraints_to_wholepose() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) add_hsstriplets() (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilter method) (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTripletSet method) add_hydrophobic_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) add_ideal_contact() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) add_if_missing() (pyrosetta.rosetta.utility.thread.MutableCache_const_core_chemical_ResidueTypeSet__star__core_pack_palette_BaseTypeList_t method) add_improper_parameter() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) add_incoming_edge() (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.utility.graph.DirectedNode method) add_index() (pyrosetta.rosetta.basic.database.schema_generator.Schema method) add_individual_constraint() (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraint method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) (pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint method) add_info() (pyrosetta.rosetta.protocols.dna.PDBOutput method) add_info_for_csts() (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) add_init_dev_penalty() (in module pyrosetta.rosetta.protocols.mpi_refinement) add_inner_cycle_step() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) add_input_file() (pyrosetta.rosetta.utility.Inline_File_Provider method) add_input_job_result_index() (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) add_inputvalue() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) add_instruction() (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.forge.components.BDR method) add_interaction() (pyrosetta.rosetta.core.scoring.custom_pair_distance.AtomPairFuncList method) add_internal_loop_rotamer() (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) add_ionized_restype() (pyrosetta.rosetta.protocols.simple_moves.IonizableResidue method) add_job_data_to_ss() (in module pyrosetta.rosetta.protocols.jd2) add_jump() (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.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.RigidBodyInfo method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceSasaFilter method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterface method) add_jump_action() (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) add_jump_clone() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) add_jump_id() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) add_jump_label() (pyrosetta.rosetta.core.environment.SequenceAnnotation method) add_jump_neighbor() (pyrosetta.rosetta.core.environment.FoldTreeSketch.Node method) add_jump_selector() (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) add_kic_mover() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) add_known_value() (pyrosetta.rosetta.numeric.interpolation.spline.SplineGenerator method) add_labels_as_remark() (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) add_layer() (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) add_leap() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) add_legacyleap() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) add_length_parameter() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) add_ligand_contact() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) add_ligand_from_file() (pyrosetta.rosetta.protocols.motifs.MotifLibrary method) add_line() (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.sequence.ABEGO method) (pyrosetta.rosetta.protocols.frags.RMSVallData method) (pyrosetta.rosetta.protocols.frags.VallData method) add_linker() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) add_linker_asymmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper method) add_linker_bonds_asymmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper method) add_linker_bonds_symmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper method) add_linker_constraints_asymmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper method) add_linker_constraints_symmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper method) add_linker_segments() (in module pyrosetta.rosetta.protocols.legacy_sewing) add_linker_symmetric() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper method) add_list_filenames() (pyrosetta.rosetta.core.import_pose.pose_stream.PDBPoseInputStream method) add_long_range_damping() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) add_longrange_twobody_energies_multithreaded() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) add_loop() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.loops.Loops method) add_loop_flank_residues_bb_to_movemap() (in module pyrosetta.rosetta.protocols.loops) ADD_LOOP_RES (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.MoveType attribute) add_loop_residue() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) add_loop_segment() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) add_loop_size() (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) add_loops_from_bool_vector() (in module pyrosetta.rosetta.protocols.antibody.design) add_lower_connect_angle_params() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) add_lower_padding() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) add_lower_terminus_type_to_conformation_residue() (in module pyrosetta.rosetta.core.conformation) add_lower_terminus_type_to_pose_residue() (in module pyrosetta.rosetta.core.pose) add_lr_gaussian() (pyrosetta.rosetta.core.scoring.CenHBPotential method) add_mainchain_segments() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) add_mainchain_segments_from_options() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) add_match() (pyrosetta.rosetta.protocols.match.output.BestMatchesCollection method) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) add_match_dspos1() (pyrosetta.rosetta.protocols.match.output.BestMatchesCollection method) add_mcfi() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) add_memb_etable() (pyrosetta.rosetta.core.scoring.ScoringManager method) add_member() (pyrosetta.rosetta.protocols.cluster.Cluster method) add_member_front() (pyrosetta.rosetta.protocols.cluster.Cluster method) add_membrane_again() (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) add_membrane_virtual() (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover method) add_metalbinding_atom() (pyrosetta.rosetta.core.chemical.MutableResidueType method) add_metapatch_connect() (pyrosetta.rosetta.core.chemical.MutableResidueType method) add_methyl() (pyrosetta.rosetta.protocols.noesy_assign.MethylNames method) add_metric() (pyrosetta.rosetta.protocols.jd3.jobs.MoverJob method) add_metric_value_getter() (pyrosetta.rosetta.protocols.multistate_design.MultiStateFitnessFunction method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) add_metrics() (pyrosetta.rosetta.protocols.jd3.jobs.MoverJob method) add_mm_atom_type_set_parameters_from_command_line() (in module pyrosetta.rosetta.core.chemical) add_mode() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams method) add_model() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) add_monomers_to_lattice() (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) add_monomers_to_layer() (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) add_monte_carlo_viewer() (in module pyrosetta.rosetta.protocols.viewer) add_motif() (pyrosetta.rosetta.core.scoring.motif.MotifHash method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilter method) add_motif_bb_constraints() (in module pyrosetta.rosetta.protocols.motifs) add_motif_sc_constraints() (in module pyrosetta.rosetta.protocols.motifs) add_motif_scorers_to_score_file() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) add_motif_set_name() (pyrosetta.rosetta.core.scoring.motif.MotifHashManager method) add_movable_chain() (pyrosetta.rosetta.protocols.simple_task_operations.InterfaceTaskOperation method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterface method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) add_movable_jump() (pyrosetta.rosetta.protocols.simple_task_operations.InterfaceTaskOperation method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterface method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) add_movemap_from_loopres() (in module pyrosetta.rosetta.protocols.mpi_refinement) add_mover() (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.jd3.jobs.MoverJob method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.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.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) add_mover_group() (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) add_MPI_rank_handling_message() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_RMSDToBestSummary method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary method) add_MSAcst_to_pose() (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) add_msg() (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.environment.EXCN_Env_Exception method) (pyrosetta.rosetta.core.environment.EXCN_FTSketchGraph method) (pyrosetta.rosetta.core.id.EXCN_AtomNotFound method) (pyrosetta.rosetta.core.kinematics.EXCN_InvalidFoldTree method) (pyrosetta.rosetta.core.pack.task.ResfileReaderException method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.EXCN_CalcFailed method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.EXCN_InitFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_CalcFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_detection_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_undefined_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_grafting_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_invalid_cdr_region_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_json_cdr_detection_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_numbering_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_scs_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_unexpected_region_length_ method) (pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Heat_Converged method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Pool_Converged method) (pyrosetta.rosetta.protocols.constraint_generator.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.denovo_design.architects.EXCN_PreFilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_PoseInconsistent method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_RemarksNotPresent method) (pyrosetta.rosetta.protocols.denovo_design.connection.EXCN_ConnectionSetupFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_NothingToFold method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Passport method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Security_Exception method) (pyrosetta.rosetta.protocols.forge.remodel.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.jd2.archive.EXCN_Archive method) (pyrosetta.rosetta.protocols.jd2.JD2Failure method) (pyrosetta.rosetta.protocols.loophash.EXCN_bbdb_Merge_Failed method) (pyrosetta.rosetta.protocols.loophash.EXCN_DB_IO_Failed method) (pyrosetta.rosetta.protocols.loophash.EXCN_Invalid_Hashmap method) (pyrosetta.rosetta.protocols.loophash.EXCN_No_Extra_Data_To_Write method) (pyrosetta.rosetta.protocols.loophash.EXCN_Wrong_DB_Format method) (pyrosetta.rosetta.protocols.loops.EXCN_Loop_not_closed method) (pyrosetta.rosetta.protocols.moves.EXCN_Converged method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_AssignmentNotFound method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_FileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_NoesyAssign method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownAtomname method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownResonance method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_FailedBroking method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_Input method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_TopologyBroker method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_Unknown method) (pyrosetta.rosetta.utility.excn.BadInput method) (pyrosetta.rosetta.utility.excn.Exception method) (pyrosetta.rosetta.utility.excn.FileNotFound method) (pyrosetta.rosetta.utility.excn.IOError method) (pyrosetta.rosetta.utility.excn.KeyError method) (pyrosetta.rosetta.utility.excn.NullPointerError method) (pyrosetta.rosetta.utility.excn.RangeError method) (pyrosetta.rosetta.utility.excn.RosettaScriptsOptionError method) (pyrosetta.rosetta.utility.excn.UserCorrectableIssue method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) add_mutant() (pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData method) add_mutant_complex() (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData method) add_mutant_to_vectors() (in module pyrosetta.rosetta.protocols.relax.membrane) add_mutant_unbounds() (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData method) add_mutation() (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData method) (pyrosetta.rosetta.protocols.pmut_scan.Mutant method) add_mutation_ddG() (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) add_n_terminal_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) add_named_selector() (pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser method) add_native() (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData method) add_native_fasta() (pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation method) add_native_pdb() (pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation method) add_native_pose() (pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation method) add_nbr_radius_ (pyrosetta.rosetta.protocols.ligand_docking.LigandArea property) add_negative_filter() (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter method) add_neighbors_mass() (pyrosetta.rosetta.core.scoring.TenANeighborNode method) add_neutral_restype() (pyrosetta.rosetta.protocols.simple_moves.IonizableResidue method) ADD_NEW (pyrosetta.rosetta.protocols.enzdes.CstAction attribute) add_new() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) add_new_chain() (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) add_new_cluster() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) add_new_data() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) add_new_RNA_jump() (pyrosetta.rosetta.core.import_pose.RNA_JumpMover method) add_new_sequence_into_global_sequence() (in module pyrosetta.rosetta.core.pose.full_model_info) add_node() (pyrosetta.rosetta.protocols.hbnet.NetworkState method) (pyrosetta.rosetta.protocols.jd3.JobDigraph method) (pyrosetta.rosetta.protocols.jd3.JobDigraphUpdater method) (pyrosetta.rosetta.utility.graph.Digraph method) add_non_protein_cst() (in module pyrosetta.rosetta.protocols.hybridization) add_npd_property_calculator_for_state() (pyrosetta.rosetta.protocols.pack_daemon.DaemonSet method) add_npdpro_calculator_creator() (pyrosetta.rosetta.protocols.pack_daemon.DaemonSet method) add_nt_seq_to_pose() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) add_nu() (pyrosetta.rosetta.core.chemical.MutableResidueType method) add_nu_action() (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) add_null_template() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) add_num_neighbors() (in module pyrosetta.rosetta.protocols.legacy_sewing) add_number_base_pairs() (in module pyrosetta.rosetta.core.pose.rna) add_number_native_base_pairs() (in module pyrosetta.rosetta.core.pose.rna) add_numeric_property() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) add_objective_function_info() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) add_obligate_pairing_set() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) add_observer() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) add_observer_cache_segments_to_set() (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface static method) add_onebody_enmeth() (pyrosetta.rosetta.core.scoring.MinimizationNode method) add_oop_constraint() (in module pyrosetta.rosetta.core.pose.ncbb) add_operation() (pyrosetta.rosetta.core.chemical.PatchCase method) add_optional_name_attribute() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) add_orbital() (pyrosetta.rosetta.core.chemical.MutableResidueType method) add_orbital_bond() (pyrosetta.rosetta.core.chemical.MutableResidueType method) add_orbitals_to_restype() (pyrosetta.rosetta.core.chemical.orbitals.AssignOrbitals method) add_ordered_subelement_set_as_optional() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) add_ordered_subelement_set_as_pick_one() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) add_ordered_subelement_set_as_pick_one_or_none() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) add_ordered_subelement_set_as_repeatable() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) add_ordered_subelement_set_as_required() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) add_other_pose() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) add_other_struct() (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) add_outgoing_edge() (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.utility.graph.DirectedNode method) add_overall_constraints() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) add_overlap_loop() (pyrosetta.rosetta.protocols.loops.Loops method) add_overlap_to_loops() (in module pyrosetta.rosetta.protocols.denovo_design.movers) add_pack_daemon() (pyrosetta.rosetta.protocols.pack_daemon.DaemonSet method) add_packer_screeners() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWiseMasterPacker method) add_pair() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing method) add_pairing() (pyrosetta.rosetta.protocols.abinitio.AlternativePairings method) (pyrosetta.rosetta.protocols.abinitio.PairingStatEntry method) (pyrosetta.rosetta.protocols.abinitio.StrandConstraints method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) add_parameter() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) add_parameters() (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) add_parameters_from_file() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) add_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) add_parent() (pyrosetta.rosetta.protocols.jd3.JGJobNode method) add_parent_entity() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) add_parent_remark() (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) add_parents_from_current_generation() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) add_pass_through() (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) add_patch_operation_line() (pyrosetta.rosetta.protocols.chemistries.PatchChemistry method) add_patches() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) add_pdb() (pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation method) add_pdb_id() (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter method) add_pdb_ids() (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter method) add_pdb_profile_pair() (pyrosetta.rosetta.protocols.splice.SpliceSegment method) add_peak() (pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator method) add_peptide_neighbor() (pyrosetta.rosetta.core.environment.FoldTreeSketch.Node method) add_per_residue_simple_metric_schema() (in module pyrosetta.rosetta.core.simple_metrics) add_perturbation_magnitude() (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) add_perturbation_type() (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) add_perturber() (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) add_point() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbAcc_t method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbDon_t method) (pyrosetta.rosetta.protocols.qsar.qsarMap method) (pyrosetta.rosetta.protocols.simple_moves.AtomHash method) add_polar_atom() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) add_polar_atom_if_doesnt_exist() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) add_polar_atoms() (pyrosetta.rosetta.protocols.hbnet.NetworkState method) add_pool() (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) add_pose() (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.protocols.loophash.BackboneDB method) (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation method) (pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation method) add_pose_input_stream() (pyrosetta.rosetta.core.import_pose.pose_stream.MetaPoseInputStream method) add_pose_segments_to_segment_vector() (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover static method) add_poseinfo_to_ss() (in module pyrosetta.rosetta.protocols.mpi_refinement) add_position() (pyrosetta.rosetta.protocols.environment.claims.EnvLabelSelector method) add_position_data() (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) add_position_in_pose() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache method) add_positive_filter() (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter method) add_postfold_mover() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) add_prefix_to_segments() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) add_prefold_mover() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) ADD_PREGENERATED (pyrosetta.rosetta.protocols.enzdes.CstAction attribute) add_pregenerated_constraints_to_pose() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) add_pregenerated_enzdes_constraints() (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) add_preparer() (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) add_primary_author() (pyrosetta.rosetta.basic.citation_manager.Citation method) add_ProCorrection_values() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) add_ProCorrection_values_for_edge() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) add_profile() (pyrosetta.rosetta.protocols.splice.SpliceSegment method) add_prohibited() (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) add_property() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector method) add_property_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) add_property_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) add_proposal_density_factor() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) add_protein() (pyrosetta.rosetta.protocols.loophash.BackboneDB method) add_proton() (pyrosetta.rosetta.protocols.noesy_assign.MethylNames method) add_proton_index() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) add_pssm_features() (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) add_query_ss() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) add_range() (pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector method) (pyrosetta.rosetta.numeric.interpolation.spline.CompoundInterpolator method) add_rcg() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) add_reactivity() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) add_ref() (pyrosetta.rosetta.cppdb.backend.connection method) (pyrosetta.rosetta.cppdb.backend.driver method) (pyrosetta.rosetta.cppdb.backend.loadable_driver method) (pyrosetta.rosetta.cppdb.backend.result method) (pyrosetta.rosetta.cppdb.backend.statement method) (pyrosetta.rosetta.cppdb.pool method) (pyrosetta.rosetta.cppdb.ref_counted method) add_reference_fragment() (pyrosetta.rosetta.protocols.drug_design.bcl.BCLReferenceSDFilesManager method) add_refiner() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) add_registered_mover() (pyrosetta.rosetta.protocols.environment.EnvMover method) add_relevant() (pyrosetta.rosetta.utility.options.OptionCollection method) add_remark() (in module pyrosetta.rosetta.protocols.denovo_design) add_remodel_constraints_to_pose() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) add_repeats() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) add_reported_value() (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric method) (pyrosetta.rosetta.protocols.filters.CalculatorFilter method) add_required_connection_for_residue() (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) add_required_connections_between_regions() (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) add_required_name_attribute() (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) add_requirement() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementSet method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) add_rerelaxed() (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) add_res() (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) add_res_identity_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) add_res_identity_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) add_resid_to_entity_list() (pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence method) add_residue() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.FragData method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.RotamerPairEnergies method) add_residue_alternative_rotamer() (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) add_residue_alternative_set() (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) add_residue_connection() (pyrosetta.rosetta.core.chemical.MutableResidueType method) add_residue_dis() (pyrosetta.rosetta.core.scoring.TMscoreStore method) add_residue_exclude_torsions() (pyrosetta.rosetta.core.scoring.GenBondedExclInfo method) add_residue_labels_back() (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) add_residue_pair() (pyrosetta.rosetta.protocols.jumping.ResiduePairJump method) add_residue_pair_jump() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) add_residue_property_by_name() (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilter method) add_residue_selector() (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) add_residue_selectors_to_datamap() (in module pyrosetta.rosetta.protocols.jd3) add_residue_single() (pyrosetta.rosetta.protocols.jumping.ResiduePairJump method) add_residue_to_perturber_residue_list() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) add_residue_type() (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) add_residue_type_by_name() (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilter method) add_residues_to_pose() (in module pyrosetta.rosetta.protocols.denovo_design) add_reslabel() (pyrosetta.rosetta.core.pose.PDBInfo method) add_reslabels_to_pose() (in module pyrosetta.rosetta.protocols.hbnet) add_resnum() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyResidueRetentionRequirement method) add_restriction() (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) add_reverse_motifs() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifs method) add_reweighter() (pyrosetta.rosetta.core.pack.task.IGEdgeReweightContainer method) add_ring() (pyrosetta.rosetta.core.chemical.MutableResidueType method) add_rms() (pyrosetta.rosetta.numeric.model_quality.RmsData method) add_rna_pairing() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) add_rosetta_options_0() (in module pyrosetta.rosetta) add_rosetta_options_1() (in module pyrosetta.rosetta) add_rosetta_options_10() (in module pyrosetta.rosetta) add_rosetta_options_11() (in module pyrosetta.rosetta) add_rosetta_options_12() (in module pyrosetta.rosetta) add_rosetta_options_13() (in module pyrosetta.rosetta) add_rosetta_options_14() (in module pyrosetta.rosetta) add_rosetta_options_15() (in module pyrosetta.rosetta) add_rosetta_options_2() (in module pyrosetta.rosetta) add_rosetta_options_3() (in module pyrosetta.rosetta) add_rosetta_options_4() (in module pyrosetta.rosetta) add_rosetta_options_5() (in module pyrosetta.rosetta) add_rosetta_options_6() (in module pyrosetta.rosetta) add_rosetta_options_7() (in module pyrosetta.rosetta) add_rosetta_options_8() (in module pyrosetta.rosetta) add_rosetta_options_9() (in module pyrosetta.rosetta) add_rotamer() (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) (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) add_rotamer_bb_torsion_index() (pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification method) add_rotamer_constraints() (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation method) add_rotamer_into_existing_group() (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) add_rotamer_line_data() (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) add_rotamer_to_rotamer_set() (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation method) add_rotamers() (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) add_rt() (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) add_rv_info() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) add_sampler() (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) add_schema() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric 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.TestPerResidueProbabilitiesMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric static method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric static method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric static method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric static method) add_schema_restrictions_for_strings() (in module pyrosetta.rosetta.utility.tag) add_score() (pyrosetta.rosetta.core.scoring.motif.XformScore method) (pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet method) (pyrosetta.rosetta.protocols.moves.MoverStatistics method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) add_score_info_to_pose() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) add_score_line_string() (in module pyrosetta.rosetta.core.pose) add_score_type() (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilter method) add_score_weights() (pyrosetta.rosetta.protocols.abinitio.CoordinateConstraintKC method) (pyrosetta.rosetta.protocols.abinitio.KinematicControl method) add_scored_pair() (pyrosetta.rosetta.core.sequence.PairScoringScheme method) add_scorer() (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyAssemblyScoreFunction method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) add_scores_for_chain() (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) add_scores_for_residue() (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) add_scoring_method() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) add_scoring_scheme() (pyrosetta.rosetta.core.sequence.CompositeScoringScheme method) add_secondary_downstream_match_geometry_for_constraint() (pyrosetta.rosetta.protocols.match.Matcher method) add_secondary_upstream_match_geometry_for_constraint() (pyrosetta.rosetta.protocols.match.Matcher method) add_section() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) add_segment() (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) add_segment_and_neighbors_to_local_segments() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) add_segment_envelopes_from_string() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector method) add_segment_fname() (pyrosetta.rosetta.protocols.splice.RotLibdb method) add_segments_for_chain() (in module pyrosetta.rosetta.protocols.denovo_design.components) add_selector() (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilter method) add_selector_rlto_pair() (pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions method) add_senior_author() (pyrosetta.rosetta.basic.citation_manager.Citation method) add_seq_label() (pyrosetta.rosetta.core.environment.SequenceAnnotation method) add_sequence() (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.SequenceAlignment method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) add_sequence_constraints() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) add_sequence_constraints_only() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) add_setup_mover() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) add_sfs_drs_enmeth() (pyrosetta.rosetta.core.scoring.MinimizationNode method) add_shear_mover() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) add_sheet() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) add_sheets() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) add_sheets_from_pose() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) add_sheets_from_spairs() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) add_shell() (in module pyrosetta.rosetta.core.membrane) add_sidechain_mc_mover() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) add_sidechain_mover() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) add_sigmoid() (pyrosetta.rosetta.core.scoring.SmoothScoreTermCoeffs method) add_similarity() (pyrosetta.rosetta.protocols.cluster.DataPoint method) add_simple_metric() (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeatures method) add_simple_subelement() (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) add_single_atom_to_power_diagram() (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) add_single_cutpoint_variant() (in module pyrosetta.rosetta.protocols.loops) add_single_magnesium() (in module pyrosetta.rosetta.protocols.magnesium) add_small_fragments() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) add_small_mover() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) add_span() (pyrosetta.rosetta.core.conformation.membrane.SpanningTopology method) add_span_embedding() (pyrosetta.rosetta.protocols.membrane.geometry.Embedding method) add_spanning_region() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) add_special_edges() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) add_sr_gaussian() (pyrosetta.rosetta.core.scoring.CenHBPotential method) add_standard_functions() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticScanner method) (pyrosetta.rosetta.numeric.expression_parser.BooleanExpressionScanner method) add_start_from() (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) add_start_res() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) add_starting_model() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) add_state() (pyrosetta.rosetta.protocols.multistate_design.MultiStateFitnessFunction method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) add_step() (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) add_str_str_data() (pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule method) add_strand() (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) add_strand_extension() (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) add_strand_pairs_cst() (in module pyrosetta.rosetta.protocols.hybridization) add_strandMover() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) add_string() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) add_string_property() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) add_string_real_pair() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) add_string_real_pair_to_current_job() (in module pyrosetta.rosetta.protocols.jd2) add_string_string_pair() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) add_string_string_pair_to_current_job() (in module pyrosetta.rosetta.protocols.jd2) add_string_to_current_job() (in module pyrosetta.rosetta.protocols.jd2) add_string_value() (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) add_strings() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) add_strings_to_current_job() (in module pyrosetta.rosetta.protocols.jd2) add_structure() (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.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.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) add_structure_replace_tag_if_necessary() (pyrosetta.rosetta.core.io.silent.SilentFileData method) add_stub_() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) add_stub_set() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) add_subelement() (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) add_subelement_for_parse_stub_sets() (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) ADD_SUBMOTIF (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.MoveType attribute) add_submotif_info() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) add_submotif_info_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) add_submover() (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) add_suckers() (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) add_sugar_ring_closure_constraints() (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential method) add_sym_dof_name() (pyrosetta.rosetta.protocols.simple_filters.InterfaceSasaFilter method) add_syn_anti_chi_constraints() (in module pyrosetta.rosetta.core.pose.rna) add_syn_chi_constraints() (in module pyrosetta.rosetta.core.pose.rna) add_tail_residue() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) add_target_constraints() (pyrosetta.rosetta.protocols.abinitio.Templates method) add_target_restype() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) add_target_selector() (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) add_task_operation() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) add_task_operations() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) add_template() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) add_template_selector() (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) add_ters_via_bonds() (in module pyrosetta.rosetta.core.io.mmtf) add_threshold_distance_allFrag() (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore method) add_to_energy_map() (pyrosetta.rosetta.core.scoring.EnergyEdge method) add_to_library() (pyrosetta.rosetta.protocols.motifs.MotifLibrary method) add_to_multimodel_pdb() (in module pyrosetta.rosetta.core.io.pdb) add_to_nodes_one_body_energy() (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) add_to_one_body_energies() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG 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.FixedBBNode 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.NodeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode 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.PrecomputedPairEnergiesNode 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.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode 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.OTFFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) add_to_one_body_energy() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NodeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) add_to_one_body_energy_for_node_state() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) add_to_onebody() (in module pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty) add_to_pose() (in module pyrosetta.rosetta.protocols.denovo_design.components) add_to_pose_list() (in module pyrosetta.rosetta.protocols.stepwise.modeler) add_to_top_level() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) add_to_two_body_energies() (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) add_to_two_body_energies_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) add_to_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) add_to_twobody() (in module pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty) add_to_weight() (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) add_top_level_element() (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) add_topology() (pyrosetta.rosetta.protocols.abinitio.PairingStatistics method) add_torerelax() (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) add_torsion() (pyrosetta.rosetta.core.fragment.rna.FragmentLibrary method) (pyrosetta.rosetta.core.kinematics.MinimizerMapBase method) (pyrosetta.rosetta.core.optimization.CartesianMinimizerMap method) (pyrosetta.rosetta.core.optimization.MinimizerMap method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) add_torsion_parameter() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) add_torsion_to_fix() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) add_torsion_to_sample() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) add_triazole_constraint() (in module pyrosetta.rosetta.core.pose.ncbb) add_trigger() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) add_trj() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) add_trj_scratch() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) add_twobody_enmeth() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) add_type() (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.pack.palette.CustomBaseTypePackerPalette method) (pyrosetta.rosetta.core.scoring.func.FuncFactory method) (pyrosetta.rosetta.core.sequence.ScoringSchemeFactory method) (pyrosetta.rosetta.protocols.comparative_modeling.features.ResidueFeatureFactory method) (pyrosetta.rosetta.protocols.moves.PyMOLObserver method) (pyrosetta.rosetta.protocols.network.UIObserver method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimerFactory method) add_unfolded_energy_data() (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor method) add_unpatchable_residue_type() (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) add_unrecognized_atoms() (pyrosetta.rosetta.core.pose.PDBInfo method) add_upper_connect_angle_params() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) add_upper_padding() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) add_upper_terminus_type_to_conformation_residue() (in module pyrosetta.rosetta.core.conformation) add_upper_terminus_type_to_pose_residue() (in module pyrosetta.rosetta.core.pose) add_upstream_restype_for_constraint() (pyrosetta.rosetta.protocols.match.Matcher method) add_user_csts() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) add_user_provided_mover() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) add_vall_cheating_fragments() (in module pyrosetta.rosetta.protocols.frags) add_vall_fragments() (in module pyrosetta.rosetta.protocols.frags) add_value_to_perturber_value_list() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) add_values_from_center() (in module pyrosetta.rosetta.core.chemical.rna) add_values_to_job() (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.jd2.JobOutputterObserver method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) add_variable() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticScanner method) (pyrosetta.rosetta.numeric.expression_parser.BooleanExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.BooleanExpressionScanner method) (pyrosetta.rosetta.numeric.expression_parser.SimpleExpressionCreator method) add_variant_type() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) add_variant_type_to_conformation_residue() (in module pyrosetta.rosetta.core.conformation) add_variant_type_to_pose_residue() (in module pyrosetta.rosetta.core.pose) add_variant_type_to_residue() (in module pyrosetta.rosetta.core.pose) add_virt_res_as_root() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) add_virtual_O2Prime_hydrogen() (in module pyrosetta.rosetta.core.pose.rna) add_virtual_res() (in module pyrosetta.rosetta.protocols.toolbox.sample_around) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) add_virtual_residue_to_cterm() (in module pyrosetta.rosetta.protocols.relax) add_virtual_sugar_res() (in module pyrosetta.rosetta.core.import_pose) add_vital_residue() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) add_warnings() (pyrosetta.rosetta.utility.tag.XMLValidationOutput method) add_water_overcoordinated_hb_score() (in module pyrosetta.rosetta.protocols.hydrate) add_weight() (pyrosetta.rosetta.numeric.random.WeightedSampler method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) add_weights_from_file() (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) add_whole_pose_context_enmeth() (pyrosetta.rosetta.core.scoring.MinimizationGraph method) add_wholeStructureMover() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) add_wildtypes() (pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet method) add_wt() (pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData method) add_wt_complex() (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData method) add_wt_unbounds() (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData method) add_xsd_options() (pyrosetta.rosetta.core.pack.palette.CustomBaseTypePackerPalette static method) AddAllPositionsMPM (class in pyrosetta.rosetta.protocols.match) AddAromaticAtomType() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) AddAssemblyConstraints (class in pyrosetta.rosetta.protocols.domain_assembly) AddAtom (class in pyrosetta.rosetta.core.chemical) AddAtom() (pyrosetta.rosetta.core.scoring.sc.ContactMolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeSimilarityCalculator method) addAtom() (pyrosetta.rosetta.RDKit.RWMol method) AddAtomAlias (class in pyrosetta.rosetta.core.chemical) AddAtomType() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) AddBehaviorRLT (class in pyrosetta.rosetta.core.pack.task.operation) AddBehaviorRLTCreator (class in pyrosetta.rosetta.core.pack.task.operation) AddBond (class in pyrosetta.rosetta.core.chemical) addBond() (pyrosetta.rosetta.RDKit.RWMol method) AddBondType (class in pyrosetta.rosetta.core.chemical) AddCavitiesMover (class in pyrosetta.rosetta.protocols.simple_moves) AddCDRProfileSetsOperation (class in pyrosetta.rosetta.protocols.antibody.task_operations) AddCDRProfileSetsOperationCreator (class in pyrosetta.rosetta.protocols.antibody.task_operations) AddCDRProfilesOperation (class in pyrosetta.rosetta.protocols.antibody.task_operations) AddCDRProfilesOperationCreator (class in pyrosetta.rosetta.protocols.antibody.task_operations) AddChainBreak (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) AddChainBreakCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) AddChainMover (class in pyrosetta.rosetta.protocols.simple_moves) AddChainMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) AddChi (class in pyrosetta.rosetta.core.chemical) AddChiRotamer (class in pyrosetta.rosetta.core.chemical) addCleanup() (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) AddCompositionConstraintMover (class in pyrosetta.rosetta.protocols.aa_composition) AddCompositionConstraintMoverCreator (class in pyrosetta.rosetta.protocols.aa_composition) addConformer() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) AddConnect (class in pyrosetta.rosetta.core.chemical) AddConnectAndTrackingVirt (class in pyrosetta.rosetta.core.chemical) AddConnectDeleteChildProton (class in pyrosetta.rosetta.core.chemical) AddConstraints (class in pyrosetta.rosetta.protocols.constraint_generator) AddConstraintsCreator (class in pyrosetta.rosetta.protocols.constraint_generator) AddConstraintsToCurrentConformationMover (class in pyrosetta.rosetta.protocols.constraint_movers) AddConstraintsToCurrentConformationMover.AtomSelector (class in pyrosetta.rosetta.protocols.constraint_movers) AddConstraintsToCurrentConformationMoverCreator (class in pyrosetta.rosetta.protocols.constraint_movers) addcount() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) ADDED_STRUCTURE_AS_INTENDED (pyrosetta.rosetta.protocols.optimize_weights.AddStatus attribute) ADDED_STRUCTURE_OPPOSITE_AS_INTENDED (pyrosetta.rosetta.protocols.optimize_weights.AddStatus attribute) addEntry() (pyrosetta.rosetta.protocols.sparta.GDB method) AddExpression (class in pyrosetta.rosetta.numeric.expression_parser) AddFlankingVirtualResiduesMover (class in pyrosetta.rosetta.protocols.pose_sewing.movers) AddFlankingVirtualResiduesMoverCreator (class in pyrosetta.rosetta.protocols.pose_sewing.movers) AddGood2BPairEnergyRotamers (class in pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations) AddHelixSequenceConstraintsMover (class in pyrosetta.rosetta.protocols.aa_composition) AddHelixSequenceConstraintsMoverCreator (class in pyrosetta.rosetta.protocols.aa_composition) AddHydrogen (class in pyrosetta.rosetta.protocols.ligand_docking) AddHydrogens (class in pyrosetta.rosetta.protocols.ligand_docking) AddHydrogensCreator (class in pyrosetta.rosetta.protocols.ligand_docking) additional_metrics() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) additional_string_output() (pyrosetta.rosetta.core.io.StructFileRep method) AdditionalOutputWrapper (class in pyrosetta.rosetta.protocols.rosetta_scripts) AdditionalOutputWrapperCreator (class in pyrosetta.rosetta.protocols.rosetta_scripts) AdditiveAtomicPolarizability (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) AddJobPairData (class in pyrosetta.rosetta.protocols.simple_moves) AddJobPairDataCreator (class in pyrosetta.rosetta.protocols.simple_moves) AddLigandMotifRotamers (class in pyrosetta.rosetta.protocols.enzdes) AddLigandMotifRotamersOperationCreator (class in pyrosetta.rosetta.protocols.enzdes) AddMembraneMover (class in pyrosetta.rosetta.protocols.membrane) AddMembraneMoverCreator (class in pyrosetta.rosetta.protocols.membrane) AddMembraneSpanConstraint (class in pyrosetta.rosetta.protocols.membrane) AddMembraneSpanConstraintCreator (class in pyrosetta.rosetta.protocols.membrane) AddMembraneSpanTermZConstraint (class in pyrosetta.rosetta.protocols.membrane) AddMembraneSpanTermZConstraintCreator (class in pyrosetta.rosetta.protocols.membrane) AddMHCEpitopeConstraintMover (class in pyrosetta.rosetta.protocols.aa_composition) AddMHCEpitopeConstraintMoverCreator (class in pyrosetta.rosetta.protocols.aa_composition) AddMover (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) AddMoverCreator (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) AddMPLigandMover (class in pyrosetta.rosetta.protocols.membrane) AddMPLigandMoverCreator (class in pyrosetta.rosetta.protocols.membrane) addnativesolution() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) AddNetChargeConstraintMover (class in pyrosetta.rosetta.protocols.aa_composition) AddNetChargeConstraintMoverCreator (class in pyrosetta.rosetta.protocols.aa_composition) AddOrDeleteMover (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) AddOrRemoveMatchCsts (class in pyrosetta.rosetta.protocols.enzdes) AddOrRemoveMatchCstsCreator (class in pyrosetta.rosetta.protocols.enzdes) AddPDBInfoMover (class in pyrosetta.rosetta.protocols.simple_moves) AddPDBInfoMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) AddProperty (class in pyrosetta.rosetta.core.chemical) AddProtonChi (class in pyrosetta.rosetta.core.chemical) AddPyMOLObserver() (in module pyrosetta.rosetta.protocols.moves) AddPyMOLObserver_to_conformation() (in module pyrosetta.rosetta.protocols.moves) AddPyMOLObserver_to_energies() (in module pyrosetta.rosetta.protocols.moves) addRemark() (pyrosetta.rosetta.protocols.sparta.GDB method) AddResidue() (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) AddResidueCouplingConstraint (class in pyrosetta.rosetta.protocols.simple_moves) AddResidueCouplingConstraintCreator (class in pyrosetta.rosetta.protocols.simple_moves) AddResidueLabelMover (class in pyrosetta.rosetta.protocols.simple_moves) AddResidueLabelMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) AddResiduesRotamerSetOperation (class in pyrosetta.rosetta.core.pack.rotamer_set) address() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) address_ (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.PoolData property) address_exists_in_cache() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) address_to_buf() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.DataBuffer method) AddRigidBodyLigandConfs (class in pyrosetta.rosetta.protocols.enzdes) AddRigidBodyLigandConfsCreator (class in pyrosetta.rosetta.protocols.enzdes) addRing() (pyrosetta.rosetta.RDKit.RingInfo method) adds_atoms() (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) adds_properties() (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) adds_properties_enums() (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) adds_property() (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.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) adds_property_enum() (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.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) AddSapConstraintMover (class in pyrosetta.rosetta.protocols.simple_moves) AddSapConstraintMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) AddSapMathConstraintMover (class in pyrosetta.rosetta.protocols.simple_moves) AddSapMathConstraintMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) addScoresForLoopParts() (in module pyrosetta.rosetta.protocols.loops) AddSearchPatternRotSetOp (class in pyrosetta.rosetta.protocols.hotspot_hashing) AddSegmentDataMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) AddSegmentDataMoverCreator (class in pyrosetta.rosetta.protocols.denovo_design.movers) AddSidechainConstraintsToHotspots (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) AddSidechainConstraintsToHotspotsCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) AddStatus (class in pyrosetta.rosetta.protocols.optimize_weights) addTag() (pyrosetta.rosetta.utility.tag.Tag method) addTypeEqualityFunc() (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) Adduct (class in pyrosetta.rosetta.core.chemical) ADDUCT (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) adduct_name() (pyrosetta.rosetta.core.chemical.Adduct method) ADDUCT_VARIANT (pyrosetta.rosetta.core.chemical.VariantType attribute) adducts() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) AddUIObserver() (in module pyrosetta.rosetta.protocols.network) AddUIObserver_to_conformation() (in module pyrosetta.rosetta.protocols.network) AddUIObserver_to_energies() (in module pyrosetta.rosetta.protocols.network) addVAR() (pyrosetta.rosetta.protocols.sparta.GDB method) addVirtualResAsRoot() (in module pyrosetta.rosetta.core.pose) addVirtualResAsRootMembrane() (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) AddZincSiteConstraints (class in pyrosetta.rosetta.protocols.metal_interface) ADJ_LIST_MODE (class in pyrosetta.rosetta.protocols.cluster.calibur) ADJ_Tab (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) adjacent_lists_ (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) AdjacentList (class in pyrosetta.rosetta.protocols.cluster.calibur) AdjacentRemainingNodes() (in module pyrosetta.rosetta.protocols.toolbox) adjFileName (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) adjust_mm_to_length() (in module pyrosetta.rosetta.protocols.seeded_abinitio) adjust_n_ter_tail_length() (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) adjust_position_for_chain() (in module pyrosetta.rosetta.protocols.tcr) adjust_relax_movemap() (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) adjust_stem_positions_by_template() (pyrosetta.rosetta.protocols.splice.SpliceManager method) adjust_stem_positions_by_template_ (pyrosetta.rosetta.protocols.splice.SpliceManager property) adjust_template_jump() (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) advance_euler_angles() (in module pyrosetta.rosetta.protocols.match) advance_to_next_pose_segment() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) affected() (pyrosetta.rosetta.cppdb.backend.statement method) (pyrosetta.rosetta.cppdb.statement method) affiliation() (pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleAuthor method) affix_has_inherent_position() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager static method) after (pyrosetta.rosetta.protocols.denovo_design.task_operations.SurroundingSS property) AFTER_APPLY (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol.FilterReportTime attribute) Ag (pyrosetta.rosetta.core.chemical.element.Elements attribute) AgglomerativeHierarchicalClusterer (class in pyrosetta.rosetta.numeric) aggregate_add() (pyrosetta.rosetta.core.scoring.motif.XformScore method) aggregate_function() (pyrosetta.rosetta.protocols.multistate_design.MultiStateFitnessFunction method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) (pyrosetta.rosetta.protocols.pack_daemon.MPIMultistateFitnessFunction method) (pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction method) aggregate_max() (pyrosetta.rosetta.core.scoring.motif.XformScore method) AHdist_long_fade_lookup() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) AHdist_poly_lookup() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) AHdist_short_fade_lookup() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) AHO_Scheme (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingSchemeEnum attribute) Ai() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) Ai_ (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo property) ai_cmp (class in pyrosetta.rosetta.core.io.mmtf) aid (pyrosetta.rosetta.core.scoring.packstat.Sphere property) Al (pyrosetta.rosetta.core.chemical.element.Elements attribute) ala_constraint_over_strength() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) ala_constraint_under_strength() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) ala_pose_loop() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) AlaScan (class in pyrosetta.rosetta.protocols.simple_ddg) AlaScanFilterCreator (class in pyrosetta.rosetta.protocols.simple_ddg) ALDONIC_ACID (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) ALDONIC_ACID_VARIANT (pyrosetta.rosetta.core.chemical.VariantType attribute) ALDOSE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) algorithm() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) algorithm_ (pyrosetta.rosetta.protocols.match.upstream.BuildSet property) algorithm_inputs() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo method) Alias (class in pyrosetta.rosetta.protocols.denovo_design.components) alias() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) aliases() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) align() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.sequence.Aligner method) (pyrosetta.rosetta.core.sequence.MCAligner method) (pyrosetta.rosetta.core.sequence.NWAligner method) (pyrosetta.rosetta.core.sequence.SWAligner method) (pyrosetta.rosetta.numeric.Py_xyzTransform_double static method) (pyrosetta.rosetta.numeric.xyzTransform_double_t static method) (pyrosetta.rosetta.numeric.xyzTransform_float_t static method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) align_and_calculate_rmsd() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) align_and_output_to_silent_file() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) align_angle() (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilter method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing method) align_by_domain() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) align_c() (pyrosetta.rosetta.protocols.sic_dock.Rose method) align_fast() (pyrosetta.rosetta.numeric.Py_xyzTransform_double static method) (pyrosetta.rosetta.numeric.xyzTransform_double_t static method) (pyrosetta.rosetta.numeric.xyzTransform_float_t static method) align_mainchain_atoms() (in module pyrosetta.rosetta.protocols.helical_bundle) align_mainchain_atoms_of_residue_range() (in module pyrosetta.rosetta.protocols.helical_bundle) align_model() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) align_motif_pose() (in module pyrosetta.rosetta.core.scoring.motif) align_motif_pose_break() (in module pyrosetta.rosetta.core.scoring.motif) align_motif_pose_by_one_frame() (in module pyrosetta.rosetta.core.scoring.motif) align_motif_pose_super() (in module pyrosetta.rosetta.core.scoring.motif) align_multipole_axes() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) align_n() (pyrosetta.rosetta.protocols.sic_dock.Rose method) align_naive() (in module pyrosetta.rosetta.core.sequence) align_output() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) align_pdb() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) align_pose() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAligner method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) align_pose_and_add_rmsd_constraints() (in module pyrosetta.rosetta.protocols.stepwise.modeler.align) align_poses() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) align_poses_naive() (in module pyrosetta.rosetta.core.sequence) align_residue_multipole_axes() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) ALIGN_RMSD (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) Align_RmsdEvaluator (class in pyrosetta.rosetta.protocols.comparative_modeling) Align_RotamerEvaluator (class in pyrosetta.rosetta.protocols.comparative_modeling) align_segment() (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) align_templates_by_domain() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) align_to_current_phore_match() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo method) align_to_native() (in module pyrosetta.rosetta.protocols.antibody) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) align_to_native_pose() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication method) align_to_residue() (pyrosetta.rosetta.core.conformation.UltraLightResidue method) align_virtual_atoms_in_carbohydrate_residue() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) (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) align_working_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker method) align_working_to_vdw_atom_id_map (pyrosetta.rosetta.core.pose.rna.VDW_RepScreenInfo property) alignaxis() (in module pyrosetta.rosetta.protocols.sic_dock) alignaxis_xform() (in module pyrosetta.rosetta.protocols.sic_dock) AlignByResidueSelectorMover (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) AlignByResidueSelectorMoverCreator (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) AlignChainMover (class in pyrosetta.rosetta.protocols.simple_moves) AlignChainMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) aligned() (pyrosetta.rosetta.protocols.star.Extender method) AlignedThreadOperation (class in pyrosetta.rosetta.protocols.task_operations) AlignedThreadOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) AlignEndsMover (class in pyrosetta.rosetta.protocols.splice) AlignEndsMoverCreator (class in pyrosetta.rosetta.protocols.splice) Aligner (class in pyrosetta.rosetta.core.sequence) AlignerFactory (class in pyrosetta.rosetta.core.sequence) AlignEvaluator (class in pyrosetta.rosetta.protocols.evaluation) alignment (pyrosetta.rosetta.core.scoring.ScoreType attribute) alignment() (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) alignment2AtomMap() (pyrosetta.rosetta.protocols.hybridization.TMalign method) alignment2strings() (pyrosetta.rosetta.protocols.hybridization.TMalign method) ALIGNMENT_ANCHOR_RES (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) alignment_anchor_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) alignment_atoms_num (pyrosetta.rosetta.protocols.sewing.data_storage.LigandDescription property) alignment_atoms_str (pyrosetta.rosetta.protocols.sewing.data_storage.LigandDescription property) alignment_file() (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation method) alignment_from_pose() (in module pyrosetta.rosetta.core.sequence) alignment_generator() (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) alignment_id() (pyrosetta.rosetta.core.sequence.SequenceAlignment method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) alignment_into_pose() (in module pyrosetta.rosetta.core.sequence) alignment_length (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult property) alignment_probabilities() (in module pyrosetta.rosetta.protocols.medal) alignment_settings() (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) alignment_settings_from_options() (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) alignment_settings_from_tag() (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover static method) AlignmentAAFinder (class in pyrosetta.rosetta.protocols.evolution) AlignmentAAFinderFilterCreator (class in pyrosetta.rosetta.protocols.evolution) AlignmentAtom (class in pyrosetta.rosetta.core.kinematics.inverse) AlignmentAtomArray (class in pyrosetta.rosetta.core.kinematics.inverse) AlignmentCluster (class in pyrosetta.rosetta.protocols.comparative_modeling) AlignmentClustering (class in pyrosetta.rosetta.protocols.comparative_modeling) AlignmentEnergy (class in pyrosetta.rosetta.protocols.rna) AlignmentEnergyCreator (class in pyrosetta.rosetta.protocols.rna) AlignmentFGMSettings (class in pyrosetta.rosetta.protocols.sewing.hashing) AlignmentFileGeneratorMover (class in pyrosetta.rosetta.protocols.sewing.hashing) AlignmentFileGeneratorMoverCreator (class in pyrosetta.rosetta.protocols.sewing.hashing) AlignmentGapInserter (class in pyrosetta.rosetta.protocols.evolution) AlignmentGapInserterFilterCreator (class in pyrosetta.rosetta.protocols.evolution) AlignmentGenerator (class in pyrosetta.rosetta.protocols.sewing.hashing) alignments() (pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet method) (pyrosetta.rosetta.protocols.jd2.InnerMultiThreadingJob method) alignments_from_cmd_line() (in module pyrosetta.rosetta.protocols.comparative_modeling) AlignmentSet (class in pyrosetta.rosetta.protocols.comparative_modeling) AlignmentSettings (class in pyrosetta.rosetta.protocols.sewing.hashing) AlignMove (class in pyrosetta.rosetta.core.sequence) AlignOption (class in pyrosetta.rosetta.protocols.hybridization) AlignPDBInfoToSequences (class in pyrosetta.rosetta.protocols.pdbinfo_manipulations) AlignPDBInfoToSequences_namer() (in module pyrosetta.rosetta.protocols.pdbinfo_manipulations) AlignPDBInfoToSequencesCreator (class in pyrosetta.rosetta.protocols.pdbinfo_manipulations) AlignPDBInfoToSequencesMode (class in pyrosetta.rosetta.protocols.pdbinfo_manipulations) alignpdbinfotosequencesmode_to_string() (in module pyrosetta.rosetta.protocols.pdbinfo_manipulations) alignPerfectCA() (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) AlignPoseToInvrotTreeMover (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) AlignResiduesMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) AlignResiduesMoverCreator (class in pyrosetta.rosetta.protocols.denovo_design.movers) AlignRMSD_Screener (class in pyrosetta.rosetta.protocols.stepwise.screener) AlignRmsdTargetEvaluatorCreator (class in pyrosetta.rosetta.protocols.comparative_modeling) alignStrand() (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) ALIPHATIC (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) (pyrosetta.rosetta.core.chemical.rings.RingSaturationType attribute) all (pyrosetta.bindings.pose.PoseScoreAccessor property)

ALL (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover.AtomSelector attribute) all() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChainNumbering method) all_add_energy() (pyrosetta.rosetta.protocols.wum.SilentStructStore method) all_aligned() (pyrosetta.rosetta.core.id.SequenceMapping method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) all_atom_center() (in module pyrosetta.rosetta.core.conformation) (in module pyrosetta.rosetta.core.pose) all_atom_mode_ (pyrosetta.rosetta.protocols.ligand_docking.LigandArea property) all_atom_rmsd() (in module pyrosetta.rosetta.core.scoring) all_atom_rmsd_incl_hydrogens() (in module pyrosetta.rosetta.core.scoring) all_atom_rmsd_nosuper() (in module pyrosetta.rosetta.core.scoring) all_atoms() (pyrosetta.rosetta.core.chemical.MutableResidueType method) all_bb() (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) all_bb_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) all_bondangles() (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) all_bondlengths() (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) all_branches() (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) all_broker_files() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) all_cdr_fold_tree() (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) all_cdr_loops (pyrosetta.rosetta.protocols.antibody_legacy.Antibody property) all_cdr_VL_VH_fold_tree() (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) all_cdrs() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) all_chi() (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) all_chunks (pyrosetta.rosetta.protocols.hybridization.AlignOption attribute) all_default() (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_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) ALL_DNA_TYPES_ON (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) all_energies() (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) all_false_selection() (in module pyrosetta.rosetta.core.select.residue_selector) all_job_results_for_node() (pyrosetta.rosetta.protocols.jd3.JobGenealogist method) all_jobs_completed() (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) all_jobs_started() (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) all_jumps() (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) all_L_dssp() (in module pyrosetta.rosetta.core.select.residue_selector) (in module pyrosetta.rosetta.protocols.pose_sewing) all_lDDT() (pyrosetta.rosetta.core.scoring.lDDT_Calculator method) all_lex_states (pyrosetta.rosetta.protocols.match.MatcherOutputStats property) all_lores_score_final() (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) all_methods() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) all_nu() (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) all_pairs_shortest_paths() (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.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Graph method) all_ref_poses() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) all_results_are_in() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.EvenlyPartitionedNodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) all_rna_fragments_file() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) ALL_SASA (pyrosetta.rosetta.core.scoring.sasa.SasaMethodHPMode attribute) all_sc_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) all_scatom_rmsd_nosuper() (in module pyrosetta.rosetta.core.scoring) all_segments() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) all_sort_silent_scores() (pyrosetta.rosetta.protocols.wum.SilentStructStore method) ALL_STAGES (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints attribute) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper attribute) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio attribute) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio.StageID attribute) (pyrosetta.rosetta.protocols.abinitio.StageID attribute) all_stats (pyrosetta.rosetta.protocols.moves.StatsType attribute) all_target_res() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleResidueInvrotTarget method) all_true_selection() (in module pyrosetta.rosetta.core.select.residue_selector) all_turn_residues_are_on_the_same_chain() (pyrosetta.rosetta.protocols.features.BetaTurnDetection method) all_types_with_variants_aa_already_cached() (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) all_types_with_variants_residuetypecops_already_cached() (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) all_waste_is_discarded() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.EvenlyPartitionedNodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) ALLAA (class in pyrosetta.rosetta.core.pack.task) ALLAAwc (class in pyrosetta.rosetta.core.pack.task) ALLAAxc (class in pyrosetta.rosetta.core.pack.task) AllAtomNormalization (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) AllBB (pyrosetta.rosetta.protocols.canonical_sampling.TorsionSpecStyle attribute) AllChi (pyrosetta.rosetta.protocols.canonical_sampling.TorsionSpecStyle attribute) AlleleMatrix (class in pyrosetta.rosetta.core.scoring.mhc_epitope_energy) alllevel() (pyrosetta.rosetta.core.sequence.ABEGOManager method) allocate_matrix() (in module pyrosetta.rosetta.protocols.frag_picker.scores) allocated() (pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t method) allocateSpaceForRMSD() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) allow_all_aa() (pyrosetta.rosetta.protocols.splice.Splice method) allow_all_aas() (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) ALLOW_ALTERNATE_BACKBONE_MATCHING (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) allow_base_pair_only_centroid_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) allow_base_pair_only_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker method) allow_bulge() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) allow_bulge_at_chainbreak() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) allow_chi_copy_ (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover property) allow_claim() (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) allow_consecutive_bulges() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) allow_delete() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) allow_design() (pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) allow_design_around() (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation method) allow_dof() (pyrosetta.rosetta.core.conformation.symmetry.SymDof method) allow_duplicates (pyrosetta.rosetta.protocols.environment.claims.ResidueElement property) allow_even_trades() (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation method) allow_fragment_moves_in_bps() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) allow_hbond() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) allow_insert_res() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) allow_internal_hinge_moves() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) allow_internal_local_moves() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) allow_peptide_flips() (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) allow_peptoid_flips() (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) allow_phosphate_virtualization() (pyrosetta.rosetta.core.pack.task.rna.RNA_ResidueLevelTask method) allow_pre_gly_flips() (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) allow_pure_movers() (pyrosetta.rosetta.protocols.environment.Environment method) allow_rama_mismatches() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher method) allow_reading_cancelled_decoys() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) allow_rebuild_bulge_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) allow_repacking() (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) allow_scoring() (pyrosetta.rosetta.core.scoring.MembraneTopology method) allow_split_off() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) allow_submotif_split() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) allow_syn_pyrimidine() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) allow_tmh_scoring() (pyrosetta.rosetta.core.scoring.MembraneTopology method) allow_virtual_o2prime_hydrogens() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) allow_virtual_side_chains() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) allowed_bulge_res() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) allowed_closure_attempts() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) allowed_current_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) allowed_cuts() (pyrosetta.rosetta.protocols.splice.SpliceManager method) allowed_failure_before_stop (pyrosetta.rosetta.protocols.LoopRebuild property) allowed_output_modes() (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric static method) allowed_output_modes_as_vector() (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric static method) allowed_res_name3_at_position() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) allowed_res_name3s() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo method) allowed_res_types() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) allowed_res_types_pointers() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) allowed_residue_types() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) allowed_restypes() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo method) allowed_seqpos() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo method) allowed_types() (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.motifs.BuildPosition method) AllowedSeqposForGeomCst (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) AllowPdbIdFilter (class in pyrosetta.rosetta.protocols.frag_picker) AllResFilter (class in pyrosetta.rosetta.core.pack.task.operation) AllResFilterCreator (class in pyrosetta.rosetta.core.pack.task.operation) AllResiduesChanged (class in pyrosetta.rosetta.protocols.abinitio) (class in pyrosetta.rosetta.protocols.hybridization) allsc() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) ALPHA (pyrosetta.rosetta.core.chemical.rna.RNA_Torsion attribute) alpha (pyrosetta.rosetta.core.optimization.lbfgs_iteration_data property) (pyrosetta.rosetta.core.scoring.fiber_diffraction.Hankel property) (pyrosetta.rosetta.protocols.protein_interface_design.Transformation property) ALPHA() (in module pyrosetta.rosetta.numeric.crick_equations) alpha() (pyrosetta.rosetta.core.io.CrystInfo method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) (pyrosetta.rosetta.protocols.dna.DNABase method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.EulerAngles method) ALPHA6_LINKS (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType attribute) ALPHA_AA (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) (pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobianTypeEnum attribute) alpha_aa_rama_check (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.filter_type attribute) alpha_aform() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) ALPHA_ATOM (pyrosetta.rosetta.core.chemical.GreekDistance attribute) alpha_components() (pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential method) alpha_deriv_func() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) alpha_func() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) ALPHA_LINKS (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType attribute) ALPHA_SUGAR (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) alphabet() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) alphamax (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName property) alphamin (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName property) ALREADY_SYMMETRIZED (pyrosetta.rosetta.core.pack.task.PackerTaskSymmetryStatus attribute) alt (pyrosetta.rosetta.core.scoring.sc._PROBE property) 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) alt_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) alt_loc() (pyrosetta.rosetta.core.pose.PDBInfo method) alt_rot_matrix() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) alt_sc_centroid() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) alt_sc_radius() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) alt_state_energy() (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) alter_espGrid() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) alter_espGrid_with_bound_ligand() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) alter_rotamer_set() (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.protocols.hotspot_hashing.SearchPatternRotSetOp method) (pyrosetta.rosetta.protocols.matdes.MotifHitsRotamersOperation method) (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2_RotamerSetOperation 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) alter_rotamer_set_from_db() (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation method) alter_rotamer_set_from_pdb() (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation method) alter_rotamer_sets() (pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminator method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetsOperation method) (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsats_RotamerSetsOperation method) alternate_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) alternate_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) alternate_state_is_being_considered() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) alternate_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) alternate_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) alternate_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) alternative_decoys_out() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) ALTERNATIVE_PROTONATION (pyrosetta.rosetta.core.chemical.VariantType attribute) AlternativePairings (class in pyrosetta.rosetta.protocols.abinitio) AlterSpecDisruptionDriver (class in pyrosetta.rosetta.protocols.pmut_scan) altitude_max (pyrosetta.rosetta.protocols.hotspot_hashing.SphericalRotationSearchPattern property) altitude_min (pyrosetta.rosetta.protocols.hotspot_hashing.SphericalRotationSearchPattern property) altitude_rotation_sampling (pyrosetta.rosetta.protocols.hotspot_hashing.SphericalRotationSearchPattern property) altLoc (pyrosetta.rosetta.core.io.AtomInformation property) (pyrosetta.rosetta.core.pose.PDBInfo.AtomRecord property) ALWAYS_CLEAR (pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum attribute) Am (pyrosetta.rosetta.core.chemical.element.Elements attribute) AmberPeriodicFunc (class in pyrosetta.rosetta.core.scoring.func) AmbigCSScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) ambiguity() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties 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) ambiguous() (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) ambiguous_hnq() (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) AmbiguousConstraint (class in pyrosetta.rosetta.core.scoring.constraints) AmbiguousConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) AmbiguousMultiConstraint (class in pyrosetta.rosetta.protocols.constraints_additional) AmbiguousNMRConstraint (class in pyrosetta.rosetta.core.scoring.constraints) AmbiguousNMRConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) AmbiguousNMRDistanceConstraint (class in pyrosetta.rosetta.core.scoring.constraints) AmbiguousNMRDistanceConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) AMINO_SUGAR (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) aminoAcidList (pyrosetta.rosetta.protocols.forge.remodel.LineObject property) AminoAcidNeighborSparseMatrix_float_t (class in pyrosetta.rosetta.core.pack.interaction_graph) amoeba_type_lookup() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) amplitude (pyrosetta.rosetta.core.chemical.rna.GaussianParameter property) amplitude() (pyrosetta.rosetta.protocols.dna.DNABase method) aN (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) ana_deriv() (pyrosetta.rosetta.core.optimization.DerivCheckDataPoint method) (pyrosetta.rosetta.core.optimization.DOF_DataPoint method) analytic_etable_derivatives() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) analytic_etable_evaluation (pyrosetta.rosetta.core.scoring.etable.EtableOptions property) analytic_etable_evaluation() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) analytic_lk_derivatives() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) analytic_lk_energy() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) analytic_membetable_evaluation (pyrosetta.rosetta.core.scoring.etable.EtableOptions property) analytic_membetable_evaluation() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) analytic_params_for_pair() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) AnalyticEtableEnergy (class in pyrosetta.rosetta.core.scoring.etable) AnalyticEtableEvaluator (class in pyrosetta.rosetta.core.scoring.etable) analyze() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetric method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.SequenceMetric method) analyze_and_filter() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) AnalyzeLoopModeling (class in pyrosetta.rosetta.protocols.pose_length_moves) AnalyzeLoopModelingCreator (class in pyrosetta.rosetta.protocols.pose_length_moves) anb (pyrosetta.rosetta.core.scoring.packstat.CavityBall property) anc_grandparent (pyrosetta.rosetta.core.chemical.Ancestor attribute) anc_greatgrandparent (pyrosetta.rosetta.core.chemical.Ancestor attribute) anc_parent (pyrosetta.rosetta.core.chemical.Ancestor attribute) Ancestor (class in pyrosetta.rosetta.core.chemical) Anchor (class in pyrosetta.rosetta.protocols.anchored_design) anchor_at_res1() (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) anchor_atom() (pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo method) anchor_end() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) anchor_noise_constraints_setup() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) anchor_offset() (pyrosetta.rosetta.protocols.multistate_design.PartitionAggregateFunction method) anchor_res() (pyrosetta.rosetta.protocols.splice.SpliceManager method) anchor_residue() (pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo method) anchor_residue_substrate() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) anchor_resnum() (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) anchor_specified() (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) anchor_start() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) ANCHOR_SUGAR (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) anchor_sugar_modeling() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) anchor_sugar_solution_number() (pyrosetta.rosetta.protocols.stepwise.screener.AnchorSugarScreener method) anchored_loop() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) AnchoredDesignMover (class in pyrosetta.rosetta.protocols.anchored_design) AnchoredGraftMover (class in pyrosetta.rosetta.protocols.grafting) AnchoredGraftMoverCreator (class in pyrosetta.rosetta.protocols.grafting) AnchoredPerturbMover (class in pyrosetta.rosetta.protocols.anchored_design) AnchoredRefineMover (class in pyrosetta.rosetta.protocols.anchored_design) AnchorMoversData (class in pyrosetta.rosetta.protocols.anchored_design) anchors() (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter method) AnchorSugarScreener (class in pyrosetta.rosetta.protocols.stepwise.screener) AND (pyrosetta.rosetta.protocols.filters.boolean_operations attribute) (pyrosetta.rosetta.protocols.task_operations.boolean_operations attribute) AND_combine() (in module pyrosetta.rosetta.core.select.residue_selector) and_extrachi_cutoff() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) and_linmem_ig() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) and_logic (pyrosetta.rosetta.core.select.residue_selector.basic_selection_logic attribute) and_max_rotbump_energy() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) AND_SYMBOL (pyrosetta.rosetta.numeric.expression_parser.TokenType attribute) and_with() (pyrosetta.rosetta.protocols.match.Bool3DGrid method) (pyrosetta.rosetta.protocols.match.BumpGrid method) AndExpression (class in pyrosetta.rosetta.numeric.expression_parser) AndJumpSelector (class in pyrosetta.rosetta.core.select.jump_selector) AndJumpSelectorCreator (class in pyrosetta.rosetta.core.select.jump_selector) ANDNOT (pyrosetta.rosetta.protocols.filters.boolean_operations attribute) (pyrosetta.rosetta.protocols.task_operations.boolean_operations attribute) AndResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) AndResidueSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) AndSelector (class in pyrosetta.rosetta.protocols.pose_selectors) AndSelectorCreator (class in pyrosetta.rosetta.protocols.pose_selectors) ang_U1D2 (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleConstraint property) ang_U1D2_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) ang_U2D1 (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleConstraint property) ang_U2D1_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) angle (pyrosetta.rosetta.core.scoring.packstat.trace property) (pyrosetta.rosetta.protocols.cartesian.MD_Angle property) (pyrosetta.rosetta.protocols.cartesian.MD_HarmonicDihedral property) (pyrosetta.rosetta.protocols.ligand_docking.Transform_info property) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble_info property) (pyrosetta.rosetta.protocols.make_rot_lib.CentroidRotNum property) angle() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) (pyrosetta.rosetta.numeric.Quaternion_double_t method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondingAtom method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ConstraintFulfilmentFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ConstraintResidueSelector method) (pyrosetta.rosetta.protocols.loophash.BackboneDB method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) angle_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) angle_constraint_energy() (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) angle_degrees() (in module pyrosetta.rosetta.numeric) angle_degrees_double() (in module pyrosetta.rosetta.numeric) angle_degrees_in_range() (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) angle_diff() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) angle_disp() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) angle_distance() (in module pyrosetta.rosetta.core.scoring.motif) angle_exponent() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions method) (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) angle_in_range() (in module pyrosetta.rosetta.basic) angle_magnitude() (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover method) angle_max() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) angle_parameters() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) angle_radians() (in module pyrosetta.rosetta.numeric) angle_radians_double() (in module pyrosetta.rosetta.numeric) angle_range_bb() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) angle_range_chi() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) angle_range_free_bb() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) angle_range_free_chi() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) angle_resl_ (pyrosetta.rosetta.core.scoring.motif.MotifHash property) (pyrosetta.rosetta.core.scoring.motif.XformScore property) angle_shift_factor() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions method) (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) angle_threshold() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) angle_tolerance() (pyrosetta.rosetta.numeric.NumericTraits_double_t static method) (pyrosetta.rosetta.numeric.NumericTraits_float_t static method) (pyrosetta.rosetta.numeric.NumericTraits_long_double_t static method) angle_weight() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) angleA (pyrosetta.rosetta.protocols.jumping.cstType attribute) angleB (pyrosetta.rosetta.protocols.jumping.cstType attribute) AngleConstraint (class in pyrosetta.rosetta.core.scoring.constraints) AngleConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) angles (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData property) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData property) (pyrosetta.rosetta.protocols.loophash.BBData property) angleTo() (pyrosetta.rosetta.RDGeom.Point3D method) AngleToVector (class in pyrosetta.rosetta.protocols.simple_filters) AngleToVectorFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) AngleUnit (class in pyrosetta.rosetta.numeric.conversions) angstroms (pyrosetta.rosetta.protocols.ligand_docking.Translate_info property) angth (pyrosetta.rosetta.protocols.kinmatch.KRSQuery property) AngularMomentumQuantumNumber_strings() (pyrosetta.rosetta.core.chemical.ElectronConfiguration static method) animate() (pyrosetta.rosetta.core.conformation.ResidueKinWriter method) (pyrosetta.rosetta.protocols.match.output.ResidueKinemageWriter method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage method) ANISOU (pyrosetta.rosetta.core.io.pdb.RecordType attribute) ANN (class in pyrosetta.rosetta.protocols.sparta) ann (pyrosetta.rosetta.protocols.environment.EnvClaimBroker.BrokerResult property) ANN_CS_OUTPUT_FULL (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) ANN_IN_MTX (pyrosetta.rosetta.protocols.sparta.ANN property) (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) ANN_IN_MTX_LEVEL1 (pyrosetta.rosetta.protocols.sparta.ANN property) ANN_IN_MTX_LEVEL2 (pyrosetta.rosetta.protocols.sparta.ANN property) ANN_OUT_MTX_LEVEL1 (pyrosetta.rosetta.protocols.sparta.ANN property) ANN_OUT_MTX_LEVEL2 (pyrosetta.rosetta.protocols.sparta.ANN property) AnnealableGraphBase (class in pyrosetta.rosetta.core.pack.interaction_graph) annealer_file() (pyrosetta.rosetta.core.pack.annealer.DebuggingAnnealer method) AnnealerFactory (class in pyrosetta.rosetta.core.pack.annealer) AnnealerObserver (class in pyrosetta.rosetta.core.pack.annealer) annotate() (pyrosetta.rosetta.protocols.environment.claims.CutBiasClaim method) (pyrosetta.rosetta.protocols.environment.claims.EnvClaim method) (pyrosetta.rosetta.protocols.environment.claims.JumpClaim method) (pyrosetta.rosetta.protocols.environment.claims.TorsionClaim method) (pyrosetta.rosetta.protocols.environment.claims.VirtResClaim method) (pyrosetta.rosetta.protocols.environment.claims.XYZClaim method) annotate_backbone() (in module pyrosetta.rosetta.core.chemical) annotated_name() (pyrosetta.rosetta.core.conformation.Residue method) annotated_sequence() (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) (pyrosetta.rosetta.protocols.topology_broker.claims.SequenceClaim method) annotated_sequence_from_IUPAC_sequence() (pyrosetta.rosetta.core.io.NomenclatureManager static method) annotated_sequence_from_modomics_oneletter_sequence() (pyrosetta.rosetta.core.io.NomenclatureManager static method) annotated_to_oneletter_sequence() (in module pyrosetta.rosetta.core.pose) AnnotatedFragData (class in pyrosetta.rosetta.core.fragment) AnnotatedSequence (class in pyrosetta.rosetta.core.sequence) annotations() (pyrosetta.rosetta.core.io.rna.RDAT method) (pyrosetta.rosetta.protocols.environment.Environment method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) anomer() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) anomeric (pyrosetta.rosetta.core.chemical.carbohydrates.RootData property) anomeric_carbon() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) anomeric_carbon_index() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) anomeric_carbon_name() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) anomeric_position_from_code() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager static method) anomeric_pseudotorsion() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) anomeric_sidechain_index() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) ANTI (pyrosetta.rosetta.core.chemical.rna.ChiState attribute) (pyrosetta.rosetta.core.fragment.rna.SYN_ANTI_RESTRICTION attribute) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType attribute) Antibody (class in pyrosetta.rosetta.protocols.antibody_legacy) antibody_DB() (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) antibody_grafting_usable() (in module pyrosetta.rosetta.protocols.antibody.grafting) antibody_modeling_insert_ter() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) antibody_region_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) antibody_region_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) AntibodyCDRGrafter (class in pyrosetta.rosetta.protocols.antibody) AntibodyCDRGrafterCreator (class in pyrosetta.rosetta.protocols.antibody) AntibodyChain (class in pyrosetta.rosetta.protocols.antibody.grafting) AntibodyChainNumbering (class in pyrosetta.rosetta.protocols.antibody.grafting) AntibodyDatabaseManager (class in pyrosetta.rosetta.protocols.antibody) AntibodyDesignEnumManager (class in pyrosetta.rosetta.protocols.antibody.design) AntibodyDesignMover (class in pyrosetta.rosetta.protocols.antibody.design) AntibodyDesignMoverCreator (class in pyrosetta.rosetta.protocols.antibody.design) AntibodyDesignProtocolEnum (class in pyrosetta.rosetta.protocols.antibody.design) AntibodyEnumManager (class in pyrosetta.rosetta.protocols.antibody) AntibodyFeatures (class in pyrosetta.rosetta.protocols.antibody) AntibodyFeaturesCreator (class in pyrosetta.rosetta.protocols.antibody) AntibodyFramework (class in pyrosetta.rosetta.protocols.antibody.grafting) AntibodyInfo (class in pyrosetta.rosetta.protocols.antibody) AntibodyModeler (class in pyrosetta.rosetta.protocols.antibody_legacy) AntibodyModelerProtocol (class in pyrosetta.rosetta.protocols.antibody) AntibodyNumbering (class in pyrosetta.rosetta.protocols.antibody) (class in pyrosetta.rosetta.protocols.antibody.grafting) AntibodyNumberingConverterMover (class in pyrosetta.rosetta.protocols.antibody) AntibodyNumberingConverterMoverCreator (class in pyrosetta.rosetta.protocols.antibody) AntibodyNumberingParser (class in pyrosetta.rosetta.protocols.antibody) AntibodyNumberingSchemeEnum (class in pyrosetta.rosetta.protocols.antibody) AntibodyNumberingSchemeEnum_start (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingSchemeEnum attribute) AntibodyNumberingSchemeEnum_total (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingSchemeEnum attribute) AntibodyRegionEnum (class in pyrosetta.rosetta.protocols.antibody) AntibodyRegionEnum_start (pyrosetta.rosetta.protocols.antibody.AntibodyRegionEnum attribute) AntibodyRegionEnum_total (pyrosetta.rosetta.protocols.antibody.AntibodyRegionEnum attribute) AntibodyRegionSelector (class in pyrosetta.rosetta.protocols.antibody.residue_selector) AntibodyRegionSelectorCreator (class in pyrosetta.rosetta.protocols.antibody.residue_selector) AntibodySeqDesignTFCreator (class in pyrosetta.rosetta.protocols.antibody.design) AntibodySequence (class in pyrosetta.rosetta.protocols.antibody.grafting) antigen_present() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) antigen_region (pyrosetta.rosetta.protocols.antibody.AntibodyRegionEnum attribute) ANTIPARALLEL (pyrosetta.rosetta.core.chemical.rna.BaseDoubletOrientation attribute) antiparallel() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.protocols.abinitio.AlternativePairings method) ANY (pyrosetta.rosetta.core.fragment.rna.SYN_ANTI_RESTRICTION attribute) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) any() (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.HBondBonusOptions method) any_active_enmeths() (pyrosetta.rosetta.core.scoring.MinimizationEdge method) ANY_BASE_DOUBLET_ORIENTATION (pyrosetta.rosetta.core.chemical.rna.BaseDoubletOrientation attribute) ANY_BASE_EDGE (pyrosetta.rosetta.core.chemical.rna.BaseEdge attribute) ANY_BASE_STACK_SIDE (pyrosetta.rosetta.core.chemical.rna.BaseStackWhichSide attribute) ANY_CHI (pyrosetta.rosetta.core.chemical.rna.ChiState attribute) any_exposed_dots() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) any_lr_residue_pair_energy() (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) ANY_LW_BASE_DOUBLET_ORIENTATION (pyrosetta.rosetta.core.chemical.rna.LW_BaseDoubletOrientation attribute) any_neighbors_for_residue() (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) ANY_OPTION (pyrosetta.rosetta.utility.options.OptionTypes attribute) ANY_PUCKER (pyrosetta.rosetta.core.chemical.rna.PuckerState attribute) ANY_TORSION (pyrosetta.rosetta.core.chemical.rna.RNA_Torsion attribute) any_type (class in pyrosetta.rosetta.utility.type_traits.has_insertion_operator_implementation) any_unassigned() (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) any_upper_neighbors_for_residue() (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) ANY_VECTOR_OPTION (pyrosetta.rosetta.utility.options.OptionTypes attribute) any_vertex_state_unassigned() (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) AnyOptionKey (class in pyrosetta.rosetta.utility.options) AnyResFilter (class in pyrosetta.rosetta.core.pack.task.operation) AnyResFilterCreator (class in pyrosetta.rosetta.core.pack.task.operation) AnyVectorOptionKey (class in pyrosetta.rosetta.utility.options) APBSConfig (class in pyrosetta.rosetta.core.scoring) APBSConfig.I_PARAM (class in pyrosetta.rosetta.core.scoring) APBSConfig.R_PARAM (class in pyrosetta.rosetta.core.scoring) APBSResult (class in pyrosetta.rosetta.core.scoring) APBSWrapper (class in pyrosetta.rosetta.core.scoring) APCluster (class in pyrosetta.rosetta.protocols.cluster) apol_calcenergy (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) apol_calcforce (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) APOLA (class in pyrosetta.rosetta.core.pack.task) APOLAR (class in pyrosetta.rosetta.core.pack.task) apolar_target() (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilter method) APolarHydrogenFilter (class in pyrosetta.rosetta.core.chemical) append() (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.epr_deer.DEERDataCache method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo 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.expression_parser.TokenSet 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.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoints 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.vector_core_io_AtomInformation method) (pyrosetta.rosetta.std.vector_core_io_RemarkInfo method) (pyrosetta.rosetta.std.vector_core_pose_Pose method) (pyrosetta.rosetta.std.vector_core_scoring_hbonds_graph_HBondInfo method) (pyrosetta.rosetta.std.vector_core_scoring_sc__DOT method) (pyrosetta.rosetta.std.vector_core_scoring_sc_Atom method) (pyrosetta.rosetta.std.vector_double method) (pyrosetta.rosetta.std.vector_float method) (pyrosetta.rosetta.std.vector_int method) (pyrosetta.rosetta.std.vector_numeric_xyzMatrix_double_t method) (pyrosetta.rosetta.std.vector_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.vector_protocols_cluster_Cluster method) (pyrosetta.rosetta.std.vector_protocols_motif_grafting_movers_MotifMatch method) (pyrosetta.rosetta.std.vector_RDGeom_Point3D method) (pyrosetta.rosetta.std.vector_RDKit_Dict_Pair method) (pyrosetta.rosetta.std.vector_std_list_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.vector_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t method) (pyrosetta.rosetta.std.vector_std_map_unsigned_long_unsigned_long_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_pair_std_shared_ptr_protocols_filters_Filter_protocols_filters_boolean_operations_t method) (pyrosetta.rosetta.std.vector_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_set_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_chemical_Orbital_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_fragment_FragSet_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_pose_Pose_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_cluster_calibur_Stru_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_hbnet_HBondNetStruct_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_std_list_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.vector_std_string method) (pyrosetta.rosetta.std.vector_std_vector_double_t method) (pyrosetta.rosetta.std.vector_std_vector_int_t method) (pyrosetta.rosetta.std.vector_std_vector_std_string_t method) (pyrosetta.rosetta.std.vector_std_vector_std_vector_double_t method) (pyrosetta.rosetta.std.vector_std_vector_unsigned_long_t method) (pyrosetta.rosetta.std.vector_unsigned_int method) (pyrosetta.rosetta.std.vector_unsigned_long method) (pyrosetta.rosetta.std.vector_utility_file_FileName method) (pyrosetta.rosetta.std.vector_utility_json_spirit_Pair_impl_utility_json_spirit_Config_vector_std_string_t method) (pyrosetta.rosetta.std.vector_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t method) (pyrosetta.rosetta.std.vector_utility_json_spirit_Value_impl_utility_json_spirit_Config_vector_std_string_t method) (pyrosetta.rosetta.std.vector_utility_signals_Link method) (pyrosetta.rosetta.std.vector_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.vector_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.std.vector_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.std.vector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.utility.deep_copy_vector1_std_shared_ptr_core_chemical_Orbital_t method) (pyrosetta.rosetta.utility.vector0_core_conformation_ppo_torsion_bin method) (pyrosetta.rosetta.utility.vector0_core_id_AtomID_Map_bool_t method) (pyrosetta.rosetta.utility.vector0_core_io_AtomInformation method) (pyrosetta.rosetta.utility.vector0_double method) (pyrosetta.rosetta.utility.vector0_float method) (pyrosetta.rosetta.utility.vector0_int method) (pyrosetta.rosetta.utility.vector0_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector0_protocols_flexpack_interaction_graph_FlexbbSparseMatrixIndex method) (pyrosetta.rosetta.utility.vector0_std_list_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.utility.vector0_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector0_std_pair_float_float_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_moves_Mover_t method) (pyrosetta.rosetta.utility.vector0_std_string method) (pyrosetta.rosetta.utility.vector0_unsigned_char method) (pyrosetta.rosetta.utility.vector0_unsigned_long method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_double_3_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_double_5_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_utility_fixedsizearray0_double_3_3_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_utility_fixedsizearray0_double_5_5_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray1_double_16_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_core_io_AtomInformation_std_allocator_core_io_AtomInformation_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_int_std_allocator_int_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_std_list_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_list_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_std_allocator_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_std_pair_int_int_std_allocator_std_pair_int_int_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_basic_citation_manager_AuthorNames method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_Column method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_ForeignKey method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_Index method) (pyrosetta.rosetta.utility.vector1_basic_sampling_orientations_QuatDBMetadata method) (pyrosetta.rosetta.utility.vector1_bool method) (pyrosetta.rosetta.utility.vector1_char method) (pyrosetta.rosetta.utility.vector1_const_utility_vector1_int_std_allocator_int__star_t method) (pyrosetta.rosetta.utility.vector1_core_chemical_AA method) (pyrosetta.rosetta.utility.vector1_core_chemical_Adduct method) (pyrosetta.rosetta.utility.vector1_core_chemical_AtomICoor method) (pyrosetta.rosetta.utility.vector1_core_chemical_AtomType method) (pyrosetta.rosetta.utility.vector1_core_chemical_BondName method) (pyrosetta.rosetta.utility.vector1_core_chemical_io_merge_residue_behavior method) (pyrosetta.rosetta.utility.vector1_core_chemical_MutableResidueConnection method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResConnID method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResidueConnection method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty method) (pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingConformer method) (pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingSaturationType method) (pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter method) (pyrosetta.rosetta.utility.vector1_core_chemical_rna_PuckerState method) (pyrosetta.rosetta.utility.vector1_core_chemical_VariantType method) (pyrosetta.rosetta.utility.vector1_core_conformation_Atom method) (pyrosetta.rosetta.utility.vector1_core_conformation_PseudoBond method) (pyrosetta.rosetta.utility.vector1_core_conformation_signals_LengthEvent method) (pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue method) (pyrosetta.rosetta.utility.vector1_core_fragment_FragData method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_scores_VallFragmentScore method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection method) (pyrosetta.rosetta.utility.vector1_core_fragment_rna_SYN_ANTI_RESTRICTION method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_bool_t method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.utility.vector1_core_id_DOF_ID method) (pyrosetta.rosetta.utility.vector1_core_id_NamedAtomID method) (pyrosetta.rosetta.utility.vector1_core_id_TorsionID method) (pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range method) (pyrosetta.rosetta.utility.vector1_core_io_AtomInformation method) (pyrosetta.rosetta.utility.vector1_core_io_HELIXInformation method) (pyrosetta.rosetta.utility.vector1_core_io_LinkInformation method) (pyrosetta.rosetta.utility.vector1_core_io_ResidueInformation method) (pyrosetta.rosetta.utility.vector1_core_io_SHEETInformation method) (pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy method) (pyrosetta.rosetta.utility.vector1_core_io_SSBondInformation method) (pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Edge method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Jump method) (pyrosetta.rosetta.utility.vector1_core_kinematics_RT method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Stub method) (pyrosetta.rosetta.utility.vector1_core_optimization_DerivCheckDataPoint method) (pyrosetta.rosetta.utility.vector1_core_optimization_DOF_DataPoint method) (pyrosetta.rosetta.utility.vector1_core_pack_annealer_PointDwell method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbond method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_sap_BlockParam method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_DotSphere method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_exposed_hydrophobic_data method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_RotamerDots method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_SparseMatrixIndex method) (pyrosetta.rosetta.utility.vector1_core_pack_rotamer_set_ContinuousRotamerSet method) (pyrosetta.rosetta.utility.vector1_core_pack_scmin_ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.utility.vector1_core_pack_task_operation_ResiduePDBIndexIs_ChainPos method) (pyrosetta.rosetta.utility.vector1_core_pack_task_ResidueLevelTask_ method) (pyrosetta.rosetta.utility.vector1_core_pose_PDBInfo_AtomRecord method) (pyrosetta.rosetta.utility.vector1_core_pose_PDBInfo_ResidueRecord method) (pyrosetta.rosetta.utility.vector1_core_pose_Pose method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_Atom_Bin method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_BaseStack method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_Datum method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_Reactivity method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_SuiteInfo method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_VDW_RepScreenInfo method) (pyrosetta.rosetta.utility.vector1_core_pose_UnrecognizedAtomRecord method) (pyrosetta.rosetta.utility.vector1_core_scoring_bin_transitions_BT_PROPERTIES method) (pyrosetta.rosetta.utility.vector1_core_scoring_CSA method) (pyrosetta.rosetta.utility.vector1_core_scoring_DC method) (pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair method) (pyrosetta.rosetta.utility.vector1_core_scoring_disulfides_DisulfideDerivativeAtom method) (pyrosetta.rosetta.utility.vector1_core_scoring_dssp_Pairing method) (pyrosetta.rosetta.utility.vector1_core_scoring_dssp_StrandPairing method) (pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector method) (pyrosetta.rosetta.utility.vector1_core_scoring_epr_deer_EPRSpinLabel method) (pyrosetta.rosetta.utility.vector1_core_scoring_etable_EtableParamsOnePair method) (pyrosetta.rosetta.utility.vector1_core_scoring_etable_etrie_GenericResidueConnectionData method) (pyrosetta.rosetta.utility.vector1_core_scoring_fiber_diffraction_OneGaussianScattering method) (pyrosetta.rosetta.utility.vector1_core_scoring_GenTorsionParams method) (pyrosetta.rosetta.utility.vector1_core_scoring_Hairpin method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_HBondEdge method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_HBondNode method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_HBEvalTuple method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_HBondWeightType method) (pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_Loop method) (pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_LoopCycle method) (pyrosetta.rosetta.utility.vector1_core_scoring_mhc_epitope_energy_AlleleMatrix method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_MotifHit method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_ResPairMotif method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_Xfres method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_pcs_PCSSingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_pre_PRESingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_rdc_RDCSingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_packing_Ball method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBall method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBallCluster method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_LR_AtomData method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_LR_MP_AtomData method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_SimplePDB_Atom method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_Sphere method) (pyrosetta.rosetta.utility.vector1_core_scoring_power_diagram_SAnode method) (pyrosetta.rosetta.utility.vector1_core_scoring_RDC method) (pyrosetta.rosetta.utility.vector1_core_scoring_RDC_Rohl method) (pyrosetta.rosetta.utility.vector1_core_scoring_rna_RNA_Motif method) (pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType method) (pyrosetta.rosetta.utility.vector1_core_scoring_SmallAtNb method) (pyrosetta.rosetta.utility.vector1_core_scoring_SmoothScoreTermCoeffs method) (pyrosetta.rosetta.utility.vector1_core_scoring_SpringParams method) (pyrosetta.rosetta.utility.vector1_core_scoring_tableID method) (pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange method) (pyrosetta.rosetta.utility.vector1_core_sequence_Line method) (pyrosetta.rosetta.utility.vector1_core_sequence_SequenceAlignment method) (pyrosetta.rosetta.utility.vector1_double method) (pyrosetta.rosetta.utility.vector1_float method) (pyrosetta.rosetta.utility.vector1_int method) (pyrosetta.rosetta.utility.vector1_long method) (pyrosetta.rosetta.utility.vector1_numeric_CubicPolynomial method) (pyrosetta.rosetta.utility.vector1_numeric_geometry_hashing_Ball method) (pyrosetta.rosetta.utility.vector1_numeric_histograms_TwoDHistogram_unsigned_long_long_t method) (pyrosetta.rosetta.utility.vector1_numeric_HomogeneousTransform_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_BicubicSpline method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_CubicSpline method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_interp_range method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_Point method) (pyrosetta.rosetta.utility.vector1_numeric_MultiDimensionalHistogram method) (pyrosetta.rosetta.utility.vector1_numeric_random_WeightedSampler method) (pyrosetta.rosetta.utility.vector1_numeric_RocPoint method) (pyrosetta.rosetta.utility.vector1_numeric_urs_Quat method) (pyrosetta.rosetta.utility.vector1_numeric_xyzMatrix_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzTransform_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzVector_float_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray1D_double_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray2D_double_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_AlternativePairings method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_ClassicAbinitio_StageID method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_PairingStatEntry method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_StageID method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_AntibodyNumberingSchemeEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRDefinitionEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRNameEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_clusters_CDRClusterEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_clusters_ClusterData method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_design_PDBNumbering method) (pyrosetta.rosetta.utility.vector1_protocols_backbone_moves_local_backbone_mover_Residue method) (pyrosetta.rosetta.utility.vector1_protocols_backrub_BackrubSegment method) (pyrosetta.rosetta.utility.vector1_protocols_branch_angle_BranchCoef1 method) (pyrosetta.rosetta.utility.vector1_protocols_branch_angle_BranchCoef2 method) (pyrosetta.rosetta.utility.vector1_protocols_canonical_sampling_DbTrajectoryRecorder_Frame method) (pyrosetta.rosetta.utility.vector1_protocols_canonical_sampling_TorsionSpec method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_CartesianAtom method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_Angle method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_Bond method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_HarmonicDihedral method) (pyrosetta.rosetta.utility.vector1_protocols_cluster_DataPoint method) (pyrosetta.rosetta.utility.vector1_protocols_cluster_Exemplar method) (pyrosetta.rosetta.utility.vector1_protocols_constraints_additional_ConstraintEvaluator method) (pyrosetta.rosetta.utility.vector1_protocols_contact_map_Contact method) (pyrosetta.rosetta.utility.vector1_protocols_cyclic_peptide_PSM_StubMode method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_BondInfo method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_StructureSlice method) (pyrosetta.rosetta.utility.vector1_protocols_features_TaskOperationFeatures_Taskop_id_name_factory_ method) (pyrosetta.rosetta.utility.vector1_protocols_fold_from_loops_utils_NubSegment method) (pyrosetta.rosetta.utility.vector1_protocols_forge_build_Interval method) (pyrosetta.rosetta.utility.vector1_protocols_frag_picker_LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareTotalScore_t method) (pyrosetta.rosetta.utility.vector1_protocols_helical_bundle_BPC_Parameters method) (pyrosetta.rosetta.utility.vector1_protocols_hotspot_hashing_VectorPair method) (pyrosetta.rosetta.utility.vector1_protocols_hybridization_detailedControlsTagSetting method) (pyrosetta.rosetta.utility.vector1_protocols_indexed_structure_store_BackboneStub method) (pyrosetta.rosetta.utility.vector1_protocols_jd2_archive_Batch method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_chunk_library_ChunkLibraryPreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_dag_node_managers_ResultElements method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_full_model_FullModelPreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_standard_PreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_DisulfPairing method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_JumpSelector_JumpWeightDef method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_JumpSetup_JumpDef method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_ResiduePairJumpSetup_JumpDef method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewAtom method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewResidue method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_AtomProperties method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_GADockStageParams method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_Pharmacophore method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_ReweightableRepEnergy method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionDistrParams method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionType method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ligand_options_InterfaceInfo method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ProtLigPair_info method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolution method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolutionStore method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_ResTorsions method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_SheetPositions method) (pyrosetta.rosetta.utility.vector1_protocols_loops_Loop method) (pyrosetta.rosetta.utility.vector1_protocols_loops_LoopFromFileData method) (pyrosetta.rosetta.utility.vector1_protocols_loops_Loops method) (pyrosetta.rosetta.utility.vector1_protocols_loops_SerializedLoop method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_CentroidRotNum method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_RotData method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_TorsionRange method) (pyrosetta.rosetta.utility.vector1_protocols_match_Hit method) (pyrosetta.rosetta.utility.vector1_protocols_match_match_dspos1 method) (pyrosetta.rosetta.utility.vector1_protocols_match_ProbeRadius method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_BuildSet method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_hit method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_SampleStrategyData method) (pyrosetta.rosetta.utility.vector1_protocols_md_Constraint method) (pyrosetta.rosetta.utility.vector1_protocols_md_MDscheduleData method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_AAMatrix method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_RotMatrix method) (pyrosetta.rosetta.utility.vector1_protocols_membrane_SpanInfo method) (pyrosetta.rosetta.utility.vector1_protocols_monte_carlo_AcceptedScores method) (pyrosetta.rosetta.utility.vector1_protocols_motif_grafting_movers_motif2scaffold_indexes method) (pyrosetta.rosetta.utility.vector1_protocols_moves_TrialCounter method) (pyrosetta.rosetta.utility.vector1_protocols_mpi_refinement_MethodParams method) (pyrosetta.rosetta.utility.vector1_protocols_multistate_design_SingleStateEntityData method) (pyrosetta.rosetta.utility.vector1_protocols_nonlocal_Chunk method) (pyrosetta.rosetta.utility.vector1_protocols_optimize_weights_WeightRangeConstraint method) (pyrosetta.rosetta.utility.vector1_protocols_pack_daemon_StructureFileNames method) (pyrosetta.rosetta.utility.vector1_protocols_pdbinfo_manipulations_SequenceSpecification method) (pyrosetta.rosetta.utility.vector1_protocols_pmut_scan_Mutant method) (pyrosetta.rosetta.utility.vector1_protocols_pmut_scan_MutationData method) (pyrosetta.rosetta.utility.vector1_protocols_pose_creation_MergePDBMover_Overlap method) (pyrosetta.rosetta.utility.vector1_protocols_pose_creation_SliceToMiniProteinMover_Chunk method) (pyrosetta.rosetta.utility.vector1_protocols_pose_metric_calculators_EnergiesData method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_mutt method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_tm_region method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_VLBInstruction method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_Transformation method) (pyrosetta.rosetta.utility.vector1_protocols_qsar_ColorGradient method) (pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBResidueRange method) (pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment method) (pyrosetta.rosetta.utility.vector1_protocols_recces_Histogram method) (pyrosetta.rosetta.utility.vector1_protocols_relax_DatabaseRelaxScript method) (pyrosetta.rosetta.utility.vector1_protocols_rigid_Partner method) (pyrosetta.rosetta.utility.vector1_protocols_rosetta_scripts_ParsedProtocol_ParsedProtocolStep method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataCenter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataLanthanide method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsEnergyParameter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsGridSearchParameter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsInputLine method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs_PCS_data_per_lanthanides method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs_PCS_line_data method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs1_PCS_data_per_lanthanides_Ts1 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs1_PCS_line_data_Ts1 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_data_per_lanthanides_Ts2 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_line_data_Ts2 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs3_PCS_data_per_lanthanides_Ts3 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs3_PCS_line_data_Ts3 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs4_PCS_data_per_lanthanides_Ts4 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs4_PCS_line_data_Ts4 method) (pyrosetta.rosetta.utility.vector1_protocols_seeded_abinitio_SegmentSpec method) (pyrosetta.rosetta.utility.vector1_protocols_sewing_data_storage_ContactDescription method) (pyrosetta.rosetta.utility.vector1_protocols_sewing_data_storage_LigandDescription method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_Quat method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_RegionalConnections method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_ResidueDepthFrag method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_IonizableResidue method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_LoggedFragmentMover_Item method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_TorsionPerturbType method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_WaterRot method) (pyrosetta.rosetta.utility.vector1_protocols_splice_BBDofs method) (pyrosetta.rosetta.utility.vector1_protocols_splice_ResidueBBDofs method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_protein_MainChainTorsionSet method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_rna_Combine_Tags_Info method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_rna_phosphate_PhosphateMove method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_monte_carlo_mover_Attachment method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_monte_carlo_mover_StepWiseMove method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_sampler_copy_dofs_ResidueAlternativeSet method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_CstResInteractions method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ExternalGeomSampler method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ResInteractions method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_SingleConstraint method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint method) (pyrosetta.rosetta.utility.vector1_protocols_trajectory_DbTrajectoryWriter_Frame method) (pyrosetta.rosetta.utility.vector1_short method) (pyrosetta.rosetta.utility.vector1_signed_char method) (pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_downstream_hit_t method) (pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_upstream_hit_t method) (pyrosetta.rosetta.utility.vector1_std_array_int_3_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_std_shared_ptr_const_protocols_match_downstream_SecMatchResiduePairEvaluator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_shared_ptr_const_numeric_expression_parser_Expression_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_shared_ptr_protocols_pack_daemon_NPDPropCalculator_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_list_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_core_chemical_AA_utility_vector1_double_std_allocator_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_protocols_jumping_cstType_unsigned_long_std_less_protocols_jumping_cstType_std_allocator_std_pair_const_protocols_jumping_cstType_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_protocols_jumping_dofType_unsigned_long_std_less_protocols_jumping_dofType_std_allocator_std_pair_const_protocols_jumping_dofType_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_shared_ptr_const_core_conformation_Residue_double_std_less_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_pair_const_std_shared_ptr_const_core_conformation_Residue_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t 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) 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(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) append_aa_composition_setup_files() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) append_atom() (pyrosetta.rosetta.core.io.ResidueInformation 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) append_atoms() (pyrosetta.rosetta.core.io.ResidueInformation method) append_attributes() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSDCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerChiDiff static 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) (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.RRProtocolReferenceStructure static 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) (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) append_attributes_for_tag_parsing() (pyrosetta.rosetta.core.io.silent.SilentFileOptions static method) append_char() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.Sequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) append_choices() (pyrosetta.rosetta.protocols.genetic_algorithm.Mutate1Randomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) append_combine_history() (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) append_comparer_attributes() (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) append_data_and_recalculate() (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTraceFactory method) append_dist_id() (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) append_downstream_atom_to_active_site_required_list() (pyrosetta.rosetta.protocols.match.MatcherTask method) append_fold_tree_to_file() (in module pyrosetta.rosetta.protocols.backrub) append_fragment() (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) append_gap() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.Sequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) append_hairpin() (pyrosetta.rosetta.core.scoring.Hairpins method) append_hbond() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) append_index() (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) append_input_source() (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) append_job_results_that_should_be_discarded() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.EvenlyPartitionedNodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) append_ligand_docking_scores() (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) append_ligands_subelement() (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover static method) append_mg_bound_water() (in module pyrosetta.rosetta.protocols.magnesium) append_mhc_epitope_setup_files() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) append_model() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) append_movie_frame() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) append_name_and_attributes_to_complex_type() (in module pyrosetta.rosetta.utility.tag) append_netcharge_setup_files() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) append_new_chain_from_template_segment() (in module pyrosetta.rosetta.protocols.denovo_design.components) append_new_residues() (in module pyrosetta.rosetta.protocols.denovo_design.components) append_op() (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) append_outputter() (pyrosetta.rosetta.protocols.jd3.output.MultipleOutputter method) append_particle() (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) append_particles() (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) append_peptide() (pyrosetta.rosetta.core.environment.FoldTreeSketch method) append_polymer_residue_after_seqpos() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) append_pose_by_bond() (in module pyrosetta.rosetta.protocols.indexed_structure_store) append_pose_by_jump() (pyrosetta.rosetta.core.pose.Pose method) append_pose_to_pose() (in module pyrosetta.rosetta.core.pose) append_pose_to_pose_keep_fold_tree() (in module pyrosetta.rosetta.protocols.fold_from_loops.utils) append_pose_with_glycan_residues() (in module pyrosetta.rosetta.core.pose) append_pose_with_overlap() (in module pyrosetta.rosetta.protocols.indexed_structure_store) append_protocol_attributes() (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) append_reporter_attributes() (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory method) append_required_name_and_attributes_to_complex_type() (in module pyrosetta.rosetta.utility.tag) append_res() (pyrosetta.rosetta.core.pose.PDBInfo method) append_residue() (pyrosetta.rosetta.core.environment.FoldTreeSketch method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.kinematics.FoldTree method) append_residue_by_atoms() (pyrosetta.rosetta.core.pose.Pose method) append_residue_by_bond() (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) append_residue_by_chemical_bond() (pyrosetta.rosetta.core.kinematics.FoldTree method) append_residue_by_jump() (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) append_residue_selector_subelements() (in module pyrosetta.rosetta.protocols.jd3) append_residue_to_sfr() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) append_residues() (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) append_residues_from_template_segment() (in module pyrosetta.rosetta.protocols.denovo_design.components) append_rotamer_operation() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) append_rotamerset_operation() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) append_rotamersets_operation() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) append_schema_attributes() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions static method) (pyrosetta.rosetta.core.io.StructFileReaderOptions static method) (pyrosetta.rosetta.core.io.StructFileRepOptions static method) (pyrosetta.rosetta.core.scoring.etable.EtableOptions static method) (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions static method) append_segments() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) append_seq() (pyrosetta.rosetta.core.environment.SequenceAnnotation method) append_single_far_away_water() (in module pyrosetta.rosetta.protocols.hydrate) append_single_scorefxn_subelement() (in module pyrosetta.rosetta.protocols.jd3) append_specification() (pyrosetta.rosetta.protocols.jd3.output.MultipleOutputSpecification method) append_subelement_and_attributes_for_parse_loops_from_tag() (in module pyrosetta.rosetta.protocols.loop_modeling.utilities) append_subelement_for_parse_movemap_factory_legacy() (in module pyrosetta.rosetta.protocols.rosetta_scripts) append_subpose_to_pose() (in module pyrosetta.rosetta.core.pose) append_to_additional_string_output() (pyrosetta.rosetta.core.io.StructFileRep method) append_to_edge_map() (pyrosetta.rosetta.protocols.sewing.hashing.EdgeMapGenerator method) append_to_fragment_store() (pyrosetta.protocols.h5_fragment_store_provider.H5PyFragmentStoreProvider method) (pyrosetta.rosetta.protocols.indexed_structure_store.BinaryFragmentStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreProvider method) append_to_tag() (pyrosetta.rosetta.protocols.stepwise.screener.TagDefinition method) append_twobody_energy() (pyrosetta.rosetta.protocols.hbnet.NetworkState method) append_upstream_resiue_as_defining_active_site() (pyrosetta.rosetta.protocols.match.MatcherTask method) append_virtual_residue_to_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) AppendAssemblyMover (class in pyrosetta.rosetta.protocols.sewing.movers) AppendAssemblyMoverCreator (class in pyrosetta.rosetta.protocols.sewing.movers) AppendMainchainAtom (class in pyrosetta.rosetta.core.chemical) AppendResidueRotamerSet (class in pyrosetta.rosetta.core.pack.task.operation) AppendResidueRotamerSetCreator (class in pyrosetta.rosetta.core.pack.task.operation) AppendRotamer (class in pyrosetta.rosetta.core.pack.task.operation) AppendRotamerCreator (class in pyrosetta.rosetta.core.pack.task.operation) AppendRotamerSet (class in pyrosetta.rosetta.core.pack.task.operation) AppendRotamerSetCreator (class in pyrosetta.rosetta.core.pack.task.operation) applicable() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.Pool_Evaluator method) (pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator method) (pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluator method) (pyrosetta.rosetta.protocols.evaluation.AlignEvaluator method) (pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator method) (pyrosetta.rosetta.protocols.evaluation.PoseEvaluator method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_long_t method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_Size method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_SSize method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_unsigned_long_t method) (pyrosetta.rosetta.protocols.evaluation.TimeEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.BatchEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.BatchNrEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.ExternalEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.JumpEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.LoopRmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.RDC_Evaluator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SelectGdtEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SelectMaxsubEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SelectRDC_Evaluator method) (pyrosetta.rosetta.protocols.simple_filters.SelectRmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.StructuralSimilarityEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricRmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.TruncatedScoreEvaluator method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluator method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper method) Application (pyrosetta.rosetta.basic.citation_manager.CitedModuleType attribute) APPLICATIONS_OR_APPLICATION_PROTOCOLS (pyrosetta.rosetta.basic.thread_manager.RosettaThreadRequestOriginatingLevel attribute) applies_to() (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) applies_to_placeholder() (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) 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(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) 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(pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SecstructSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.UpJumpSRFD method) (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric method) (pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminatorTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLT 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.ClashBasedRepackShell method) 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(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.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.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) 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(pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.numeric.Quaternion_double_t 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.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.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.design.ResnumFromStringsWithRangesSelector method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastComparator method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastComparator_BitScore_Resolution method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_alignment_length method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_outlier method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_pdbid method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_length method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_bfactor method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_resolution method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_nonmatching_prolines method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Comparator method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Functor 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.free_peptide_movers.CircularPermuteFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.FreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.LongAxisRotationFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.ShearFreePeptideMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers.TranslationFreePeptideMover 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.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.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.Pool_Evaluator 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.chemistries.Chemistry method) (pyrosetta.rosetta.protocols.chemistries.PatchChemistry method) (pyrosetta.rosetta.protocols.chemistries.WrappedBaseChemistry 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.Align_RmsdEvaluator method) (pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator 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_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.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.CombinedConstraintEvaluator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluator 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.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.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber 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.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.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.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.environment.claims.EnvLabelSelector 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.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.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric method) (pyrosetta.rosetta.protocols.evaluation.AlignEvaluator method) (pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator method) (pyrosetta.rosetta.protocols.evaluation.PoseEvaluator method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_long_t method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_Size method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_SSize method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_unsigned_long_t method) (pyrosetta.rosetta.protocols.evaluation.TimeEvaluator method) (pyrosetta.rosetta.protocols.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.ProteinSilentReport method) (pyrosetta.rosetta.protocols.features.Report 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.FilterCollection 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.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator 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.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.fold_from_loops.utils.Nub 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.RemodelEnzdesCstModule 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.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.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.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.BundleGridSampler 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.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.helix_capper.HelixNCapperMover 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.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.TMalign 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.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution 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.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.EntropyEstimator method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAligner 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.LoopComparator method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution 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.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.LoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ShortLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_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_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.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.match.MatcherMover 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.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.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.Clusterer method) (pyrosetta.rosetta.protocols.mpi_refinement.Serial_Refine 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.pack_interface.ProteinProteinInterfaceUpweighter method) (pyrosetta.rosetta.protocols.parser.FragmentReader method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter 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.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_interface_design.Revert 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.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage 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.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.RepeatProteinRelax 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.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.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.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.BatchEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.BatchNrEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.COFilter method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluator 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.ExternalEvaluator 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.JScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.JumpEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LoopRmsdEvaluator 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.PalesEvaluator 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.PredictedBurialEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.RangeFilter method) (pyrosetta.rosetta.protocols.simple_filters.RDC_Evaluator 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.RmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter method) (pyrosetta.rosetta.protocols.simple_filters.SAXSScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter method) (pyrosetta.rosetta.protocols.simple_filters.SelectGdtEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SelectMaxsubEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SelectRDC_Evaluator method) (pyrosetta.rosetta.protocols.simple_filters.SelectRmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.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.StructuralSimilarityEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilter method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricRmsdEvaluator 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.TruncatedScoreEvaluator 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.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_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.sparta.ChemicalShiftEvaluator 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.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.legacy.modeler.rna.StepWiseWorkingParametersSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner 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.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.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider 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.SymmetrySlider 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.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.ProteinInterfaceDesignOperation 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.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.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker 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.vip.VIP_Mover method) apply_A_LH_foldtree() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) apply_adducts_to_residue() (in module pyrosetta.rosetta.core.chemical) apply_Aform_torsions() (in module pyrosetta.rosetta.core.pose.rna) apply_after_jump_change() (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) apply_and_return_jump() (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) apply_and_to_subset() (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) apply_at_all_positions() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) apply_at_domain() (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) APPLY_BB_MOVE (pyrosetta.rosetta.basic.ProfTag attribute) apply_best_fragment() (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) (pyrosetta.rosetta.core.fragment.rna.RNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) apply_best_scoring_fragdata() (in module pyrosetta.rosetta.core.fragment) apply_binder_selector() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) apply_binder_selector_as_ranges() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) apply_body() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) apply_check() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) apply_chi_cst() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) apply_closure() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.GapCloser method) apply_const() (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) apply_current_pose_segment() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) apply_delta_torsion_values() (pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1 method) apply_disulfides() (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) apply_dofs() (in module pyrosetta.rosetta.core.pose.copydofs) (pyrosetta.rosetta.core.pose.copydofs.CopyDofsInfo method) apply_filter() (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) apply_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) apply_frame() (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) apply_from_template_pose() (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) apply_full_to_sub_mapping() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) apply_helper() (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.simple_filters.EnergyPerResidueFilter method) apply_holes() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) apply_ideal_c2endo_sugar_coords() (in module pyrosetta.rosetta.core.pose.rna) apply_if_reasonable() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureSolution method) apply_legacy() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) apply_linked_constraints() (pyrosetta.rosetta.protocols.recon_design.MSDMover method) APPLY_MOVE (pyrosetta.rosetta.basic.ProfTag attribute) apply_mover() (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) apply_mpi() (pyrosetta.rosetta.protocols.filters.VectorPoseFilter method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.FitnessFilter method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) apply_multi() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) apply_non_main_chain_sugar_coords() (in module pyrosetta.rosetta.core.pose.rna) apply_nucleoside_torsion_Aform() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) apply_on_pose() (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) apply_or_to_subset() (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) apply_parsed_protocol_mpi() (pyrosetta.rosetta.protocols.jd2.VectorPoseJobDistributor method) apply_patch_from_file() (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) apply_probability() (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) apply_profile() (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) apply_protonated_H1_adenosine_variant_type() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) apply_pucker() (in module pyrosetta.rosetta.core.pose.rna) (pyrosetta.rosetta.core.pose.rna.RNA_IdealCoord method) apply_random() (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) apply_random_fragment() (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) (pyrosetta.rosetta.core.fragment.rna.RNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) apply_random_nucleoside_torsion() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) apply_random_suite_torsion() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) apply_ranked_fragment() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) apply_repeat() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) apply_residue_entries_to_pose() (in module pyrosetta.rosetta.protocols.indexed_structure_store) apply_rigid_body_only() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) apply_rotate() (in module pyrosetta.rosetta.protocols.ligand_docking) APPLY_SC_MOVE (pyrosetta.rosetta.basic.ProfTag attribute) apply_selector() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) apply_selector_as_ranges() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) apply_sequence_mapping() (in module pyrosetta.rosetta.protocols.loops) (pyrosetta.rosetta.core.kinematics.FoldTree method) apply_set_weights() (in module pyrosetta.rosetta.core.scoring) apply_sheets() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) apply_ss() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.fragment.BBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.DownJumpSRFD method) (pyrosetta.rosetta.core.fragment.FragData method) (pyrosetta.rosetta.core.fragment.FragID method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SecstructSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.UpJumpSRFD method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) apply_sub_to_full_mapping() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) apply_suite_torsion_Aform() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) apply_superposition_transform() (in module pyrosetta.rosetta.protocols.toolbox) apply_superposition_transform_to_jump() (in module pyrosetta.rosetta.protocols.toolbox) apply_symm_b3g_corrections() (in module pyrosetta.rosetta.core.chemical) apply_symm_gly_corrections() (in module pyrosetta.rosetta.core.chemical) apply_tensor_transformation() (in module pyrosetta.rosetta.core.scoring.nmr) apply_to_cdr() (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) apply_to_pose() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.loophash.BackboneSegment method) apply_to_rotpack() (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) apply_transform() (in module pyrosetta.bindings.pose) (in module pyrosetta.rosetta.protocols.electron_density) (pyrosetta.rosetta.core.pose.Pose method) apply_transform_Rx_plus_v() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) apply_transformation() (in module pyrosetta.rosetta.protocols.forge.methods) (in module pyrosetta.rosetta.protocols.hybridization) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.simple_filters.RepeatParameterFilter method) apply_transformation_norecompute() (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) apply_vector_rotation() (in module pyrosetta.rosetta.core.scoring.nmr) apply_vector_transformation() (in module pyrosetta.rosetta.core.scoring.nmr) apply_virtual_rna_residue_variant_type() (in module pyrosetta.rosetta.core.pose.rna) apply_without_merge() (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) applyANNTransformation() (pyrosetta.rosetta.protocols.sparta.ANN method) ApplyChemistryMover (class in pyrosetta.rosetta.protocols.drug_design) ApplyChemistryMoverCreator (class in pyrosetta.rosetta.protocols.drug_design) ApplyRandomStoredRBConf (class in pyrosetta.rosetta.protocols.enzdes) applyRotation() (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) applySpin() (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) applyTransformation() (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) applyTranslation() (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) applyVecAverage() (pyrosetta.rosetta.protocols.sparta.ANN method) applyVecNormalization() (pyrosetta.rosetta.protocols.sparta.ANN method) approved() (pyrosetta.rosetta.protocols.topology_broker.claims.BBClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.CutClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.LegacyRootClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.SequenceClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.SymmetryClaim method) approx_lever_distance() (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.xyzTransform_double_t method) (pyrosetta.rosetta.numeric.xyzTransform_float_t method) approximate_buried_unsat_penalty (pyrosetta.rosetta.core.scoring.ScoreType attribute) approximate_buried_unsat_penalty_assume_const_backbone() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) approximate_buried_unsat_penalty_burial_atomic_depth() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) approximate_buried_unsat_penalty_burial_probe_radius() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) approximate_buried_unsat_penalty_burial_resolution() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) approximate_buried_unsat_penalty_hbond_bonus_cross_chain() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) approximate_buried_unsat_penalty_hbond_energy_threshold() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) approximate_buried_unsat_penalty_lys_ok_with_1() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) approximate_buried_unsat_penalty_natural_corrections1() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) approximate_buried_unsat_penalty_oversat_penalty() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) APPROXIMATE_UNSAT_POSE_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) approximate_vdw_radius() (pyrosetta.rosetta.core.scoring.AtomVDW method) ApproximateBuriedUnsatPenalty (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty) ApproximateBuriedUnsatPenaltyCreator (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty) AqueousPoreFinder (class in pyrosetta.rosetta.protocols.membrane) AqueousPoreFinderCreator (class in pyrosetta.rosetta.protocols.membrane) AqueousPoreParameters (class in pyrosetta.rosetta.core.conformation.membrane) Ar (pyrosetta.rosetta.core.chemical.element.Elements attribute) ARAMID (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) ARBITRARY_FLOAT_DATA (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) ARBITRARY_STRING_DATA (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) architect() (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover method) architect_group_name() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectFactory static method) architect_name() (pyrosetta.rosetta.protocols.denovo_design.architects.MotifArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect static method) ARCHIVE_BLOCK_FILE (pyrosetta.rosetta.basic.ProfTag attribute) ARCHIVE_CRITICAL_JOBSCOMPLETE (pyrosetta.rosetta.basic.ProfTag attribute) ARCHIVE_EVAL_DECOYS (pyrosetta.rosetta.basic.ProfTag attribute) ARCHIVE_EVALUATORS (pyrosetta.rosetta.basic.ProfTag attribute) ARCHIVE_FILL_POSE (pyrosetta.rosetta.basic.ProfTag attribute) ARCHIVE_GEN_BATCH (pyrosetta.rosetta.basic.ProfTag attribute) ARCHIVE_JOBSCOMPLETE (pyrosetta.rosetta.basic.ProfTag attribute) ARCHIVE_READ_DECOYS (pyrosetta.rosetta.basic.ProfTag attribute) ARCHIVE_SCORE_POSE (pyrosetta.rosetta.basic.ProfTag attribute) ARCHIVE_SYNC_BATCHES (pyrosetta.rosetta.basic.ProfTag attribute) ArchiveBase (class in pyrosetta.rosetta.protocols.jd2.archive) ArchiveManager (class in pyrosetta.rosetta.protocols.jd2.archive) arcs_ (pyrosetta.rosetta.core.scoring.packstat.trace property) are_aa_pres() (pyrosetta.rosetta.protocols.constel.PresenceCommon static method) are_atomid_vector_maps_enabled() (in module pyrosetta.rosetta.core.scoring) are_atoms_pres() (pyrosetta.rosetta.protocols.constel.PresenceCommon static method) are_colliding() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) are_coplanar() (in module pyrosetta.rosetta.numeric.geometry) are_selections_equal() (in module pyrosetta.rosetta.core.select.residue_selector) are_seqs_different() (in module pyrosetta.rosetta.protocols.vip) are_they_neighbors() (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) area (pyrosetta.rosetta.core.scoring.packstat.CavityBall property) (pyrosetta.rosetta.core.scoring.packstat.LR_AtomData property) (pyrosetta.rosetta.core.scoring.packstat.LR_MP_AtomData property) (pyrosetta.rosetta.core.scoring.sc._DOT property) (pyrosetta.rosetta.core.scoring.sc._RESULTS property) area_cav_ball_required_exposed (pyrosetta.rosetta.core.scoring.packstat.SasaOptions property) AreaAccumulator (class in pyrosetta.rosetta.core.scoring.packstat) AreConnectablePredicate (class in pyrosetta.rosetta.protocols.denovo_design.connection) arg_cation_pi (pyrosetta.rosetta.core.scoring.ScoreType attribute) arg_cation_pi_his_can_be_pi() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) ARG_METHYLATION (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes attribute) arg_min() (in module pyrosetta.rosetta.utility) ArgCationPiEnergy (class in pyrosetta.rosetta.core.energy_methods) ArgCationPiEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) argrot_dna_dis2() (in module pyrosetta.rosetta.protocols.dna) args (pyrosetta.network.rosetta_udp_to_tcp_bridge.StartUpError attribute) (pyrosetta.PyRosettaException attribute) ArithmeticASTAndClause (class in pyrosetta.rosetta.numeric.expression_parser) ArithmeticASTExpression (class in pyrosetta.rosetta.numeric.expression_parser) ArithmeticASTFactor (class in pyrosetta.rosetta.numeric.expression_parser) ArithmeticASTFunction (class in pyrosetta.rosetta.numeric.expression_parser) ArithmeticASTNode (class in pyrosetta.rosetta.numeric.expression_parser) ArithmeticASTOrClause (class in pyrosetta.rosetta.numeric.expression_parser) ArithmeticASTRestAndClause (class in pyrosetta.rosetta.numeric.expression_parser) ArithmeticASTRestExpression (class in pyrosetta.rosetta.numeric.expression_parser) ArithmeticASTRestOrClause (class in pyrosetta.rosetta.numeric.expression_parser) ArithmeticASTRestTerm (class in pyrosetta.rosetta.numeric.expression_parser) ArithmeticASTTerm (class in pyrosetta.rosetta.numeric.expression_parser) ArithmeticASTValue (class in pyrosetta.rosetta.numeric.expression_parser) ArithmeticScanner (class in pyrosetta.rosetta.numeric.expression_parser) Armijo() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) armijo_max_step_limit() (pyrosetta.rosetta.core.optimization.MinimizerOptions method) ArmijoLineMinimization (class in pyrosetta.rosetta.core.optimization) aro2double (pyrosetta.rosetta.core.chemical.rdkit.RestypeToRDMolOptions property) AROMATIC (class in pyrosetta.rosetta.core.pack.task) (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) (pyrosetta.rosetta.core.chemical.rings.RingSaturationType attribute) AROMATIC_CARBON_WITH_FREE_VALENCE (pyrosetta.rosetta.core.chemical.AtomProperty attribute) aromatic_dG_fraction (pyrosetta.rosetta.protocols.analysis.InterfaceData property) aromatic_dSASA_fraction (pyrosetta.rosetta.protocols.analysis.InterfaceData property) AROMATIC_HYDROGEN (pyrosetta.rosetta.core.chemical.AtomProperty attribute) aromatic_nres (pyrosetta.rosetta.protocols.analysis.InterfaceData property) aromatic_restraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) AromaticAtomFilter (class in pyrosetta.rosetta.core.chemical) AromaticBackboneRestraintEnergy (class in pyrosetta.rosetta.core.energy_methods) AromaticBackboneRestraintEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) AromaticBond (pyrosetta.rosetta.core.chemical.BondName attribute) aromaticity() (pyrosetta.rosetta.core.chemical.Bond method) Aroop (pyrosetta.rosetta.protocols.antibody.CDRDefinitionEnum attribute) array() (pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t method) Array0_double_t (class in pyrosetta.rosetta.utility.graph) Array2D (class in pyrosetta.rosetta.core.scoring.packstat) array_core_kinematics_inverse_AlignmentAtom_3_t (class in pyrosetta.rosetta.std) array_pool() (pyrosetta.rosetta.core.scoring.EnergyGraph method) array_size() (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) 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(pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) array_to_farray() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.DataBuffer method) array_type (pyrosetta.rosetta.utility.json_spirit.Value_type attribute) ArrayPool_double_t (class in pyrosetta.rosetta.utility.graph) ArrayPoolElement_double_t (class in pyrosetta.rosetta.utility.graph) arrow() (pyrosetta.rosetta.core.fragment.ConstFrameIterator method) (pyrosetta.rosetta.core.fragment.FragID_Iterator method) (pyrosetta.rosetta.core.fragment.FrameIterator method) (pyrosetta.rosetta.core.io.raw_data.DecoyFileData.const_iterator method) (pyrosetta.rosetta.core.io.raw_data.DecoyFileData.iterator method) (pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator method) (pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator method) (pyrosetta.rosetta.core.io.raw_data.ScoreFileData.const_iterator method) (pyrosetta.rosetta.core.io.raw_data.ScoreFileData.iterator method) (pyrosetta.rosetta.core.io.silent.SilentFileData.const_iterator method) (pyrosetta.rosetta.core.io.silent.SilentFileData.iterator method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose.const_iterator method) (pyrosetta.rosetta.cppdb.ref_ptr_cppdb_backend_connection_t method) (pyrosetta.rosetta.cppdb.ref_ptr_cppdb_backend_loadable_driver_t method) (pyrosetta.rosetta.cppdb.ref_ptr_cppdb_backend_statement_t method) (pyrosetta.rosetta.cppdb.ref_ptr_cppdb_pool_t method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash.const_iterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator method) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.EdgeListIterator method) (pyrosetta.rosetta.utility.graph.LowMemEdgeListConstIter method) (pyrosetta.rosetta.utility.graph.LowMemEdgeListIter method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_core_kinematics_MoveMap_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_core_pose_Pose_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_core_scoring_bin_transitions_BinTransitionCalculator_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_protocols_antibody_AntibodyInfo_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_protocols_loops_Loops_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_chemical_AtomProperties_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_chemical_ResidueProperties_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_chemical_rotamers_RotamerLibrarySpecification_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_kinematics_MoveMap_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_pose_Pose_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_scoring_ScoreFunction_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_interpolation_spline_BicubicSpline_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_interpolation_spline_CubicSpline_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_interpolation_spline_PolycubicSplineBase_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_MathNTensorBase_double_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_protocols_loops_Loops_t method) article_title() (pyrosetta.rosetta.basic.citation_manager.Citation method) As (pyrosetta.rosetta.core.chemical.element.Elements attribute) as_array() (in module pyrosetta.bindings.homogeneous_transform) (in module pyrosetta.bindings.rt) (pyrosetta.rosetta.core.kinematics.RT method) (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) aseq_posi() (pyrosetta.rosetta.protocols.tcr.TCRseqInfo method) aspartimide_penalty (pyrosetta.rosetta.core.scoring.ScoreType attribute) aspartimide_penalty_lr (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) aspartimide_penalty_value() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) AspartimidePenaltyEnergy (class in pyrosetta.rosetta.core.energy_methods) AspartimidePenaltyEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) asR() (pyrosetta.rosetta.numeric.urs_Quat method) assemble_enzdes_fragdata() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) assemble_remark_line() (in module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) assemble_remark_lines() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) AssembleLinkerMover (class in pyrosetta.rosetta.protocols.domain_assembly) Assembly (class in pyrosetta.rosetta.protocols.legacy_sewing) assembly_meets_requirements() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) assembly_mover_subtag_ct_namer() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover static method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover static method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover static method) assembly_requirement_ct_namer() (pyrosetta.rosetta.protocols.sewing.requirements.AssemblyRequirementFactory static method) assembly_requirement_group_name() (pyrosetta.rosetta.protocols.sewing.requirements.AssemblyRequirementFactory static method) assembly_scorer_ct_namer() (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorerFactory static method) assembly_scorer_group_name() (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorerFactory static method) AssemblyFactory (class in pyrosetta.rosetta.protocols.legacy_sewing) AssemblyMover (class in pyrosetta.rosetta.protocols.sewing.movers) AssemblyMoverCreator (class in pyrosetta.rosetta.protocols.sewing.movers) AssemblyRequirement (class in pyrosetta.rosetta.protocols.sewing.requirements) AssemblyRequirementCreator (class in pyrosetta.rosetta.protocols.sewing.requirements) AssemblyRequirementFactory (class in pyrosetta.rosetta.protocols.sewing.requirements) AssemblyScorer (class in pyrosetta.rosetta.protocols.sewing.scoring) AssemblyScorerCreator (class in pyrosetta.rosetta.protocols.sewing.scoring) AssemblyScorerFactory (class in pyrosetta.rosetta.protocols.sewing.scoring) assert_() (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) assert_atoms_are_downstream_of_jump() (in module pyrosetta.rosetta.core.kinematics.inverse) assert_atoms_are_upstream_of_jump() (in module pyrosetta.rosetta.core.kinematics.inverse) assert_phosphate_nomenclature_matches_mini() (in module pyrosetta.rosetta.core.pose.rna) assertAlmostEqual() (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) assertAlmostEquals() (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) assertCountEqual() (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) assertDictContainsSubset() (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) assertDictEqual() (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) assertEqual() (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) assertEquals() (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) assertFalse() (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) assertGreater() (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) assertGreaterEqual() (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) assertIn() (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) assertIs() (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) assertIsInstance() (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) assertIsNone() (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) assertIsNot() (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) assertIsNotNone() (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) assertLess() (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) assertLessEqual() (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) assertListEqual() (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) assertLogs() (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) assertMultiLineEqual() (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) assertNotAlmostEqual() (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) assertNotAlmostEquals() (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) assertNotEqual() (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) assertNotEquals() (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) assertNotIn() (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) assertNotIsInstance() (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) assertNotRegex() (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) assertNotRegexpMatches() (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) assertRaises() (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) assertRaisesRegex() (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) assertRaisesRegexp() (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) assertRegex() (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) assertRegexpMatches() (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) assertSequenceEqual() (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) assertSetEqual() (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) assertTrue() (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) assertTupleEqual() (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) assertWarns() (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) assertWarnsRegex() (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) assign() (pyrosetta.protocols.h5_fragment_store_provider.H5PyFragmentStoreProvider method) (pyrosetta.protocols.h5_structure_store_provider.H5StructureStoreProvider method) (pyrosetta.PythonPyExitCallback method) (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.CitationCollectionBase method) (pyrosetta.rosetta.basic.citation_manager.CitationCollectionList method) (pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleAuthor method) (pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleInfo method) (pyrosetta.rosetta.basic.database.insert_statement_generator.InsertGenerator method) (pyrosetta.rosetta.basic.database.insert_statement_generator.RowDataBase method) (pyrosetta.rosetta.basic.database.schema_generator.Column method) (pyrosetta.rosetta.basic.database.schema_generator.Constraint method) (pyrosetta.rosetta.basic.database.schema_generator.DbBigInt method) (pyrosetta.rosetta.basic.database.schema_generator.DbDataType method) (pyrosetta.rosetta.basic.database.schema_generator.DbDouble method) (pyrosetta.rosetta.basic.database.schema_generator.DbInteger method) (pyrosetta.rosetta.basic.database.schema_generator.DbReal method) (pyrosetta.rosetta.basic.database.schema_generator.DbText method) (pyrosetta.rosetta.basic.database.schema_generator.DbTextKey method) (pyrosetta.rosetta.basic.database.schema_generator.DbUUID method) (pyrosetta.rosetta.basic.database.schema_generator.ForeignKey method) (pyrosetta.rosetta.basic.database.schema_generator.GreaterThanConstraint method) (pyrosetta.rosetta.basic.database.schema_generator.PrimaryKey method) (pyrosetta.rosetta.basic.database.schema_generator.Schema method) (pyrosetta.rosetta.basic.database.schema_generator.UniqueConstraint method) (pyrosetta.rosetta.basic.datacache.BasicDataCache 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.ConstDataMap method) (pyrosetta.rosetta.basic.datacache.DataCache_basic_datacache_CacheableData_t method) (pyrosetta.rosetta.basic.datacache.DataCache_CacheableData method) (pyrosetta.rosetta.basic.datacache.DataCache_core_pose_datacache_CacheableObserver_t method) (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.basic.datacache.DiagnosticData method) (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap method) (pyrosetta.rosetta.basic.datacache.ResRotPairHasher method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableData method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.basic.DynamicProfileThis method) (pyrosetta.rosetta.basic.ExecutionResult method) (pyrosetta.rosetta.basic.MetricValueBase method) (pyrosetta.rosetta.basic.mpi.DbMoverMessageListener method) (pyrosetta.rosetta.basic.mpi.MessageListener method) (pyrosetta.rosetta.basic.random.RandomGeneratorSettings method) (pyrosetta.rosetta.basic.Report method) (pyrosetta.rosetta.basic.Reporter method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullStream method) (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoader method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceStream method) (pyrosetta.rosetta.basic.sampling.orientations.QuatDBMetadata method) (pyrosetta.rosetta.basic.sampling.orientations.QuaternionGrid method) (pyrosetta.rosetta.basic.sampling.orientations.QuatSet method) (pyrosetta.rosetta.basic.svd.SVD_Solver method) (pyrosetta.rosetta.basic.tensorflow_manager.RosettaTensorflowProtocolBase method) (pyrosetta.rosetta.basic.thread_manager.RosettaThreadAssignmentInfo method) (pyrosetta.rosetta.core.chemical.AcceptorAtomFilter method) (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.Adduct method) (pyrosetta.rosetta.core.chemical.APolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.AromaticAtomFilter method) (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t method) (pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t method) (pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO method) (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.bcl.BCLFragmentHandler method) (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) (pyrosetta.rosetta.core.chemical.carbohydrates.RootData method) (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow 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.ElectronConfiguration method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.ElementSet method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) (pyrosetta.rosetta.core.chemical.HeavyAtomFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter method) (pyrosetta.rosetta.core.chemical.HydrogenAtomFilter method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) (pyrosetta.rosetta.core.chemical.mainchain_potential.MainchainScoreTable method) (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.mmCIF.mmCIFParser method) (pyrosetta.rosetta.core.chemical.modifications.ChemistryBase method) (pyrosetta.rosetta.core.chemical.MutableICoorRecord method) (pyrosetta.rosetta.core.chemical.MutableResidueConnection method) (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData method) (pyrosetta.rosetta.core.chemical.orbitals.OrbitalType method) (pyrosetta.rosetta.core.chemical.orbitals.OrbitalTypeSet method) (pyrosetta.rosetta.core.chemical.Patch method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PatchOperationCreator method) (pyrosetta.rosetta.core.chemical.PolarHydrogenFilter method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.rdkit.RestypeToRDMolOptions method) (pyrosetta.rosetta.core.chemical.RealFilter 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.ResConnID method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) (pyrosetta.rosetta.core.chemical.ResidueDatabaseIO method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueTypeKinWriter method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle method) (pyrosetta.rosetta.core.chemical.RestypeDestructionEvent method) (pyrosetta.rosetta.core.chemical.rings.RingConformer method) (pyrosetta.rosetta.core.chemical.rings.RingConformerSet method) (pyrosetta.rosetta.core.chemical.rna.GaussianParameter method) (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) (pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecificationCreator method) (pyrosetta.rosetta.core.chemical.sdf.CtabParserBase method) (pyrosetta.rosetta.core.chemical.sdf.CtabV2000Parser method) (pyrosetta.rosetta.core.chemical.sdf.CtabV3000Parser method) (pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom method) (pyrosetta.rosetta.core.chemical.sdf.MolFileIOBond method) (pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule method) (pyrosetta.rosetta.core.chemical.sdf.MolFileIOReader method) (pyrosetta.rosetta.core.chemical.sdf.SDFParser method) (pyrosetta.rosetta.core.chemical.Selector_AA method) (pyrosetta.rosetta.core.chemical.Selector_BASENAME method) (pyrosetta.rosetta.core.chemical.Selector_CMDFLAG method) (pyrosetta.rosetta.core.chemical.Selector_HAS_ATOMS method) (pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_NAME1 method) (pyrosetta.rosetta.core.chemical.Selector_NAME3 method) (pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS method) (pyrosetta.rosetta.core.chemical.Selector_PROPERTY method) (pyrosetta.rosetta.core.chemical.Selector_UPPER_ATOM method) (pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE 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.VDDistanceMatrix method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) (pyrosetta.rosetta.core.conformation.AbstractRotamerTrie method) (pyrosetta.rosetta.core.conformation.Atom method) (pyrosetta.rosetta.core.conformation.AtomGraphVertexData 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.ConformationKinWriter method) (pyrosetta.rosetta.core.conformation.ExactResidueMatcher method) (pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) (pyrosetta.rosetta.core.conformation.membrane.Span method) (pyrosetta.rosetta.core.conformation.membrane.SpanningTopology method) (pyrosetta.rosetta.core.conformation.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.PointGraphPy method) (pyrosetta.rosetta.core.conformation.PointGraphVertexData method) (pyrosetta.rosetta.core.conformation.PseudoBond method) (pyrosetta.rosetta.core.conformation.PseudoBondCollection method) (pyrosetta.rosetta.core.conformation.ResidueKinWriter method) (pyrosetta.rosetta.core.conformation.ResidueMatcher method) (pyrosetta.rosetta.core.conformation.RotamerSetBase method) (pyrosetta.rosetta.core.conformation.signals.ConnectionEvent method) (pyrosetta.rosetta.core.conformation.signals.GeneralEvent method) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent method) (pyrosetta.rosetta.core.conformation.signals.LengthEvent method) (pyrosetta.rosetta.core.conformation.signals.XYZEvent method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymDof method) (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) (pyrosetta.rosetta.core.conformation.symmetry.SymmDataLoader method) (pyrosetta.rosetta.core.conformation.symmetry.SymmDataLoaderCreator 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.conformation.symmetry.SymSlideInfo method) (pyrosetta.rosetta.core.conformation.symmetry.VirtualCoordinate method) (pyrosetta.rosetta.core.conformation.UltraLightResidue method) (pyrosetta.rosetta.core.conformation.WatsonCrickResidueMatcher method) (pyrosetta.rosetta.core.energy_methods.AACompositionEnergy method) (pyrosetta.rosetta.core.energy_methods.AACompositionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.AARepeatEnergy method) (pyrosetta.rosetta.core.energy_methods.AARepeatEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.Abego method) (pyrosetta.rosetta.core.energy_methods.AbegoEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.BranchEnergy method) (pyrosetta.rosetta.core.energy_methods.BranchEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.Burial_v2Energy method) (pyrosetta.rosetta.core.energy_methods.Burial_v2EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CCS_IMMSEnergy method) (pyrosetta.rosetta.core.energy_methods.CCS_IMMSEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifDegreeEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifDegreeEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.ChainbreakEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ChemicalShiftAnisotropyEnergy method) (pyrosetta.rosetta.core.energy_methods.ChemicalShiftAnisotropyEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ContactOrderEnergy method) (pyrosetta.rosetta.core.energy_methods.ContactOrderEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.D2H_SA_Energy method) (pyrosetta.rosetta.core.energy_methods.D2H_SA_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.DipolarCouplingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.energy_methods.DirectReadoutEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.DistanceChainbreakEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_EnvPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAllCreator method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAroCreator method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FAElecContextData method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FastSAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.FastSAXSEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyDens method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyDensCreator method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.GoapRsdType method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.HolesEnergy method) (pyrosetta.rosetta.core.energy_methods.HolesEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.IntermolEnergy method) (pyrosetta.rosetta.core.energy_methods.IntermolEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearBranchEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearChainbreakEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_hackCreator method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.LoopCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.LoopCloseEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvPenalties method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvPenaltiesCreator method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MembraneLipo method) (pyrosetta.rosetta.core.energy_methods.MembraneLipoCreator method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MgEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergy method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MissingEnergy method) (pyrosetta.rosetta.core.energy_methods.MissingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergy method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebodyCreator method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.OtherPoseEnergy method) (pyrosetta.rosetta.core.energy_methods.OtherPoseEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.PackStatEnergy method) (pyrosetta.rosetta.core.energy_methods.PackStatEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.PBLifetimeCache method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.pHEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.PoseSequence method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ProQ_Energy method) (pyrosetta.rosetta.core.energy_methods.ProQ_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2BCreator method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonicalCreator method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy_Rohl method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy_RohlCreator method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_Fast method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_FastCreator method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_RNA method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_RNACreator method) (pyrosetta.rosetta.core.energy_methods.RG_Local_MinData method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergy method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RG_MinData method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RMS_Energy method) (pyrosetta.rosetta.core.energy_methods.RMS_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalMappingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalMappingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalShiftEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphateCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_PartitionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PartitionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SA_Energy method) (pyrosetta.rosetta.core.energy_methods.SA_EnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy 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.ScoreCache method) (pyrosetta.rosetta.core.energy_methods.SecondaryStructureEnergy method) (pyrosetta.rosetta.core.energy_methods.SecondaryStructureEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergy method) (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SurfEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SurfVolEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfVolEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.XtalMLEnergy method) (pyrosetta.rosetta.core.energy_methods.XtalMLEnergyCreator method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergyCreator method) (pyrosetta.rosetta.core.environment.DofPassport method) (pyrosetta.rosetta.core.environment.EXCN_Env_Exception method) (pyrosetta.rosetta.core.environment.EXCN_FTSketchGraph method) (pyrosetta.rosetta.core.environment.FoldTreeSketch.Node method) (pyrosetta.rosetta.core.environment.LocalPosition method) (pyrosetta.rosetta.core.environment.SequenceAnnotation method) (pyrosetta.rosetta.core.enzymes.EnzymeData 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.CacheWrapper_protocols_simple_moves_GunnTuple_core_fragment_MapCacheUnit_protocols_simple_moves_GunnTuple_t method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.DownJumpSRFD method) (pyrosetta.rosetta.core.fragment.FragCache_protocols_simple_moves_GunnTuple_t method) (pyrosetta.rosetta.core.fragment.FragData method) (pyrosetta.rosetta.core.fragment.FragID method) (pyrosetta.rosetta.core.fragment.FragmentRmsd method) (pyrosetta.rosetta.core.fragment.FragmentSetLoader method) (pyrosetta.rosetta.core.fragment.FragmentSetLoaderCreator method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragSetCollection method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.FrameList 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.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.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.picking_old.vall.scores.VallFragmentScore method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue 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.fragment.rna.FragmentLibrary method) (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) (pyrosetta.rosetta.core.fragment.rna.RNA_Fragments method) (pyrosetta.rosetta.core.fragment.rna.TorsionSet method) (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.fragment.SecstructSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.UpJumpSRFD method) (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.AtomID_Map_AtomID method) (pyrosetta.rosetta.core.id.AtomID_Map_bool method) (pyrosetta.rosetta.core.id.AtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_MP_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_Real method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.EXCN_AtomNotFound method) (pyrosetta.rosetta.core.id.NamedAtomID 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.NamedStubID method) (pyrosetta.rosetta.core.id.PartialAtomID method) (pyrosetta.rosetta.core.id.SequenceMapping method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepSequence method) (pyrosetta.rosetta.core.import_pose.libraries.ChunkSet method) (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) (pyrosetta.rosetta.core.import_pose.libraries.RNA_JumpLibrary 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.import_pose.PDBSilentStructCreator method) (pyrosetta.rosetta.core.import_pose.pose_stream.ExtendedPoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.LazySilentFilePoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.MetaPoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.PDBPoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.PoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.SilentFilePoseInputStream method) (pyrosetta.rosetta.core.import_pose.PoseResource method) (pyrosetta.rosetta.core.import_pose.PoseResourceLoader method) (pyrosetta.rosetta.core.import_pose.PoseResourceLoaderCreator method) (pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler method) (pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup method) (pyrosetta.rosetta.core.import_pose.RNA_JumpMover method) (pyrosetta.rosetta.core.io.AtomInformation method) (pyrosetta.rosetta.core.io.CisPeptideInformation method) (pyrosetta.rosetta.core.io.CrystInfo method) (pyrosetta.rosetta.core.io.external.PsiPredResult method) (pyrosetta.rosetta.core.io.HeaderInformation method) (pyrosetta.rosetta.core.io.HELIXInformation method) (pyrosetta.rosetta.core.io.LinkInformation method) (pyrosetta.rosetta.core.io.mmtf.ExtraDataEnumManager method) (pyrosetta.rosetta.core.io.ModifiedResidueInformation method) (pyrosetta.rosetta.core.io.nmr.AtomSelection method) (pyrosetta.rosetta.core.io.nmr.ParaIon method) (pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry method) (pyrosetta.rosetta.core.io.pdb.Field method) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder method) (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) (pyrosetta.rosetta.core.io.raw_data.DecoyFileData method) (pyrosetta.rosetta.core.io.raw_data.DecoyFileData.const_iterator method) (pyrosetta.rosetta.core.io.raw_data.DecoyFileData.iterator method) (pyrosetta.rosetta.core.io.raw_data.DecoyStruct method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator method) (pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreFileData method) (pyrosetta.rosetta.core.io.raw_data.ScoreFileData.const_iterator method) (pyrosetta.rosetta.core.io.raw_data.ScoreFileData.iterator method) (pyrosetta.rosetta.core.io.raw_data.ScoreMap method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructJSON method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.RemarkInfo method) (pyrosetta.rosetta.core.io.Remarks method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.io.rna.RDAT method) (pyrosetta.rosetta.core.io.rna.RNA_DataReader method) (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) (pyrosetta.rosetta.core.io.SHEETInformation method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.EnergyNames method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStruct_SinglePrecCreator method) (pyrosetta.rosetta.core.io.silent.ProteinSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStructCreator method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStructCreator method) (pyrosetta.rosetta.core.io.silent.SharedSilentData method) (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileData.iterator method) (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStructCreator method) (pyrosetta.rosetta.core.io.silent.SimpleSequenceData method) (pyrosetta.rosetta.core.io.SSBondInformation method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.kinematics.EXCN_InvalidFoldTree 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.Jump method) (pyrosetta.rosetta.core.kinematics.MinimizerMapBase method) (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) (pyrosetta.rosetta.core.kinematics.RT method) (pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree method) (pyrosetta.rosetta.core.kinematics.Stub method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.optimization.AtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.CartesianMinimizer method) (pyrosetta.rosetta.core.optimization.CartesianMinimizerMap method) (pyrosetta.rosetta.core.optimization.ConvergenceTest method) (pyrosetta.rosetta.core.optimization.DerivCheckDataPoint method) (pyrosetta.rosetta.core.optimization.DFPMinConvergedAbsolute method) (pyrosetta.rosetta.core.optimization.DFPMinConvergedFractional method) (pyrosetta.rosetta.core.optimization.DOF_DataPoint method) (pyrosetta.rosetta.core.optimization.DOF_Node method) (pyrosetta.rosetta.core.optimization.MinimizerMap method) (pyrosetta.rosetta.core.optimization.MinimizerOptions method) (pyrosetta.rosetta.core.optimization.NumDerivCheckData method) (pyrosetta.rosetta.core.optimization.NumericalDerivCheckResult method) (pyrosetta.rosetta.core.optimization.Particle method) (pyrosetta.rosetta.core.optimization.ParticleSwarmMinimizer method) (pyrosetta.rosetta.core.optimization.SimpleDerivCheckResult method) (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.annealer.AnnealerObserver method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBIndNRChiSample_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergyCreator method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibraryCreator method) (pyrosetta.rosetta.core.pack.dunbrack.ChiSet method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergyCreator method) (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.MainchainTorsionReporter 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) (pyrosetta.rosetta.core.pack.dunbrack.PeptideTorsionReporter method) (pyrosetta.rosetta.core.pack.dunbrack.PeptoidGeneralDOFReporter method) (pyrosetta.rosetta.core.pack.dunbrack.PeptoidOmegaReporter method) (pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericData_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryInterpolationScratch method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibraryCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenaltyCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.HBondBonusOptions method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.UnsatCorrectionOptions method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenaltyCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdgeData method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphContainer method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup 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.hbnet_energy.HBNetEnergyCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomePackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomePackEnergyCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.MyTemplatePointerHash1_core_conformation_Residue_t method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetricCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.RotamerRotamerHasher 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.SapConstraintEnergyCreator 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.SapParameterOptions method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetricCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergyCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid 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.DotSphere 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.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergyCreator method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots 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.RotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SparseMatrixIndex method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergyCreator 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.core.pack.palette.BaseTypeList method) (pyrosetta.rosetta.core.pack.palette.CustomBaseTypePackerPalette method) (pyrosetta.rosetta.core.pack.palette.CustomBaseTypePackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.DefaultPackerPalette method) (pyrosetta.rosetta.core.pack.palette.DefaultPackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.NCAADefaultPackerPalette method) (pyrosetta.rosetta.core.pack.palette.NCAADefaultPackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.NoDesignPackerPalette method) (pyrosetta.rosetta.core.pack.palette.NoDesignPackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.PackerPalette method) (pyrosetta.rosetta.core.pack.palette.PackerPaletteCreator method) (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminator method) (pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminatorTaskOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerCouplings method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerLinks method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetFactory method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetsFactory method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetsOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo method) (pyrosetta.rosetta.core.pack.rotamer_set.WaterPackingInfo 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.pack.scmin.AtomTreeCollection method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment 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.IGEdgeReweightContainer 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.AddBehaviorRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.AllResFilter method) (pyrosetta.rosetta.core.pack.task.operation.AllResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.AnyResFilter method) (pyrosetta.rosetta.core.pack.task.operation.AnyResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSetCreator method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerCreator method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSetCreator method) (pyrosetta.rosetta.core.pack.task.operation.ChainIs method) (pyrosetta.rosetta.core.pack.task.operation.ChainIsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ChainIsnt method) (pyrosetta.rosetta.core.pack.task.operation.ChainIsntCreator method) (pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShell method) (pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShellCreator method) (pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions method) (pyrosetta.rosetta.core.pack.task.operation.DesignRestrictionsCreator method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeCreator method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLT method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealerCreator method) (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealerCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLT method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamerSamplingData method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrent method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentCreator method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLT method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandline method) (pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandlineCreator method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandline method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandlineCreator method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollectionCreator method) (pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry method) (pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetryCreator method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfidesCreator method) (pyrosetta.rosetta.core.pack.task.operation.NoResFilter method) (pyrosetta.rosetta.core.pack.task.operation.NoResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResiduesCreator method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubsetCreator method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHGCreator method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.OptHCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBeta method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLT method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepackingCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLT method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitResiduePropertiesCreator method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypesCreator method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfile method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEventsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileCreator 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.ResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasPropertyCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIs method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsnt method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsntCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueLacksProperty method) (pyrosetta.rosetta.core.pack.task.operation.ResidueLacksPropertyCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3Is method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3IsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3Isnt method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3IsntCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIs method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsnt method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsntCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoHasLabel method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoHasLabelCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoLacksLabel method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoLacksLabelCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueTypeFilter method) (pyrosetta.rosetta.core.pack.task.operation.ResidueTypeFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAAS method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASExceptNativeRLT method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASExceptNativeRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASRLT method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictInteractionGraphThreadsOperation method) (pyrosetta.rosetta.core.pack.task.operation.RestrictInteractionGraphThreadsOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepackingCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepackingCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepackingRLT method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepackingRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToResidueProperties method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToResiduePropertiesCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToSpecifiedBaseResidueTypes method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToSpecifiedBaseResidueTypesCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesignCreator method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosionCreator method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerCouplings method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerCouplingsCreator method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerLinks method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerLinksCreator method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.UseMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.UseMultiCoolAnnealerCreator 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.ResfileContents method) (pyrosetta.rosetta.core.pack.task.ResfileReaderException method) (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector method) (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelectorCreator method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.core.pack.task.rna.RNA_ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) (pyrosetta.rosetta.core.pack_basic.RotamerSetsBase method) (pyrosetta.rosetta.core.pose.copydofs.CopyDofsInfo 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.ObserverCache 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.PoseMetricContainer 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.MiniPose method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.pose.PDBInfo.ResidueRecord method) (pyrosetta.rosetta.core.pose.PDBPoseMap 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.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionChainEnd method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionLastResidue method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPDB method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPoseNum method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionRefPose method) (pyrosetta.rosetta.core.pose.RID_FileSource method) (pyrosetta.rosetta.core.pose.RID_Source method) (pyrosetta.rosetta.core.pose.rna.BasePair method) (pyrosetta.rosetta.core.pose.rna.BasePairStep method) (pyrosetta.rosetta.core.pose.rna.BaseStack method) (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SecStruct method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteAssignment method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteInfo method) (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName method) (pyrosetta.rosetta.core.pose.rna.secstruct_legacy.RNA_SecStructLegacyInfo method) (pyrosetta.rosetta.core.pose.rna.VDW_Grid method) (pyrosetta.rosetta.core.pose.rna.VDW_RepScreenInfo method) (pyrosetta.rosetta.core.pose.signals.ConformationEvent method) (pyrosetta.rosetta.core.pose.signals.DestructionEvent method) (pyrosetta.rosetta.core.pose.signals.EnergyEvent method) (pyrosetta.rosetta.core.pose.signals.GeneralEvent method) (pyrosetta.rosetta.core.pose.toolbox.AtomID_Mapper method) (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) (pyrosetta.rosetta.core.scoring.annealing.ResidueArrayAnnealableEnergy method) (pyrosetta.rosetta.core.scoring.APBSConfig method) (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM method) (pyrosetta.rosetta.core.scoring.APBSConfig.R_PARAM method) (pyrosetta.rosetta.core.scoring.APBSResult method) (pyrosetta.rosetta.core.scoring.APBSWrapper method) (pyrosetta.rosetta.core.scoring.atomic_depth.AtomicDepth method) (pyrosetta.rosetta.core.scoring.atomic_depth.point3d method) (pyrosetta.rosetta.core.scoring.AtomNeighbor method) (pyrosetta.rosetta.core.scoring.AtomVDW method) (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculator method) (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergyCreator method) (pyrosetta.rosetta.core.scoring.CenHBPotential method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.CenRotEnvPairPotential method) (pyrosetta.rosetta.core.scoring.ChemicalShiftAnisotropy 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.BoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintGraph method) (pyrosetta.rosetta.core.scoring.constraints.Constraints method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergyCreator method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.CstEnergyContainer method) (pyrosetta.rosetta.core.scoring.constraints.CstMinimizationData method) (pyrosetta.rosetta.core.scoring.constraints.CstResNeighbConstIterator method) (pyrosetta.rosetta.core.scoring.constraints.CstResNeighbIterator 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.Obsolet_NamedAtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintCreator method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResiduesCreator method) (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.AtomPairFuncList method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.DistanceFunc method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergyCreator method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.DerivVectorPair 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.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingDatabase method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbIterator method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.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.dna.DNA_BasePotential method) (pyrosetta.rosetta.core.scoring.dna.DNA_EnvPairPotential method) (pyrosetta.rosetta.core.scoring.dna.DNABFormPotential method) (pyrosetta.rosetta.core.scoring.dna.TorsionFourierComponent method) (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.dssp.Dssp method) (pyrosetta.rosetta.core.scoring.dssp.Pairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.core.scoring.elec.CountPairRepresentative method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergyCreator method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) (pyrosetta.rosetta.core.scoring.electron_density.poseCoord method) (pyrosetta.rosetta.core.scoring.electron_density_atomwise.ElectronDensityAtomwise method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) (pyrosetta.rosetta.core.scoring.epr_deer.EPRSpinLabel method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERChiSqMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERData method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDecayData method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceBounds method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceDistribution method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJaccardMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJSMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERMiscMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEEROverlapMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTrace method) (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTraceFactory 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.count_pair.CountPairAll method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover3 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover34 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover3full method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairCrossover4 method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairGeneric method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairNone method) (pyrosetta.rosetta.core.scoring.etable.count_pair.Invoker method) (pyrosetta.rosetta.core.scoring.etable.EtableClassicIntraEnergyCreator method) (pyrosetta.rosetta.core.scoring.etable.EtableEnergyCreator method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableOptions method) (pyrosetta.rosetta.core.scoring.etable.etrie.EtableAtom method) (pyrosetta.rosetta.core.scoring.etable.etrie.TrieCountPair1BC3 method) (pyrosetta.rosetta.core.scoring.etable.etrie.TrieCountPair1BC4 method) (pyrosetta.rosetta.core.scoring.etable.etrie.TrieCountPairAll method) (pyrosetta.rosetta.core.scoring.etable.etrie.TrieCountPairGeneric method) (pyrosetta.rosetta.core.scoring.etable.etrie.TrieCountPairNone method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) (pyrosetta.rosetta.core.scoring.ExcludedResPredicate 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.facts.FACTSRsdTypeInfo method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.CentroidScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FAScatter method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffraction 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.ConformationXYZ 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.FourPointsFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.FuncFactory 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.ResiduePairXYZ method) (pyrosetta.rosetta.core.scoring.func.ResidueXYZ method) (pyrosetta.rosetta.core.scoring.func.ScalarWeightedFunc method) (pyrosetta.rosetta.core.scoring.func.SigmoidFunc method) (pyrosetta.rosetta.core.scoring.func.SkipViolFunc method) (pyrosetta.rosetta.core.scoring.func.SmoothStepFunc method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SplineFunc method) (pyrosetta.rosetta.core.scoring.func.SquareWell2Func method) (pyrosetta.rosetta.core.scoring.func.SquareWellFunc method) (pyrosetta.rosetta.core.scoring.func.SumFunc method) (pyrosetta.rosetta.core.scoring.func.TopOutFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.func.XYZ_Func 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.GenericBondedPotential method) (pyrosetta.rosetta.core.scoring.GenTorsionParams method) (pyrosetta.rosetta.core.scoring.Hairpin method) (pyrosetta.rosetta.core.scoring.Hairpins method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfoSet method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.LKHBondInfo method) (pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple method) (pyrosetta.rosetta.core.scoring.hbonds.HBond method) (pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergyCreator method) (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBCountPairFunction method) (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBondsTrieVsTrieCachedDataContainer method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.Polynomial_1d method) (pyrosetta.rosetta.core.scoring.Helices method) (pyrosetta.rosetta.core.scoring.HydroxylTorsionPotential method) (pyrosetta.rosetta.core.scoring.interface_.DDPlookup method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.interface_.DDPscoreCreator method) (pyrosetta.rosetta.core.scoring.IsHeavyAtomPredicate method) (pyrosetta.rosetta.core.scoring.IsMainAtomPredicate method) (pyrosetta.rosetta.core.scoring.IsProteinBackboneIncludingOPredicate method) (pyrosetta.rosetta.core.scoring.IsProteinBackbonePredicate method) (pyrosetta.rosetta.core.scoring.IsProteinCAPredicate method) (pyrosetta.rosetta.core.scoring.IsSpecificAtomsPredicate method) (pyrosetta.rosetta.core.scoring.lDDT_Calculator method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergyCreator method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergyCreator 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.lkball.WaterBuilderForRestype method) (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) (pyrosetta.rosetta.core.scoring.loop_graph.LoopCycle method) (pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph method) (pyrosetta.rosetta.core.scoring.LREnergyContainer method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenaltyCreator method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenaltyCreator 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.BBDepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.methods.BBIndepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.methods.CartBondedParameters 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.dfire.DFIRE_Potential method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergyCreator method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergyCreator method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInterCreator method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntraCreator method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergyCreator method) (pyrosetta.rosetta.core.scoring.methods.NeighborListData method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergyCreator method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergyCreator method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergyCreator method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ResidueAtomOverlaps 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.AlleleMatrix method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorExternal method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorMatrix method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorSVM method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet method) (pyrosetta.rosetta.core.scoring.mm.MMBondLengthLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary method) (pyrosetta.rosetta.core.scoring.mm.mmtrie.MMEnergyTableAtom method) (pyrosetta.rosetta.core.scoring.motif.MotifHits method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotifs method) (pyrosetta.rosetta.core.scoring.motif.XformScore 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.netcharge_energy.NetChargeEnergySetup method) (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelAtom method) (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer method) (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelEnsemble method) (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelVoxelGrid method) (pyrosetta.rosetta.core.scoring.nmr.NMRGridSearch method) (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel method) (pyrosetta.rosetta.core.scoring.nmr.NMRTensor method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSData method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingle method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREData method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingle method) (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingleSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCData method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingle method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) (pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint method) (pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint_AA method) (pyrosetta.rosetta.core.scoring.nv.NVlookup method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.core.scoring.nv.NVscoreCreator method) (pyrosetta.rosetta.core.scoring.OmegaTether method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsLookup method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScoreCreator method) (pyrosetta.rosetta.core.scoring.P_AA method) (pyrosetta.rosetta.core.scoring.P_AA_ABEGO3 method) (pyrosetta.rosetta.core.scoring.P_AA_ss method) (pyrosetta.rosetta.core.scoring.packing.Ball method) (pyrosetta.rosetta.core.scoring.packing.HolesEnergyRes method) (pyrosetta.rosetta.core.scoring.packing.HolesParamsRes method) (pyrosetta.rosetta.core.scoring.packing.HolesResult method) (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) (pyrosetta.rosetta.core.scoring.packing.PoseBallsLite method) (pyrosetta.rosetta.core.scoring.packstat.Accumulator method) (pyrosetta.rosetta.core.scoring.packstat.AreaAccumulator method) (pyrosetta.rosetta.core.scoring.packstat.Array2D method) (pyrosetta.rosetta.core.scoring.packstat.LR_AtomData method) (pyrosetta.rosetta.core.scoring.packstat.LR_MP_AtomData method) (pyrosetta.rosetta.core.scoring.packstat.MultiProbePerSphereAccumulator method) (pyrosetta.rosetta.core.scoring.packstat.MultiProbePoseAccumulator method) (pyrosetta.rosetta.core.scoring.packstat.PerSphereAccumulator method) (pyrosetta.rosetta.core.scoring.packstat.PosePackData method) (pyrosetta.rosetta.core.scoring.packstat.SasaOptions method) (pyrosetta.rosetta.core.scoring.packstat.SasaResult method) (pyrosetta.rosetta.core.scoring.packstat.SimplePDB method) (pyrosetta.rosetta.core.scoring.packstat.SimplePDB_Atom method) (pyrosetta.rosetta.core.scoring.packstat.Slice method) (pyrosetta.rosetta.core.scoring.PairEPotential method) (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.PDinter method) (pyrosetta.rosetta.core.scoring.PDvertex method) (pyrosetta.rosetta.core.scoring.PointWaterPotential method) (pyrosetta.rosetta.core.scoring.PoissonBoltzmannPotential method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) (pyrosetta.rosetta.core.scoring.PQR method) (pyrosetta.rosetta.core.scoring.Predicate method) (pyrosetta.rosetta.core.scoring.ProQPotential method) (pyrosetta.rosetta.core.scoring.Ramachandran method) (pyrosetta.rosetta.core.scoring.RamaPrePro method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling_Rohl method) (pyrosetta.rosetta.core.scoring.ResidueExclParams method) (pyrosetta.rosetta.core.scoring.ResidueNblistData method) (pyrosetta.rosetta.core.scoring.ResidueNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.ResidueNeighborIterator method) (pyrosetta.rosetta.core.scoring.ResiduePairNeighborList method) (pyrosetta.rosetta.core.scoring.ResPairMinimizationData method) (pyrosetta.rosetta.core.scoring.ResRangePredicate method) (pyrosetta.rosetta.core.scoring.ResSingleMinimizationData method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData method) (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_AtomVDW method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotentialCreator method) (pyrosetta.rosetta.core.scoring.rna.RNA_Motif method) (pyrosetta.rosetta.core.scoring.rna.RNA_Motifs method) (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.core.scoring.SAnode 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.scoring.SASAPotential method) (pyrosetta.rosetta.core.scoring.saxs.DistanceHistogram method) (pyrosetta.rosetta.core.scoring.saxs.FormFactor method) (pyrosetta.rosetta.core.scoring.sc._RESULTS method) (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.core.scoring.sc.ContactMolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.scoring.sc.ShapeSimilarityCalculator method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunctionKey method) (pyrosetta.rosetta.core.scoring.SecondaryStructureWeights method) (pyrosetta.rosetta.core.scoring.SelectedResPredicate method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) (pyrosetta.rosetta.core.scoring.SmoothScoreTermCoeffs method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.SplitUnfoldedTwoBodyPotential method) (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) (pyrosetta.rosetta.core.scoring.Strands method) (pyrosetta.rosetta.core.scoring.sym_e.symECreator 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.tableID method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.trie.RotamerTrieBase method) (pyrosetta.rosetta.core.scoring.trie.TrieCollection method) (pyrosetta.rosetta.core.scoring.trie.TrieCountPairBase method) (pyrosetta.rosetta.core.scoring.trie.TrieVsTrieCachedDataContainerBase method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_EnergyCreator method) (pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieCountPair1B method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.ExclusivelySharedJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.ExclusivelySharedJumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.JumpForResidue method) (pyrosetta.rosetta.core.select.jump_selector.JumpForResidueCreator method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.JumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelectorCreator method) (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelector method) (pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.BFactorSelector method) (pyrosetta.rosetta.core.select.residue_selector.BFactorSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.BlockSelector method) (pyrosetta.rosetta.core.select.residue_selector.BlockSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset method) (pyrosetta.rosetta.core.select.residue_selector.ChainSelector method) (pyrosetta.rosetta.core.select.residue_selector.ChainSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ConfluentSelector method) (pyrosetta.rosetta.core.select.residue_selector.ConfluentSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.FractionSelector method) (pyrosetta.rosetta.core.select.residue_selector.FractionSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector method) (pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRanges method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueVector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelector method) (pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector method) (pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser method) (pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelector method) (pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelector method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelectorCreator method) (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.core.sequence.Aligner method) (pyrosetta.rosetta.core.sequence.AnnotatedSequence method) (pyrosetta.rosetta.core.sequence.Blosum62Map method) (pyrosetta.rosetta.core.sequence.Cell method) (pyrosetta.rosetta.core.sequence.CharPairHash method) (pyrosetta.rosetta.core.sequence.ChemicalShiftScoringScheme method) (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.ChemicalShiftSequenceCreator method) (pyrosetta.rosetta.core.sequence.CompassScoringScheme method) (pyrosetta.rosetta.core.sequence.CompositeScoringScheme method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.CompositeSequenceCreator method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.core.sequence.DP_Matrix method) (pyrosetta.rosetta.core.sequence.DPScoringScheme method) (pyrosetta.rosetta.core.sequence.L1ScoringScheme method) (pyrosetta.rosetta.core.sequence.Line method) (pyrosetta.rosetta.core.sequence.MatrixScoringScheme method) (pyrosetta.rosetta.core.sequence.MCAligner method) (pyrosetta.rosetta.core.sequence.NWAligner 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.SequenceCouplingCreator method) (pyrosetta.rosetta.core.sequence.SequenceCreator method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) (pyrosetta.rosetta.core.sequence.SequenceProfileCreator method) (pyrosetta.rosetta.core.sequence.SimpleScoringScheme method) (pyrosetta.rosetta.core.sequence.SimpleSequenceCreator method) (pyrosetta.rosetta.core.sequence.SSManager method) (pyrosetta.rosetta.core.sequence.SWAligner method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetricCreator 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.composite_metrics.ProtocolSettingsMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetricCreator 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.AverageProbabilitiesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_CalcFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_InitFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetricCreator 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.SimpleMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricData method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetricCreator method) (pyrosetta.rosetta.core.util.ChainbreakUtil method) (pyrosetta.rosetta.cppdb.connection_info method) (pyrosetta.rosetta.cppdb.ref_ptr_cppdb_backend_connection_t method) (pyrosetta.rosetta.cppdb.ref_ptr_cppdb_backend_loadable_driver_t method) (pyrosetta.rosetta.cppdb.ref_ptr_cppdb_backend_statement_t method) (pyrosetta.rosetta.cppdb.ref_ptr_cppdb_pool_t method) (pyrosetta.rosetta.cppdb.result method) (pyrosetta.rosetta.cppdb.session method) (pyrosetta.rosetta.cppdb.statement method) (pyrosetta.rosetta.numeric.AgglomerativeHierarchicalClusterer method) (pyrosetta.rosetta.numeric.AverageLinkClusterer method) (pyrosetta.rosetta.numeric.Calculator method) (pyrosetta.rosetta.numeric.ClusteringTreeNode method) (pyrosetta.rosetta.numeric.CompleteLinkClusterer method) (pyrosetta.rosetta.numeric.CubicPolynomial method) (pyrosetta.rosetta.numeric.DiscreteIntervalEncodingTree_unsigned_long_t method) (pyrosetta.rosetta.numeric.expression_parser.AbsoluteValueExpression method) (pyrosetta.rosetta.numeric.expression_parser.AddExpression method) (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTAndClause method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTExpression method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTFactor method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTFunction method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTOrClause method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestAndClause method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestExpression method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestOrClause method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestTerm method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTTerm method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticScanner method) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter method) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor method) (pyrosetta.rosetta.numeric.expression_parser.BinaryExpression method) (pyrosetta.rosetta.numeric.expression_parser.BooleanExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.BooleanExpressionScanner method) (pyrosetta.rosetta.numeric.expression_parser.DivideExpression method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.Expression method) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.FunctionToken method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.ITEExpression method) (pyrosetta.rosetta.numeric.expression_parser.LiteralExpression method) (pyrosetta.rosetta.numeric.expression_parser.LiteralToken method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.MaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMaxExpression method) (pyrosetta.rosetta.numeric.expression_parser.MetaMinExpression method) (pyrosetta.rosetta.numeric.expression_parser.MinExpression method) (pyrosetta.rosetta.numeric.expression_parser.MultiplyExpression method) (pyrosetta.rosetta.numeric.expression_parser.NaryExpression method) (pyrosetta.rosetta.numeric.expression_parser.NotExpression method) (pyrosetta.rosetta.numeric.expression_parser.OrExpression method) (pyrosetta.rosetta.numeric.expression_parser.SimpleExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.SimpleToken method) (pyrosetta.rosetta.numeric.expression_parser.SquarerootExpression method) (pyrosetta.rosetta.numeric.expression_parser.SubtractExpression method) (pyrosetta.rosetta.numeric.expression_parser.Token method) (pyrosetta.rosetta.numeric.expression_parser.TokenSet method) (pyrosetta.rosetta.numeric.expression_parser.UnaryExpression method) (pyrosetta.rosetta.numeric.expression_parser.VariableExpression method) (pyrosetta.rosetta.numeric.expression_parser.VariableToken method) (pyrosetta.rosetta.numeric.fourier.kiss_fft_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t method) (pyrosetta.rosetta.numeric.geometry.hashing.bin_index_hasher method) (pyrosetta.rosetta.numeric.geometry.hashing.MinimalClashHash method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) (pyrosetta.rosetta.numeric.histograms.TwoDHistogram_unsigned_long_long_t method) (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) (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) 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(pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.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) 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(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.FArraySection_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArraySection_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArraySection_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArraySection_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMoverCreator method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMoverCreator method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMoverCreator method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.abinitio._HashEntry method) (pyrosetta.rosetta.protocols.abinitio._MergableEntries method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCMCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMoverCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparerCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCMCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCMCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.JumpSampleData method) (pyrosetta.rosetta.protocols.abinitio.abscript.JumpSampleDataCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCMCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCMCreator method) (pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.CoordinateConstraintKC method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DomainAssemblyCreator method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FixTemplateJumpSetup method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicControl method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.PairingStatistics method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.abinitio.StrandConstraints method) (pyrosetta.rosetta.protocols.abinitio.Template method) (pyrosetta.rosetta.protocols.abinitio.TemplateJumpSetup method) (pyrosetta.rosetta.protocols.abinitio.Templates method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetricCreator method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMoverCreator method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMoverCreator method) (pyrosetta.rosetta.protocols.analysis.InterfaceData method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMoverCreator method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetricCreator method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMoverCreator method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetricCreator method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafterCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumbering method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMoverCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingParser method) (pyrosetta.rosetta.protocols.antibody.CDRDBPose method) (pyrosetta.rosetta.protocols.antibody.CDRDBSequence 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.clusters.CDRClusterEnumManager method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeatures method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeaturesCreator method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterMatcher method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMoverCreator method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMoverCreator method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMoverCreator method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignEnumManager method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMoverCreator 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.MutantPosition method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForClusterCreator method) (pyrosetta.rosetta.protocols.antibody.design.NativeAntibodySeq method) (pyrosetta.rosetta.protocols.antibody.design.ResnumFromStringsWithRangesSelector method) (pyrosetta.rosetta.protocols.antibody.FrameWork method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_detection_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_undefined_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_grafting_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_invalid_cdr_region_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_json_cdr_detection_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_numbering_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_scs_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_unexpected_region_length_ method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework method) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds method) (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.Chothia_Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.FRH_FRL method) (pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception method) (pyrosetta.rosetta.protocols.antibody.grafting.Json_based_CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.Numberer method) (pyrosetta.rosetta.protocols.antibody.grafting.RegEx_based_CDR_Detector method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastComparator method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastComparator_BitScore_Resolution method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_alignment_length method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_outlier method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_pdbid method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_length method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_bfactor method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_template_resolution method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_nonmatching_prolines method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastPlus method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Comparator method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Functor method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_LoopOverSCs method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultVector method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrix method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult 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.ParatopeMetric_long_t method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelectorCreator method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelectorCreator method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockCreator method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperationCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperationCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperationCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperationCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighborsCreator method) (pyrosetta.rosetta.protocols.antibody_legacy.Antibody 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.local_backbone_mover.LocalBackboneMoverCreator method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPreProCreator method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMoverCreator method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocolCreator method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMoverCreator method) (pyrosetta.rosetta.protocols.buns.BuriedUnsatHbondFilter2Creator method) (pyrosetta.rosetta.protocols.buns.BuriedUnsatisfiedPolarsCalculator2 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.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMoverCreator method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMoverCreator method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMoverCreator 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.DbTrajectoryRecorder.Frame method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.DataBuffer method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Heat_Converged method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Pool_Converged method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.Heat_ConvergenceCheck 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_ConvergenceCheck method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.Pool_Evaluator method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.Pool_RMSD method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MultiTemperatureTrialCounter method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator 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.TorsionSpec method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSamplerCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModelerCreator method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogensCreator method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMoverCreator method) (pyrosetta.rosetta.protocols.cartesian.MolecularDynamics method) (pyrosetta.rosetta.protocols.checkpoint.CheckPointer method) (pyrosetta.rosetta.protocols.checkpoint.FileBuffer method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMoverCreator method) (pyrosetta.rosetta.protocols.chemistries.Chemistry method) (pyrosetta.rosetta.protocols.chemistries.ChemistryCreator method) (pyrosetta.rosetta.protocols.chemistries.ChemistryLoader method) (pyrosetta.rosetta.protocols.chemistries.ChemistryLoaderCreator method) (pyrosetta.rosetta.protocols.chemistries.PatchChemistry method) (pyrosetta.rosetta.protocols.chemistries.PatchChemistryCreator method) (pyrosetta.rosetta.protocols.chemistries.WrappedBaseChemistry method) (pyrosetta.rosetta.protocols.chromophore.ChromophoreDataReader method) (pyrosetta.rosetta.protocols.chromophore.ReadResidueCoordinatesFromPDB method) (pyrosetta.rosetta.protocols.cluster.APCluster method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) (pyrosetta.rosetta.protocols.cluster.calibur.PreloadedPDB method) (pyrosetta.rosetta.protocols.cluster.calibur.SimPDB 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.Align_RmsdEvaluator method) (pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignmentClustering method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator 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.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator 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.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constel.ResidueMask 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.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraintsCreator method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondingAtom method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraintsCreator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMoverCreator method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMoverCreator method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMoverCreator method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMoverCreator method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraintCreator method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluator method) (pyrosetta.rosetta.protocols.constraints_additional.CombinedConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluator method) (pyrosetta.rosetta.protocols.constraints_additional.ConstraintEvaluatorCreator method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet 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.contact_map.Contact method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.contact_map.ContactMapCreator method) (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocolCreator method) (pyrosetta.rosetta.protocols.cryst.CheshireCell method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.CrystRMSCreator method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMoverCreator method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMoverCreator method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMoverCreator method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMoverCreator method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMoverCreator method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMoverCreator method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMoverCreator method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMoverCreator method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMoverCreator method) (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMoverCreator method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfoCreator method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMoverCreator method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomainCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraintCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraintCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraintCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilterCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilterCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilterCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetricCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelectorCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlignCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutationsCreator 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.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.EXCN_PreFilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.MotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.MotifArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.SecStructInfo method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.calculators.CavityCalculator method) (pyrosetta.rosetta.protocols.denovo_design.components.Alias method) (pyrosetta.rosetta.protocols.denovo_design.components.BondInfo method) (pyrosetta.rosetta.protocols.denovo_design.components.BuildPhases 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.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.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_PoseInconsistent method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_RemarksNotPresent method) (pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder method) (pyrosetta.rosetta.protocols.denovo_design.components.FoldGraph 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.NamedSolution method) (pyrosetta.rosetta.protocols.denovo_design.components.NamedSolutions 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.ResidueDihedrals method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairSet method) (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataCreator method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber 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.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.connection.AreConnectablePredicate method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.connection.EXCN_ConnectionSetupFailed method) (pyrosetta.rosetta.protocols.denovo_design.constraints.FileConstraintGenerator method) (pyrosetta.rosetta.protocols.denovo_design.constraints.FileConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMoverCreator 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.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_NothingToFold method) (pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesignCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.RelaxScriptCommand method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotationRange method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelectorCreator method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelectorCreator method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequencies method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequency method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperationCreator method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.LoopInfo method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.SurroundingSS method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMoverCreator 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.DesignProteinBackboneAroundDNACreator method) (pyrosetta.rosetta.protocols.dna.DnaChains method) (pyrosetta.rosetta.protocols.dna.DnaDesignDef method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceFinder method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMoverCreator method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesignCreator method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePackerCreator method) (pyrosetta.rosetta.protocols.dna.DNAParameters method) (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterface method) (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterfaceCreator method) (pyrosetta.rosetta.protocols.dna.RotamerDNAHBondFilter method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDnaCreator method) (pyrosetta.rosetta.protocols.dna.WatsonCrickRotamerCouplings method) (pyrosetta.rosetta.protocols.dna.WatsonCrickRotamerCouplingsCreator method) (pyrosetta.rosetta.protocols.dna_dock.DNAClashCheckFilterCreator method) (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilterCreator method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMoverCreator method) (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacyCreator method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbationCreator method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocolCreator method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocolCreator method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContactCreator method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocolCreator method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockMinMoverCreator method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.DockTaskFactory method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMoverCreator 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.MPDockingMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.docking.RigidBodyInfo 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.docking.TemperedDockingCreator 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.ApplyChemistryMoverCreator method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMoverCreator method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetric method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricCreator method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMoverCreator method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMoverCreator method) (pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions method) (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DensityZscoresCreator 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.ReportFSCCreator method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensitiesCreator method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMoverCreator method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMoverCreator 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.AutoCutDataCreator method) (pyrosetta.rosetta.protocols.environment.claims.ClaimStrength method) (pyrosetta.rosetta.protocols.environment.claims.CutBiasClaim method) (pyrosetta.rosetta.protocols.environment.claims.CutBiasElement method) (pyrosetta.rosetta.protocols.environment.claims.CutElement 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.JumpElement method) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement 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.CoMTrackerCMCreator method) (pyrosetta.rosetta.protocols.environment.EnvClaimBroker.BrokerResult method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.EnvMoverCreator method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Passport method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Security_Exception method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.environment.ScriptCMCreator method) (pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamers method) (pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamersOperationCreator method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCstsCreator method) (pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfs method) (pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfsCreator method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.BackboneSamplerCreator method) (pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterfaceOperationCreator method) (pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesConstraintReporter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputterCreator method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputterCreator method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimizeCreator method) (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.LigBurialFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.LigDSasaFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.LigInterfaceEnergyFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedyCreator method) (pyrosetta.rosetta.protocols.enzdes.PoseFoundResiduesCombination method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMoverCreator method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighterOperationCreator method) (pyrosetta.rosetta.protocols.enzdes.RemoveLigandFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.RepackWithoutLigandFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehaviorCreator method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMoverCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMoverCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.esm_perplexity.EsmPerplexityTensorflowProtocol method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetricCreator method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetricCreator method) (pyrosetta.rosetta.protocols.evaluation.AlignEvaluator method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorCreator method) (pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator method) (pyrosetta.rosetta.protocols.evaluation.PCA method) (pyrosetta.rosetta.protocols.evaluation.PoseEvaluator method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_long_t method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_Size method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_SSize method) (pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_unsigned_long_t method) (pyrosetta.rosetta.protocols.evaluation.TimeEvaluator method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCostFilterCreator method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinderFilterCreator method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserterFilterCreator method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMoverCreator method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutationCreator method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMoverCreator method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMoverCreator method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomTypesFeatures method) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.BatchFeatures method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeatures method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.DatabaseFilter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputterCreator method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputterCreator method) (pyrosetta.rosetta.protocols.features.DdGFeatures method) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporter method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeatures method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondFeatures method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeatures method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTest method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelicalFragment method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeatures method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeatures method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMoverCreator method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator method) (pyrosetta.rosetta.protocols.features.JobDataFeatures method) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeatures method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator method) (pyrosetta.rosetta.protocols.features.MetricData method) (pyrosetta.rosetta.protocols.features.ModelFeatures method) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator method) (pyrosetta.rosetta.protocols.features.OrbitalsFeatures method) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PairFeatures method) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PdbDataFeatures method) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeatures method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseConformationFeatures method) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinSilentReport method) (pyrosetta.rosetta.protocols.features.ProtocolFeatures method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeatures method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.Report method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.ReportToDBCreator method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeatures method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeatures method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueFeatures method) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeatures method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeatures method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeatures method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerFeatures method) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeatures method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RuntimeFeatures method) (pyrosetta.rosetta.protocols.features.RuntimeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeatures method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeatures method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeatures method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScreeningFeatures method) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegment method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeatures method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator method) (pyrosetta.rosetta.protocols.features.Segment method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeatures method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SmotifFeatures method) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeatures method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFragment method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandFragment method) (pyrosetta.rosetta.protocols.features.StructureFeatures method) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureScoresFeatures method) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TaskOperationFeatures method) (pyrosetta.rosetta.protocols.features.TaskOperationFeatures.Taskop_id_name_factory_ method) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TopCountOfAllInputs method) (pyrosetta.rosetta.protocols.features.TopCountOfEachInput method) (pyrosetta.rosetta.protocols.features.TopPercentOfAllInputs method) (pyrosetta.rosetta.protocols.features.TopPercentOfEachInput method) (pyrosetta.rosetta.protocols.features.TotalScoreFeatures method) (pyrosetta.rosetta.protocols.features.TotalScoreFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeatures method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDBCreator method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeatures method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator method) (pyrosetta.rosetta.protocols.features.WaterFeatures method) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CalculatorFilterCreator method) (pyrosetta.rosetta.protocols.filters.CombinedFilterCreator method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilterCreator method) (pyrosetta.rosetta.protocols.filters.ContingentFilterCreator method) (pyrosetta.rosetta.protocols.filters.FalseFilterCreator method) (pyrosetta.rosetta.protocols.filters.FilterCollection method) (pyrosetta.rosetta.protocols.filters.FilterCreator method) (pyrosetta.rosetta.protocols.filters.FilterValueMetric method) (pyrosetta.rosetta.protocols.filters.FilterValueMetricCreator 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.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDRCreator method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutationCreator 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.fldsgn.MatchResidues method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMoverCreator method) (pyrosetta.rosetta.protocols.fldsgn.NcontactsCalculator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergyCreator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotentialCreator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergiesCreator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergyCreator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential method) (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairings 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.HSSTripletSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.Sheet method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand 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.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbSparseMatrixIndex 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.flexpack.OtherContextScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocolCreator method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.CombinedTaskOperation method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal 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.FlxbbDesignCreator method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.flxbb.InterlockAromaCreator method) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperationCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.ConstraintConditions method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGeneratorCreator 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.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ConstraintResidueSelector method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ConstraintResidueSelectorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.CutpointResidueSelector method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.CutpointResidueSelectorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ProteinResidueSelector method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ProteinResidueSelectorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub 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.Interval 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.InverseRotamersCstGeneratorCreator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeCstGeneratorCreator method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCstsCreator method) (pyrosetta.rosetta.protocols.forge.remodel.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.LineObject method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelData method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule 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.RemodelMoverCreator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinks method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinksCreator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityCstGeneratorCreator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector 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.CompareByScoreCombination method) (pyrosetta.rosetta.protocols.frag_picker.CompareQueryPosition method) (pyrosetta.rosetta.protocols.frag_picker.CompareScoreComponent method) (pyrosetta.rosetta.protocols.frag_picker.CompareTotalScore method) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector method) (pyrosetta.rosetta.protocols.frag_picker.Contact method) (pyrosetta.rosetta.protocols.frag_picker.ContactCounts method) (pyrosetta.rosetta.protocols.frag_picker.CSTalosIO method) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector method) (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) (pyrosetta.rosetta.protocols.frag_picker.FragmentComparatorBase method) (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilterCreator method) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.JCouplingIO method) (pyrosetta.rosetta.protocols.frag_picker.LAMBEGO_IO 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.PdbIdChunkFilter method) (pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Map 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.QuotaConfig method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frag_picker.scores.ABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.AdaptiveScoreHistogram method) (pyrosetta.rosetta.protocols.frag_picker.scores.AmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsData method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.BFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.CachingScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.ConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.CSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.DisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.FourAtomsConstraintData method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.GunnCost 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.MakeABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.PartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.PCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.Phi method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.PhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.ProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.Psi method) (pyrosetta.rosetta.protocols.frag_picker.scores.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.SecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.SolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.TalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.TorsionBinSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.SidechainContactDistCutoff method) (pyrosetta.rosetta.protocols.frag_picker.TorsionBinIO method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallChunkFilter method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary 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.GeneralizedKICCreator method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.GeneralizedKICselector method) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementCreator method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementsEqual method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.FitnessFunction method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) (pyrosetta.rosetta.protocols.genetic_algorithm.Mutate1Randomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.Vec1Hash method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocolCreator 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.glycopeptide_docking.GlycopeptideDockingProtocolCreator method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMoverCreator method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMoverCreator method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMoverCreator method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMoverCreator method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMoverCreator method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMoverCreator method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetworkCreator method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetCreator method) (pyrosetta.rosetta.protocols.hbnet.HBNetScoreFilterCreator method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterfaceCreator method) (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct method) (pyrosetta.rosetta.protocols.hbnet.HBondResStruct method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelector method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelectorCreator method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerCreator method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerCreator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterCreator method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixCreator method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleCreator method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelixCreator 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.PerturbBundleCreator method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelixCreator 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.helix_capper.HelixNCapperMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.AddSearchPatternRotSetOp method) (pyrosetta.rosetta.protocols.hotspot_hashing.CartesianSearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.ComposeSearchPatterns method) (pyrosetta.rosetta.protocols.hotspot_hashing.ConstPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStub method) (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) (pyrosetta.rosetta.protocols.hotspot_hashing.LSMSearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbeCreator method) (pyrosetta.rosetta.protocols.hotspot_hashing.PartitionedSearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.RotationSearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.SearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.SearchPatternExpansion method) (pyrosetta.rosetta.protocols.hotspot_hashing.SearchPatternRotSetOp method) (pyrosetta.rosetta.protocols.hotspot_hashing.SearchPatternTransform method) (pyrosetta.rosetta.protocols.hotspot_hashing.SICPatternAtTransform method) (pyrosetta.rosetta.protocols.hotspot_hashing.SphericalRotationSearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.SurfaceSearchPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.TestPattern method) (pyrosetta.rosetta.protocols.hotspot_hashing.VectorPair method) (pyrosetta.rosetta.protocols.hybridization.AllResiduesChanged method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbationCreator method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSamplerCreator method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianSamplerCreator method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.detailedControlsTagSetting method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.FragmentBiasAssigner method) (pyrosetta.rosetta.protocols.hybridization.HybridizeFoldtreeDynamic method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocolCreator method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.TemplateHistory method) (pyrosetta.rosetta.protocols.hybridization.TMalign 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.idealize.IdealizeMoverCreator method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.BinaryFragmentStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.DirectSegmentLookupConfig method) (pyrosetta.rosetta.protocols.indexed_structure_store.DirStructureStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilterCreator method) (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookup method) (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentSpecification method) (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreProvider method) (pyrosetta.rosetta.protocols.indexed_structure_store.JSONStructureStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMoverCreator method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMoverCreator method) (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueBackboneEntry method) (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueOrientEntry method) (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueSidechainEntry method) (pyrosetta.rosetta.protocols.indexed_structure_store.SegmentSequenceProfileConfig method) (pyrosetta.rosetta.protocols.indexed_structure_store.SilentStructureStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreProvider method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.EXCN_Archive method) (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.BOINCJobDistributor method) (pyrosetta.rosetta.protocols.jd2.DebugOut_MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd2.EmptyPoseJobInputter method) (pyrosetta.rosetta.protocols.jd2.EmptyPoseJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.FileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.JD2Failure method) (pyrosetta.rosetta.protocols.jd2.JobDistributor method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.JobOutputterObserver method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.LazySilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.LazySilentFileJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.mmtfJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.MpiFileBuffer 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.NoOutputJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.ScreeningJobInputter method) (pyrosetta.rosetta.protocols.jd2.ScreeningJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobInputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.ShuffleFileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputterCreator method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputterCreator method) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.VectorPoseJobDistributor method) (pyrosetta.rosetta.protocols.jd2.WriteFileSFB method) (pyrosetta.rosetta.protocols.jd2.WriteOut_MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobQueen method) (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobResult method) (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryPreliminaryLarvalJob method) (pyrosetta.rosetta.protocols.jd3.chunk_library.MoverAndChunkLibraryJob method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputSource method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputter method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputterCreator method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.PDBChunkLibraryInputter method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.PDBChunkLibraryInputterCreator method) (pyrosetta.rosetta.protocols.jd3.compare_job_nodes 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.ResultElements method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) (pyrosetta.rosetta.protocols.jd3.deallocation.DeallocationMessage method) (pyrosetta.rosetta.protocols.jd3.deallocation.InputPoseDeallocationMessage method) (pyrosetta.rosetta.protocols.jd3.deallocation.ResourceDeallocationMessage method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelPreliminaryLarvalJob method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputSource method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputter method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputterCreator method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.PDBFullModelInputter method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.PDBFullModelInputterCreator method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.SilentFileFullModelInputter method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.SilentFileFullModelInputterCreator method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.InputSource method) (pyrosetta.rosetta.protocols.jd3.JGJobNode method) (pyrosetta.rosetta.protocols.jd3.JGResultNode method) (pyrosetta.rosetta.protocols.jd3.Job method) (pyrosetta.rosetta.protocols.jd3.job_distributors.JobExtractor method) (pyrosetta.rosetta.protocols.jd3.job_distributors.VanillaJobDistributor method) (pyrosetta.rosetta.protocols.jd3.job_results.PoseJobResult method) (pyrosetta.rosetta.protocols.jd3.job_summaries.EnergyJobSummary method) (pyrosetta.rosetta.protocols.jd3.job_summaries.StandardPoseJobSummary method) (pyrosetta.rosetta.protocols.jd3.JobDigraph method) (pyrosetta.rosetta.protocols.jd3.JobDistributor method) (pyrosetta.rosetta.protocols.jd3.JobGenealogist method) (pyrosetta.rosetta.protocols.jd3.JobOutputIndex method) (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.JobResult method) (pyrosetta.rosetta.protocols.jd3.jobs.MoverJob method) (pyrosetta.rosetta.protocols.jd3.JobSummary method) (pyrosetta.rosetta.protocols.jd3.JobTracker method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) (pyrosetta.rosetta.protocols.jd3.output.MultipleOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.output.MultipleOutputter method) (pyrosetta.rosetta.protocols.jd3.output.OutputSpecification method) (pyrosetta.rosetta.protocols.jd3.output.ResultOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputter method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputSource method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputter method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputter method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJob method) (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJobTracker method) (pyrosetta.rosetta.protocols.jd3.standard.StandardInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) (pyrosetta.rosetta.protocols.jumping.BaseDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.BaseJumpSetup method) (pyrosetta.rosetta.protocols.jumping.BasePairingLibrary method) (pyrosetta.rosetta.protocols.jumping.ChainbreakDistFunc method) (pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.DisulfTemplate method) (pyrosetta.rosetta.protocols.jumping.JumpSample method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings method) (pyrosetta.rosetta.protocols.jumping.MembraneJump method) (pyrosetta.rosetta.protocols.jumping.PairingLibrary method) (pyrosetta.rosetta.protocols.jumping.PairingTemplate method) (pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJump method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) (pyrosetta.rosetta.protocols.jumping.SameStrand method) (pyrosetta.rosetta.protocols.jumping.SheetBuilder method) (pyrosetta.rosetta.protocols.jumping.SpecificGeometryLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary method) (pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMoverCreator method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.Basis method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.coord_equal_to method) (pyrosetta.rosetta.protocols.legacy_sewing.coord_hash method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragmentsCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFileCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFileCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.Model method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalLengthRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalLengthRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyIntraSegmentRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyIntraSegmentRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementSet method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyResidueRetentionRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyResidueRetentionRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentDsspRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentDsspRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentLengthRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentLengthRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyAssemblyScoreFunction method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyAssemblyScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyBlosumScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyCalciumMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyClashScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyInterModelMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyPartnerMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewResidue method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogensCreator 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.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslateCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDFCreator method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizerCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfo method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfoComp method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.EntropyEstimator method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GADockStageParams method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDockCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GAOptimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbAcc_t method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbDon_t method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAlignerOptions method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.RotamerPairEnergies method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfo method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfoComp method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfoCompdH method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionSampler method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigandCreator 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.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDockerCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsembleCreator method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilder method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoaderCreator method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculatorCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.ligand_docking.LigandArea method) (pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoader method) (pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoaderCreator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesignCreator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackboneCreator method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilder method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoaderCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsembleCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigPair_info method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformersCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate_info method) (pyrosetta.rosetta.protocols.ligand_docking.RotateCreator method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.RotatesCreator method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogetherCreator method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.StartFromCreator method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.Transform_info method) (pyrosetta.rosetta.protocols.ligand_docking.TransformCreator method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble_info method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsembleCreator method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.Translate_info method) (pyrosetta.rosetta.protocols.ligand_docking.TranslateCreator method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFileCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapperCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator method) (pyrosetta.rosetta.protocols.loop_grower.DensSkeleton method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtensionCreator method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) (pyrosetta.rosetta.protocols.loop_grower.ResTorsions method) (pyrosetta.rosetta.protocols.loop_grower.SheetPositions method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModelerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilderCreator method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocolCreator method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefinerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefinerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefinerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSamplerCreator 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.PrepareForCentroidCreator method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatomCreator method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.loophash.BackboneDB method) (pyrosetta.rosetta.protocols.loophash.BBExtraData method) (pyrosetta.rosetta.protocols.loophash.EXCN_bbdb_Merge_Failed method) (pyrosetta.rosetta.protocols.loophash.EXCN_DB_IO_Failed method) (pyrosetta.rosetta.protocols.loophash.EXCN_Invalid_Hashmap method) (pyrosetta.rosetta.protocols.loophash.EXCN_No_Extra_Data_To_Write method) (pyrosetta.rosetta.protocols.loophash.EXCN_Wrong_DB_Format method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LocalInserter method) (pyrosetta.rosetta.protocols.loophash.LocalInserter_SimpleMin method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifierCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapperCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.loophash.MPI_LoopHashRefine method) (pyrosetta.rosetta.protocols.loophash.MPI_LoopHashRefine_Emperor method) (pyrosetta.rosetta.protocols.loophash.MPI_LoopHashRefine_Master method) (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash.WU_Header method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.EXCN_Loop_not_closed method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilterCreator method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoopsCreator method) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.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.ShortLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCMCreator 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_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator 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.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_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator 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.LoopRefineInnerCycleContainerCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoaderCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsStringDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsStringDefinerCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileData method) (pyrosetta.rosetta.protocols.loops.LoopsFileIO method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator method) (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader 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.magnesium.SampleGrid method) (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotential method) (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputterCreator method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibOptionsData method) (pyrosetta.rosetta.protocols.make_rot_lib.TorsionRange method) (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM method) (pyrosetta.rosetta.protocols.match.BfactorMPM method) (pyrosetta.rosetta.protocols.match.Bool3DGrid method) (pyrosetta.rosetta.protocols.match.Bool3DGridKinemageWriter method) (pyrosetta.rosetta.protocols.match.BumpGrid method) (pyrosetta.rosetta.protocols.match.downstream.ActiveSiteGrid method) (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.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) (pyrosetta.rosetta.protocols.match.downstream.ScoringSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor method) (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.match_lite_equals method) (pyrosetta.rosetta.protocols.match.match_lite_hasher method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.match.MatcherMoverCreator method) (pyrosetta.rosetta.protocols.match.MatcherTask method) (pyrosetta.rosetta.protocols.match.MatchPositionModifier method) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.DownstreamCoordinateKinemageWriter method) (pyrosetta.rosetta.protocols.match.output.DownstreamRMSEvaluator method) (pyrosetta.rosetta.protocols.match.output.LimitHitsPerRotamerFilter method) (pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.MatchConsolidator method) (pyrosetta.rosetta.protocols.match.output.MatchEvaluator method) (pyrosetta.rosetta.protocols.match.output.MatchFilter method) (pyrosetta.rosetta.protocols.match.output.MatchGrouper method) (pyrosetta.rosetta.protocols.match.output.MatchOutputter method) (pyrosetta.rosetta.protocols.match.output.MatchProcessor method) (pyrosetta.rosetta.protocols.match.output.MatchScoreWriter method) (pyrosetta.rosetta.protocols.match.output.OutputWriter method) (pyrosetta.rosetta.protocols.match.output.PDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseInserter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.ProcessorFactory method) (pyrosetta.rosetta.protocols.match.output.ResidueKinemageWriter method) (pyrosetta.rosetta.protocols.match.output.SameChiBinComboGrouper method) (pyrosetta.rosetta.protocols.match.output.SameRotamerComboGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) (pyrosetta.rosetta.protocols.match.output.SingleDownstreamResidueWriter method) (pyrosetta.rosetta.protocols.match.output.StateAccumulatingMatchFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamHitCacher method) (pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage method) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM method) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM method) (pyrosetta.rosetta.protocols.match.TaskOperationMPM method) (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) (pyrosetta.rosetta.protocols.match.upstream.DunbrackSCSampler method) (pyrosetta.rosetta.protocols.match.upstream.OriginalBackboneBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.ProteinBackboneBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.ProteinSCSampler method) (pyrosetta.rosetta.protocols.match.upstream.ProteinUpstreamBuilder method) (pyrosetta.rosetta.protocols.match.upstream.ScaffoldBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamBuilder method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResidueProcessor method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) (pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperation method) (pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperationCreator method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilterCreator method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMoverCreator method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValuesCreator method) (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilterCreator method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMoverCreator method) (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) (pyrosetta.rosetta.protocols.matdes.MotifHitsRotamersOperation method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilterCreator method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMoverCreator method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMoverCreator method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilterCreator method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.CartesianMDCreator method) (pyrosetta.rosetta.protocols.md.Constraint method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.md.MDscheduleData method) (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.EnergiesByTaskCalculator method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMoverCreator 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.ResHasher method) (pyrosetta.rosetta.protocols.mean_field.ResPred method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraintCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraintCreator method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinderCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelixCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAnglesCreator method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator method) (pyrosetta.rosetta.protocols.membrane.geometry.Embedding method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequenceCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibilityCreator method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergyCreator method) (pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSamplerCreator method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMoverCreator method) (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) (pyrosetta.rosetta.protocols.metal_interface.MatchGrafter method) (pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMoverCreator method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincSiteFinder method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.ChainGroupDiscriminator method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMoverCreator 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.MinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazyCreator method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMoverCreator 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.SymMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.UserDefinedGroupDiscriminator method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMoverCreator method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealerCreator method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecoverCreator method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloResetCreator method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTestCreator method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMoverCreator method) (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftCreator method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motifs.BuildPosition method) (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPackerCreator method) (pyrosetta.rosetta.protocols.motifs.MotifHit method) (pyrosetta.rosetta.protocols.motifs.MotifLibrary method) (pyrosetta.rosetta.protocols.motifs.MotifSearch 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.DsspMoverCreator method) (pyrosetta.rosetta.protocols.moves.EXCN_Converged method) (pyrosetta.rosetta.protocols.moves.FastLinearFunc method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMoverCreator method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.GeometricFunc method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IfMoverCreator method) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMoverCreator method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.LinearFunc method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloExceptionConverge 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.MoverCreator method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.MoverStatistics method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.PoseCondition method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMoverCreator method) (pyrosetta.rosetta.protocols.moves.PyMOLObserver method) (pyrosetta.rosetta.protocols.moves.RampingFunc method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RampingMoverCreator method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RandomMoverCreator method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.ResId method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SequenceMoverCreator method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.SwitchMoverCreator method) (pyrosetta.rosetta.protocols.moves.TrialCounter method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.UDPSocketClient method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.Clusterer method) (pyrosetta.rosetta.protocols.mpi_refinement.MethodParams method) (pyrosetta.rosetta.protocols.mpi_refinement.MPI_Refine_Emperor method) (pyrosetta.rosetta.protocols.mpi_refinement.MPI_Refine_Master method) (pyrosetta.rosetta.protocols.mpi_refinement.MPI_Refinement method) (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) (pyrosetta.rosetta.protocols.mpi_refinement.Serial_Refine method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss.WU_Header method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose.WU_Header method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert.WU_Header method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser.WU_Header method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash.WU_Header method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD.WU_Header method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode.WU_Header method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio.WU_Header method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber.WU_Header method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax.WU_Header method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Sampler method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Sampler.WU_Header method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetric method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricCreator method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetric method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetricCreator method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.SequenceMetric method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.SequenceMetricCreator method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.mover_or_filter method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobSummary method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.NoFailDataMap method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.PoseForPoseID method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.SortByLowEnergy method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.TagManager method) (pyrosetta.rosetta.protocols.multistate_design.MetricCalculatorFitnessFunction method) (pyrosetta.rosetta.protocols.multistate_design.MultiStateAggregateFunction method) (pyrosetta.rosetta.protocols.multistate_design.MultiStateEntity method) (pyrosetta.rosetta.protocols.multistate_design.MultiStateFitnessFunction method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) (pyrosetta.rosetta.protocols.multistate_design.PackingState method) (pyrosetta.rosetta.protocols.multistate_design.PartitionAggregateFunction method) (pyrosetta.rosetta.protocols.multistate_design.PosType method) (pyrosetta.rosetta.protocols.multistate_design.PosTypeCreator method) (pyrosetta.rosetta.protocols.multistate_design.SingleState method) (pyrosetta.rosetta.protocols.multistate_design.SingleStateEntityData method) (pyrosetta.rosetta.protocols.multistate_design.SingleStateFitnessFunction method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocolCreator method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMoverCreator method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocolCreator method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMoverCreator method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinderCreator method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMoverCreator method) (pyrosetta.rosetta.protocols.neighbor.Neighborhood method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.network.UIObserver method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMoverCreator method) (pyrosetta.rosetta.protocols.nmr.pcs.AtomGrid method) (pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergyCreator method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMoverCreator method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSTensorOptimizer method) (pyrosetta.rosetta.protocols.nmr.pre.PREDistanceRecord method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergy method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergyCreator method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMoverCreator method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergy method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergyCreator method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D.Spin method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D.Spin method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_AssignmentNotFound method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_FileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_NoesyAssign method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownAtomname method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownResonance method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.FoldResonance method) (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.NoesyModule method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.PeakCalibratorMap method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator method) (pyrosetta.rosetta.protocols.normalmode.NormalMode method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizerCreator method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMoverCreator method) (pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc method) (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEVariableExpression method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptERotamerData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptERotamerData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData method) (pyrosetta.rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pack_daemon.BasicSimAnnealerRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.DaemonSet method) (pyrosetta.rosetta.protocols.pack_daemon.DenseIGRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.DoubleDenseIGRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction method) (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunctionDriver method) (pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence method) (pyrosetta.rosetta.protocols.pack_daemon.EntityFunc method) (pyrosetta.rosetta.protocols.pack_daemon.EntityFuncExpressionCreator method) (pyrosetta.rosetta.protocols.pack_daemon.ExpExpression method) (pyrosetta.rosetta.protocols.pack_daemon.FASTER_IG_Repacker method) (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) (pyrosetta.rosetta.protocols.pack_daemon.IterativeVectorExpression method) (pyrosetta.rosetta.protocols.pack_daemon.LnExpression method) (pyrosetta.rosetta.protocols.pack_daemon.Mean method) (pyrosetta.rosetta.protocols.pack_daemon.MPIMultistateFitnessFunction method) (pyrosetta.rosetta.protocols.pack_daemon.MultistateAggregateFunction method) (pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction method) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator method) (pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculatorCreator method) (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) (pyrosetta.rosetta.protocols.pack_daemon.PowExpression method) (pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.RotamerSubsetRepacker method) (pyrosetta.rosetta.protocols.pack_daemon.StructureFileNames method) (pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression method) (pyrosetta.rosetta.protocols.pack_daemon.TopEntitySet method) (pyrosetta.rosetta.protocols.pack_daemon.VariableVectorExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VectorExpression method) (pyrosetta.rosetta.protocols.pack_daemon.VectorExpressionCreator method) (pyrosetta.rosetta.protocols.pack_daemon.VectorFunction method) (pyrosetta.rosetta.protocols.pack_daemon.VectorFunction2 method) (pyrosetta.rosetta.protocols.pack_daemon.VMax method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMin method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) (pyrosetta.rosetta.protocols.pack_interface.ProteinProteinInterfaceUpweighter method) (pyrosetta.rosetta.protocols.pack_interface.ProteinProteinInterfaceUpweighterTaskOperationCreator method) (pyrosetta.rosetta.protocols.parser.BluePrint method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DatabaseSessionLoader method) (pyrosetta.rosetta.protocols.parser.DatabaseSessionLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DataLoader method) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator method) (pyrosetta.rosetta.protocols.parser.FragmentReader method) (pyrosetta.rosetta.protocols.parser.FragSetLoader method) (pyrosetta.rosetta.protocols.parser.FragSetLoaderCreator method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoaderCreator method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoaderCreator method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoaderCreator method) (pyrosetta.rosetta.protocols.parser.PackerPaletteLoader method) (pyrosetta.rosetta.protocols.parser.PackerPaletteLoaderCreator method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoaderCreator method) (pyrosetta.rosetta.protocols.parser.ResLvlTaskOperationLoader method) (pyrosetta.rosetta.protocols.parser.ResLvlTaskOperationLoaderCreator method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoaderCreator method) (pyrosetta.rosetta.protocols.parser.SimpleMetricLoader method) (pyrosetta.rosetta.protocols.parser.SimpleMetricLoaderCreator method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoaderCreator method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotentialCreator method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequencesCreator method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.SequenceSpecification method) (pyrosetta.rosetta.protocols.peptide_deriver.CyclizedPeptideInfo method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilterCreator 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) (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver method) (pyrosetta.rosetta.protocols.pockets.CCluster.Cxyz method) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.DarcParticleSwarmMinimizer method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.FingerprintBase method) (pyrosetta.rosetta.protocols.pockets.GenPharmacophore method) (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraintCreator method) (pyrosetta.rosetta.protocols.pockets.PocketExemplarMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.SmallMol method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover.Design method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover.Chunk method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover.SSElement method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMoverCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModelingCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMoverCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMoverCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMoverCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloserCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop 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.EmptyVertexData method) (pyrosetta.rosetta.protocols.pose_metric_calculators.EnergiesData 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.MetricValueGetter 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_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporterCreator method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporterCreator method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporterCreator method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelectorCreator method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelectorCreator method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.FilterCreator method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelectorCreator method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByPropertyCreator 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.CoreScorerCreator method) (pyrosetta.rosetta.protocols.pose_sewing.filters.HasDisulfideFilterCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetricCreator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetricCreator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetricCreator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetricCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNativeResidue method) (pyrosetta.rosetta.protocols.protein_interface_design.FavorNonNativeResidue 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.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreakCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspotsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPoseCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.CoordinateConstraintStack method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbondsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechainsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycleCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycleCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinderCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChangeCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLineCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodelCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspotCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransformCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoopCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutationCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimizeCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechainsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover.mutt method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover.tm_region method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTreeCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactorCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCstsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TryRotamersCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBInstruction method) (pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputter method) (pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportPSSMDifferences method) (pyrosetta.rosetta.protocols.protein_interface_design.ReportSequenceDifferences method) (pyrosetta.rosetta.protocols.protein_interface_design.Revert method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMoverCreator method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetricCreator method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetricCreator method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionTensorflowProtocol method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionTensorflowProtocolBase method) (pyrosetta.rosetta.protocols.qsar.ColorGradient method) (pyrosetta.rosetta.protocols.qsar.qsarCreator method) (pyrosetta.rosetta.protocols.qsar.qsarMap method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.qsarOptData method) (pyrosetta.rosetta.protocols.qsar.qsarOptFunc method) (pyrosetta.rosetta.protocols.qsar.qsarPoint method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemageCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.AllAtomNormalization method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChiAngleNormalization method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HeavyAtomNormalization method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScoreCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.MolecularWeightNormalization method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoreNormalization method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoaderCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGridCreator method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoaderCreator method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetricCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMoverCreator 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.IdealizeHelicesMoverCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMoverCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMoverCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment 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.Histogram method) (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) (pyrosetta.rosetta.protocols.recces.params.RECCES_Parameters 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.ThermalMinimizerCreator method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMoverCreator method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequenceCreator method) (pyrosetta.rosetta.protocols.recon_design.FitnessFilterCreator method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.recon_design.MSDMoverCreator method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMoverCreator method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMoverCreator method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelaxCreator method) (pyrosetta.rosetta.protocols.relax.DatabaseRelaxScript method) (pyrosetta.rosetta.protocols.relax.EnergyMapContainer method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.FastRelaxCreator method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelaxCreator method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMoverCreator method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator 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.RelaxScriptCommand method) (pyrosetta.rosetta.protocols.relax.RelaxScriptFileContents method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelaxCreator method) (pyrosetta.rosetta.protocols.relax.VariableSubstitutionPair method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax.WU_Header method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore.WU_Header method) (pyrosetta.rosetta.protocols.residue_optimization.MetapatchEnumeration method) (pyrosetta.rosetta.protocols.residue_selectors.HBondSelector method) (pyrosetta.rosetta.protocols.residue_selectors.HBondSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.NativeSelector method) (pyrosetta.rosetta.protocols.residue_selectors.NativeSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMoverCreator method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelectorCreator 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.RigidBodyPerturbNoCenterMoverCreator 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.RigidBodyTiltMoverCreator method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMoverCreator method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RollMoverCreator method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCMCreator method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMoverCreator 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.AlignmentEnergyCreator method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.SourcePositions 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_DeNovoProtocolMoverCreator 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_DeNovoProtocolCreator method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2ProtocolCreator method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMoverCreator method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_CoarsifyCreator method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DecoarsifyCreator 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.RNAIdealizeMoverCreator method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMoverCreator 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.AdditionalOutputWrapperCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapperCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMoverCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol.ParsedProtocolStep method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocolCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporter method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelector method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMoverCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects method) (pyrosetta.rosetta.protocols.rotamer_recovery.PerNativeRRReporterHuman method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecovery method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMoverCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSDCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerChiDiff method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerChiDiffCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerElecDensDiff method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerElecDensDiffCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerRotBins method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerRotBinsCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolMinPack method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolMinPackCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolMoverCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolPackRotamers method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolPackRotamersCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolReferenceStructure method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolReferenceStructureCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRelax method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRelaxCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRotamerTrials method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRotamerTrialsCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRTMin method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRTMinCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporter method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHuman method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterHumanCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSimple method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSimpleCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSQLite method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRReporterSQLiteCreator method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.rpc.BasicCmdLineInit method) (pyrosetta.rosetta.protocols.rpc.BasicInit method) (pyrosetta.rosetta.protocols.rpc.JSON_RPC 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.scoring.ImplicitFastClashCheck method) (pyrosetta.rosetta.protocols.scoring.Interface method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.scoring.methods.EnsembleEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.EnsembleEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.GridSearchIterator method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_input method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_per_lanthanides method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_file_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_tensor method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PseudocontactShiftEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.GridSearchIteratorCA method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManager method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.GridSearchIterator_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_input_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_per_lanthanides_Ts1 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.pcsTs1.PCS_file_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_tensor_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PseudocontactShiftEnergyCreator_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.GridSearchIterator_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2 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.pcsTs2.PCS_file_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PseudocontactShiftEnergyCreator_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.GridSearchIterator_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_input_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_per_lanthanides_Ts3 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.pcsTs3.PCS_file_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_tensor_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PseudocontactShiftEnergyCreator_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.GridSearchIterator_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_input_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_per_lanthanides_Ts4 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.pcsTs4.PCS_file_data_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_tensor_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PseudocontactShiftEnergyCreator_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.ResidualDipolarCouplingEnergyRigidSegments 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.SpecialRotamerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergyCreator method) (pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments method) (pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergyCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGeneratorCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFoldCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCstCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoopsCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptidesCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTreeCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMoverCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizerCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegmentCreator method) (pyrosetta.rosetta.protocols.sewing.data_storage.Basis method) (pyrosetta.rosetta.protocols.sewing.data_storage.ContactDescription method) (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.LigandDescription 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.AlignmentFGMSettings method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMoverCreator method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentGenerator method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentSettings method) (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) (pyrosetta.rosetta.protocols.sewing.hashing.coord_equal_to method) (pyrosetta.rosetta.protocols.sewing.hashing.coord_hash method) (pyrosetta.rosetta.protocols.sewing.hashing.EdgeMapGenerator method) (pyrosetta.rosetta.protocols.sewing.hashing.Hasher method) (pyrosetta.rosetta.protocols.sewing.hashing.HasherSettings method) (pyrosetta.rosetta.protocols.sewing.hashing.LigandBindingResPlacer method) (pyrosetta.rosetta.protocols.sewing.hashing.LigandCoordInfo method) (pyrosetta.rosetta.protocols.sewing.hashing.ModelFileReader method) (pyrosetta.rosetta.protocols.sewing.hashing.SegmentVector method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMoverCreator method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.AssemblyRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.AssemblyRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.ClashRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.ClashRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.DsspSpecificLengthRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.DsspSpecificLengthRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.KeepLigandContactsRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.KeepLigandContactsRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.LengthInResiduesRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LengthInResiduesRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandAssemblyRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandClashRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandClashRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.NonTerminalStartingSegmentRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.NonTerminalStartingSegmentRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.SizeInSegmentsRequirement method) (pyrosetta.rosetta.protocols.sewing.requirements.SizeInSegmentsRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandAssemblyScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorerCreator method) (pyrosetta.rosetta.protocols.sic_dock.AtomIDHashFunction method) (pyrosetta.rosetta.protocols.sic_dock.BuriedPolarScore method) (pyrosetta.rosetta.protocols.sic_dock.CBScore method) (pyrosetta.rosetta.protocols.sic_dock.ConstraintSetScore method) (pyrosetta.rosetta.protocols.sic_dock.EdgeStandScore method) (pyrosetta.rosetta.protocols.sic_dock.HelixScore method) (pyrosetta.rosetta.protocols.sic_dock.JointScore method) (pyrosetta.rosetta.protocols.sic_dock.LinkerScore method) (pyrosetta.rosetta.protocols.sic_dock.RigidScore method) (pyrosetta.rosetta.protocols.sic_dock.Rose method) (pyrosetta.rosetta.protocols.sic_dock.scores.MotifHashRigidScore method) (pyrosetta.rosetta.protocols.sic_dock.scores.TrisBpyScore method) (pyrosetta.rosetta.protocols.sic_dock.SICFast method) (pyrosetta.rosetta.protocols.simple_ddg.AlaScanFilterCreator method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_ddg.ddGCreator 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.AtomicContactFilter 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.BatchEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.BatchNrEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.CamShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreakFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.ChiWellRmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.ContactMapEvaluatorCreator 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.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.simple_filters.ExpiryFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ExternalEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.ExtraScoreEvaluatorCreator 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.InterfaceHbondsFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHydrophobicResidueContactsFilter 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.JScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.JScoreEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.JumpEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.JumpNrEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.LoopRmsdEvaluator 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.NativeEvaluatorCreator 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.PalesEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.PalesEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoolEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoseCommentFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.PredictedBurialFnEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RangeFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.RDC_Evaluator method) (pyrosetta.rosetta.protocols.simple_filters.RdcEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcSelectEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RdcTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.ReadPoseExtraScoreFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections 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.ResidueDepthCalculator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFrag 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.RmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.RmsdTargetEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter.mutt method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter.tm_region method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SelectGdtEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SelectMaxsubEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.SelectRDC_Evaluator method) (pyrosetta.rosetta.protocols.simple_filters.SelectRmsdEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.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.StructuralSimilarityEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.StructureSimilarityEvaluatorCreator method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricRmsdEvaluator 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.TruncatedScoreEvaluator method) (pyrosetta.rosetta.protocols.simple_filters.Worst9merFilterCreator 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.AddChainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairDataCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AtomHash 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.BBDihedralSamplerMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBinsCreator method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBinsCreator method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMoverCreator 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.ConcatenatePosesMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond 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.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdbCreator method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamersCreator method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfileCreator method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequenceCreator method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotifCreator method) (pyrosetta.rosetta.protocols.simple_moves.FragmentCost method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.GunnCost method) (pyrosetta.rosetta.protocols.simple_moves.GunnTuple method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.IonizableResidue method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopologyCreator method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidueCreator 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.PDBReloadMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKACreator method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZCreator method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTreeCreator method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMoverCreator 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.RingConformationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilitiesCreator method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsionCreator method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMoverCreator 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.StorePoseSnapshotCreator method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData 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.TumbleCreator 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.VirtualRootMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.WaterRot method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPoseCreator method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMoverCreator 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.RestrictToInterfaceCreator method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoops method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighborsCreator method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsCreator method) (pyrosetta.rosetta.protocols.sparta.ANN method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluator method) (pyrosetta.rosetta.protocols.sparta.ChemicalShiftEvaluatorCreator method) (pyrosetta.rosetta.protocols.sparta.GDB method) (pyrosetta.rosetta.protocols.sparta.PDB method) (pyrosetta.rosetta.protocols.sparta.PDB_Entry method) (pyrosetta.rosetta.protocols.sparta.RingData method) (pyrosetta.rosetta.protocols.sparta.Sparta method) (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMoverCreator method) (pyrosetta.rosetta.protocols.splice.BBDofs method) (pyrosetta.rosetta.protocols.splice.BBMatching method) (pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation method) (pyrosetta.rosetta.protocols.splice.DesignInterfacesOperationCreator method) (pyrosetta.rosetta.protocols.splice.FindEndpointsOperation method) (pyrosetta.rosetta.protocols.splice.FindEndpointsOperationCreator method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBInMoverCreator method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RBOutMoverCreator method) (pyrosetta.rosetta.protocols.splice.ResidueBBDofs method) (pyrosetta.rosetta.protocols.splice.ROT method) (pyrosetta.rosetta.protocols.splice.RotLibdb method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.RotLibOutCreator method) (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB method) (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation method) (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDBCreator method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceCreator method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibodyCreator method) (pyrosetta.rosetta.protocols.splice.SpliceInCreator method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceInTailCreator method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibodyCreator method) (pyrosetta.rosetta.protocols.splice.SpliceOutCreator method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.splice.SpliceOutTailCreator method) (pyrosetta.rosetta.protocols.splice.SpliceSegment method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.splice.TailSegmentMoverCreator method) (pyrosetta.rosetta.protocols.ss_prediction.SS_predictor 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.SlicedPoseWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.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.align.StepWiseClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased 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.StepWiseMasterPacker 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.InputStreamWithResidueInfo 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.MainChainTorsionSet 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.Combine_Tags_Info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Filterer_Count method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Jump_point 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.PhosphateMove method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Residue_info method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarModeling 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.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMoverCreator method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMoverCreator method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.FromScratchMoverCreator 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.ResampleMoverCreator 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.ResidueAlternativeSet method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.EulerAngles method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange 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.screener.RNA_TorsionScreener method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.stepwise.screener.AlignRMSD_Screener method) (pyrosetta.rosetta.protocols.stepwise.screener.AnchorSugarScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.BaseBinMapUpdater method) (pyrosetta.rosetta.protocols.stepwise.screener.BaseCentroidScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.BulgeApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.CentroidDistanceScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.FastForwardToNextResidueAlternative method) (pyrosetta.rosetta.protocols.stepwise.screener.FastForwardToNextRigidBody method) (pyrosetta.rosetta.protocols.stepwise.screener.IntegrationTestBreaker method) (pyrosetta.rosetta.protocols.stepwise.screener.O2PrimeScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PackScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PartitionContactScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PhosphateScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PoseSelectionScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.ProteinCCD_ClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.ResidueContactScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryResidueBasedScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryStubBasedScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.SampleApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.Scorer method) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseResiduePairScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.StubApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.StubDistanceScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.SugarInstantiator method) (pyrosetta.rosetta.protocols.stepwise.screener.TagDefinition method) (pyrosetta.rosetta.protocols.stepwise.screener.VDW_BinScreener method) (pyrosetta.rosetta.protocols.stepwise.StepWiseSampleAndScreen method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator 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.surface_docking.SurfaceVectorLoader method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoaderCreator method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator 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.SymDockProtocolCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMoverCreator 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.DetectSymmetryMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.NCSResMapping method) (pyrosetta.rosetta.protocols.symmetry.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperation method) (pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThreadCreator method) (pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation method) (pyrosetta.rosetta.protocols.task_operations.DesignAroundOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperation method) (pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosionCreator method) (pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation method) (pyrosetta.rosetta.protocols.task_operations.JointSequenceOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2_RotamerSetOperation method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2OperationCreator method) (pyrosetta.rosetta.protocols.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.task_operations.LinkResiduesCreator method) (pyrosetta.rosetta.protocols.task_operations.ModifyAnnealer method) (pyrosetta.rosetta.protocols.task_operations.ModifyAnnealerCreator method) (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ProteinCore method) (pyrosetta.rosetta.protocols.task_operations.ProteinCoreFilterCreator method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsats_RotamerSetsOperation method) (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation method) (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB method) (pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDBCreator method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities method) (pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilitiesCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3Loop method) (pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3LoopCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperation method) (pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.STMStoredTask method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMoverCreator method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMoverCreator method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMoverCreator method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperationCreator method) (pyrosetta.rosetta.protocols.tcr.TCRloopRefine method) (pyrosetta.rosetta.protocols.tcr.TCRmodel method) (pyrosetta.rosetta.protocols.tcr.TCRmodel.tcrtmplts method) (pyrosetta.rosetta.protocols.tcr.TCRmodel.tmpltinfo method) (pyrosetta.rosetta.protocols.tcr.TCRseqInfo method) (pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrposi method) (pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMoverCreator method) (pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup method) (pyrosetta.rosetta.protocols.toolbox.ClusterBase method) (pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DummyClass method) (pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.InteratomicVarianceMatrix method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KClusterData method) (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesSeqRecoveryCache method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTree method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleResidueInvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree method) (pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator method) (pyrosetta.rosetta.protocols.toolbox.Node method) (pyrosetta.rosetta.protocols.toolbox.py_inheritance_test.Base method) (pyrosetta.rosetta.protocols.toolbox.py_inheritance_test.O_1A method) (pyrosetta.rosetta.protocols.toolbox.py_inheritance_test.O_1B method) (pyrosetta.rosetta.protocols.toolbox.py_inheritance_test.O_2A method) (pyrosetta.rosetta.protocols.toolbox.py_inheritance_test.O_2A2B method) (pyrosetta.rosetta.protocols.toolbox.py_inheritance_test.O_2B method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork 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.ScoreRmsPoint method) (pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoints 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.ClaimerMessage method) (pyrosetta.rosetta.protocols.topology_broker.claims.BBClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.CutClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.LegacyRootClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.SequenceClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.SymmetryClaim method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapper method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintEvaluatorWrapperCreator 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.EXCN_FailedBroking method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_Input method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_TopologyBroker method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_Unknown method) (pyrosetta.rosetta.protocols.topology_broker.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.RigidChunkClaimer.CM_SuggestFixResidue method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceNumberResolver method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SuggestValueMessage method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.weights.AbinitioMoverWeight method) (pyrosetta.rosetta.protocols.topology_broker.weights.ConstAbinitioMoverWeight method) (pyrosetta.rosetta.protocols.topology_broker.weights.LargeFragWeight method) (pyrosetta.rosetta.protocols.topology_broker.weights.SmallFragWeight method) (pyrosetta.rosetta.protocols.topology_broker.weights.SmoothFragWeight method) (pyrosetta.rosetta.protocols.trajectory.DbTrajectoryWriter.Frame 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.constraint_generators.trRosettaConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMoverCreator method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMoverCreator method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDistSasaCalculator method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) (pyrosetta.rosetta.protocols.vip.VIP_Mover method) (pyrosetta.rosetta.protocols.vip.VIP_Report method) (pyrosetta.rosetta.protocols.wum.DatabaseEntryWorkUnit method) (pyrosetta.rosetta.protocols.wum.DatabaseEntryWorkUnit.WU_Header method) (pyrosetta.rosetta.protocols.wum.find_SilentStructOPs method) (pyrosetta.rosetta.protocols.wum.MPI_WorkUnitManager method) (pyrosetta.rosetta.protocols.wum.MPI_WorkUnitManager_Slave method) (pyrosetta.rosetta.protocols.wum.SilentStructStore method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper.WU_Header method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore.WU_Header method) (pyrosetta.rosetta.protocols.wum.WorkUnit_Wait method) (pyrosetta.rosetta.protocols.wum.WorkUnit_Wait.WU_Header method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase.WU_Header method) (pyrosetta.rosetta.protocols.wum.WorkUnitList method) (pyrosetta.rosetta.protocols.wum.WorkUnitManager method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue_Swapped method) (pyrosetta.rosetta.RDGeom.Point method) (pyrosetta.rosetta.RDGeom.Point3D method) (pyrosetta.rosetta.RDKit.Atom method) (pyrosetta.rosetta.RDKit.Bond method) (pyrosetta.rosetta.RDKit.Conformer method) (pyrosetta.rosetta.RDKit.Dict method) (pyrosetta.rosetta.RDKit.Dict.Pair method) (pyrosetta.rosetta.RDKit.RDProps method) (pyrosetta.rosetta.RDKit.RDValue method) (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) (pyrosetta.rosetta.std.binary_function_unsigned_long_unsigned_long_bool_t method) (pyrosetta.rosetta.std.equal_to_unsigned_long_t method) (pyrosetta.rosetta.std.exception method) (pyrosetta.rosetta.std.hash_unsigned_long_t method) (pyrosetta.rosetta.std.ios_base.failure 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.locale method) (pyrosetta.rosetta.std.multimap_double_std_pair_unsigned_long_std_pair_std_shared_ptr_protocols_hotspot_hashing_HotspotStubSet_std_shared_ptr_protocols_hotspot_hashing_HotspotStub_t method) (pyrosetta.rosetta.std.multimap_double_std_shared_ptr_protocols_hotspot_hashing_HotspotStub_t method) (pyrosetta.rosetta.std.priority_queue_protocols_motif_grafting_movers_MotifMatch_std_vector_protocols_motif_grafting_movers_MotifMatch_std_less_protocols_motif_grafting_movers_MotifMatch_t method) (pyrosetta.rosetta.std.set_core_chemical_gasteiger_GasteigerAtomTypeData_AtomicOrbitalTypes_t method) (pyrosetta.rosetta.std.set_core_id_DOF_ID_t method) (pyrosetta.rosetta.std.set_core_id_PartialAtomID_t method) (pyrosetta.rosetta.std.set_double_t method) (pyrosetta.rosetta.std.set_int_t method) (pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t method) (pyrosetta.rosetta.std.set_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.set_std_set_unsigned_long_t method) (pyrosetta.rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_t method) (pyrosetta.rosetta.std.set_std_string_t method) (pyrosetta.rosetta.std.set_unsigned_long_t method) (pyrosetta.rosetta.std.unordered_map_basic_datacache_ResRotPair_float_basic_datacache_ResRotPairHasher_std_equal_to_basic_datacache_ResRotPair_std_allocator_std_pair_const_basic_datacache_ResRotPair_float_t method) (pyrosetta.rosetta.std.unordered_map_std_pair_char_char_int_core_sequence_CharPairHash_std_equal_to_std_pair_char_char_std_allocator_std_pair_const_std_pair_char_char_int_t method) (pyrosetta.rosetta.std.unordered_map_unsigned_long_numeric_MathMatrix_float_t method) (pyrosetta.rosetta.std.weak_ptr_const_basic_datacache_HierarchicalDataMap_t method) (pyrosetta.rosetta.std.weak_ptr_const_core_chemical_AtomTypeSet_t method) (pyrosetta.rosetta.std.weak_ptr_const_core_chemical_ElementSet_t method) (pyrosetta.rosetta.std.weak_ptr_const_core_chemical_MMAtomTypeSet_t method) (pyrosetta.rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t method) (pyrosetta.rosetta.std.weak_ptr_const_core_environment_EnvCore_t method) (pyrosetta.rosetta.std.weak_ptr_const_core_environment_FoldTreeSketch_Node_t method) (pyrosetta.rosetta.std.weak_ptr_const_core_scoring_etable_Etable_t method) (pyrosetta.rosetta.std.weak_ptr_const_core_scoring_etable_MembEtable_t method) (pyrosetta.rosetta.std.weak_ptr_const_protocols_environment_Environment_t method) (pyrosetta.rosetta.std.weak_ptr_const_protocols_enzdes_EnzdesFlexBBProtocol_t method) (pyrosetta.rosetta.std.weak_ptr_const_protocols_enzdes_SecondaryMatchProtocol_t method) (pyrosetta.rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t method) (pyrosetta.rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintIO_t method) (pyrosetta.rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintParameters_t method) (pyrosetta.rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t method) (pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t method) (pyrosetta.rosetta.std.weak_ptr_core_environment_FoldTreeSketch_Node_t method) (pyrosetta.rosetta.std.weak_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.std.weak_ptr_core_pose_Pose_t method) (pyrosetta.rosetta.std.weak_ptr_numeric_ClusteringTreeNode_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_forge_components_VarLengthBuild_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_frag_picker_VallProvider_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_jd3_JGJobNode_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_optimize_weights_WrapperOptEMultifunc_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t method) (pyrosetta.rosetta.std.weak_ptr_utility_tag_XMLSchemaRepeatableCTNode_t method) (pyrosetta.rosetta.utility.Bound_bool_t method) (pyrosetta.rosetta.utility.Bound_double_t method) (pyrosetta.rosetta.utility.Bound_int_t method) (pyrosetta.rosetta.utility.Bound_std_string_t method) (pyrosetta.rosetta.utility.Bound_utility_file_FileName_t method) (pyrosetta.rosetta.utility.Bound_utility_file_PathName_t method) (pyrosetta.rosetta.utility.CSI_Sequence method) (pyrosetta.rosetta.utility.deep_copy_vector1_std_shared_ptr_core_chemical_Orbital_t method) (pyrosetta.rosetta.utility.DenseBoolMap_5_0_t 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.factory.WidgetFactory_protocols_genetic_algorithm_EntityElementCreator_t method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.fixedsizearray0_double_3_t method) (pyrosetta.rosetta.utility.fixedsizearray0_double_5_t method) (pyrosetta.rosetta.utility.fixedsizearray0_utility_fixedsizearray0_double_3_3_t method) (pyrosetta.rosetta.utility.fixedsizearray0_utility_fixedsizearray0_double_5_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_bool_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_bool_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_bool_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_bool_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_bool_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_bool_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepNRChiSample_float_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepNRChiSample_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepNRChiSample_float_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepNRChiSample_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepNRChiSample_float_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepScoreInterpData_1_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepScoreInterpData_2_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepScoreInterpData_3_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepScoreInterpData_4_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepScoreInterpData_5_64_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_64_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_7_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_float_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_float_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_float_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_int_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_CatmullRomSplineBoundaryType_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_CatmullRomSplineBoundaryType_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_spline_BorderFlag_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_spline_BorderFlag_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_spline_BorderFlag_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_spline_BorderFlag_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_spline_BorderFlag_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_spline_BorderFlag_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathNTensor_double_1_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathNTensor_double_2_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathNTensor_double_3_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathNTensor_double_4_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathNTensor_double_5_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathNTensor_double_6_64_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathVector_double_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathVector_double_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathVector_double_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathVector_double_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_ObjexxFCL_FArray1D_double_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_ObjexxFCL_FArray1D_double_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_ObjexxFCL_FArray1D_double_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_ObjexxFCL_FArray1D_double_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_ObjexxFCL_FArray1D_double_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_protocols_match_ProbeRadius_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_std_pair_double_double_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_std_pair_double_double_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_std_pair_double_double_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_std_pair_double_double_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_std_pair_double_double_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_std_pair_double_double_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_char_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_char_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_7_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_short_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_16_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_2_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_32_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_4_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_5_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_64_64_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_8_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_vector1_unsigned_long_std_allocator_unsigned_long_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_vector1_unsigned_long_std_allocator_unsigned_long_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_vector1_unsigned_long_std_allocator_unsigned_long_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_vector1_unsigned_long_std_allocator_unsigned_long_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_vector1_unsigned_long_std_allocator_unsigned_long_5_t method) (pyrosetta.rosetta.utility.graph.Array0_double_t method) (pyrosetta.rosetta.utility.graph.ArrayPool_double_t method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator method) (pyrosetta.rosetta.utility.graph.DisjointSets method) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.EdgeListIterator method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS 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.LowMemGraphBase method) (pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t method) (pyrosetta.rosetta.utility.graph.UEEdge_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) (pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) (pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t method) (pyrosetta.rosetta.utility.heap method) (pyrosetta.rosetta.utility.Inline_File_Provider_Hook method) (pyrosetta.rosetta.utility.io.FileContentsMap method) (pyrosetta.rosetta.utility.io.GeneralFileContents method) (pyrosetta.rosetta.utility.io.GeneralFileContentsVector method) (pyrosetta.rosetta.utility.json_spirit.Pair_impl_utility_json_spirit_Config_vector_std_string_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_string_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t 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.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.keys.VariantKey_utility_options_OptionKey_t method) (pyrosetta.rosetta.utility.LexicographicalIterator method) (pyrosetta.rosetta.utility.libsvm.Svm_node_rosetta method) (pyrosetta.rosetta.utility.libsvm.Svm_rosetta 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.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.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.VectorOptionKey method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_core_kinematics_MoveMap_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_core_pose_Pose_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_core_scoring_bin_transitions_BinTransitionCalculator_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_protocols_antibody_AntibodyInfo_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_const_protocols_loops_Loops_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_chemical_AtomProperties_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_chemical_ResidueProperties_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_chemical_rotamers_RotamerLibrarySpecification_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_kinematics_MoveMap_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_pose_Pose_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_core_scoring_ScoreFunction_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_interpolation_spline_BicubicSpline_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_interpolation_spline_CubicSpline_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_interpolation_spline_PolycubicSplineBase_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_numeric_MathNTensorBase_double_t method) (pyrosetta.rosetta.utility.pointer.DeepCopyOP_protocols_loops_Loops_t method) (pyrosetta.rosetta.utility.py.Base method) (pyrosetta.rosetta.utility.py.OverloadTest method) (pyrosetta.rosetta.utility.py.PyExitCallback method) (pyrosetta.rosetta.utility.py.Value method) (pyrosetta.rosetta.utility.recent_history_queue method) (pyrosetta.rosetta.utility.Show method) (pyrosetta.rosetta.utility.signals.Link method) (pyrosetta.rosetta.utility.SimulateMPIMessage method) (pyrosetta.rosetta.utility.sql_database.session method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_GlobalJobID_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_JobDAGNodeID_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_NStructIndex_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_PrelimJobNodeID_t method) (pyrosetta.rosetta.utility.subset_mapping method) (pyrosetta.rosetta.utility.tag.Tag method) (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) (pyrosetta.rosetta.utility.tag.XMLSchemaRepeatableCTNode method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList.ElementSummary method) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaType method) (pyrosetta.rosetta.utility.thread.MutableCache_const_core_chemical_ResidueTypeSet__star__core_pack_palette_BaseTypeList_t method) (pyrosetta.rosetta.utility_exit_detail.Stringifier method) (pyrosetta.rosetta.utility_exit_detail.Stringy method) assign_abase_derivs() (in module pyrosetta.rosetta.core.scoring.hbonds) assign_achain_CDRs_using_REGEX() (in module pyrosetta.rosetta.protocols.tcr) assign_all_amoeba_types() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) assign_bchain_CDRs_using_REGEX() (in module pyrosetta.rosetta.protocols.tcr) assign_best_rotamer() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) assign_BMEC() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) assign_CDRs_using_anarci() (in module pyrosetta.rosetta.protocols.tcr) assign_CDRs_using_numbers() (in module pyrosetta.rosetta.protocols.tcr) assign_chain_ids() (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover static method) assign_conformer_group_to_residue() (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) assign_dofs_to_mobile_residues() (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) assign_energy() (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) assign_esp_for_atom_grid_points() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) assign_esp_for_protein_grid_points() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) assign_esp_for_surface_grid_points() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) assign_esp_for_surface_grid_points_by_nn() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) assign_from_res_to_res() (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) assign_gasteiger_atom_types() (in module pyrosetta.rosetta.core.chemical.gasteiger) assign_group_for_match() (pyrosetta.rosetta.protocols.match.output.MatchGrouper method) (pyrosetta.rosetta.protocols.match.output.SameChiBinComboGrouper method) (pyrosetta.rosetta.protocols.match.output.SameRotamerComboGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceAndDSPositionGrouper method) (pyrosetta.rosetta.protocols.match.output.SameSequenceGrouper method) assign_haro_derivs_one_way() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) assign_hpol_derivs_one_way() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) assign_if() (pyrosetta.rosetta.ObjexxFCL.Dimension method) assign_if_bigger() (pyrosetta.rosetta.ObjexxFCL.Dimension method) assign_if_bigger_nic() (pyrosetta.rosetta.ObjexxFCL.Dimension method) assign_if_half() (pyrosetta.rosetta.ObjexxFCL.Dimension method) assign_if_half_nic() (pyrosetta.rosetta.ObjexxFCL.Dimension method) assign_if_nic() (pyrosetta.rosetta.ObjexxFCL.Dimension method) assign_internal_coordinates() (pyrosetta.rosetta.core.chemical.MutableResidueType method) assign_labelled_spin() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) assign_last_rotamers_to_pose() (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) assign_ligand_trans() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) assign_neighbor_atom() (pyrosetta.rosetta.core.chemical.MutableResidueType method) assign_new_cluster_tag (pyrosetta.rosetta.protocols.toolbox.ClusterOptions property) assign_no_notify() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) assign_only_pi_orbitals_to_atom() (pyrosetta.rosetta.core.chemical.orbitals.AssignOrbitals method) assign_orb_H_derivs() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) assign_orb_orb_derivs() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) assign_orbitals() (pyrosetta.rosetta.core.chemical.orbitals.AssignOrbitals method) assign_pucker() (in module pyrosetta.rosetta.core.pose.rna) assign_random_chi() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) assign_random_rotamer() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) assign_random_rotamer_with_bias() (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) assign_residue_amoeba_type() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) assign_seq() (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) assign_sp2_orbitals_to_one_bonded_atom() (pyrosetta.rosetta.core.chemical.orbitals.AssignOrbitals method) assign_sp2_sp_orbitals_to_one_bonded_atom() (pyrosetta.rosetta.core.chemical.orbitals.AssignOrbitals method) assign_spin() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) assign_ss_dssp() (in module pyrosetta.rosetta.protocols.jumping) assign_state() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) assign_type_data() (pyrosetta.rosetta.protocols.toolbox.KClusterElement method) assign_value_of() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) assign_zero_state() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NodeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) assigned() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) assignment() (pyrosetta.rosetta.core.scoring.hbonds.HBDerivAssigner method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D.Spin method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D.Spin method) assignment_ (pyrosetta.rosetta.protocols.noesy_assign.EXCN_AssignmentNotFound property) assignment_index() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D.Spin method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D.Spin method) assignments() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) AssignmentScaleAndDerivVectID (class in pyrosetta.rosetta.core.scoring.hbonds) AssignOrbitals (class in pyrosetta.rosetta.core.chemical.orbitals) AssignToClustersMover (class in pyrosetta.rosetta.protocols.cluster) ast_string() (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter method) ASTPrinter (class in pyrosetta.rosetta.numeric.expression_parser) astr (pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet property) ASTVisitor (class in pyrosetta.rosetta.numeric.expression_parser) AsymFoldandDockClaimer (class in pyrosetta.rosetta.protocols.topology_broker) AsymFoldandDockMoveRbJumpMover (class in pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock) AsymFoldandDockMoveRbJumpMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock) AsymFoldandDockRbTrialMover (class in pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock) AsymFoldandDockRbTrialMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock) asymm_residues (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) asymmetric_dof() (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) asymmetric_unit() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) AsymmetricUnitSelector (class in pyrosetta.rosetta.core.select.residue_selector) AsymmetricUnitSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) AsyncMPITemperingBase (class in pyrosetta.rosetta.protocols.canonical_sampling) At (pyrosetta.rosetta.core.chemical.element.Elements attribute) at() (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) (pyrosetta.rosetta.core.scoring.epr_deer.EPRSpinLabel method) (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.Sequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.protocols.denovo_design.components.EnumeratedVectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.denovo_design.components.VectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.frag_picker.scores.AdaptiveScoreHistogram method) (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreMap method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.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.std.array_core_kinematics_inverse_AlignmentAtom_3_t method) (pyrosetta.rosetta.std.unordered_map_basic_datacache_ResRotPair_float_basic_datacache_ResRotPairHasher_std_equal_to_basic_datacache_ResRotPair_std_allocator_std_pair_const_basic_datacache_ResRotPair_float_t method) (pyrosetta.rosetta.std.unordered_map_std_pair_char_char_int_core_sequence_CharPairHash_std_equal_to_std_pair_char_char_std_allocator_std_pair_const_std_pair_char_char_int_t method) (pyrosetta.rosetta.std.unordered_map_unsigned_long_numeric_MathMatrix_float_t method) (pyrosetta.rosetta.utility.deep_copy_vector1_std_shared_ptr_core_chemical_Orbital_t method) (pyrosetta.rosetta.utility.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) at1 (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionType property) at2 (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionType property) at3 (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionType property) at4 (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionType property) AT_END (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol.FilterReportTime attribute) at_end() (pyrosetta.rosetta.protocols.match.VoxelSetIterator method) (pyrosetta.rosetta.utility.LexicographicalIterator method) at_inds() (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) at_interface() (in module pyrosetta.rosetta.protocols.constel) atcr() (pyrosetta.rosetta.protocols.tcr.TCRseqInfo method) atm (pyrosetta.rosetta.core.scoring.TorsionParams property) atm() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore method) atm1() (pyrosetta.rosetta.protocols.simple_filters.AngleToVector method) atm2() (pyrosetta.rosetta.protocols.simple_filters.AngleToVector method) atm_excluded() (pyrosetta.rosetta.core.scoring.ResidueExclParams method) atmid() (pyrosetta.rosetta.core.energy_methods.GoapRsdType method) atmInfo (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) atmname_using() (pyrosetta.rosetta.core.energy_methods.GoapRsdType method) atmplt() (pyrosetta.rosetta.protocols.tcr.TCRmodel method) atms (pyrosetta.rosetta.core.scoring.elec.ElecGroup property) atms() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore method) Atom (class in pyrosetta.rosetta.core.chemical) (class in pyrosetta.rosetta.core.conformation) (class in pyrosetta.rosetta.core.kinematics.tree) (class in pyrosetta.rosetta.core.scoring.sc) (class in pyrosetta.rosetta.RDKit) ATOM (pyrosetta.rosetta.core.io.pdb.RecordType attribute) atom (pyrosetta.rosetta.core.scoring.constraints.XYZs property) (pyrosetta.rosetta.core.scoring.packstat.Circle property) ATOM (pyrosetta.rosetta.core.scoring.packstat.SimplePDB_Atom property) atom (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.atmInfo property) atom() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.id.EXCN_AtomNotFound method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.id.NamedStubID method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap 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.elec.electrie.ElecAtom method) (pyrosetta.rosetta.core.scoring.lkball.lkbtrie.LKBAtom method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.core.scoring.packstat.SimplePDB method) (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere 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.noesy_assign.EXCN_UnknownResonance method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) atom1 (pyrosetta.rosetta.core.id.BondID property) (pyrosetta.rosetta.core.id.NamedStubID property) (pyrosetta.rosetta.core.id.StubID property) (pyrosetta.rosetta.protocols.denovo_design.components.BondInfo property) (pyrosetta.rosetta.protocols.environment.claims.JumpElement property) atom1() (pyrosetta.rosetta.core.chemical.sdf.MolFileIOBond method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Obsolet_NamedAtomPairConstraint method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) (pyrosetta.rosetta.core.scoring.RDC method) atom1_atom2_atom3_angle() (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) atom1_atom2_distance() (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) atom1_belongs_in_active_site() (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) atom1_derivs() (pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo method) atom1_radius() (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) atom2 (pyrosetta.rosetta.core.id.BondID property) (pyrosetta.rosetta.core.id.NamedStubID property) (pyrosetta.rosetta.core.id.StubID property) (pyrosetta.rosetta.protocols.denovo_design.components.BondInfo property) (pyrosetta.rosetta.protocols.environment.claims.JumpElement property) atom2() (pyrosetta.rosetta.core.chemical.sdf.MolFileIOBond method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Obsolet_NamedAtomPairConstraint method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondingAtom method) atom2_atom3_distance() (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) atom2_belongs_in_active_site() (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) atom2_derivs() (pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo method) atom2_radius() (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) atom3 (pyrosetta.rosetta.core.id.NamedStubID property) (pyrosetta.rosetta.core.id.StubID property) atom3() (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondingAtom method) atom3_belongs_in_active_site() (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) atom3_derivs() (pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo method) atom3_radius() (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) Atom_ (class in pyrosetta.rosetta.core.kinematics.tree) atom_alias() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) atom_aliases() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) atom_atom_distance (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData property) atom_base() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) atom_being_shadowed() (pyrosetta.rosetta.core.chemical.ResidueType method) Atom_Bin (class in pyrosetta.rosetta.core.pose.rna) atom_charge() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.ResidueType method) atom_controlled_by_any_chi() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) atom_data() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) atom_dependent_calibration_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) atom_depends_on_connection() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_depends_on_lower() (pyrosetta.rosetta.core.conformation.Residue method) atom_depends_on_lower_polymeric_connection() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_depends_on_polymeric_connection() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_depends_on_upper() (pyrosetta.rosetta.core.conformation.Residue method) atom_depends_on_upper_polymeric_connection() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_derivatives() (pyrosetta.rosetta.core.optimization.CartesianMinimizerMap method) (pyrosetta.rosetta.core.optimization.MinimizerMap method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) atom_distance() (in module pyrosetta.rosetta.protocols.protein_interface_design.filters) (in module pyrosetta.rosetta.protocols.simple_filters) atom_dont_do_update() (pyrosetta.rosetta.core.kinematics.AtomTree method) atom_forms_residue_connection() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_geom_rpes() (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) atom_gets_derivatives() (pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices method) atom_gradient() (pyrosetta.rosetta.core.scoring.electron_density_atomwise.ElectronDensityAtomwise method) atom_has_nonchi_coordinate() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) atom_has_orbital() (pyrosetta.rosetta.core.chemical.AtomType method) atom_has_property() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_hbonds() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) atom_hbonds_all() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) atom_hbonds_to_bridging_water() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) atom_id (pyrosetta.rosetta.protocols.cartesian.CartesianAtom property) atom_id() (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.id.DOF_ID 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.DOF_Node method) atom_id_1 (pyrosetta.rosetta.protocols.cartesian.MD_Angle property) (pyrosetta.rosetta.protocols.cartesian.MD_Bond property) (pyrosetta.rosetta.protocols.cartesian.MD_HarmonicDihedral property) atom_id_2 (pyrosetta.rosetta.protocols.cartesian.MD_Angle property) (pyrosetta.rosetta.protocols.cartesian.MD_Bond property) (pyrosetta.rosetta.protocols.cartesian.MD_HarmonicDihedral property) atom_id_3 (pyrosetta.rosetta.protocols.cartesian.MD_Angle property) (pyrosetta.rosetta.protocols.cartesian.MD_HarmonicDihedral property) atom_id_4 (pyrosetta.rosetta.protocols.cartesian.MD_HarmonicDihedral property) atom_id_mapper() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) atom_id_to_named_atom_id() (in module pyrosetta.rosetta.core.conformation) (in module pyrosetta.rosetta.core.pose) atom_ids_in_res() (pyrosetta.rosetta.core.pose.toolbox.AtomID_Mapper method) atom_index() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.sdf.MolFileIOMolecule method) (pyrosetta.rosetta.core.conformation.Residue method) atom_index_ (pyrosetta.rosetta.core.scoring.custom_pair_distance.resatom_and_func_struct property) atom_inds_for_restype() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) atom_is_acceptor() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) atom_is_aro_hydrogen() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_is_backbone() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) atom_is_backbone_norefold() (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) atom_is_chitip() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) atom_is_donorH() (pyrosetta.rosetta.core.scoring.hbonds.HBond method) atom_is_heavy() (pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator method) atom_is_hydratable() (in module pyrosetta.rosetta.protocols.hydrate) atom_is_hydrogen() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) atom_is_independent() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) atom_is_moving() (pyrosetta.rosetta.core.optimization.CartesianMinimizerMap method) atom_is_on_path_from_root() (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) atom_is_phosphate() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) atom_is_polar_hydrogen() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) atom_is_sidechain() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_is_virtual() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) atom_iterators() (pyrosetta.rosetta.core.chemical.MutableResidueType method) atom_lDDT() (pyrosetta.rosetta.core.scoring.lDDT_Calculator method) atom_level_domain_map() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) (pyrosetta.rosetta.core.import_pose.RNA_JumpMover method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) atom_map_ (pyrosetta.rosetta.core.scoring.packstat.MultiProbePerSphereAccumulator property) (pyrosetta.rosetta.core.scoring.packstat.MultiProbePoseAccumulator property) (pyrosetta.rosetta.core.scoring.packstat.PerSphereAccumulator property) atom_map_from_score_result() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) atom_map_valid_size() (in module pyrosetta.rosetta.protocols.hybridization) atom_mode() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) atom_name (pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData property) atom_name() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.AtomGraphVertexData method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord method) (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelAtom method) (pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint method) (pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint_AA method) (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) (pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) atom_name1() (pyrosetta.rosetta.core.import_pose.libraries.RNA_PairingTemplate method) atom_name2() (pyrosetta.rosetta.core.import_pose.libraries.RNA_PairingTemplate method) atom_names_list() (pyrosetta.rosetta.core.pose.MiniPose method) atom_names_soft() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) atom_neighbors() (pyrosetta.rosetta.core.scoring.ResidueNblistData method) (pyrosetta.rosetta.core.scoring.ResiduePairNeighborList method) atom_num() (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) (pyrosetta.rosetta.core.scoring.packing.PoseBallsLite method) atom_numbers_for_mg_calculation() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) atom_numbers_for_vdw_calculation() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) atom_overlap_is_exposed() (pyrosetta.rosetta.core.pack.interaction_graph.InvRotamerDots method) atom_overlaps_voxel() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) atom_pair_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) atom_pair_constraint_energy() (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) atom_pair_constraint_weight() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) atom_pair_distance (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.filter_type attribute) atom_pair_energy() (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.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) atom_pair_energy_v() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) atom_pair_lk_energy_and_deriv_v() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) atom_pair_lk_energy_and_deriv_v_efficient() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) atom_properties() (pyrosetta.rosetta.core.chemical.ResidueType method) atom_radii_ (pyrosetta.rosetta.protocols.match.upstream.BuildSet property) atom_radius() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) atom_radius_squared() (pyrosetta.rosetta.core.conformation.AtomGraphVertexData method) atom_score() (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) atom_scores (pyrosetta.rosetta.core.scoring.packing.HolesResult property) atom_selector() (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) atom_set() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) atom_specific_rms() (in module pyrosetta.rosetta.protocols.motifs) atom_square_deviation() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) atom_to_modify (pyrosetta.rosetta.core.enzymes.EnzymeData property) atom_tree() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) atom_tree_dfunc() (in module pyrosetta.rosetta.core.optimization) (in module pyrosetta.rosetta.core.optimization.symmetry) ATOM_TREE_FILE (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum attribute) atom_tree_get_atompairE_deriv() (in module pyrosetta.rosetta.core.optimization) (in module pyrosetta.rosetta.core.optimization.symmetry) ATOM_TREE_UPDATE_INTERNAL_COORDS (pyrosetta.rosetta.basic.ProfTag attribute) ATOM_TREE_UPDATE_XYZ_COORDS (pyrosetta.rosetta.basic.ProfTag attribute) atom_type (pyrosetta.rosetta.protocols.pockets.CCluster.Cxyz property) atom_type() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.etrie.EtableAtom method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.MultipoleParameter method) (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) (pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom method) (pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator static method) (pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator static method) (pyrosetta.rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator static method) atom_type_index() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) atom_type_name() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.orbitals.OrbitalType method) (pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams method) atom_type_radius (pyrosetta.rosetta.core.scoring.sc.Atom property) atom_type_set() (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.conformation.Residue method) atom_type_set_name() (pyrosetta.rosetta.core.scoring.AtomVDW method) atom_type_set_ptr() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) atom_vdw_atom_type_set_name() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) atom_vertex() (pyrosetta.rosetta.core.chemical.MutableResidueType method) atom_weights() (pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo method) (pyrosetta.rosetta.core.scoring.lkball.lkbtrie.LKBAtom method) (pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilderForRestype method) atom_z_position() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) AtomAngleSecMatchRPE (class in pyrosetta.rosetta.protocols.match.downstream) AtomAtomPairFeatures (class in pyrosetta.rosetta.protocols.features) AtomAtomPairFeaturesCreator (class in pyrosetta.rosetta.protocols.features) AtomBasedConstraintsScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) AtomCoordinateCstMover (class in pyrosetta.rosetta.protocols.relax) AtomCoordinateCstMoverCreator (class in pyrosetta.rosetta.protocols.relax) AtomCountFilter (class in pyrosetta.rosetta.protocols.ligand_docking) AtomCountFilterCreator (class in pyrosetta.rosetta.protocols.ligand_docking) AtomDihedralSecMatchRPE (class in pyrosetta.rosetta.protocols.match.downstream) AtomDistanceSecMatchRPE (class in pyrosetta.rosetta.protocols.match.downstream) atomGDTha() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) AtomGeometrySecMatchRPE (class in pyrosetta.rosetta.protocols.match.downstream) AtomGraphEdgeData (class in pyrosetta.rosetta.core.conformation) AtomGraphVertexData (class in pyrosetta.rosetta.core.conformation) AtomGrid (class in pyrosetta.rosetta.protocols.nmr.pcs) AtomGridPoint (class in pyrosetta.rosetta.protocols.nmr.pcs) AtomHash (class in pyrosetta.rosetta.protocols.simple_moves) AtomHashNode (class in pyrosetta.rosetta.protocols.simple_moves) atomic_charge() (pyrosetta.rosetta.core.conformation.Residue method) atomic_depth() (in module pyrosetta.rosetta.core.scoring.atomic_depth) atomic_depth_cutoff() (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation method) atomic_depth_probe_radius() (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation method) atomic_depth_resolution() (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation method) atomic_interaction_cutoff() (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.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.BranchEnergy method) (pyrosetta.rosetta.core.energy_methods.Burial_v2Energy 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.CenRotPairEnergy 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.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.D2H_SA_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.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy 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.GaussianOverlapEnergy 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.HybridVDW_Energy 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.MembraneCenPairEnergy 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.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.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.OtherPoseEnergy method) (pyrosetta.rosetta.core.energy_methods.PackStatEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.ProQ_Energy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy_Rohl method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_Fast method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_RNA method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergy method) (pyrosetta.rosetta.core.energy_methods.RMS_Energy 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_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_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.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) (pyrosetta.rosetta.core.energy_methods.SecondaryStructureEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy 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.SurfEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfVolEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.XtalMLEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomePackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.geometric_solvation.DatabaseOccSolEne method) (pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.packing.HolesEnergyRes method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieEvaluator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergy method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.EnsembleEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.ResidualDipolarCouplingEnergyRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergy method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy method) atomic_radius() (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) atomicCharge (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.atmInfo property) AtomicContactCountFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) AtomicContactCountFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) AtomicContactFilter (class in pyrosetta.rosetta.protocols.simple_filters) AtomicContactFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) AtomicDepth (class in pyrosetta.rosetta.core.scoring.atomic_depth) AtomicDistanceFilter (class in pyrosetta.rosetta.protocols.simple_filters) AtomicDistanceFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) AtomICoor (class in pyrosetta.rosetta.core.chemical) AtomicOrbitalTypes_strings() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData static method) AtomID (class in pyrosetta.rosetta.core.id) atomid() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo method) atomid_ (pyrosetta.rosetta.core.kinematics.AtomWithDOFChange property) AtomID_Map_AtomID (class in pyrosetta.rosetta.core.id) AtomID_Map_bool (class in pyrosetta.rosetta.core.id) AtomID_Map_bool_t (class in pyrosetta.rosetta.core.id) AtomID_Map_core_id_AtomID_t (class in pyrosetta.rosetta.core.id) AtomID_Map_core_id_TorsionID_t (class in pyrosetta.rosetta.core.id) AtomID_Map_core_scoring_packstat_LR_AtomData_t (class in pyrosetta.rosetta.core.id) AtomID_Map_core_scoring_packstat_LR_MP_AtomData_t (class in pyrosetta.rosetta.core.id) AtomID_Map_double_t (class in pyrosetta.rosetta.core.id) AtomID_Map_numeric_xyzVector_double_t (class in pyrosetta.rosetta.core.id) AtomID_Map_Real (class in pyrosetta.rosetta.core.id) AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t (class in pyrosetta.rosetta.core.id) AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t (class in pyrosetta.rosetta.core.id) AtomID_Map_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.core.id) AtomID_Map_utility_vector1_unsigned_long_std_allocator_unsigned_long_t (class in pyrosetta.rosetta.core.id) AtomID_Map_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.core.id) AtomID_Mapper (class in pyrosetta.rosetta.core.pose.toolbox) AtomIDHashFunction (class in pyrosetta.rosetta.protocols.sic_dock) atomids() (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) AtomInfo (class in pyrosetta.rosetta.core.scoring.hbonds.graph) AtomInformation (class in pyrosetta.rosetta.core.io) AtomInfoSet (class in pyrosetta.rosetta.core.scoring.hbonds.graph) AtomInResidueAtomInResiduePairFeatures (class in pyrosetta.rosetta.protocols.features) AtomInResidueAtomInResiduePairFeaturesCreator (class in pyrosetta.rosetta.protocols.features) atomistic_energy() (pyrosetta.rosetta.core.energy_methods.AACompositionEnergy method) (pyrosetta.rosetta.core.energy_methods.AARepeatEnergy method) (pyrosetta.rosetta.core.energy_methods.Abego method) (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.BranchEnergy method) (pyrosetta.rosetta.core.energy_methods.Burial_v2Energy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CCS_IMMSEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifDegreeEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.ChemicalShiftAnisotropyEnergy method) (pyrosetta.rosetta.core.energy_methods.ContactOrderEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.D2H_SA_Energy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.energy_methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FastSAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyDens method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HolesEnergy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.IntermolEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.LoopCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvPenalties method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneLipo method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergy method) (pyrosetta.rosetta.core.energy_methods.MissingEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.OtherPoseEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.PackStatEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.ProQ_Energy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy_Rohl method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_Fast method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_RNA method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergy method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RMS_Energy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalMappingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PartitionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SA_Energy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) (pyrosetta.rosetta.core.energy_methods.SecondaryStructureEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfVolEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.XtalMLEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomePackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.packing.HolesEnergyRes method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergy method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.EnsembleEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.ResidualDipolarCouplingEnergyRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergy method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy method) atomistic_pair_energy() (pyrosetta.rosetta.core.energy_methods.AACompositionEnergy method) (pyrosetta.rosetta.core.energy_methods.AARepeatEnergy method) (pyrosetta.rosetta.core.energy_methods.Abego method) (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.BranchEnergy method) (pyrosetta.rosetta.core.energy_methods.Burial_v2Energy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CCS_IMMSEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifDegreeEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.ChemicalShiftAnisotropyEnergy method) (pyrosetta.rosetta.core.energy_methods.ContactOrderEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.D2H_SA_Energy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.energy_methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FastSAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyDens method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HolesEnergy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.IntermolEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.LoopCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvPenalties method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneLipo method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergy method) (pyrosetta.rosetta.core.energy_methods.MissingEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.OtherPoseEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.PackStatEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.ProQ_Energy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy_Rohl method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_Fast method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_RNA method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergy method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RMS_Energy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalMappingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PartitionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SA_Energy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) (pyrosetta.rosetta.core.energy_methods.SecondaryStructureEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfVolEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.XtalMLEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomePackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.packing.HolesEnergyRes method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergy method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.EnsembleEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.ResidualDipolarCouplingEnergyRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergy method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy method) atomitem (class in pyrosetta.rosetta.core.scoring.rna.chemical_shift) AtomLevelDomainMap (class in pyrosetta.rosetta.core.pose.toolbox) atomName (pyrosetta.rosetta.protocols.sparta.PDB_Entry property) atomname() (pyrosetta.rosetta.protocols.contact_map.ContactPartner method) AtomNeighbor (class in pyrosetta.rosetta.core.scoring) atomno (pyrosetta.rosetta.protocols.legacy_sewing.HashValue property) (pyrosetta.rosetta.protocols.sewing.hashing.HashValue property) atomNo (pyrosetta.rosetta.protocols.sparta.RingData property) atomno() (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.PartialAtomID method) (pyrosetta.rosetta.core.optimization.DOF_Node method) (pyrosetta.rosetta.core.scoring.AtomNeighbor method) (pyrosetta.rosetta.numeric.geometry.hashing.Ball method) atomno1() (pyrosetta.rosetta.core.scoring.SmallAtNb method) atomno2() (pyrosetta.rosetta.core.scoring.SmallAtNb method) atomno_ (pyrosetta.rosetta.numeric.geometry.hashing.Ball property) (pyrosetta.rosetta.protocols.legacy_sewing.SewAtom property) atomNum (pyrosetta.rosetta.protocols.sparta.PDB_Entry property) AtomPairConstraint (class in pyrosetta.rosetta.core.scoring.constraints) AtomPairConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) AtomPairConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) AtomPairConstraintGenerator.MappedAtom (class in pyrosetta.rosetta.protocols.constraint_generator) AtomPairConstraintGeneratorCreator (class in pyrosetta.rosetta.protocols.constraint_generator) AtomPairConstraintsData (class in pyrosetta.rosetta.protocols.frag_picker.scores) AtomPairConstraintsScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) AtomPairData (class in pyrosetta.rosetta.protocols.ligand_docking.rdf) AtomPairEnergy (class in pyrosetta.rosetta.core.scoring.etable) AtomPairFuncList (class in pyrosetta.rosetta.core.scoring.custom_pair_distance) AtomProperties (class in pyrosetta.rosetta.core.chemical) (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) AtomPropertiesManager (class in pyrosetta.rosetta.core.chemical) AtomProperty (class in pyrosetta.rosetta.core.chemical) AtomRadiusMap (class in pyrosetta.rosetta.core.scoring.packstat) atomRec (pyrosetta.rosetta.core.pose.PDBInfo.ResidueRecord property) AtomRefMapping_unsigned_long_void__star__t (class in pyrosetta.rosetta.core.chemical) AtomRefMapping_void__star__unsigned_long_t (class in pyrosetta.rosetta.core.chemical) AtomRefMapping_void__star__void__star__t (class in pyrosetta.rosetta.core.chemical) atomRings() (pyrosetta.rosetta.RDKit.RingInfo method) atomRingSizes() (pyrosetta.rosetta.RDKit.RingInfo method) atoms (pyrosetta.rosetta.core.kinematics.inverse.AlignmentAtomArray property) ATOMS (pyrosetta.rosetta.protocols.sparta.PDB property) atoms() (pyrosetta.rosetta.core.chemical.Metapatch method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.optimization.DOF_Node method) (pyrosetta.rosetta.core.scoring.packstat.SimplePDB method) (pyrosetta.rosetta.core.scoring.PDinter method) (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) (pyrosetta.rosetta.protocols.environment.claims.JumpClaim method) atoms_and_func_struct (class in pyrosetta.rosetta.core.scoring.custom_pair_distance) atoms_are_bonded() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) atoms_deeper_than() (in module pyrosetta.rosetta.core.scoring.atomic_depth) atoms_downstream_ (pyrosetta.rosetta.protocols.jumping.DisulfTemplate property) (pyrosetta.rosetta.protocols.jumping.PairingTemplate property) atoms_interact() (in module pyrosetta.rosetta.core.scoring.methods) atoms_last_controlled_by_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) atoms_upstream_ (pyrosetta.rosetta.protocols.jumping.DisulfTemplate property) (pyrosetta.rosetta.protocols.jumping.PairingTemplate property) atoms_w_dof_derivatives() (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) atoms_with_orb_index() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) atoms_within_one_bond_of_a_residue_connection() (pyrosetta.rosetta.core.chemical.ResidueType method) atoms_within_two_bonds_of_a_residue_connection() (pyrosetta.rosetta.core.chemical.ResidueType method) AtomSelection (class in pyrosetta.rosetta.core.io.nmr) AtomSurfaceFullList (pyrosetta.rosetta.protocols.sparta.PDB property) AtomSurfacePartList (pyrosetta.rosetta.protocols.sparta.PDB property) AtomToAxisConstraint (class in pyrosetta.rosetta.core.scoring.constraints) AtomTree (class in pyrosetta.rosetta.core.kinematics) AtomTreeCollection (class in pyrosetta.rosetta.core.pack.scmin) AtomTreeDiff (class in pyrosetta.rosetta.core.import_pose.atom_tree_diffs) AtomTreeDiffJobDistributor (class in pyrosetta.rosetta.protocols.jobdist) AtomTreeDiffJobInputter (class in pyrosetta.rosetta.protocols.jd2) AtomTreeDiffJobInputterCreator (class in pyrosetta.rosetta.protocols.jd2) AtomTreeDiffJobOutputter (class in pyrosetta.rosetta.protocols.jd2) AtomTreeDiffJobOutputterCreator (class in pyrosetta.rosetta.protocols.jd2) AtomTreeMinimizer (class in pyrosetta.rosetta.core.optimization) AtomTreeMultifunc (class in pyrosetta.rosetta.core.optimization) AtomTreeSCMinMinimizerMap (class in pyrosetta.rosetta.core.pack.scmin) AtomType (class in pyrosetta.rosetta.core.chemical) atomtype_to_block_param() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapDatabase method) AtomTypeDatabaseIO (class in pyrosetta.rosetta.core.chemical) AtomTypeSet (class in pyrosetta.rosetta.core.chemical) AtomTypesFeatures (class in pyrosetta.rosetta.protocols.features) AtomTypesFeaturesCreator (class in pyrosetta.rosetta.protocols.features) AtomVDW (class in pyrosetta.rosetta.core.scoring) atomWaters (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.atmInfo property) AtomWithDOFChange (class in pyrosetta.rosetta.core.kinematics) atr (pyrosetta.rosetta.protocols.ligand_docking.Ligand_info property) ATR_REP (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) atr_rep_screen() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) atr_rep_screen_for_docking() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) atr_weight() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) AtrGrid (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) AtrGridCreator (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) ats_n_func_list() (pyrosetta.rosetta.core.scoring.custom_pair_distance.AtomPairFuncList method) attach() (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t method) (pyrosetta.rosetta.protocols.moves.PyMOLObserver method) (pyrosetta.rosetta.protocols.network.UIObserver method) attach_boinc_ghost_observer() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) attach_impl() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) attach_ligand() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) attach_n_and_c_unfolded_poses_to_pose() (in module pyrosetta.rosetta.protocols.fold_from_loops.utils) attach_next_part() (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) attach_observer() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) attach_rotamer_clouds_to_pose_and_rotset() (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) attach_secondary_structure_pools() (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) attach_to() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) (pyrosetta.rosetta.protocols.moves.PyMOLObserver method) (pyrosetta.rosetta.protocols.network.UIObserver method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver method) (pyrosetta.rosetta.protocols.viewer.SilentObserver method) attach_to_conformation() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) attach_unfolded_pose_to_pose_c_term() (in module pyrosetta.rosetta.protocols.fold_from_loops.utils) attach_unfolded_pose_to_pose_n_term() (in module pyrosetta.rosetta.protocols.fold_from_loops.utils) attach_unowned_ligand() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) attached_H_begin() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) attached_H_end() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) attached_res() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) attaches_to_residue_type() (pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo method) Attachment (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) attachment_type() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.Attachment method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) attachment_type_from_string() (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) attachments() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) AttachmentType (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) attempt_insert() (pyrosetta.rosetta.protocols.mean_field.ResHashMap method) atten (pyrosetta.rosetta.core.scoring.sc.Atom property) attractive (pyrosetta.rosetta.core.scoring.etable.AtomPairEnergy property) attribute_w_default() (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute static method) attribute_w_name_in_attribute_list() (in module pyrosetta.rosetta.utility.tag) attributes (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList.ElementSummary property) attributes() (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator static method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter static method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid static method) attributes_for_append_assembly_mover() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover static method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover static method) attributes_for_get_ab_design_global_scorefxn() (in module pyrosetta.rosetta.protocols.antibody.design) attributes_for_get_ab_design_min_scorefxn() (in module pyrosetta.rosetta.protocols.antibody.design) attributes_for_get_cdr_bool_from_tag() (in module pyrosetta.rosetta.protocols.antibody) attributes_for_get_resnum_selector() (in module pyrosetta.rosetta.core.pose) attributes_for_get_resnum_string() (in module pyrosetta.rosetta.core.pose) attributes_for_get_score_function_name() (in module pyrosetta.rosetta.core.scoring) attributes_for_get_score_function_name_w_description() (in module pyrosetta.rosetta.core.scoring) attributes_for_hbnet() (pyrosetta.rosetta.protocols.hbnet.HBNet static method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface static method) attributes_for_load_loop_definitions() (in module pyrosetta.rosetta.protocols.loops.loops_definers) attributes_for_parse_center_normal_from_tag() (pyrosetta.rosetta.protocols.membrane.AddMembraneMover static method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover static method) attributes_for_parse_constraint_generators() (in module pyrosetta.rosetta.protocols.constraint_generator) attributes_for_parse_database_connection() (in module pyrosetta.rosetta.basic.database) attributes_for_parse_database_session() (in module pyrosetta.rosetta.protocols.rosetta_scripts) attributes_for_parse_grid_set_from_tag() (in module pyrosetta.rosetta.protocols.qsar.scoring_grid) attributes_for_parse_jump_selector() (in module pyrosetta.rosetta.core.select.jump_selector) attributes_for_parse_jump_selector_default_option_name() (in module pyrosetta.rosetta.core.select.jump_selector) attributes_for_parse_jump_selector_when_required() (in module pyrosetta.rosetta.core.select.jump_selector) attributes_for_parse_movemap_factory() (in module pyrosetta.rosetta.core.select.movemap) attributes_for_parse_movemap_factory_default_attr_name() (in module pyrosetta.rosetta.core.select.movemap) attributes_for_parse_movemap_factory_when_required() (in module pyrosetta.rosetta.core.select.movemap) attributes_for_parse_movemap_factory_when_required_default_name() (in module pyrosetta.rosetta.core.select.movemap) attributes_for_parse_my_tag() (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.DeNovoArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.MotifArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect static method) attributes_for_parse_optional_grid_set_from_tag() (in module pyrosetta.rosetta.protocols.qsar.scoring_grid) attributes_for_parse_residue_level_operations() (in module pyrosetta.rosetta.core.pack.task.operation) attributes_for_parse_residue_selector() (in module pyrosetta.rosetta.core.select.residue_selector) (in module pyrosetta.rosetta.protocols.rosetta_scripts) attributes_for_parse_residue_selector_default_option_name() (in module pyrosetta.rosetta.core.select.residue_selector) attributes_for_parse_residue_selector_logic_string() (in module pyrosetta.rosetta.core.select.residue_selector) attributes_for_parse_residue_selector_when_required() (in module pyrosetta.rosetta.core.select.residue_selector) attributes_for_parse_resnum() (in module pyrosetta.rosetta.core.pose) attributes_for_parse_score_function() (in module pyrosetta.rosetta.core.scoring) attributes_for_parse_score_function_w_description() (in module pyrosetta.rosetta.core.scoring) attributes_for_parse_score_function_w_description_when_required() (in module pyrosetta.rosetta.core.scoring) attributes_for_parse_task_operations() (in module pyrosetta.rosetta.core.pack.task) attributes_for_parse_task_operations_w_factory() (in module pyrosetta.rosetta.core.pack.task) attributes_for_parse_xyz_vector() (in module pyrosetta.rosetta.protocols.rosetta_scripts) attributes_for_remodel_constraint_generator() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator static method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG static method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG static method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGenerator static method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator static method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG static method) attributes_for_report_to_db() (pyrosetta.rosetta.protocols.features.ReportToDB static method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB static method) attributes_for_saved_reference_pose() (in module pyrosetta.rosetta.core.pose) (in module pyrosetta.rosetta.protocols.rosetta_scripts) attributes_for_saved_reference_pose_w_description() (in module pyrosetta.rosetta.core.pose) (in module pyrosetta.rosetta.protocols.rosetta_scripts) attributes_for_set_scorefxn_from_tag() (in module pyrosetta.rosetta.protocols.loop_modeling.utilities) attributes_for_set_task_factory_from_tag() (in module pyrosetta.rosetta.protocols.loop_modeling.utilities) attributes_for_sheet_constraint_generator() (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator static method) attributes_for_tempering_base() (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase static method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange static method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering static method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering static method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase static method) attributes_for_trajectory_recorder() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder static method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder static method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder static method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder static method) Au (pyrosetta.rosetta.core.chemical.element.Elements attribute) auction_results() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) AUTHOR (pyrosetta.rosetta.core.io.pdb.RecordType attribute) author_in_progress() (pyrosetta.rosetta.core.io.HeaderInformation method) author_name() (pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleAuthor method) AuthorNames (class in pyrosetta.rosetta.basic.citation_manager) authors() (pyrosetta.rosetta.core.io.HeaderInformation method) AUTO (class in pyrosetta.rosetta.core.pack.task) Auto (pyrosetta.rosetta.utility.tag.AutoBool attribute) auto_choose_cutpoint() (pyrosetta.rosetta.protocols.loops.Loop method) auto_choose_cutpoints() (pyrosetta.rosetta.protocols.loops.Loops method) auto_clash() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) auto_cut() (pyrosetta.rosetta.protocols.environment.Environment method) auto_cuts (pyrosetta.rosetta.protocols.environment.EnvClaimBroker.BrokerResult property) auto_design (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) auto_detect_contacts (pyrosetta.rosetta.protocols.sewing.data_storage.LigandDescription property) auto_detect_glycan_connections() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) auto_detect_symmetry() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) auto_download() (pyrosetta.rosetta.protocols.esm_perplexity.EsmPerplexityTensorflowProtocol method) auto_generate_kink_constraint() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) auto_increment() (pyrosetta.rosetta.basic.database.schema_generator.Column method) auto_increment_base() (pyrosetta.rosetta.basic.database.schema_generator.Column method) auto_setup_all_metal_bonds() (in module pyrosetta.rosetta.core.util) auto_setup_all_metal_constraints() (in module pyrosetta.rosetta.core.util) auto_trim_floppy_termini() (in module pyrosetta.rosetta.protocols.sic_dock) autoAdjustPercentile (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) AutoBool (class in pyrosetta.rosetta.utility.tag) AutoCutData (class in pyrosetta.rosetta.protocols.environment) AutoCutDataCreator (class in pyrosetta.rosetta.protocols.environment) autodetermine_chi_bonds() (pyrosetta.rosetta.core.chemical.MutableResidueType method) autoexpanding_pocket_eval() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) autofill() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) autofilter() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) autofilter_score_quantile() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) autogenerate_constseq_frags() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) autogenerate_design_frags() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) autogenerate_frags() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) AutoKey_utility_options_Option_utility_keys_Key_utility_keys_NoClient_t (class in pyrosetta.rosetta.utility.keys) AUTOMATIC (pyrosetta.rosetta.core.conformation.Strategy attribute) automatic_distance_cutoff() (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) AutomaticSheetConstraintGenerator (class in pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator) AutomaticSheetConstraintGeneratorCreator (class in pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator) automode() (pyrosetta.rosetta.protocols.hybridization.FragmentBiasAssigner method) automode_scores() (pyrosetta.rosetta.protocols.hybridization.FragmentBiasAssigner method) automorphic_rmsd() (in module pyrosetta.rosetta.core.scoring) AutomorphismIterator (class in pyrosetta.rosetta.core.chemical) AutoRBMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) auxClustering() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) available_AAs_file() (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) available_lower_termini() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) available_resource_loaders() (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) available_upper_termini() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) ave_abs_diff() (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) average_antiparallel_embeddings() (in module pyrosetta.rosetta.protocols.membrane) average_change_in_rama_score_over_range() (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) average_dist() (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist.DistanceRecord method) average_dist6() (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist.DistanceRecord method) average_embeddings() (in module pyrosetta.rosetta.protocols.membrane) average_residue_hASA() (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) average_score() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) average_shortest_path_length() (pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork method) (pyrosetta.rosetta.protocols.toolbox.ResidueNetwork method) AverageDegreeFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) AverageDegreeFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) AverageLinkClusterer (class in pyrosetta.rosetta.numeric) AveragePathLengthFilter (class in pyrosetta.rosetta.protocols.simple_filters) AveragePathLengthFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) AverageProbabilitiesMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) AverageProbabilitiesMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.metrics) avg_rank_as_energy() (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) avg_stdev() (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERChiSqMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERData method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDecayData method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceBounds method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceDistribution method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJaccardMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJSMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERMiscMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEEROverlapMethod method) AvNAPSA_negative() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) AvNAPSA_positive() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) AvNAPSA_values() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) avoid_negative_zero() (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) avoid_sc_hbonds() (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBCPData method) ax_init() (pyrosetta.rosetta.core.optimization.MinimizerOptions method) AxEqDesignation (class in pyrosetta.rosetta.core.chemical.rings) AXIAL (pyrosetta.rosetta.core.chemical.rings.AxEqDesignation attribute) axis() (pyrosetta.rosetta.numeric.Quaternion_double_t method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) axis1 (pyrosetta.rosetta.core.scoring.constraints.XYZs property) axis2 (pyrosetta.rosetta.core.scoring.constraints.XYZs property) AxisRotationSampler (class in pyrosetta.rosetta.numeric) axs (pyrosetta.rosetta.protocols.kinmatch.KRSQuery property) azmiuth_max (pyrosetta.rosetta.protocols.hotspot_hashing.SphericalRotationSearchPattern property) azmiuth_min (pyrosetta.rosetta.protocols.hotspot_hashing.SphericalRotationSearchPattern property) azmiuth_rotation_sampling (pyrosetta.rosetta.protocols.hotspot_hashing.SphericalRotationSearchPattern property)