Index – O

O (pyrosetta.rosetta.core.chemical.element.Elements attribute) (pyrosetta.rosetta.protocols.comparative_modeling.features.TorsionBin attribute) (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueOrientEntry property) O() (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) O1_ACETYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O1_BUTYRYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O1_LACTYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O1_METHYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O1_PROPARGYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O2_ACETYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O2_BUTYRYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O2_LACTYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O2_METHYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O2_PROPARGYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O2H (pyrosetta.rosetta.core.chemical.rna.RNA_Torsion attribute) O2PRIME (pyrosetta.rosetta.core.chemical.rna.BaseEdge attribute) o2prime_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) o2prime_index_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) o2prime_legacy_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) O2PRIME_PACK (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) o2prime_trials() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) O2PrimePacker (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime) O2PrimeScreener (class in pyrosetta.rosetta.protocols.stepwise.screener) O3_ACETYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O3_BUTYRYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O3_C5_distance (pyrosetta.rosetta.protocols.stepwise.modeler.rna.output_data_struct property) O3_LACTYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O3_METHYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O3_PROPARGYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O3P_TO_O5P (pyrosetta.rosetta.core.pose.rna.StubStubType attribute) o3prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) o3prime_index_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) O4_ACETYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O4_BUTYRYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O4_LACTYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O4_METHYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O4_PROPARGYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) o4prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) o4prime_index_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) O5_ACETYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O5_BUTYRYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O5_LACTYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O5_METHYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O5_PROPARGYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) o5prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) o5prime_index_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) O6_ACETYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O6_BUTYRYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O6_LACTYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O6_METHYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O6_PROPARGYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O7_ACETYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O7_BUTYRYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O7_LACTYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O7_METHYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O7_PROPARGYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O8_ACETYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O8_BUTYRYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O8_LACTYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O8_METHYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O8_PROPARGYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O9_ACETYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O9_BUTYRYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O9_LACTYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O9_METHYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O9_PROPARGYL_SUGAR (pyrosetta.rosetta.core.chemical.VariantType attribute) O_1A (class in pyrosetta.rosetta.protocols.toolbox.py_inheritance_test) O_1B (class in pyrosetta.rosetta.protocols.toolbox.py_inheritance_test) O_2A (class in pyrosetta.rosetta.protocols.toolbox.py_inheritance_test) O_2A2B (class in pyrosetta.rosetta.protocols.toolbox.py_inheritance_test) O_2B (class in pyrosetta.rosetta.protocols.toolbox.py_inheritance_test) O_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) O_CONNECT (pyrosetta.rosetta.core.chemical.VariantType attribute) O_LINKED_GLYCOSYLATION (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes attribute) O_p_sp2 (pyrosetta.rosetta.core.chemical.orbitals.orbital_type_enum attribute) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics attribute) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics.orbital_type_name attribute) O_p_sp2_bb (pyrosetta.rosetta.core.chemical.orbitals.orbital_type_enum attribute) O_p_sp3 (pyrosetta.rosetta.core.chemical.orbitals.orbital_type_enum attribute) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics attribute) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics.orbital_type_name attribute) O_pi_sp2 (pyrosetta.rosetta.core.chemical.orbitals.orbital_type_enum attribute) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics attribute) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics.orbital_type_name attribute) O_pi_sp2_bb (pyrosetta.rosetta.core.chemical.orbitals.orbital_type_enum attribute) O_pos() (pyrosetta.rosetta.protocols.match.upstream.OriginalBackboneBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.ProteinBackboneBuildPoint method) oatom1_oatom2_distance() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) oatom1_oatom2_oatom3_angle() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) oatom2_oatom3_distance() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) obey_ENDMDL() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) obj_type (pyrosetta.rosetta.utility.json_spirit.Value_type attribute) object_name() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub static method) obligate_pairing_sets() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) observe_after_metropolis() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.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.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) observe_mc() (pyrosetta.rosetta.core.pack.annealer.AnnealerObserver method) Observer (class in pyrosetta.rosetta.ObjexxFCL) observer_attached() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) observer_cache() (pyrosetta.rosetta.core.pose.Pose method) observer_p() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) ObserverCache (class in pyrosetta.rosetta.core.pose.datacache) ObserverGraph (class in pyrosetta.rosetta.ObjexxFCL.internal) ObserverMulti (class in pyrosetta.rosetta.ObjexxFCL) ObserverSingle (class in pyrosetta.rosetta.ObjexxFCL) OBSIG (pyrosetta.rosetta.core.scoring.nmr.SINGLE_NMR_VALUE_WEIGHTING attribute) OBSLTE (pyrosetta.rosetta.core.io.pdb.RecordType attribute) Obsolet_NamedAtomPairConstraint (class in pyrosetta.rosetta.core.scoring.constraints) obsolete() (pyrosetta.rosetta.core.pose.PDBInfo method) obtain_rtypes_for_target_sequence() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) occ (pyrosetta.rosetta.core.scoring.packstat.SimplePDB_Atom property) occ_sol_exact (pyrosetta.rosetta.core.scoring.ScoreType attribute) occ_sol_fitted (pyrosetta.rosetta.core.scoring.ScoreType attribute) occ_sol_fitted_onebody (pyrosetta.rosetta.core.scoring.ScoreType attribute) occ_space_bounding_box() (pyrosetta.rosetta.protocols.match.MatcherTask method) occ_space_hash() (pyrosetta.rosetta.protocols.match.Matcher method) OccFitParam (class in pyrosetta.rosetta.core.scoring.geometric_solvation) OccFitParam_amp (pyrosetta.rosetta.core.scoring.geometric_solvation.OccFitParam attribute) OccFitParam_cos_angle_mu (pyrosetta.rosetta.core.scoring.geometric_solvation.OccFitParam attribute) OccFitParam_dist_mu (pyrosetta.rosetta.core.scoring.geometric_solvation.OccFitParam attribute) OccFitParam_max_sq_dist (pyrosetta.rosetta.core.scoring.geometric_solvation.OccFitParam attribute) OccFitParam_min_cos_angle (pyrosetta.rosetta.core.scoring.geometric_solvation.OccFitParam attribute) OccFitParam_num_params (pyrosetta.rosetta.core.scoring.geometric_solvation.OccFitParam attribute) OccFitParam_twice_cos_angle_sigma_sq (pyrosetta.rosetta.core.scoring.geometric_solvation.OccFitParam attribute) OccFitParam_twice_dist_sigma_sq (pyrosetta.rosetta.core.scoring.geometric_solvation.OccFitParam attribute) OccludedHbondSolEnergy (class in pyrosetta.rosetta.core.energy_methods) OccludedHbondSolEnergy_onebody (class in pyrosetta.rosetta.core.energy_methods) OccludedHbondSolEnergy_onebodyCreator (class in pyrosetta.rosetta.core.energy_methods) OccludedHbondSolEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) occlusion_max() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) occlusion_min() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) occupancy (pyrosetta.rosetta.core.io.AtomInformation property) (pyrosetta.rosetta.core.pose.PDBInfo.AtomRecord property) occupancy() (pyrosetta.rosetta.core.pose.PDBInfo method) occupied() (pyrosetta.rosetta.protocols.match.Bool3DGrid method) (pyrosetta.rosetta.protocols.match.BumpGrid method) (pyrosetta.rosetta.protocols.match.downstream.ActiveSiteGrid method) OccupiedSpaceHash (class in pyrosetta.rosetta.protocols.match) occurrence_data() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) ocstream (class in pyrosetta.rosetta.utility.io) octahedral_metal (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker attribute) OctahedralMetal_Helper (class in pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) OCTOSE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) OCTREE (pyrosetta.rosetta.core.conformation.Strategy attribute) Octree2D (class in pyrosetta.rosetta.core.scoring.packstat) OD1_CONNECT (pyrosetta.rosetta.core.chemical.VariantType attribute) OD2_CONNECT (pyrosetta.rosetta.core.chemical.VariantType attribute) odd() (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.FindEndpointsOperation method) OE1_CONNECT (pyrosetta.rosetta.core.chemical.VariantType attribute) OE2_CONNECT (pyrosetta.rosetta.core.chemical.VariantType attribute) off (pyrosetta.rosetta.protocols.hybridization.sampleEnum attribute) off_rotamer_pack() (in module pyrosetta.rosetta.core.pack) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) off_rotamer_pack_optimize() (in module pyrosetta.rosetta.core.pack) off_rotamer_pack_setup() (in module pyrosetta.rosetta.core.pack) off_rotamer_pack_update_pose() (in module pyrosetta.rosetta.core.pack) offset (pyrosetta.rosetta.protocols.loophash.LeapIndex property) offset() (pyrosetta.rosetta.core.io.rna.RDAT method) (pyrosetta.rosetta.core.scoring.GenTorsionParams method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.topology_broker.SequenceNumberResolver method) offset_data_up_to_date() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) OffsetPeriodicBoundFunc (class in pyrosetta.rosetta.core.scoring.constraints) ofrac (pyrosetta.rosetta.core.scoring.APBSConfig property) ofstream (class in pyrosetta.rosetta.std) ofstream.sentry (class in pyrosetta.rosetta.std) OG1_CONNECT (pyrosetta.rosetta.core.chemical.VariantType attribute) OG_CONNECT (pyrosetta.rosetta.core.chemical.VariantType attribute) OL_features (pyrosetta.rosetta.protocols.rotamer_recovery.OutputLevel attribute) OL_full (pyrosetta.rosetta.protocols.rotamer_recovery.OutputLevel attribute) OL_none (pyrosetta.rosetta.protocols.rotamer_recovery.OutputLevel attribute) old_eval_atom_derivative() (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) old_force (pyrosetta.rosetta.protocols.cartesian.CartesianAtom property) old_position (pyrosetta.rosetta.protocols.cartesian.CartesianAtom property) old_seqpos() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) old_velocity (pyrosetta.rosetta.protocols.cartesian.CartesianAtom property) OligomericAverageDegreeFilter (class in pyrosetta.rosetta.protocols.matdes) OligomericAverageDegreeFilterCreator (class in pyrosetta.rosetta.protocols.matdes) OLIGOUREA (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) omega (pyrosetta.rosetta.core.fragment.torsions property) OMEGA (pyrosetta.rosetta.core.scoring.ProteinTorsion attribute) omega (pyrosetta.rosetta.core.scoring.ScoreType attribute) (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueBackboneEntry property) (pyrosetta.rosetta.protocols.jumping.DisulfTemplate property) (pyrosetta.rosetta.protocols.jumping.PairingTemplate property) omega() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.io.raw_data.DecoyStruct method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frags.RMSVallData method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.loophash.BackboneSegment method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.splice.BBDofs method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) omega0_range() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters method) omega2_dihedral (pyrosetta.rosetta.core.id.MainchainTorsionType attribute) omega3_dihedral (pyrosetta.rosetta.core.id.MainchainTorsionType attribute) omega_ (pyrosetta.rosetta.protocols.loop_grower.ResTorsions property) OMEGA_ANGLES (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) omega_dihedral (pyrosetta.rosetta.core.id.MainchainTorsionType attribute) omega_index() (pyrosetta.rosetta.core.scoring.OmegaTether method) omega_mean_sd (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData property) omega_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) OmegaBundleParameter (class in pyrosetta.rosetta.protocols.helical_bundle.parameters) OmegaPerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) OmegaPreferenceSamplingData (class in pyrosetta.rosetta.core.scoring.carbohydrates) OmegaPreferencesFunction (class in pyrosetta.rosetta.core.scoring.carbohydrates) OmegaPreferenceType (class in pyrosetta.rosetta.core.scoring.carbohydrates) OmegaTether (class in pyrosetta.rosetta.core.scoring) OmegaTetherEnergy (class in pyrosetta.rosetta.core.energy_methods) OmegaTetherEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) omg() (pyrosetta.rosetta.core.scoring.motif.Xfres method) OMICRON_ATOM (pyrosetta.rosetta.core.chemical.GreekDistance attribute) OMIT (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation attribute) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation.LayerOperationType attribute) OmnibusDisulfideAnalysisLabelerMover (class in pyrosetta.rosetta.protocols.pose_sewing.movers) OmnibusDisulfideAnalysisLabelerMoverCreator (class in pyrosetta.rosetta.protocols.pose_sewing.movers) on (pyrosetta.rosetta.protocols.hybridization.sampleEnum attribute) on_connection_change() (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) on_energy_change() (pyrosetta.rosetta.protocols.viewer.SilentObserver method) on_identity_change() (pyrosetta.rosetta.core.pose.PDBInfo method) on_length_change() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.pose.PDBInfo 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.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) on_new_fragments() (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) on_pose_conf_change() (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) on_pose_destruction_change() (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) on_pose_energy_change() (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) on_residue_append() (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) on_residue_delete() (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) on_residue_prepend() (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) on_segment() (in module pyrosetta.rosetta.core.membrane) once_called() (pyrosetta.rosetta.cppdb.backend.connection method) (pyrosetta.rosetta.cppdb.session method) (pyrosetta.rosetta.utility.sql_database.session method) One (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType attribute) one() (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) one_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) one_body_energy() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) ONE_DOF (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) One_Four_BBMB (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker attribute) One_Four_BBMB_Helper (class in pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) one_indexed_chr_chains() (in module pyrosetta.rosetta.core.chemical) one_letter() (pyrosetta.rosetta.core.sequence.AnnotatedSequence method) one_letter_code() (pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry method) one_letter_sequence() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.sequence.AnnotatedSequence method) one_line_report() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) ONE_TORSION (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) ONE_VALUE (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) ONE_VALUE_COMB (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) oneb_wtd_ (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy property) onebody_energies() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) OneBodyEnergy (class in pyrosetta.rosetta.core.scoring.methods) OneDDistPotential (class in pyrosetta.rosetta.core.scoring) OneGaussianScattering (class in pyrosetta.rosetta.core.scoring.electron_density) (class in pyrosetta.rosetta.core.scoring.fiber_diffraction) ONELETTER_CODE (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricMode attribute) oneletter_code_from_aa() (in module pyrosetta.rosetta.core.chemical) oneletter_code_specifies_aa() (in module pyrosetta.rosetta.core.chemical) OnePerStruct (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover attribute) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover.ExecutionMode attribute) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe attribute) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe.ExecutionMode attribute) onError() (in module pyrosetta.rosetta.core.pack.task) OneToAllEnergyContainer (class in pyrosetta.rosetta.core.scoring) OneToAllNeighborConstIterator (class in pyrosetta.rosetta.core.scoring) OneToAllNeighborIterator (class in pyrosetta.rosetta.core.scoring) ONLY_ALPHA_AA_AT_ALPHA_POSITIONS (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) ONLY_ARAMID_AT_ARAMID_POSITIONS (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) ONLY_BETA_AA_AT_BETA_POSITIONS (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) only_clean_seq_num() (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) ONLY_DESIGN_POLYMER_RESIDUES (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) ONLY_DESIGN_PROTEIN_PEPTIOID_DNA_AND_SACCHARIDES (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) ONLY_DNA_AT_DNA_POSITIONS (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) only_enumerate_non_match_redundant_ligand_rotamers() (pyrosetta.rosetta.protocols.match.MatcherTask method) ONLY_GAMMA_AA_AT_GAMMA_POSITIONS (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) ONLY_LIGAND_AT_LIGAND_POSITIONS (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) ONLY_MATCHING_LIGAND_NAMES (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) only_native() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) ONLY_OLIGOUREA_AT_OLIGOUREA_POSITIONS (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) ONLY_RNA_AT_RNA_POSITIONS (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) ONLY_SACCHARIDES_AT_SACCHARIDE_POSITIONS (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) OnTheFlyEdge (class in pyrosetta.rosetta.core.pack.interaction_graph) OnTheFlyInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) OnTheFlyNode (class in pyrosetta.rosetta.core.pack.interaction_graph) OOP_POST (pyrosetta.rosetta.core.chemical.VariantType attribute) OOP_PRE (pyrosetta.rosetta.core.chemical.VariantType attribute) OopCreatorMover (class in pyrosetta.rosetta.protocols.ncbb.oop) OopCreatorMoverCreator (class in pyrosetta.rosetta.protocols.ncbb.oop) OopDockDesignProtocol (class in pyrosetta.rosetta.protocols.ncbb.oop) OopDockDesignProtocolCreator (class in pyrosetta.rosetta.protocols.ncbb.oop) OopDPuckMinusMover (class in pyrosetta.rosetta.protocols.simple_moves.oop) OopDPuckPlusMover (class in pyrosetta.rosetta.protocols.simple_moves.oop) OopMover (class in pyrosetta.rosetta.protocols.simple_moves.oop) OopPatcher (class in pyrosetta.rosetta.protocols.simple_moves.oop) OopPuckMinusMover (class in pyrosetta.rosetta.protocols.simple_moves.oop) OopPuckPlusMover (class in pyrosetta.rosetta.protocols.simple_moves.oop) OopRandomPuckMover (class in pyrosetta.rosetta.protocols.simple_moves.oop) OopRandomSmallMover (class in pyrosetta.rosetta.protocols.simple_moves.oop) op() (pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) op1_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) op1_atom_index_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) op2_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) op2_atom_index_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) open() (in module pyrosetta.rosetta.basic.database) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream method) (pyrosetta.rosetta.cppdb.backend.driver method) (pyrosetta.rosetta.cppdb.backend.loadable_driver method) (pyrosetta.rosetta.cppdb.pool method) (pyrosetta.rosetta.cppdb.session method) (pyrosetta.rosetta.std.filebuf method) (pyrosetta.rosetta.std.ifstream method) (pyrosetta.rosetta.std.ofstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ozstream method) (pyrosetta.rosetta.utility.sql_database.session method) open_append() (pyrosetta.rosetta.utility.io.ozstream method) open_append_if_existed() (pyrosetta.rosetta.utility.io.ozstream method) open_compressed() (in module pyrosetta.io.silent_file_map) open_mysql_session() (pyrosetta.rosetta.utility.sql_database.session method) open_postgres_session() (pyrosetta.rosetta.utility.sql_database.session method) open_sqlite3_session() (pyrosetta.rosetta.utility.sql_database.session method) opening() (pyrosetta.rosetta.protocols.dna.DNABasepair method) operate_on_ex1() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) operate_on_ex2() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) operate_on_ex3() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) operate_on_ex4() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) OperateOnCertainResidues (class in pyrosetta.rosetta.core.pack.task.operation) OperateOnCertainResiduesCreator (class in pyrosetta.rosetta.core.pack.task.operation) OperateOnResidueSubset (class in pyrosetta.rosetta.core.pack.task.operation) OperateOnResidueSubsetCreator (class in pyrosetta.rosetta.core.pack.task.operation) Operation (class in pyrosetta.rosetta.protocols.calc_taskop_filters) operation() (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) Operator (class in pyrosetta.rosetta.protocols.calc_taskop_filters) operator_filter() (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) OperatorFilterCreator (class in pyrosetta.rosetta.protocols.calc_taskop_filters) opposite_designation() (in module pyrosetta.rosetta.core.chemical.rings) oprev_cprev_n_h_interres_improper_params() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) opt_bckg() (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTraceFactory method) OptCysHG (class in pyrosetta.rosetta.core.pack.task.operation) OptCysHGCreator (class in pyrosetta.rosetta.core.pack.task.operation) optE_type_from_name() (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataFactory static method) optE_type_name() (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataFactory static method) OptEData (class in pyrosetta.rosetta.protocols.optimize_weights) OptEMultifunc (class in pyrosetta.rosetta.protocols.optimize_weights) OptEMultifuncMPIMessages (class in pyrosetta.rosetta.protocols.optimize_weights) OptEPositionData (class in pyrosetta.rosetta.protocols.optimize_weights) OptEPositionDataFactory (class in pyrosetta.rosetta.protocols.optimize_weights) OptEPositionDataType (class in pyrosetta.rosetta.protocols.optimize_weights) OptEVariableExpression (class in pyrosetta.rosetta.protocols.optimize_weights) OptH (class in pyrosetta.rosetta.core.pack.task.operation) OPTH_FLEXIBLE_SIDECHAINS (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OptHMode attribute) OPTH_FULL (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OptHMode attribute) OPTH_NO_FLIP_HNQ (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OptHMode attribute) OPTH_NONE (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OptHMode attribute) OPTH_REDEFINE_SIDECHAINS (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OptHMode attribute) OptHCreator (class in pyrosetta.rosetta.core.pack.task.operation) OptHMode (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) optimal_connection_point() (in module pyrosetta.rosetta.protocols.protein_interface_design) optimization_loop() (pyrosetta.rosetta.protocols.relax.LocalRelax method) optimize() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) optimize_angles() (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) optimize_branch_angles() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) optimize_cov_bond() (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) optimize_foldtree() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) optimize_h() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) optimize_H_and_notify() (in module pyrosetta.rosetta.core.pack) optimize_kurtosis() (pyrosetta.rosetta.protocols.toolbox.InteratomicVarianceMatrix method) optimize_membrane() (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) optimize_paraion_position() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) optimize_structure() (in module pyrosetta.rosetta.protocols.ddg.CartesianddG) optimize_tensors() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSData method) optimized_transform() (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) optimizeH() (in module pyrosetta.rosetta.core.pack) OptimizeMembranePositionMover (class in pyrosetta.rosetta.protocols.membrane) OptimizeMembranePositionMoverCreator (class in pyrosetta.rosetta.protocols.membrane) OptimizeProteinEmbeddingMover (class in pyrosetta.rosetta.protocols.membrane) OptimizeProteinEmbeddingMoverCreator (class in pyrosetta.rosetta.protocols.membrane) optimizeSolventMask() (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) optimizeSolvParams() (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) optimizeSolvParamsAndMask() (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) OptimizeThreadingMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) OptimizeThreadingMoverCreator (class in pyrosetta.rosetta.protocols.rbsegment_relax) Option (class in pyrosetta.rosetta.utility.options) option() (pyrosetta.rosetta.utility.options.OptionCollection method) option_type_from_key() (in module pyrosetta.rosetta.protocols.jd3) option_vdw_rep_screen_info_user() (in module pyrosetta.rosetta.protocols.scoring) optional_name_attribute() (in module pyrosetta.rosetta.utility.tag) optional_output_name() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.InnerMultiThreadingJob method) optional_positive_intafteroption() (in module pyrosetta.rosetta.basic.options) OptionCollection (class in pyrosetta.rosetta.utility.options) OptionKey (class in pyrosetta.rosetta.utility.options) options() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintHelper method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) options_ (pyrosetta.rosetta.core.optimization.NelderMeadSimplex property) options_for_generate_relax_from_cmd() (in module pyrosetta.rosetta.protocols.relax) options_for_get_cst_fa_file_option() (in module pyrosetta.rosetta.core.scoring.constraints) options_for_get_cst_file_option() (in module pyrosetta.rosetta.core.scoring.constraints) options_for_job() (in module pyrosetta.rosetta.protocols.jd3) options_for_set_native_in_mover() (in module pyrosetta.rosetta.protocols.jd2) options_from_tag() (in module pyrosetta.rosetta.protocols.jd3) options_read_in_ctor() (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover static method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover static method) OptionTypes (class in pyrosetta.rosetta.utility.options) OR (pyrosetta.rosetta.protocols.filters.boolean_operations attribute) (pyrosetta.rosetta.protocols.task_operations.boolean_operations attribute) or_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) or_by_box_liberal() (pyrosetta.rosetta.protocols.match.Bool3DGrid method) or_by_sphere() (pyrosetta.rosetta.protocols.match.BumpGrid method) or_by_sphere_conservative() (pyrosetta.rosetta.protocols.match.Bool3DGrid method) or_by_sphere_liberal() (pyrosetta.rosetta.protocols.match.Bool3DGrid method) or_by_spheres_conservative() (pyrosetta.rosetta.protocols.match.Bool3DGrid method) OR_combine() (in module pyrosetta.rosetta.core.select.residue_selector) or_double_lazy_ig() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) or_ex1() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex1_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex1aro() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex1aro_exposed() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex1aro_exposed_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method)

or_ex1aro_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex2() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex2_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex2aro() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex2aro_exposed() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex2aro_exposed_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex2aro_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex3() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex3_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex4() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex4_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_exdna_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_fix_his_tautomer() (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) or_flip_HNQ() (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) or_include_current() (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) or_include_virtual_side_chain() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_lazy_ig() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) or_linmem_ig() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) or_logic (pyrosetta.rosetta.core.select.residue_selector.basic_selection_logic attribute) or_multi_cool_annealer() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) or_operate_on_ex1() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_operate_on_ex2() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_operate_on_ex3() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_operate_on_ex4() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_optimize_h() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_optimize_h_mode() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) or_precompute_ig() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) or_preserve_c_beta() (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) or_randomize2() (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) OR_SYMBOL (pyrosetta.rosetta.numeric.expression_parser.TokenType attribute) or_with() (pyrosetta.rosetta.protocols.match.Bool3DGrid method) (pyrosetta.rosetta.protocols.match.BumpGrid method) or_within_radius_of_backbone() (pyrosetta.rosetta.protocols.match.downstream.ActiveSiteGrid method) or_within_radius_of_residue() (pyrosetta.rosetta.protocols.match.downstream.ActiveSiteGrid method) or_within_radius_of_sidechain() (pyrosetta.rosetta.protocols.match.downstream.ActiveSiteGrid method) orb_orb_rules() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) OrbHdist_cosAOH_energy() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsLookup method) OrbHdist_cosDHO_energy() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsLookup method) Orbital (class in pyrosetta.rosetta.core.chemical) orbital() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) orbital_enum() (pyrosetta.rosetta.core.chemical.orbitals.OrbitalType method) orbital_icoor_data() (pyrosetta.rosetta.core.chemical.ResidueType method) orbital_index() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) orbital_name() (pyrosetta.rosetta.core.chemical.orbitals.OrbitalType method) (pyrosetta.rosetta.core.conformation.Residue method) orbital_type() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.conformation.Residue method) orbital_type_enum (class in pyrosetta.rosetta.core.chemical.orbitals) orbital_type_index() (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.orbitals.OrbitalTypeSet method) (pyrosetta.rosetta.core.conformation.Residue method) orbital_type_set() (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) orbital_types_ptr() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) orbital_xyz() (pyrosetta.rosetta.core.conformation.Residue method) OrbitalBond (pyrosetta.rosetta.core.chemical.BondName attribute) OrbitalBondOrder (pyrosetta.rosetta.core.chemical.BondOrder attribute) orbitals_hpol_bb (pyrosetta.rosetta.core.scoring.ScoreType attribute) OrbitalsFeatures (class in pyrosetta.rosetta.protocols.features) OrbitalsFeaturesCreator (class in pyrosetta.rosetta.protocols.features) OrbitalsLookup (class in pyrosetta.rosetta.core.scoring.orbitals) OrbitalsLookup.h_type (class in pyrosetta.rosetta.core.scoring.orbitals) OrbitalsScore (class in pyrosetta.rosetta.core.scoring.orbitals) OrbitalsScoreCreator (class in pyrosetta.rosetta.core.scoring.orbitals) OrbitalsStatistics (class in pyrosetta.rosetta.core.scoring.orbitals) OrbitalsStatistics.orbital_type_name (class in pyrosetta.rosetta.core.scoring.orbitals) OrbitalType (class in pyrosetta.rosetta.core.chemical.orbitals) OrbitalTypeMapper (class in pyrosetta.rosetta.core.chemical.orbitals) OrbitalTypeSet (class in pyrosetta.rosetta.core.chemical.orbitals) OrbitalXYZCoords (class in pyrosetta.rosetta.core.conformation.orbitals) OrbOrbDist_cosAOD_energy() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsLookup method) OrbOrbDist_cosDOA_energy() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsLookup method) ord (pyrosetta.rosetta.numeric.kinematic_closure.p property) order (pyrosetta.rosetta.protocols.fold_from_loops.utils.NubSegment property) order() (in module pyrosetta.rosetta.protocols.forge.methods) (pyrosetta.rosetta.core.chemical.Bond method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) order_by_energy() (pyrosetta.rosetta.core.io.silent.SilentFileData method) order_parameter() (pyrosetta.rosetta.protocols.toolbox.InteratomicVarianceMatrix method) order_strand() (pyrosetta.rosetta.protocols.fldsgn.topology.Sheet method) order_strands() (pyrosetta.rosetta.protocols.fldsgn.topology.Sheet method) order_tensor_parameters() (in module pyrosetta.rosetta.core.scoring.nmr) OrderCBC (class in pyrosetta.rosetta.core.scoring.packstat) ordered_constrained_positions() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) ordered_pt_wat_penalty() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) ORDERED_SEQUENTIAL (pyrosetta.rosetta.core.conformation.symmetry.SlideType attribute) ordered_wat_penalty() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) OrderedFragSet (class in pyrosetta.rosetta.core.fragment) OrderedFragSetIterator_ (class in pyrosetta.rosetta.core.fragment) OrderedSequentialSymmetrySlider (class in pyrosetta.rosetta.protocols.symmetry) OrExpression (class in pyrosetta.rosetta.numeric.expression_parser) ori (pyrosetta.rosetta.protocols.kinmatch.KRSQuery property) (pyrosetta.rosetta.protocols.pockets.spherical_coor_triplet property) (pyrosetta.rosetta.protocols.tcr.TCRmodel.tcrtmplts property) orient (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueEntry property) (pyrosetta.rosetta.protocols.membrane.SpanInfo property) orient() (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing method) orient1() (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing method) orient2() (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing method) orient_onto_location() (pyrosetta.rosetta.core.conformation.Residue method) orient_onto_residue() (pyrosetta.rosetta.core.conformation.Residue method) orient_onto_residue_peptoid() (pyrosetta.rosetta.core.conformation.Residue method) orient_residue_for_ideal_bond() (in module pyrosetta.rosetta.core.conformation) orient_rotamer_set_to_symmetric_partner() (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets static method) orient_rotamer_to_symmetric_partner() (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) orient_strand() (pyrosetta.rosetta.protocols.fldsgn.topology.Sheet method) orient_strands() (pyrosetta.rosetta.protocols.fldsgn.topology.Sheet method) orient_tcr_chain() (in module pyrosetta.rosetta.protocols.tcr) Orientation (class in pyrosetta.rosetta.core.conformation.membrane) orientation (pyrosetta.rosetta.core.import_pose.libraries.BasePairType property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultSet property) (pyrosetta.rosetta.protocols.fldsgn.ResiduePair property) Orientation() (pyrosetta.rosetta.basic.sampling.orientations.QuatSet method) orientation() (pyrosetta.rosetta.core.conformation.membrane.Span method) (pyrosetta.rosetta.core.pose.rna.BasePair method) (pyrosetta.rosetta.core.pose.rna.BaseStack method) Orientation() (pyrosetta.rosetta.core.scoring.dssp.Pairing method) orientations() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) ORIENTATIONS_END (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation attribute) OrientCommon (class in pyrosetta.rosetta.protocols.constel) orig_num_nodes() (pyrosetta.rosetta.protocols.jd3.JobDigraphUpdater method) orig_rotamer_id_for_moltenres() (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) origin() (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputSource method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputSource method) (pyrosetta.rosetta.protocols.jd3.InputSource method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputSource method) (pyrosetta.rosetta.protocols.pockets.FingerprintBase method) (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) original2modified() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) original2modified_interval_endpoints() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) original_deleted_positions() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) original_end() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) original_fixed_positions() (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) original_index (pyrosetta.rosetta.protocols.forge.remodel.LineObject property) original_insertion_point() (pyrosetta.rosetta.protocols.match.upstream.OriginalBackboneBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.ProteinBackboneBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.ScaffoldBuildPoint method) original_interval() (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) original_interval_valid() (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) original_kept_positions() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) original_mutable_positions() (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) original_pose_residue_is_in_residue_map() (in module pyrosetta.rosetta.protocols.generalized_kinematic_closure) original_resid() (pyrosetta.rosetta.protocols.match.upstream.OriginalBackboneBuildPoint method) original_sequence() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) original_weights() (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) OriginalBackboneBuildPoint (class in pyrosetta.rosetta.protocols.match.upstream) originating_geom_cst_for_dspos (pyrosetta.rosetta.protocols.match.match_dspos1 property) originating_mpi_node() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_PNearToArbitraryStateSummary method) originating_node_MPI_rank() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_RMSDToBestSummary method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary method) originnum (pyrosetta.rosetta.protocols.pockets.triplet_and_originnum property) ORIGX1 (pyrosetta.rosetta.core.io.pdb.RecordType attribute) ORIGX2 (pyrosetta.rosetta.core.io.pdb.RecordType attribute) ORIGX3 (pyrosetta.rosetta.core.io.pdb.RecordType attribute) OrJumpSelector (class in pyrosetta.rosetta.core.select.jump_selector) OrJumpSelectorCreator (class in pyrosetta.rosetta.core.select.jump_selector) ORNOT (pyrosetta.rosetta.protocols.filters.boolean_operations attribute) (pyrosetta.rosetta.protocols.task_operations.boolean_operations attribute) OrResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) OrResidueSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) OrSelector (class in pyrosetta.rosetta.protocols.pose_selectors) OrSelectorCreator (class in pyrosetta.rosetta.protocols.pose_selectors) orstream (class in pyrosetta.rosetta.utility.io) ORTHO_ARAMID (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) ortho_check() (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.RT method) ORTHORHOMBIC (pyrosetta.rosetta.protocols.cryst.SpacegroupSetting attribute) Os (pyrosetta.rosetta.core.chemical.element.Elements attribute) oshi (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) ostream (class in pyrosetta.rosetta.std) ostream.sentry (class in pyrosetta.rosetta.std) ostringstream (class in pyrosetta.rosetta.std) ostringstream.sentry (class in pyrosetta.rosetta.std) Ot (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder property) otfedge_note_substitution_accepted() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) OTFFlexbbEdge (class in pyrosetta.rosetta.protocols.flexpack.interaction_graph) OTFFlexbbInteractionGraph (class in pyrosetta.rosetta.protocols.flexpack.interaction_graph) OTFFlexbbInteractionGraph.Subsitution (class in pyrosetta.rosetta.protocols.flexpack.interaction_graph) OTFFlexbbNode (class in pyrosetta.rosetta.protocols.flexpack.interaction_graph) Other (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference attribute) OTHER (pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobianTypeEnum attribute) other_atom() (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) (pyrosetta.rosetta.core.scoring.SAnode method) other_atoms() (pyrosetta.rosetta.protocols.pose_metric_calculators.SHOBuriedUnsatisfiedPolarsCalculator method) OTHER_DETAILS (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation.CompoundToken attribute) other_energies() (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) other_neighbor_atom_indices() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) other_neighbor_id() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) other_pose (pyrosetta.rosetta.core.scoring.ScoreType attribute) other_pose() (pyrosetta.rosetta.protocols.dna.PDBOutput method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmtfJobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) other_pose_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) other_struct_list() (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) OtherContextScoreFunction (class in pyrosetta.rosetta.protocols.flexpack) OtherPoseEnergy (class in pyrosetta.rosetta.core.energy_methods) OtherPoseEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) ou3_aib (pyrosetta.rosetta.core.chemical.AA attribute) ou3_ala (pyrosetta.rosetta.core.chemical.AA attribute) ou3_arg (pyrosetta.rosetta.core.chemical.AA attribute) ou3_asn (pyrosetta.rosetta.core.chemical.AA attribute) ou3_asp (pyrosetta.rosetta.core.chemical.AA attribute) ou3_cys (pyrosetta.rosetta.core.chemical.AA attribute) ou3_gln (pyrosetta.rosetta.core.chemical.AA attribute) ou3_glu (pyrosetta.rosetta.core.chemical.AA attribute) ou3_gly (pyrosetta.rosetta.core.chemical.AA attribute) ou3_his (pyrosetta.rosetta.core.chemical.AA attribute) ou3_ile (pyrosetta.rosetta.core.chemical.AA attribute) ou3_leu (pyrosetta.rosetta.core.chemical.AA attribute) ou3_lys (pyrosetta.rosetta.core.chemical.AA attribute) ou3_met (pyrosetta.rosetta.core.chemical.AA attribute) ou3_phe (pyrosetta.rosetta.core.chemical.AA attribute) ou3_pro (pyrosetta.rosetta.core.chemical.AA attribute) ou3_ser (pyrosetta.rosetta.core.chemical.AA attribute) ou3_thr (pyrosetta.rosetta.core.chemical.AA attribute) ou3_trp (pyrosetta.rosetta.core.chemical.AA attribute) ou3_tyr (pyrosetta.rosetta.core.chemical.AA attribute) ou3_val (pyrosetta.rosetta.core.chemical.AA attribute) out (pyrosetta.rosetta.core.conformation.membrane.Orientation attribute) out_fname() (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification method) out_of_bounds() (pyrosetta.rosetta.core.scoring.PoissonBoltzmannPotential method) out_of_bounds_memory_access() (in module pyrosetta.rosetta.protocols.toolbox) out_pair_constel() (in module pyrosetta.rosetta.protocols.constel) out_path() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) out_prefix() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) out_silent_struct_type() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) out_silent_struct_type_set() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) out_torsions() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) out_triple_constel() (in module pyrosetta.rosetta.protocols.constel) out_user_tag() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) out_user_tag_set() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) out_weight_silent_scores() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) outbound() (pyrosetta.rosetta.protocols.loophash.MPI_LoopHashRefine method) (pyrosetta.rosetta.protocols.loophash.MPI_LoopHashRefine_Emperor method) (pyrosetta.rosetta.protocols.loophash.MPI_LoopHashRefine_Master method) (pyrosetta.rosetta.protocols.mpi_refinement.MPI_Refine_Emperor method) (pyrosetta.rosetta.protocols.mpi_refinement.MPI_Refine_Master method) (pyrosetta.rosetta.protocols.mpi_refinement.MPI_Refinement method) (pyrosetta.rosetta.protocols.wum.MPI_WorkUnitManager method) (pyrosetta.rosetta.protocols.wum.MPI_WorkUnitManager_Slave method) (pyrosetta.rosetta.protocols.wum.WorkUnitManager method) outdegree() (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.utility.graph.DirectedNode method) outer_cycles() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) outer_product() (in module pyrosetta.rosetta.numeric) outgoing_edge_list_begin() (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.utility.graph.DirectedNode method) outgoing_edge_list_end() (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.utility.graph.DirectedNode method) outgoing_message_queue_is_empty() (pyrosetta.rosetta.utility.SimulateMPI static method) outnml (pyrosetta.rosetta.core.scoring.sc._DOT property) OutOfBoundsMode (class in pyrosetta.rosetta.core.select.residue_selector.slice_enums) output (pyrosetta.rosetta.basic.ExecutionResult property) output() (pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster method) output_all_tag_options() (in module pyrosetta.rosetta.utility.xsd_util) output_alternate_atomids() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) output_alternative_states() (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) output_base_pairs() (in module pyrosetta.rosetta.core.pose.rna) output_base_stacks() (in module pyrosetta.rosetta.core.pose.rna) output_base_stats() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) output_bool_list() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) output_boolean() (in module pyrosetta.rosetta.core.pose.rna) (in module pyrosetta.rosetta.protocols.stepwise.modeler) output_build_positions_only() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) output_callback() (pyrosetta.logging_support.PythonLoggingSink method) (pyrosetta.rosetta.basic.PyTracer method) output_checkpoint_file() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) output_cluster_size() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) output_connectivity() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph 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.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.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.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.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.jd3.JobDigraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) output_constraints_file() (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) output_count() (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) output_counts() (pyrosetta.rosetta.protocols.stepwise.StepWiseSampleAndScreen method) output_data() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) (pyrosetta.rosetta.core.io.rna.RDAT method) output_data_struct (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna) output_debug_structure() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) output_decoy() (pyrosetta.toolbox.py_jobdistributor.PyJobDistributor method) output_diagnosis() (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) output_dimacs() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph 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.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.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.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.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.jd3.JobDigraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) output_etable() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) output_extra_RMSDs() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) output_fasta_file() (in module pyrosetta.rosetta.core.sequence) output_file_name() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) (pyrosetta.rosetta.protocols.match.MatcherTask method) output_filename() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) output_filters() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) output_fn_ (pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions property) output_fold_tree_info() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) output_fragments() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) output_histogram_file() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) output_hit() (pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage method) output_id() (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilter method) output_index() (pyrosetta.rosetta.protocols.jd3.output.MultipleOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.output.OutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification method) output_info_on_random_trials() (pyrosetta.rosetta.protocols.stepwise.StepWiseSampleAndScreen method) output_interface_deltas() (in module pyrosetta.rosetta.protocols.ligand_docking) output_intermediate_pose() (in module pyrosetta.rosetta.protocols.jd2) output_is_prepend_map() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) output_jump_chainbreak() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) output_jump_o3p_to_o5p() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) output_jump_reference_RT_string() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) output_jump_res() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) output_jump_target_xyz() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) output_ligands_as_separate_chains() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) output_lookup_count() (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) output_lookup_length() (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) output_lores_silent_file() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) output_matchres_only() (pyrosetta.rosetta.protocols.match.MatcherTask method) output_min_pose() (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) output_minimized_pose_list() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) output_motifs_to_pymol() (in module pyrosetta.rosetta.core.scoring.rna) output_movemap() (in module pyrosetta.rosetta.protocols.stepwise.modeler) output_moves() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) output_name() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.dna.PDBOutput method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmtfJobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter method) output_only_asymmetric_unit() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) output_only_cluster_transitions() (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) output_other_contacts() (in module pyrosetta.rosetta.core.pose.rna) output_packstat() (in module pyrosetta.rosetta.protocols.vip) output_packstat_pdb() (in module pyrosetta.rosetta.core.scoring.packstat) output_pair_size() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) output_pdb() (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) output_pose() (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) output_pose_cache() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) output_pose_count (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) output_pose_energies_table() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) output_pose_list() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) output_poseOP (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover.Overlap property) output_prefix() (pyrosetta.rosetta.basic.MemTracerImpl static method) (pyrosetta.rosetta.basic.TracerImpl static method) output_prefix_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) output_pssm_filename() (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) output_pssm_inline() (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) output_rdat_to_file() (pyrosetta.rosetta.core.io.rna.RDAT method) output_repacked_poses() (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) output_res_map() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) output_residue() (pyrosetta.rosetta.core.chemical.sdf.MolWriter method) output_residue_pair_energies() (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilter method) output_results() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) output_rna_motif() (in module pyrosetta.rosetta.core.scoring.rna) output_rna_motifs() (in module pyrosetta.rosetta.core.scoring.rna) output_rna_motifs_detailed() (in module pyrosetta.rosetta.core.scoring.rna) output_rotation_vector() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) output_running_info() (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) output_score_file() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) output_score_frequency() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) output_scorefile() (in module pyrosetta.toolbox.py_jobdistributor) output_scores() (pyrosetta.rosetta.protocols.match.MatcherTask method) output_secondary_structure() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) output_seq_num_list() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) output_sequence_profile() (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric static method) (pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric static method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric static method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric static method) output_silent() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) output_silent_file() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_Clusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased method) output_silent_struct() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) output_simple_text_files() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) output_size_list() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) output_specifications() (pyrosetta.rosetta.protocols.jd3.output.MultipleOutputSpecification method) output_sqc_file() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) output_statistics() (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) output_stats() (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) output_stems() (in module pyrosetta.rosetta.core.pose.rna) output_tag() (pyrosetta.rosetta.protocols.jobdist.BasicJob method) output_title_text() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) output_to_silent_file() (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) output_torsions() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) output_type() (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) output_upstream_coordinates() (pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage method) output_virtual() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) output_virtual_zero_occ() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) output_writer() (pyrosetta.rosetta.protocols.match.output.MatchConsolidator method) (pyrosetta.rosetta.protocols.match.output.MatchOutputter method) (pyrosetta.rosetta.protocols.match.output.MatchProcessor method) output_writer_name() (pyrosetta.rosetta.protocols.match.MatcherTask method) output_yet (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover.Overlap property) outputed (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover.Chunk property) outputed() (pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop method) OutputLevel (class in pyrosetta.rosetta.protocols.rotamer_recovery) outputpose() (pyrosetta.rosetta.protocols.rpc.JSON_RPC method) OutputSpecification (class in pyrosetta.rosetta.protocols.jd3.output) OutputStructureStore (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) outputter() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.standard.StandardInnerLarvalJob method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) outputter_for_job() (pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter method) outputter_specified_by_command_line() (pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputter static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputterCreator method) outputter_type() (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification method) outputters() (pyrosetta.rosetta.protocols.jd3.output.MultipleOutputter method) OutputWriter (class in pyrosetta.rosetta.protocols.match.output) outstring (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) overall_constraints_strength() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) overall_energy0() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) overall_Ktheta() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) overall_max_count() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) overall_params() (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) overall_theta0() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) overflow() (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_streambuf_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) overlap() (pyrosetta.rosetta.core.scoring.packstat.Circle method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) overlap1() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) overlap2() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) overlap_chainbreak (pyrosetta.rosetta.core.scoring.ScoreType attribute) overlap_chainbreak() (in module pyrosetta.rosetta.protocols.forge.methods) OverlapDeleteMode (class in pyrosetta.rosetta.protocols.indexed_structure_store) overlapping_with_region() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragSetCollection method) (pyrosetta.rosetta.core.fragment.MinimalFragSet method) (pyrosetta.rosetta.core.fragment.OrderedFragSet method) overlaps() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.protocols.match.BumpGrid method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) overlay() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) OverloadTest (class in pyrosetta.rosetta.utility.py) override_option_input() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) override_refine_pose_rounds() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) OversaturatedHbondAcceptorFilter (class in pyrosetta.rosetta.protocols.cyclic_peptide) OversaturatedHbondAcceptorFilterCreator (class in pyrosetta.rosetta.protocols.cyclic_peptide) overwrite() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) overwrite_stored_subset() (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) owner() (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.protocols.environment.claims.CutBiasClaim method) (pyrosetta.rosetta.protocols.environment.claims.EnvClaim method) (pyrosetta.rosetta.protocols.environment.claims.JumpClaim method) (pyrosetta.rosetta.protocols.environment.claims.TorsionClaim method) (pyrosetta.rosetta.protocols.environment.claims.VirtResClaim method) (pyrosetta.rosetta.protocols.environment.claims.XYZClaim method) (pyrosetta.rosetta.protocols.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) owner_nodes_and_locations() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) OXETOSE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) OXIROSE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) OXY (pyrosetta.rosetta.protocols.match.ProbeRadius attribute) ozstream (class in pyrosetta.rosetta.utility.io)