Index – O

O() (pyrosetta.rosetta.core.scoring.BB_Pos method) (pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos method) o2prime_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) o2prime_legacy_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) o2prime_trials() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) o3prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) o4prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) o5prime_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) O_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) obey_ENDMDL() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) observe_after_metropolis() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering 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.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover 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.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover 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) 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) obsolete() (pyrosetta.rosetta.core.pose.PDBInfo method) obtain_rtypes_for_target_sequence() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) occ_space_hash() (pyrosetta.rosetta.protocols.match.Matcher method) occupancy() (pyrosetta.rosetta.core.pose.PDBInfo method) OccupiedSpaceHash (class in pyrosetta.rosetta.protocols.match) ocstream (class in pyrosetta.rosetta.utility.io) off_rotamer_pack() (in module pyrosetta.rosetta.core.pack) (pyrosetta.rosetta.protocols.simple_moves.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.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) OffsetPeriodicBoundFunc (class in pyrosetta.rosetta.core.scoring.constraints) old_seqpos() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) omega() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue 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.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) omega0() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) omega0_copies_pitch_instead() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) omega1() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) OmegaPreferenceSamplingData (class in pyrosetta.rosetta.core.scoring.carbohydrates) OmegaPreferencesFunction (class in pyrosetta.rosetta.core.scoring.carbohydrates) OmegaPreferenceType (class in pyrosetta.rosetta.core.scoring.carbohydrates) on_connection_change() (pyrosetta.rosetta.core.pose.PDBInfo method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet 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.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.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) one_letter_sequence() (pyrosetta.rosetta.core.io.silent.SilentStruct method) one_line_report() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) one_random_loop() (pyrosetta.rosetta.protocols.loops.Loops method) onebody_energies() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) OneGaussianScattering (class in pyrosetta.rosetta.core.scoring.electron_density) (class in pyrosetta.rosetta.core.scoring.fiber_diffraction) oneletter_code_from_aa() (in module pyrosetta.rosetta.core.chemical) oneletter_code_specifies_aa() (in module pyrosetta.rosetta.core.chemical) 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_clean_seq_num() (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) op() (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) op1_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) op2_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) open() (in module pyrosetta.rosetta.basic.database) (pyrosetta.rosetta.basic.resource_manager.locator.FileStream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ozstream method) open_append() (pyrosetta.rosetta.utility.io.ozstream method) open_append_if_existed() (pyrosetta.rosetta.utility.io.ozstream method) operate_on_ex1() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) operate_on_ex2() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) operate_on_ex3() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) operate_on_ex4() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) OperateOnResidueSubset (class in pyrosetta.rosetta.core.pack.task.operation) operation() (pyrosetta.rosetta.protocols.simple_filters.Operator method) Operator (class in pyrosetta.rosetta.protocols.simple_filters) operator_filter() (pyrosetta.rosetta.protocols.simple_filters.MultipleSigmoids method) OptCysHG (class in pyrosetta.rosetta.core.pack.task.operation) OptEData (class in pyrosetta.rosetta.protocols.optimize_weights) OptEMultifunc (class in pyrosetta.rosetta.protocols.optimize_weights) OptEPositionData (class in pyrosetta.rosetta.protocols.optimize_weights) OptH (class in pyrosetta.rosetta.core.pack.task.operation) optimal_connection_point() (in module pyrosetta.rosetta.protocols.protein_interface_design) optimize_branch_angles() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) optimize_foldtree() (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.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) optimize_h() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) optimize_H_and_notify() (in module pyrosetta.rosetta.core.pack) optimizeH() (in module pyrosetta.rosetta.core.pack) OptimizeMembranePositionMoverCreator (class in pyrosetta.rosetta.protocols.membrane) OptimizeProteinEmbeddingMoverCreator (class in pyrosetta.rosetta.protocols.membrane) Option (class in pyrosetta.rosetta.utility.options) option() (pyrosetta.rosetta.utility.options.OptionCollection method) option_vdw_rep_screen_info_user() (in module pyrosetta.rosetta.protocols.scoring) optional_name_attribute() (in module pyrosetta.rosetta.utility.tag) 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.io.silent.SilentStruct method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) options_type() (pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator method) (pyrosetta.rosetta.core.io.silent.SilentFileRMOptionsCreator method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffractionOptionsCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryOptionsCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileOptionsCreator method) OptionTypes (class in pyrosetta.rosetta.utility.options) or_adducts() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) 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) or_ex1_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex1aro() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex1aro_exposed() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex1aro_exposed_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex1aro_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex2() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex2_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex2aro() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex2aro_exposed() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex2aro_exposed_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex2aro_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex3() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex3_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex4() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_ex4_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_exdna_sample_level() (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) or_flip_HNQ() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ 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) or_include_virtual_side_chain() (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_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) or_operate_on_ex2() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_operate_on_ex3() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_operate_on_ex4() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) or_optimize_h() (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_preserve_c_beta() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) Orbital (class in pyrosetta.rosetta.core.chemical) orbital() (pyrosetta.rosetta.core.chemical.ResidueType method) orbital_icoor_data() (pyrosetta.rosetta.core.chemical.ResidueType method) orbital_index() (pyrosetta.rosetta.core.chemical.ResidueType method) orbital_name() (pyrosetta.rosetta.core.conformation.Residue method) orbital_type() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) orbital_type_index() (pyrosetta.rosetta.core.chemical.Orbital 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.ResidueType method) orbital_xyz() (pyrosetta.rosetta.core.conformation.Residue method) OrbitalsFeaturesCreator (class in pyrosetta.rosetta.protocols.features) order() (in module pyrosetta.rosetta.protocols.forge.methods) (pyrosetta.rosetta.core.chemical.Bond method) order_by_energy() (pyrosetta.rosetta.core.io.silent.SilentFileData method) ordered_constrained_positions() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) orient() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand 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) orientations() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) orig_rotamer_id_for_moltenres() (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment 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_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_sequence() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) originating_node_MPI_rank() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) OrJumpSelector (class in pyrosetta.rosetta.core.select.jump_selector) OrResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) OrSelector (class in pyrosetta.rosetta.protocols.pose_selectors) orstream (class in pyrosetta.rosetta.utility.io) ortho_check() (pyrosetta.rosetta.core.kinematics.Jump method) other_atom() (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) other_helix() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) other_pose() (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.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter 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.io.silent.SilentStruct method) outer_product() (in module pyrosetta.rosetta.numeric) output_all_tag_options() (in module pyrosetta.rosetta.utility.xsd_util) output_alternative_states() (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover 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_callback() (pyrosetta.rosetta.basic.PyTracer method) output_cluster_size() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) output_connectivity() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.protocols.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_data() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) output_debug_structure() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) output_dimacs() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.protocols.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_file_name() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) output_fold_tree_info() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) output_fragments() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) output_intermediate_pose() (in module pyrosetta.rosetta.protocols.jd2) output_is_prepend_map() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) output_min_pose() (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) output_minimized_pose_list() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) output_movemap() (in module pyrosetta.rosetta.protocols.stepwise.modeler) output_name() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover 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.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) 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_pose_cache() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) output_pose_energies_table() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) output_pose_list() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) output_prefix() (pyrosetta.rosetta.basic.Tracer method) output_res_map() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) 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_scorefile() (in module pyrosetta) output_secondary_structure() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) output_seq_num_list() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) 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_size_list() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) output_sqc_file() (pyrosetta.rosetta.core.io.sequence_comparation.DesignContrast method) output_string_real_pairs_begin() (pyrosetta.rosetta.protocols.jd2.Job method) output_string_real_pairs_end() (pyrosetta.rosetta.protocols.jd2.Job method) output_string_string_pairs_begin() (pyrosetta.rosetta.protocols.jd2.Job method) output_string_string_pairs_end() (pyrosetta.rosetta.protocols.jd2.Job method) output_strings_begin() (pyrosetta.rosetta.protocols.jd2.Job method) output_strings_end() (pyrosetta.rosetta.protocols.jd2.Job method) 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) output_type() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) output_virtual() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) output_virtual_zero_occ() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) 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_theta0() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) overlap() (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) overlap_chainbreak() (in module pyrosetta.rosetta.protocols.forge.methods) overlapping_with_region() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) overlaps() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) overlay() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) OversaturatedHbondAcceptorFilter (class in pyrosetta.rosetta.protocols.cyclic_peptide) owner_nodes_and_locations() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) ozstream (class in pyrosetta.rosetta.utility.io)