Index – U

u() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) u_initialized() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) u_no_notify() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) ub() (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) ubyte (class in pyrosetta.rosetta.ObjexxFCL) UDPSocketClient (class in pyrosetta.rosetta.protocols.moves) uint_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) ulong_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) unassigned() (pyrosetta.rosetta.core.pose.ResidueIndexDescription method) (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionFromFile method) unbind() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) unblock() (pyrosetta.rosetta.utility.signals.Link method) unblock_signals() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) unbound_struct() (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) unbounded() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) unbounded_value() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) UnboundRotamersOperation (class in pyrosetta.rosetta.core.pack.rotamer_set) uncompressed() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) UnconstrainedTorsionsMover (class in pyrosetta.rosetta.protocols.ligand_docking) undefined_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) unfinished_batches() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) unfolded_energies_type() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) UnfoldedStatePotential (class in pyrosetta.rosetta.core.scoring) unfreeze() (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) unget() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) uniform() (in module pyrosetta.rosetta.numeric.random) (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) uniform_dof_distribution() (in module pyrosetta.rosetta.protocols.simple_moves) uniform_RG (class in pyrosetta.rosetta.numeric.random) uniform_vector_sphere() (in module pyrosetta.rosetta.numeric.random) UniformPerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) UniformPolicy (class in pyrosetta.rosetta.protocols.nonlocal) UniformRotationMover (class in pyrosetta.rosetta.protocols.simple_moves) UniformSphereTransMover (class in pyrosetta.rosetta.protocols.rigid) UniformTranslationMover (class in pyrosetta.rosetta.protocols.simple_moves) union_interval() (in module pyrosetta.rosetta.protocols.forge.methods) union_of_intervals_containing_undefined_positions() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) unique() (in module pyrosetta.rosetta.ObjexxFCL) uniqued() (in module pyrosetta.rosetta.ObjexxFCL) universal_main() (in module pyrosetta.rosetta.protocols.jobdist) unpaired_valence_electrons_sp() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) unpatchable_residue_types() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) unperturbed_sequence() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) UnrecognizedAtomFeaturesCreator (class in pyrosetta.rosetta.protocols.features) UnrecognizedAtomRecord (class in pyrosetta.rosetta.core.pose) UnsatSelector (class in pyrosetta.rosetta.protocols.residue_selectors) unset_acceptor_ether_oxygens() (in module pyrosetta.rosetta.core.chemical) unset_parent() (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap method) unsigned_periodic_range() (in module pyrosetta.rosetta.basic) unused_hbond() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) upcase() (in module pyrosetta.rosetta.ObjexxFCL) update() (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) (pyrosetta.rosetta.core.scoring.TMscoreStore method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) update_actcoord() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) update_actcoords() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) update_active_enmeths_for_residue() (pyrosetta.rosetta.core.scoring.MinimizationNode method) update_after_boltzmann() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) update_atom_information_based_on_occupancy() (in module pyrosetta.rosetta.core.io.pose_from_sfr) update_atom_map() (in module pyrosetta.rosetta.protocols.hybridization) update_atom_tree() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) update_chemshiftscore_from_peak() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) update_commutative() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) update_connections_to_other_residue() (pyrosetta.rosetta.core.conformation.Residue method) update_connectivity_data() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) update_constraint_set_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) update_coords_from_pose() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) update_counting_last_PDR() (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) update_cutpoint_virtual_atoms_if_connected() (in module pyrosetta.rosetta.core.conformation) (in module pyrosetta.rosetta.core.pose) update_derived_rna_data() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) update_disulfides_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) update_domain_map() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) update_edge_label() (pyrosetta.rosetta.core.kinematics.FoldTree method) update_enumeration_shell() (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) update_fixed_domain_from_extra_minimize_jump_res() (in module pyrosetta.rosetta.core.import_pose) update_fold_tree_at_virtual_sugars() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) update_from_momento() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) update_full_model_info_from_pose() (in module pyrosetta.rosetta.core.pose.full_model_info) update_internal_coords() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) update_intersection() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) update_jobs_list() (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) update_jump_atoms_for_mg_bound_water() (in module pyrosetta.rosetta.protocols.magnesium) update_jump_res() (in module pyrosetta.rosetta.core.import_pose) update_membrane_position() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) update_mg_hoh_fold_tree() (in module pyrosetta.rosetta.protocols.magnesium) update_noncanonical_connection() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) update_numbers_in_pdb_info() (in module pyrosetta.rosetta.protocols.magnesium) update_nus() (pyrosetta.rosetta.core.conformation.Residue method) update_on_length_change() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) update_one_body_energies() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) update_orbital_coords() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) update_partner_embeddings() (in module pyrosetta.rosetta.protocols.membrane) update_pdb_info_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) update_pdb_remarks() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) update_pdblist_file() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) update_polymer_bond_dependent_atoms() (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) update_polymer_dependent() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) update_polymeric_connection() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) update_pose_chains_from_pdb_chains() (pyrosetta.rosetta.core.pose.Pose method) update_pose_fold_tree() (in module pyrosetta.rosetta.core.import_pose) update_pose_objects_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) update_res_list_in_full_model_info_and_pdb_info() (in module pyrosetta.rosetta.core.pose.full_model_info) update_residue() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) update_residue_commutative() (pyrosetta.rosetta.core.pack.task.PackerTask_ method) update_residue_for_packing() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.FACTSPotential method) (pyrosetta.rosetta.core.scoring.GenBornPotential method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) update_residue_identities() (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) update_residue_intersection() (pyrosetta.rosetta.core.pack.task.PackerTask_ method) update_residue_links() (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) update_residue_neighbors() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method)

update_residue_union() (pyrosetta.rosetta.core.pack.task.PackerTask_ method) update_rna_base_base_interactions() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) update_rna_base_pair_list() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) update_rna_centroid_info() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) update_rot_trans_mag() (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) update_scores() (in module pyrosetta.rosetta.protocols.recces) update_sequence() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) update_sequence_numbering() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.kinematics.AtomTree method) update_start_position() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) update_stub() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) update_submotif_info_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) update_task_and_neighbors() (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) update_to_move_chunks_with_domain() (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap method) update_to_move_rosetta_library_chunks() (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_ChunkLibrary method) update_type() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) update_union() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) update_upperdistance_score() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) update_xyz_coords() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) UpdateEnzdesHeaderMover (class in pyrosetta.rosetta.protocols.enzdes) updates_jobs_list() (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerJobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) upper() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) upper_atom_neighbors() (pyrosetta.rosetta.core.scoring.NeighborList method) upper_bound() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) upper_bound_score() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) upper_chain() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation method) upper_connect() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) upper_connect_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) upper_connect_id() (pyrosetta.rosetta.core.chemical.ResidueType method) upper_dihedrals() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) upper_edge_list_begin() (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) upper_edge_list_end() (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) upper_is_symm_equivalent_of_lower() (in module pyrosetta.rosetta.core.conformation) upper_local() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) upper_neighbor_id() (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) upper_neighbor_iterator_begin() (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) upper_neighbor_iterator_end() (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) upper_padding() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) upper_residue() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) upper_segment() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) upper_threshold() (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) upper_value() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) uppercase() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) uppercased() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) upstream_atom() (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.kinematics.FoldTree method) upstream_builder() (pyrosetta.rosetta.protocols.match.Matcher method) upstream_centroid_by_jump() (in module pyrosetta.rosetta.protocols.geometry) upstream_combine() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) upstream_jump_residue() (pyrosetta.rosetta.core.kinematics.FoldTree method) upstream_jump_stub() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) upstream_only() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) upstream_pose() (pyrosetta.rosetta.protocols.match.Matcher method) upstream_restypes() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) UpstreamCollisionFilter (class in pyrosetta.rosetta.protocols.match.output) UpstreamDownstreamCollisionFilter (class in pyrosetta.rosetta.protocols.match.output) UpstreamResTypeGeometry (class in pyrosetta.rosetta.protocols.match.upstream) urs_norm4() (in module pyrosetta.rosetta.numeric) urs_R2ang() (in module pyrosetta.rosetta.numeric) us_secmatch_hit_compare (class in pyrosetta.rosetta.protocols.match.downstream) use_cartesian() (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) use_cartmin() (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) use_coarse_vdw() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) use_coordinate_constraints() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) use_default_membrane() (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) use_defaults() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) use_extended_intrares_energy_interface() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) use_extended_residue_energy_interface() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) use_extended_residue_pair_energy_interface() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) use_fract_expected_values_any() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) use_fract_ranges() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) use_fract_ranges_any() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) use_fragments() (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) use_fullmer() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) use_gen_kirkwood() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) use_green_packer() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) use_input_for_ref() (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) USE_INPUT_SC (class in pyrosetta.rosetta.core.pack.task) use_late_scoring_for_zeros() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) use_loops_from_threading_job() (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) use_mover_status() (pyrosetta.rosetta.protocols.moves.SequenceMover method) use_multicool_annealer() (pyrosetta.rosetta.core.pack.task.operation.OptH method) use_nblist() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) use_nblist_auto_update() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) use_nblist_of_type() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) use_nobias() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) use_origseq_for_not_dsgned_layer() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) use_packer_instead_of_rotamer_trials() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) use_pdb_format_HETNAM_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) use_phenix_geo() (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) use_polarization() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) use_pose_sequence_as_native() (pyrosetta.rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation method) use_preset_task() (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) use_radial_lookup() (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) use_rama_2B() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) use_random_conformer() (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) use_rt() (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) use_sc_neighbors() (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) user() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) user_chain1() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) user_chain2() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) user_options() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) user_or() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) user_provided_movers_apply_cycle() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) ushort_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) USOGFunc (class in pyrosetta.rosetta.core.scoring.func) uz() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method)