Index – U

U (pyrosetta.rosetta.core.chemical.element.Elements attribute) u() (pyrosetta.rosetta.core.fragment.FrameList method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.scoring.motif.MotifHits method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotifs method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRanges method) (pyrosetta.rosetta.core.select.residue_selector.ResidueVector method) (pyrosetta.rosetta.numeric.Xforms method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.FArray1_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_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.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultVector method) (pyrosetta.rosetta.protocols.denovo_design.components.BuildPhases method) (pyrosetta.rosetta.protocols.denovo_design.components.EnumeratedVectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.denovo_design.components.NamedSolution method) (pyrosetta.rosetta.protocols.denovo_design.components.NamedSolutions method) (pyrosetta.rosetta.protocols.denovo_design.components.VectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairings method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) (pyrosetta.rosetta.protocols.sewing.hashing.SegmentVector method) (pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoints method) (pyrosetta.rosetta.utility.deep_copy_vector1_std_shared_ptr_core_chemical_Orbital_t method) (pyrosetta.rosetta.utility.vector0_core_conformation_ppo_torsion_bin method) (pyrosetta.rosetta.utility.vector0_core_id_AtomID_Map_bool_t method) (pyrosetta.rosetta.utility.vector0_core_io_AtomInformation method) (pyrosetta.rosetta.utility.vector0_double method) (pyrosetta.rosetta.utility.vector0_float method) (pyrosetta.rosetta.utility.vector0_int method) (pyrosetta.rosetta.utility.vector0_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector0_protocols_flexpack_interaction_graph_FlexbbSparseMatrixIndex method) (pyrosetta.rosetta.utility.vector0_std_list_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.utility.vector0_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector0_std_pair_float_float_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_moves_Mover_t method) (pyrosetta.rosetta.utility.vector0_std_string method) (pyrosetta.rosetta.utility.vector0_unsigned_char method) (pyrosetta.rosetta.utility.vector0_unsigned_long method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_double_3_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_double_5_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_utility_fixedsizearray0_double_3_3_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_utility_fixedsizearray0_double_5_5_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray1_double_16_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_core_io_AtomInformation_std_allocator_core_io_AtomInformation_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_int_std_allocator_int_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_std_list_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_list_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_std_allocator_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_std_pair_int_int_std_allocator_std_pair_int_int_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_basic_citation_manager_AuthorNames method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_Column method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_ForeignKey method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_Index method) (pyrosetta.rosetta.utility.vector1_basic_sampling_orientations_QuatDBMetadata method) (pyrosetta.rosetta.utility.vector1_bool method) (pyrosetta.rosetta.utility.vector1_char method) (pyrosetta.rosetta.utility.vector1_const_utility_vector1_int_std_allocator_int__star_t method) (pyrosetta.rosetta.utility.vector1_core_chemical_AA method) (pyrosetta.rosetta.utility.vector1_core_chemical_Adduct method) (pyrosetta.rosetta.utility.vector1_core_chemical_AtomICoor method) (pyrosetta.rosetta.utility.vector1_core_chemical_AtomType method) (pyrosetta.rosetta.utility.vector1_core_chemical_BondName method) (pyrosetta.rosetta.utility.vector1_core_chemical_io_merge_residue_behavior method) (pyrosetta.rosetta.utility.vector1_core_chemical_MutableResidueConnection method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResConnID method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResidueConnection method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty method) (pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingConformer method) (pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingSaturationType method) (pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter method) (pyrosetta.rosetta.utility.vector1_core_chemical_rna_PuckerState method) (pyrosetta.rosetta.utility.vector1_core_chemical_VariantType method) (pyrosetta.rosetta.utility.vector1_core_conformation_Atom method) (pyrosetta.rosetta.utility.vector1_core_conformation_PseudoBond method) (pyrosetta.rosetta.utility.vector1_core_conformation_signals_LengthEvent method) (pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue method) (pyrosetta.rosetta.utility.vector1_core_fragment_FragData method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_scores_VallFragmentScore method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection method) (pyrosetta.rosetta.utility.vector1_core_fragment_rna_SYN_ANTI_RESTRICTION method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_bool_t method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.utility.vector1_core_id_DOF_ID method) (pyrosetta.rosetta.utility.vector1_core_id_NamedAtomID method) (pyrosetta.rosetta.utility.vector1_core_id_TorsionID method) (pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range method) (pyrosetta.rosetta.utility.vector1_core_io_AtomInformation method) (pyrosetta.rosetta.utility.vector1_core_io_HELIXInformation method) (pyrosetta.rosetta.utility.vector1_core_io_LinkInformation method) (pyrosetta.rosetta.utility.vector1_core_io_ResidueInformation method) (pyrosetta.rosetta.utility.vector1_core_io_SHEETInformation method) (pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy method) (pyrosetta.rosetta.utility.vector1_core_io_SSBondInformation method) (pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Edge method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Jump method) (pyrosetta.rosetta.utility.vector1_core_kinematics_RT method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Stub method) (pyrosetta.rosetta.utility.vector1_core_optimization_DerivCheckDataPoint method) (pyrosetta.rosetta.utility.vector1_core_optimization_DOF_DataPoint method) (pyrosetta.rosetta.utility.vector1_core_pack_annealer_PointDwell method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbond method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_sap_BlockParam method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_DotSphere method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_exposed_hydrophobic_data method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_RotamerDots method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_SparseMatrixIndex method) (pyrosetta.rosetta.utility.vector1_core_pack_rotamer_set_ContinuousRotamerSet method) (pyrosetta.rosetta.utility.vector1_core_pack_scmin_ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.utility.vector1_core_pack_task_operation_ResiduePDBIndexIs_ChainPos method) (pyrosetta.rosetta.utility.vector1_core_pack_task_ResidueLevelTask_ method) (pyrosetta.rosetta.utility.vector1_core_pose_PDBInfo_AtomRecord method) (pyrosetta.rosetta.utility.vector1_core_pose_PDBInfo_ResidueRecord method) (pyrosetta.rosetta.utility.vector1_core_pose_Pose method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_Atom_Bin method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_BaseStack method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_Datum method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_Reactivity method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_SuiteInfo method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_VDW_RepScreenInfo method) (pyrosetta.rosetta.utility.vector1_core_pose_UnrecognizedAtomRecord method) (pyrosetta.rosetta.utility.vector1_core_scoring_bin_transitions_BT_PROPERTIES method) (pyrosetta.rosetta.utility.vector1_core_scoring_CSA method) (pyrosetta.rosetta.utility.vector1_core_scoring_DC method) (pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair method) (pyrosetta.rosetta.utility.vector1_core_scoring_disulfides_DisulfideDerivativeAtom method) (pyrosetta.rosetta.utility.vector1_core_scoring_dssp_Pairing method) (pyrosetta.rosetta.utility.vector1_core_scoring_dssp_StrandPairing method) (pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector method) (pyrosetta.rosetta.utility.vector1_core_scoring_epr_deer_EPRSpinLabel method) (pyrosetta.rosetta.utility.vector1_core_scoring_etable_EtableParamsOnePair method) (pyrosetta.rosetta.utility.vector1_core_scoring_etable_etrie_GenericResidueConnectionData method) (pyrosetta.rosetta.utility.vector1_core_scoring_fiber_diffraction_OneGaussianScattering method) (pyrosetta.rosetta.utility.vector1_core_scoring_GenTorsionParams method) (pyrosetta.rosetta.utility.vector1_core_scoring_Hairpin method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_HBondEdge method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_HBondNode method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_HBEvalTuple method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_HBondWeightType method) (pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_Loop method) (pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_LoopCycle method) (pyrosetta.rosetta.utility.vector1_core_scoring_mhc_epitope_energy_AlleleMatrix method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_MotifHit method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_ResPairMotif method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_Xfres method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_pcs_PCSSingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_pre_PRESingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_rdc_RDCSingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_packing_Ball method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBall method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBallCluster method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_LR_AtomData method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_LR_MP_AtomData method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_SimplePDB_Atom method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_Sphere method) (pyrosetta.rosetta.utility.vector1_core_scoring_power_diagram_SAnode method) (pyrosetta.rosetta.utility.vector1_core_scoring_RDC method) (pyrosetta.rosetta.utility.vector1_core_scoring_RDC_Rohl method) (pyrosetta.rosetta.utility.vector1_core_scoring_rna_RNA_Motif method) (pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType method) (pyrosetta.rosetta.utility.vector1_core_scoring_SmallAtNb method) (pyrosetta.rosetta.utility.vector1_core_scoring_SmoothScoreTermCoeffs method) (pyrosetta.rosetta.utility.vector1_core_scoring_SpringParams method) (pyrosetta.rosetta.utility.vector1_core_scoring_tableID method) (pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange method) (pyrosetta.rosetta.utility.vector1_core_sequence_Line method) (pyrosetta.rosetta.utility.vector1_core_sequence_SequenceAlignment method) (pyrosetta.rosetta.utility.vector1_double method) (pyrosetta.rosetta.utility.vector1_float method) (pyrosetta.rosetta.utility.vector1_int method) (pyrosetta.rosetta.utility.vector1_long method) (pyrosetta.rosetta.utility.vector1_numeric_CubicPolynomial method) (pyrosetta.rosetta.utility.vector1_numeric_geometry_hashing_Ball method) (pyrosetta.rosetta.utility.vector1_numeric_histograms_TwoDHistogram_unsigned_long_long_t method) (pyrosetta.rosetta.utility.vector1_numeric_HomogeneousTransform_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_BicubicSpline method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_CubicSpline method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_interp_range method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_Point method) (pyrosetta.rosetta.utility.vector1_numeric_MultiDimensionalHistogram method) (pyrosetta.rosetta.utility.vector1_numeric_random_WeightedSampler method) (pyrosetta.rosetta.utility.vector1_numeric_RocPoint method) (pyrosetta.rosetta.utility.vector1_numeric_urs_Quat method) (pyrosetta.rosetta.utility.vector1_numeric_xyzMatrix_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzTransform_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzVector_float_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray1D_double_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray2D_double_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_AlternativePairings method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_ClassicAbinitio_StageID method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_PairingStatEntry method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_StageID method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_AntibodyNumberingSchemeEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRDefinitionEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRNameEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_clusters_CDRClusterEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_clusters_ClusterData method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_design_PDBNumbering method) (pyrosetta.rosetta.utility.vector1_protocols_backbone_moves_local_backbone_mover_Residue method) (pyrosetta.rosetta.utility.vector1_protocols_backrub_BackrubSegment method) (pyrosetta.rosetta.utility.vector1_protocols_branch_angle_BranchCoef1 method) (pyrosetta.rosetta.utility.vector1_protocols_branch_angle_BranchCoef2 method) (pyrosetta.rosetta.utility.vector1_protocols_canonical_sampling_DbTrajectoryRecorder_Frame method) (pyrosetta.rosetta.utility.vector1_protocols_canonical_sampling_TorsionSpec method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_CartesianAtom method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_Angle method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_Bond method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_HarmonicDihedral method) (pyrosetta.rosetta.utility.vector1_protocols_cluster_DataPoint method) (pyrosetta.rosetta.utility.vector1_protocols_cluster_Exemplar method) (pyrosetta.rosetta.utility.vector1_protocols_constraints_additional_ConstraintEvaluator method) (pyrosetta.rosetta.utility.vector1_protocols_contact_map_Contact method) (pyrosetta.rosetta.utility.vector1_protocols_cyclic_peptide_PSM_StubMode method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_BondInfo method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_StructureSlice method) (pyrosetta.rosetta.utility.vector1_protocols_features_TaskOperationFeatures_Taskop_id_name_factory_ method) (pyrosetta.rosetta.utility.vector1_protocols_fold_from_loops_utils_NubSegment method) (pyrosetta.rosetta.utility.vector1_protocols_forge_build_Interval method) (pyrosetta.rosetta.utility.vector1_protocols_frag_picker_LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareTotalScore_t method) (pyrosetta.rosetta.utility.vector1_protocols_helical_bundle_BPC_Parameters method) (pyrosetta.rosetta.utility.vector1_protocols_hotspot_hashing_VectorPair method) (pyrosetta.rosetta.utility.vector1_protocols_hybridization_detailedControlsTagSetting method) (pyrosetta.rosetta.utility.vector1_protocols_indexed_structure_store_BackboneStub method) (pyrosetta.rosetta.utility.vector1_protocols_jd2_archive_Batch method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_chunk_library_ChunkLibraryPreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_dag_node_managers_ResultElements method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_full_model_FullModelPreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_standard_PreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_DisulfPairing method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_JumpSelector_JumpWeightDef method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_JumpSetup_JumpDef method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_ResiduePairJumpSetup_JumpDef method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewAtom method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewResidue method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_AtomProperties method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_GADockStageParams method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_Pharmacophore method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_ReweightableRepEnergy method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionDistrParams method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionType method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ligand_options_InterfaceInfo method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ProtLigPair_info method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolution method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolutionStore method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_ResTorsions method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_SheetPositions method) (pyrosetta.rosetta.utility.vector1_protocols_loops_Loop method) (pyrosetta.rosetta.utility.vector1_protocols_loops_LoopFromFileData method) (pyrosetta.rosetta.utility.vector1_protocols_loops_Loops method) (pyrosetta.rosetta.utility.vector1_protocols_loops_SerializedLoop method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_CentroidRotNum method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_RotData method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_TorsionRange method) (pyrosetta.rosetta.utility.vector1_protocols_match_Hit method) (pyrosetta.rosetta.utility.vector1_protocols_match_match_dspos1 method) (pyrosetta.rosetta.utility.vector1_protocols_match_ProbeRadius method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_BuildSet method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_hit method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_SampleStrategyData method) (pyrosetta.rosetta.utility.vector1_protocols_md_Constraint method) (pyrosetta.rosetta.utility.vector1_protocols_md_MDscheduleData method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_AAMatrix method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_RotMatrix method) (pyrosetta.rosetta.utility.vector1_protocols_membrane_SpanInfo method) (pyrosetta.rosetta.utility.vector1_protocols_monte_carlo_AcceptedScores method) (pyrosetta.rosetta.utility.vector1_protocols_motif_grafting_movers_motif2scaffold_indexes method) (pyrosetta.rosetta.utility.vector1_protocols_moves_TrialCounter method) (pyrosetta.rosetta.utility.vector1_protocols_mpi_refinement_MethodParams method) (pyrosetta.rosetta.utility.vector1_protocols_multistate_design_SingleStateEntityData method) (pyrosetta.rosetta.utility.vector1_protocols_nonlocal_Chunk method) (pyrosetta.rosetta.utility.vector1_protocols_optimize_weights_WeightRangeConstraint method) (pyrosetta.rosetta.utility.vector1_protocols_pack_daemon_StructureFileNames method) (pyrosetta.rosetta.utility.vector1_protocols_pdbinfo_manipulations_SequenceSpecification method) (pyrosetta.rosetta.utility.vector1_protocols_pmut_scan_Mutant method) (pyrosetta.rosetta.utility.vector1_protocols_pmut_scan_MutationData method) (pyrosetta.rosetta.utility.vector1_protocols_pose_creation_MergePDBMover_Overlap method) (pyrosetta.rosetta.utility.vector1_protocols_pose_creation_SliceToMiniProteinMover_Chunk method) (pyrosetta.rosetta.utility.vector1_protocols_pose_metric_calculators_EnergiesData method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_mutt method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_tm_region method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_VLBInstruction method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_Transformation method) (pyrosetta.rosetta.utility.vector1_protocols_qsar_ColorGradient method) (pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBResidueRange method) (pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment method) (pyrosetta.rosetta.utility.vector1_protocols_recces_Histogram method) (pyrosetta.rosetta.utility.vector1_protocols_relax_DatabaseRelaxScript method) (pyrosetta.rosetta.utility.vector1_protocols_rigid_Partner method) (pyrosetta.rosetta.utility.vector1_protocols_rosetta_scripts_ParsedProtocol_ParsedProtocolStep method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataCenter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataLanthanide method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsEnergyParameter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsGridSearchParameter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsInputLine method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs_PCS_data_per_lanthanides method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs_PCS_line_data method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs1_PCS_data_per_lanthanides_Ts1 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs1_PCS_line_data_Ts1 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_data_per_lanthanides_Ts2 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_line_data_Ts2 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs3_PCS_data_per_lanthanides_Ts3 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs3_PCS_line_data_Ts3 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs4_PCS_data_per_lanthanides_Ts4 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs4_PCS_line_data_Ts4 method) (pyrosetta.rosetta.utility.vector1_protocols_seeded_abinitio_SegmentSpec method) (pyrosetta.rosetta.utility.vector1_protocols_sewing_data_storage_ContactDescription method) (pyrosetta.rosetta.utility.vector1_protocols_sewing_data_storage_LigandDescription method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_Quat method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_RegionalConnections method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_ResidueDepthFrag method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_IonizableResidue method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_LoggedFragmentMover_Item method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_TorsionPerturbType method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_WaterRot method) (pyrosetta.rosetta.utility.vector1_protocols_splice_BBDofs method) (pyrosetta.rosetta.utility.vector1_protocols_splice_ResidueBBDofs method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_protein_MainChainTorsionSet method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_rna_Combine_Tags_Info method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_rna_phosphate_PhosphateMove method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_monte_carlo_mover_Attachment method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_monte_carlo_mover_StepWiseMove method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_sampler_copy_dofs_ResidueAlternativeSet method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_CstResInteractions method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ExternalGeomSampler method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ResInteractions method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_SingleConstraint method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint method) (pyrosetta.rosetta.utility.vector1_protocols_trajectory_DbTrajectoryWriter_Frame method) (pyrosetta.rosetta.utility.vector1_short method) (pyrosetta.rosetta.utility.vector1_signed_char method) (pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_downstream_hit_t method) (pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_upstream_hit_t method) (pyrosetta.rosetta.utility.vector1_std_array_int_3_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_std_shared_ptr_const_protocols_match_downstream_SecMatchResiduePairEvaluator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_shared_ptr_const_numeric_expression_parser_Expression_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_shared_ptr_protocols_pack_daemon_NPDPropCalculator_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_list_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_core_chemical_AA_utility_vector1_double_std_allocator_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_protocols_jumping_cstType_unsigned_long_std_less_protocols_jumping_cstType_std_allocator_std_pair_const_protocols_jumping_cstType_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_protocols_jumping_dofType_unsigned_long_std_less_protocols_jumping_dofType_std_allocator_std_pair_const_protocols_jumping_dofType_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_shared_ptr_const_core_conformation_Residue_double_std_less_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_pair_const_std_shared_ptr_const_core_conformation_Residue_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_core_id_NamedAtomID_std_less_std_string_std_allocator_std_pair_const_std_string_core_id_NamedAtomID_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_numeric_xyzVector_double_std_less_std_string_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_unsigned_long_std_less_std_string_std_allocator_std_pair_const_std_string_unsigned_long_t method) 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(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) u4() (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) u5() (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) 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) U_TURN (pyrosetta.rosetta.core.scoring.rna.RNA_MotifType attribute) UA_HANDLE (pyrosetta.rosetta.core.scoring.rna.RNA_MotifType attribute) ub (pyrosetta.rosetta.numeric.interpolation.spline.interp_range property) ub() (pyrosetta.rosetta.core.scoring.constraints.BoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) ubi_e2c_modeler (class in pyrosetta.rosetta.protocols.ub_e2c) UBIQUITINATION (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes attribute) UBQ_GTPaseMover (class in pyrosetta.rosetta.protocols.chemically_conjugated_docking) UBQ_GTPaseMoverCreator (class in pyrosetta.rosetta.protocols.chemically_conjugated_docking) ubq_ras_distance() (in module pyrosetta.rosetta.protocols.chemically_conjugated_docking) ubq_ras_rotation_angle() (in module pyrosetta.rosetta.protocols.chemically_conjugated_docking) ubyte (class in pyrosetta.rosetta.ObjexxFCL) udp_main() (in module pyrosetta.network.rosetta_udp_to_tcp_bridge) UDPSocketClient (class in pyrosetta.rosetta.protocols.moves) UEEdge_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t (class in pyrosetta.rosetta.utility.graph) UEEdge_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t (class in pyrosetta.rosetta.utility.graph) UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t (class in pyrosetta.rosetta.utility.graph) UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t (class in pyrosetta.rosetta.utility.graph) ui_mover() (pyrosetta.rosetta.protocols.network.UIObserver method) UI_OBSERVER (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType attribute) UIMover (class in pyrosetta.rosetta.protocols.network) uint_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) UIObserver (class in pyrosetta.rosetta.protocols.network) UIObserver.ObserverType (class in pyrosetta.rosetta.protocols.network) ulong_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) UltraLightResidue (class in pyrosetta.rosetta.core.conformation) unaligned() (pyrosetta.rosetta.protocols.star.Extender method) UNAMBIG_MED_PROB (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.QualityClass attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D.QualityClass attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D.QualityClass attribute) UnaryExpression (class in pyrosetta.rosetta.numeric.expression_parser) unassigned_deallocation_msg (pyrosetta.rosetta.protocols.jd3.deallocation.deallocation_msg_type attribute) unbind() (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) unblock() (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_chemical_RestypeDestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_ConnectionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_IdentityEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_LengthEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_XYZEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_ConformationEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_DestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_EnergyEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.Link method) (pyrosetta.rosetta.utility.signals.PausableSignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_chemical_RestypeDestructionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_ConnectionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_IdentityEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_LengthEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_XYZEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_ConformationEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_DestructionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_EnergyEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_GeneralEvent_t method) unblock_signals() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) unbound() (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter method) unbound_score() (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker 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) unchecked (pyrosetta.rosetta.protocols.hotspot_hashing.StubStatus attribute) unchimerize_ligand_segment() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) 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) undelete_segment() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) Underline (pyrosetta.rosetta.utility.CSI.CSI_Enum attribute) undo_optimized_transform() (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) unfinished_batches() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) unfix_tensor() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) unfix_tensors() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSMultiSet method) UNFOLD (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) unfolded (pyrosetta.rosetta.core.scoring.ScoreType attribute) unfolded_energies_type() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) unfolded_energy_emap_vector() (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) unfolded_jump() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) unfolded_pose() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) UnfoldedStateEnergy (class in pyrosetta.rosetta.core.energy_methods) UnfoldedStateEnergyCalculatorJobDistributor (class in pyrosetta.rosetta.protocols.unfolded_state_energy_calculator) UnfoldedStateEnergyCalculatorMover (class in pyrosetta.rosetta.protocols.unfolded_state_energy_calculator) UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor (class in pyrosetta.rosetta.protocols.unfolded_state_energy_calculator) UnfoldedStateEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) UnfoldedStatePotential (class in pyrosetta.rosetta.core.scoring) unfreeze() (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover 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.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) ungapped_length() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.Sequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) ungapped_sequence() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.Sequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) unget() (pyrosetta.rosetta.std.ifstream method) (pyrosetta.rosetta.std.iostream method) (pyrosetta.rosetta.std.istream method) (pyrosetta.rosetta.std.istringstream method) (pyrosetta.rosetta.std.stringstream method) (pyrosetta.rosetta.std.wistream method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) Unhybridized (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.HybridOrbitalType attribute) Uniform (pyrosetta.rosetta.protocols.ligand_docking.Distribution attribute) uniform() (in module pyrosetta.rosetta.numeric.random) (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.protocols.hybridization.FragmentBiasAssigner method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) uniform_coord_constrained() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) uniform_dof_distribution() (in module pyrosetta.rosetta.protocols.simple_moves) uniform_modeler() (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) uniform_phipsi_from_allowed_rama() (pyrosetta.rosetta.core.scoring.Ramachandran method) 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) UniformRigidBodyCM (class in pyrosetta.rosetta.protocols.rigid) UniformRigidBodyCMCreator (class in pyrosetta.rosetta.protocols.rigid) UniformRigidBodyMover (class in pyrosetta.rosetta.protocols.rigid) UniformRigidBodyMoverCreator (class in pyrosetta.rosetta.protocols.rigid) UniformRotationMover (class in pyrosetta.rosetta.protocols.simple_moves) UniformRotationSampler (class in pyrosetta.rosetta.numeric) UniformSphereTransMover (class in pyrosetta.rosetta.protocols.rigid) UniformTranslationMover (class in pyrosetta.rosetta.protocols.simple_moves) unimplemented_method_error() (pyrosetta.rosetta.core.sequence.ChemicalShiftScoringScheme method) (pyrosetta.rosetta.core.sequence.CompassScoringScheme method) (pyrosetta.rosetta.core.sequence.CompositeScoringScheme method) (pyrosetta.rosetta.core.sequence.DPScoringScheme method) (pyrosetta.rosetta.core.sequence.L1ScoringScheme method) (pyrosetta.rosetta.core.sequence.MatrixScoringScheme method) (pyrosetta.rosetta.core.sequence.PairScoringScheme method) (pyrosetta.rosetta.core.sequence.ProfSimScoringScheme method) (pyrosetta.rosetta.core.sequence.ScoringScheme method) (pyrosetta.rosetta.core.sequence.SimpleScoringScheme method) union_interval() (in module pyrosetta.rosetta.protocols.forge.methods) union_of_intervals_containing_undefined_positions() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) UnionEdge (class in pyrosetta.rosetta.protocols.pockets) unique() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.basic.database.schema_generator.Index method) unique_id() (pyrosetta.rosetta.protocols.motifs.IRCollection method) UniqueConstraint (class in pyrosetta.rosetta.basic.database.schema_generator) uniqued() (in module pyrosetta.rosetta.ObjexxFCL) universal_main() (in module pyrosetta.rosetta.protocols.jobdist) unixtime_creation_ (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Sampler.WU_Header property) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax.WU_Header property) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore.WU_Header property) (pyrosetta.rosetta.protocols.wum.DatabaseEntryWorkUnit.WU_Header property) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper.WU_Header property) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore.WU_Header property) (pyrosetta.rosetta.protocols.wum.WorkUnit_Wait.WU_Header property) (pyrosetta.rosetta.protocols.wum.WorkUnitBase.WU_Header property) unixtime_start_ (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Sampler.WU_Header property) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax.WU_Header property) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore.WU_Header property) (pyrosetta.rosetta.protocols.wum.DatabaseEntryWorkUnit.WU_Header property) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper.WU_Header property) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore.WU_Header property) (pyrosetta.rosetta.protocols.wum.WorkUnit_Wait.WU_Header property) (pyrosetta.rosetta.protocols.wum.WorkUnitBase.WU_Header property) unixtime_stop_ (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Sampler.WU_Header property) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax.WU_Header property) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore.WU_Header property) (pyrosetta.rosetta.protocols.wum.DatabaseEntryWorkUnit.WU_Header property) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper.WU_Header property) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore.WU_Header property) (pyrosetta.rosetta.protocols.wum.WorkUnit_Wait.WU_Header property) (pyrosetta.rosetta.protocols.wum.WorkUnitBase.WU_Header property) UNK (pyrosetta.rosetta.protocols.frag_picker.ContactType attribute) UNKNOW (pyrosetta.rosetta.core.io.pdb.RecordType attribute) UNKNOWN (pyrosetta.rosetta.basic.thread_manager.RosettaThreadRequestOriginatingLevel attribute) Unknown (pyrosetta.rosetta.protocols.antibody.H3BaseTypeEnum attribute) unknown (pyrosetta.rosetta.protocols.antibody.LightChainTypeEnum attribute) UNKNOWN (pyrosetta.rosetta.protocols.cluster.calibur.INPUT_FILE_TYPE attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing.PairingType attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing.PairingType attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing.PairingType attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing.PairingType attribute) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum attribute) unknown_ab_region (pyrosetta.rosetta.protocols.antibody.AntibodyRegionEnum attribute) UNKNOWN_CMPD (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation.CompoundToken attribute) unknown_crosslinker (pyrosetta.rosetta.protocols.cyclic_peptide.CrossLinker attribute) unknown_effect (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) UNKNOWN_EXPDTA (pyrosetta.rosetta.core.io.rcsb.ExperimentalTechnique attribute) Unknown_file (pyrosetta.rosetta.core.import_pose.FileType attribute) unknown_filter (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.filter_type attribute) UNKNOWN_HYBRID (pyrosetta.rosetta.core.chemical.Hybridization attribute) UNKNOWN_MODE (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMoverMode attribute) unknown_num (pyrosetta.rosetta.core.io.raw_data.DisulfideFile attribute) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile.NumberingSystem attribute) UNKNOWN_OPTION (pyrosetta.rosetta.utility.options.OptionTypes attribute) unknown_ramatable_type (pyrosetta.rosetta.core.scoring.Rama_Table_Type attribute) unknown_selector (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.selector_type attribute) UnknownAromaticity (pyrosetta.rosetta.core.chemical.BondAromaticity attribute) UnknownBond (pyrosetta.rosetta.core.chemical.BondName attribute) UnknownBondOrder (pyrosetta.rosetta.core.chemical.BondOrder attribute) UnknownConjugability (pyrosetta.rosetta.core.chemical.BondConjugability attribute) UnknownElement (pyrosetta.rosetta.core.chemical.element.Elements attribute) UnknownIsometry (pyrosetta.rosetta.core.chemical.BondIsometry attribute) UnknownRingness (pyrosetta.rosetta.core.chemical.BondRingness attribute) unlabel() (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) unmuted (pyrosetta.rosetta.basic.TracerOptions property) unordered_map_basic_datacache_ResRotPair_float_basic_datacache_ResRotPairHasher_std_equal_to_basic_datacache_ResRotPair_std_allocator_std_pair_const_basic_datacache_ResRotPair_float_t (class in pyrosetta.rosetta.std) unordered_map_std_pair_char_char_int_core_sequence_CharPairHash_std_equal_to_std_pair_char_char_std_allocator_std_pair_const_std_pair_char_char_int_t (class in pyrosetta.rosetta.std) unordered_map_unsigned_long_numeric_MathMatrix_float_t (class in pyrosetta.rosetta.std) unpack() (in module pyrosetta.rosetta.core.scoring.epr_deer) 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) unpause() (pyrosetta.rosetta.utility.signals.PausableSignalHub_void_core_conformation_signals_GeneralEvent_t method) unperturbed_sequence() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) UnpublishedModuleAuthor (class in pyrosetta.rosetta.basic.citation_manager) UnpublishedModuleInfo (class in pyrosetta.rosetta.basic.citation_manager) UnrecognizedAtomFeatures (class in pyrosetta.rosetta.protocols.features) UnrecognizedAtomFeaturesCreator (class in pyrosetta.rosetta.protocols.features) UnrecognizedAtomRecord (class in pyrosetta.rosetta.core.pose) unsample_ligand() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) unsat_accs (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) unsat_Hpols (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) UnsatCorrectionOptions (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty) UnsatSelector (class in pyrosetta.rosetta.protocols.hbnet) UnsatSelectorCreator (class in pyrosetta.rosetta.protocols.hbnet) unselection_positions() (in module pyrosetta.rosetta.core.select.residue_selector) unset (pyrosetta.rosetta.protocols.hybridization.sampleEnum attribute) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequencesMode attribute) unset_acceptor_ether_oxygens() (in module pyrosetta.rosetta.core.chemical) unset_native_pose() (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) unset_parent() (pyrosetta.rosetta.basic.datacache.HierarchicalDataMap method) unsetf() (pyrosetta.rosetta.std.ios_base method) unsigned_periodic_range() (in module pyrosetta.rosetta.basic) unswitch_segment() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) unused_hbond() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) unvisit() (pyrosetta.rosetta.core.environment.FoldTreeSketch.Node method) unweighted (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.ConstraintConditions property) UP (pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation attribute) up_coll_filt() (pyrosetta.rosetta.protocols.match.output.MatchConsolidator method) (pyrosetta.rosetta.protocols.match.output.MatchOutputter method) (pyrosetta.rosetta.protocols.match.output.MatchProcessor method) up_down_filt() (pyrosetta.rosetta.protocols.match.output.MatchConsolidator method) (pyrosetta.rosetta.protocols.match.output.MatchOutputter method) (pyrosetta.rosetta.protocols.match.output.MatchProcessor method) upcase() (in module pyrosetta.rosetta.ObjexxFCL) update() (pyrosetta.bindings.pose.PoseScoreAccessor method) (pyrosetta.io.silent_file_map.SilentFileMap method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph method) (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) (pyrosetta.rosetta.core.scoring.TMscoreStore method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) (pyrosetta.rosetta.protocols.trajectory.DbTrajectoryWriter method) (pyrosetta.rosetta.protocols.viewer.triangle method) (pyrosetta.rosetta.RDKit.Dict method) update_actcoord() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) 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) (pyrosetta.rosetta.protocols.environment.ProtectedConformation 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) (pyrosetta.rosetta.protocols.simple_moves.DOFHistogramRecorder method) update_allow_sc_vectors() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) update_and_writelps() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower 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_atom_type_set() (pyrosetta.rosetta.core.chemical.MutableResidueType method) update_base_stub_list_and_check_centroid_interaction() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker method) update_base_stub_list_and_check_that_terminal_res_are_unstacked() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker method) update_cached_lkb_resinfo() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) update_center() (pyrosetta.rosetta.protocols.pockets.SmallMol method) update_chemshiftscore() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList method) update_chemshiftscore_from_peak() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) update_com() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore 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_conf() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) update_conf_from_minipose() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) update_conformation() (pyrosetta.rosetta.core.conformation.UltraLightResidue 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.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) update_core_and_boundary_residues() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) update_counting_last_PDR() (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) update_cumulative_distribution() (pyrosetta.rosetta.numeric.random.WeightedSampler method) update_current_energy() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge 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) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) update_edge_label() (pyrosetta.rosetta.core.kinematics.FoldTree method) update_edge_paired() (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential method) update_energies_after_passive_change() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) update_energy() (pyrosetta.rosetta.protocols.moves.PyMOLMover method) update_enumeration_shell() (pyrosetta.rosetta.core.scoring.facts.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_fragment_library_pointers() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) update_from_momento() (pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection method) update_from_pose() (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) update_full_model_info_from_pose() (in module pyrosetta.rosetta.core.pose.full_model_info) update_hydrogens() (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) 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_internal_energy_sums() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) update_intersection() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) update_interval() (pyrosetta.rosetta.protocols.moves.PyMOLMover method) update_job_dag() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobQueen method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen method) (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) update_jobs_list() (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EmptyPoseJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.LazySilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.ScreeningJobInputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) (pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputter 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_library_NSGAII() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) update_library_seeds() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) update_ligand_conf() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) update_ligchi_types() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) update_loops() (pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph method) update_loops_and_cycles() (pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph method) update_matrix_A() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) update_matrix_A_all() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_Ts4 method) update_matrix_A_all_for_cstyle() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter method) update_matrix_A_all_for_svd() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter method) update_membrane_position() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) update_mg_hoh_fold_tree() (in module pyrosetta.rosetta.protocols.magnesium) update_movemap() (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) update_mp_geo_pore() (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) update_multiple_format_residue_numbering() (pyrosetta.rosetta.protocols.pdbinfo_manipulations.SequenceSpecification method) update_my_A_matrix() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data_per_lanthanides method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_per_lanthanides_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_per_lanthanides_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_per_lanthanides_Ts4 method) update_my_A_matrix_for_cstyle() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide method) update_my_A_matrix_for_svd() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide method) update_nmonomer_jumps() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) update_noesy_filter_files() (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) update_noncanonical_connection() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) update_numbering() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) update_numbers_in_pdb_info() (in module pyrosetta.rosetta.protocols.magnesium) update_nus() (pyrosetta.rosetta.core.conformation.Residue method) update_offset_data() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) update_on_length_change() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) update_one_body_energies() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) update_one_body_energy() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NodeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) 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) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) update_packer_task() (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover 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_pdb_remarks_for_backbone_params() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) update_PDBInfo() (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) update_pdblist_file() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) update_peak_volumina() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList 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) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) update_pose_and_cst_set_from_cst_string() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters 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_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection method) update_pose_objects_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) update_pose_stem_positions() (pyrosetta.rosetta.protocols.splice.SpliceManager method) update_proposed_energy() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge method) update_radii() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) update_radius() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) 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_COORDINATES (pyrosetta.rosetta.basic.ProfTag attribute) update_residue_for_packing() (pyrosetta.rosetta.core.energy_methods.AACompositionEnergy method) (pyrosetta.rosetta.core.energy_methods.AARepeatEnergy method) (pyrosetta.rosetta.core.energy_methods.Abego method) (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.BranchEnergy method) (pyrosetta.rosetta.core.energy_methods.Burial_v2Energy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CCS_IMMSEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifDegreeEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.ChemicalShiftAnisotropyEnergy method) (pyrosetta.rosetta.core.energy_methods.ContactOrderEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.D2H_SA_Energy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.energy_methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FastSAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyDens method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HolesEnergy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.IntermolEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.LoopCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvPenalties method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneLipo method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergy method) (pyrosetta.rosetta.core.energy_methods.MissingEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.OtherPoseEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.PackStatEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.ProQ_Energy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy_Rohl method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_Fast method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_RNA method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergy method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RMS_Energy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalMappingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PartitionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SA_Energy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) (pyrosetta.rosetta.core.energy_methods.SecondaryStructureEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfVolEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.XtalMLEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomePackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.facts.FACTSPotential method) (pyrosetta.rosetta.core.scoring.GenBornPotential method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.packing.HolesEnergyRes method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergy method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.EnsembleEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.ResidualDipolarCouplingEnergyRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergy method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy method) 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.basic.ProfTag attribute) update_residue_neighbors() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) UPDATE_RESIDUE_TORSIONS (pyrosetta.rosetta.basic.ProfTag attribute) update_residue_type() (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) update_residue_union() (pyrosetta.rosetta.core.pack.task.PackerTask_ method) update_residue_variants() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) update_restraint() (pyrosetta.rosetta.protocols.md.CartesianMD 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_rotamer_offsets() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) update_sampler_weights() (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) update_score_multiply_factor() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) update_scores() (in module pyrosetta.rosetta.protocols.recces) (pyrosetta.distributed.packed_pose.core.PackedPose method) update_segments() (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) update_sequence() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) update_sequence_numbering() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.id.AtomID_Map_AtomID method) (pyrosetta.rosetta.core.id.AtomID_Map_bool method) (pyrosetta.rosetta.core.id.AtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_MP_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_Real method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_NamedAtomID method) (pyrosetta.rosetta.core.kinematics.AtomTree method) update_sequences() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework method) update_single_rdc_weighting() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) update_spin_coordinates() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSSingleSet method) (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet 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_symmetry_score() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList method) update_task_and_neighbors() (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) update_template() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) update_template_files() (in module pyrosetta.rosetta.protocols.tcr) update_to_move_chunks_with_domain() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) update_to_move_rosetta_library_chunks() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) update_to_stored() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower 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.CrossPeakList method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) update_value_from_list() (pyrosetta.rosetta.protocols.optimize_weights.OptEVariableExpression method) update_VDW_screen_bin() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker method) update_vl_vh_cut() (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) update_X_Y_Z_all() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_data_Ts4 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) updateChains() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) updateChainsAndAnchors_fromParamsFile() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) UpdateCrystInfo (class in pyrosetta.rosetta.protocols.cryst) UpdateCrystInfoCreator (class in pyrosetta.rosetta.protocols.cryst) UpdateEnzdesHeaderMover (class in pyrosetta.rosetta.protocols.enzdes) UpdateEnzdesHeaderMoverCreator (class in pyrosetta.rosetta.protocols.enzdes) updateFcalc() (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) updatePropertyCache() (pyrosetta.rosetta.RDKit.Atom method) (pyrosetta.rosetta.RDKit.Bond method) (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) updateProps() (pyrosetta.rosetta.RDKit.Atom method) (pyrosetta.rosetta.RDKit.Bond method) (pyrosetta.rosetta.RDKit.Conformer method) (pyrosetta.rosetta.RDKit.RDProps method) (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) updates_jobs_list() (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EmptyPoseJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.LazySilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.ScreeningJobInputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) (pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputter method) updateSolventMask() (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) UpdateSolventMover (class in pyrosetta.rosetta.protocols.cryst) UpdateSolventMoverCreator (class in pyrosetta.rosetta.protocols.cryst) updateWithDsspAssignment() (pyrosetta.rosetta.protocols.forge.remodel.RemodelData method) UpJumpSRFD (class in pyrosetta.rosetta.core.fragment) upper (pyrosetta.rosetta.core.chemical.sdf.BondData property) upper() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t method) (pyrosetta.rosetta.numeric.kdtree.HyperRectangle method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.Torsion method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter 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.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) upper_anchor() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) upper_bound (pyrosetta.rosetta.protocols.qsar.ColorGradient property) upper_bound() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERChiSqMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceDistribution method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJaccardMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJSMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERMiscMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEEROverlapMethod method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.PoissonBoltzmannPotential method) upper_bound_score() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) upper_chain() (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) upper_connect() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) upper_connect_angle_params() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) upper_connect_atom() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) upper_connect_id() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) UPPER_CONNECTION_RNA (pyrosetta.rosetta.core.chemical.VariantType attribute) upper_dihedrals() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) upper_edge_list_begin() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.utility.graph.Node method) upper_edge_list_end() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.utility.graph.Node method) 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.constraints.CstResNeighbConstIterator method) (pyrosetta.rosetta.core.scoring.constraints.CstResNeighbIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbIterator method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.ResidueNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.ResidueNeighborIterator method) upper_neighbor_iterator_begin() (pyrosetta.rosetta.core.scoring.constraints.CstEnergyContainer method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.LREnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) upper_neighbor_iterator_end() (pyrosetta.rosetta.core.scoring.constraints.CstEnergyContainer method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.LREnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) upper_omega() (pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals method) upper_padding() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) upper_psi() (pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals method) upper_residue() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) upper_segment() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) UPPER_TERMINUS (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) UPPER_TERMINUS_VARIANT (pyrosetta.rosetta.core.chemical.VariantType attribute) upper_threshold() (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilter method) upper_vertex() (pyrosetta.rosetta.utility.graph.UEEdge_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t method) (pyrosetta.rosetta.utility.graph.UEEdge_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t 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) UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t (class in pyrosetta.rosetta.utility.graph) UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t (class in pyrosetta.rosetta.utility.graph) UPPERTERM_CAP (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) UPPERTERM_TRUNC (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) UPPERTERM_TRUNC_VARIANT (pyrosetta.rosetta.core.chemical.VariantType attribute) UPSILON_ATOM (pyrosetta.rosetta.core.chemical.GreekDistance attribute) 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.id.SequenceMapping method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) upstream_conf_id() (pyrosetta.rosetta.protocols.match.Hit method) (pyrosetta.rosetta.protocols.match.upstream_hit method) upstream_conformation_for_hit() (pyrosetta.rosetta.protocols.match.output.UpstreamHitCacher method) upstream_downstream_atom_collision_tolerance() (pyrosetta.rosetta.protocols.match.MatcherTask method) upstream_downstream_residue_collision_score_cutoff() (pyrosetta.rosetta.protocols.match.MatcherTask method) upstream_downstream_residue_collision_Wfa_atr() (pyrosetta.rosetta.protocols.match.MatcherTask method) upstream_downstream_residue_collision_Wfa_rep() (pyrosetta.rosetta.protocols.match.MatcherTask method) upstream_downstream_residue_collision_Wfa_sol() (pyrosetta.rosetta.protocols.match.MatcherTask method) upstream_hit (class in pyrosetta.rosetta.protocols.match) upstream_hits (pyrosetta.rosetta.protocols.match.match_dspos1 property) 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) (pyrosetta.rosetta.protocols.environment.ProtectedConformation 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) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) upstream_only_geom_cst() (pyrosetta.rosetta.protocols.match.MatcherTask method) upstream_pose() (pyrosetta.rosetta.protocols.match.Matcher method) (pyrosetta.rosetta.protocols.match.MatcherTask method) upstream_pose_build_resids_for_geometric_constraint() (pyrosetta.rosetta.protocols.match.MatcherTask method) upstream_pose_name() (pyrosetta.rosetta.protocols.match.MatcherTask method) upstream_res() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo method) upstream_resids_and_radii_defining_active_site() (pyrosetta.rosetta.protocols.match.MatcherTask method) upstream_residue_collision_score_cutoff() (pyrosetta.rosetta.protocols.match.MatcherTask method) upstream_residue_collision_tolerance() (pyrosetta.rosetta.protocols.match.MatcherTask method) upstream_residue_collision_Wfa_atr() (pyrosetta.rosetta.protocols.match.MatcherTask method) upstream_residue_collision_Wfa_rep() (pyrosetta.rosetta.protocols.match.MatcherTask method) upstream_residue_collision_Wfa_sol() (pyrosetta.rosetta.protocols.match.MatcherTask method) upstream_restypes() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) UpstreamBuilder (class in pyrosetta.rosetta.protocols.match.upstream) UpstreamCollisionFilter (class in pyrosetta.rosetta.protocols.match.output) UpstreamDownstreamCollisionFilter (class in pyrosetta.rosetta.protocols.match.output) UpstreamHitCacher (class in pyrosetta.rosetta.protocols.match.output) UpstreamResidueProcessor (class in pyrosetta.rosetta.protocols.match.upstream) UpstreamResTypeGeometry (class in pyrosetta.rosetta.protocols.match.upstream) upweight_starting_twobody_energy() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) ur() (pyrosetta.rosetta.core.conformation.PseudoBond method) ur_conn_id() (pyrosetta.rosetta.core.conformation.PseudoBond method) ur_resconnid() (pyrosetta.rosetta.core.conformation.PseudoBond method) url() (pyrosetta.rosetta.utility.Version static method) URONIC_ACID (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) URONIC_ACID_VARIANT (pyrosetta.rosetta.core.chemical.VariantType attribute) urs_norm4() (in module pyrosetta.rosetta.numeric) urs_Quat (class in pyrosetta.rosetta.numeric) urs_R2ang() (in module pyrosetta.rosetta.numeric) us_secmatch_hit_compare (class in pyrosetta.rosetta.protocols.match.downstream) use_abego_bias() (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) use_all_blocks() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) use_backbone_only_blocks() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) use_bounded_func() (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) use_cache_ (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric property) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric property) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric property) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric property) use_cartesian() (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) use_cartmin() (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) use_CB_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) use_charge (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) use_chem_shift_data() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) use_coarse_vdw() (pyrosetta.rosetta.protocols.relax.ClassicRelax method) use_coordinate_constraints() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) use_correction_weights() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) use_count() (pyrosetta.rosetta.cppdb.backend.connection method) (pyrosetta.rosetta.cppdb.backend.driver method) (pyrosetta.rosetta.cppdb.backend.loadable_driver method) (pyrosetta.rosetta.cppdb.backend.result method) (pyrosetta.rosetta.cppdb.backend.statement method) (pyrosetta.rosetta.cppdb.pool method) (pyrosetta.rosetta.cppdb.ref_counted method) use_cst() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) use_current_pose() (pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation method) use_custom_task() (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) use_default_membrane() (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) use_degrees() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) use_diel (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) use_different_build_points_for_each_geometric_constraint() (pyrosetta.rosetta.protocols.match.MatcherTask method) use_distance_cst() (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) use_dssp() (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) use_extended_intrares_energy_interface() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) use_extended_residue_energy_interface() (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) use_extended_residue_pair_energy_interface() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) use_fast_frame_heuristic() (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) use_fast_heuristic() (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) use_first_jump_for_submotif() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) use_fold_tree_from_silent_file() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) use_foldtree() (pyrosetta.rosetta.protocols.fold_from_loops.selectors.CutpointResidueSelector 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_franklin() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) use_fullmer() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.forge.components.BDR method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) use_gen_kirkwood() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) use_gma_templates() (pyrosetta.rosetta.protocols.tcr.TCRmodel method) use_gmb_templates() (pyrosetta.rosetta.protocols.tcr.TCRmodel method) use_green_packer() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) use_harmonic (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.ConstraintConditions property) use_harmonic_func() (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) use_hb_env_dep() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) use_hb_env_dep_DNA() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) use_hierarchical_clustering() (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) use_incorrect_deriv() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) use_input_for_ref() (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) USE_INPUT_SC (class in pyrosetta.rosetta.core.pack.task) use_input_sc() (pyrosetta.rosetta.protocols.match.MatcherTask method) use_interface() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) use_job_pose() (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) use_kappa (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) use_largest_ddg() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) use_late_scoring_for_zeros() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) use_legacy_setup() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) use_local_distviol_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) use_loops_from_threading_job() (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) use_mean() (pyrosetta.rosetta.protocols.ddg.ddGMover method) use_min() (pyrosetta.rosetta.protocols.ddg.ddGMover method) use_mover_status() (pyrosetta.rosetta.protocols.moves.SequenceMover method) use_MPI_bcast() (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) use_MPI_sync_pools() (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) use_multicool_annealer() (pyrosetta.rosetta.core.pack.task.operation.OptH method) use_natro() (pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation method) use_nblist() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.core.optimization.MinimizerOptions method) (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) use_nblist_auto_update() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) use_nblist_of_type() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) use_nbr() (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) use_nobias() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) use_numbers() (pyrosetta.rosetta.protocols.pose_metric_calculators.ResidueDecompositionByChainCalculator method) use_occurrence_data() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation method) use_only_calpha() (pyrosetta.rosetta.protocols.fldsgn.NcontactsCalculator method) use_orientation_dep_rna_ch_o_bonds() (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) use_original_seq() (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) use_original_weights() (pyrosetta.rosetta.protocols.pose_metric_calculators.EnergiesData 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.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) use_pdb_format_HETNAM_records() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) use_pharmacophore() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner method) use_phenix_geo() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) (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) use_polarization() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) use_pose_numbering (pyrosetta.rosetta.protocols.loops.LoopConfiguration attribute) use_pose_sequence_as_native() (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) use_pot (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) use_precomputed_library() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) use_prefiltering() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) use_preset_task() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) use_pssm_features() (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy 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_rama_power() (pyrosetta.rosetta.core.scoring.Ramachandran method) use_random_conformer() (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) use_rattle() (pyrosetta.rosetta.protocols.md.CartesianMD method) use_residue_type_theta0() (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet method) use_rosetta_numbering() (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) use_rosetta_radii() (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter 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) use_sequence_bias() (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.forge.components.BDR method) use_sequence_profiles() (pyrosetta.rosetta.protocols.splice.SpliceManager method) use_sidechain_neighbors() (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) use_smallest_dscore() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) use_sp2_chi_penalty() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) use_threeletter() (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) use_time_as_seed() (pyrosetta.rosetta.basic.random.RandomGeneratorSettings method) use_trRosetta_constraints() (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) use_virtual_waters_as_placeholders() (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) used_for_phore() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties method) used_template_ranges() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) used_template_selector() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) UseMultiCoolAnnealer (class in pyrosetta.rosetta.core.pack.task.operation) UseMultiCoolAnnealerCreator (class in pyrosetta.rosetta.core.pack.task.operation) user() (pyrosetta.rosetta.protocols.hybridization.FragmentBiasAssigner method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) user_chain1() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) user_chain2() (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) user_defined_cycles() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) user_defined_peptide_chain() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) user_defined_receptor_chain() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) user_input() (pyrosetta.rosetta.core.import_pose.libraries.ChunkSet method) user_inputted_VDW_screen_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker 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.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) user_provided_movers_apply_cycle() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) USER_SPECIFIED (pyrosetta.rosetta.protocols.cluster.calibur.EST_THRESHOLD_MODE attribute) UserCorrectableIssue (class in pyrosetta.rosetta.utility.excn) UserDefinedGroupDiscriminator (class in pyrosetta.rosetta.protocols.minimization_packing) useres1() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) useres1_ph() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) useres1_po() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) useres2() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) useres2_ph() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) useres2_po() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery 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) Uuo (pyrosetta.rosetta.core.chemical.element.Elements attribute) Uup (pyrosetta.rosetta.core.chemical.element.Elements attribute) Uus (pyrosetta.rosetta.core.chemical.element.Elements attribute) Uut (pyrosetta.rosetta.core.chemical.element.Elements attribute) uz() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method)