Identifier Index

[ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _ ]

U

ub() (in BoundFunc)	update_residue_for_packing() (in SurfaceEnergy)	upstream_residue_collision_tolerance() (in MatcherTask)
UDPSocketClient (in rosetta.protocols.moves._protocols_moves_)	update_residue_for_packing() (in GenBornPotential)	upstream_residue_collision_Wfa_atr() (in MatcherTask)
UDPSocketClientAP (in rosetta.protocols.moves._protocols_moves_)	update_residue_for_packing() (in ScoreFunction)	upstream_residue_collision_Wfa_rep() (in MatcherTask)
UDPSocketClientCAP (in rosetta.protocols.moves._protocols_moves_)	update_residue_for_packing() (in CarbonHBondEnergy)	upstream_residue_collision_Wfa_sol() (in MatcherTask)
UltraLightResidue (in rosetta.core.conformation._core_conformation_)	update_residue_for_packing() (in ConstraintsEnergy)	upstream_restypes() (in MatchConstraintFileInfoList)
UltraLightResidueAP (in rosetta.core.conformation._core_conformation_)	update_residue_for_packing() (in XtalMLEnergy)	UpstreamBuilder (in rosetta.protocols.match.upstream._protocols_match_upstream_)
UltraLightResidueCAP (in rosetta.core.conformation._core_conformation_)	update_residue_for_packing() (in FullatomCustomPairDistanceEnergy)	UpstreamBuilderAP (in rosetta.protocols.match.upstream._protocols_match_upstream_)
UnaryExpression (in rosetta.numeric.expression_parser._numeric_expression_parser_)	update_residue_for_packing() (in CentroidDisulfideEnergy)	UpstreamBuilderCAP (in rosetta.protocols.match.upstream._protocols_match_upstream_)
UnaryExpressionAP (in rosetta.numeric.expression_parser._numeric_expression_parser_)	update_residue_for_packing() (in DisulfideMatchingEnergy)	UpstreamCollisionFilter (in rosetta.protocols.match.output._protocols_match_output_)
UnaryExpressionCAP (in rosetta.numeric.expression_parser._numeric_expression_parser_)	update_residue_for_packing() (in FullatomDisulfideEnergy)	UpstreamCollisionFilterAP (in rosetta.protocols.match.output._protocols_match_output_)
unassigned() (in ResidueIndexDescription)	update_residue_for_packing() (in DNAChiEnergy)	UpstreamCollisionFilterCAP (in rosetta.protocols.match.output._protocols_match_output_)
unblock() (in Link)	update_residue_for_packing() (in DNATorsionEnergy)	UpstreamDownstreamCollisionFilter (in rosetta.protocols.match.output._protocols_match_output_)
unblock_signals() (in Conformation)	update_residue_for_packing() (in FA_ElecEnergy)	UpstreamDownstreamCollisionFilterAP (in rosetta.protocols.match.output._protocols_match_output_)
unbound() (in FilterScanFilter)	update_residue_for_packing() (in FA_ElecEnergyAroAll)	UpstreamDownstreamCollisionFilterCAP (in rosetta.protocols.match.output._protocols_match_output_)
unbound() (in DeltaFilter)	update_residue_for_packing() (in FA_ElecEnergyAroAro)	UpstreamHitCacher (in rosetta.protocols.match.output._protocols_match_output_)
unbound() (in RelativePoseFilter)	update_residue_for_packing() (in FA_GrpElecEnergy)	UpstreamHitCacherAP (in rosetta.protocols.match.output._protocols_match_output_)
unbound() (in RotamerBoltzmannWeight)	update_residue_for_packing() (in RNA_FA_ElecEnergy)	UpstreamHitCacherCAP (in rosetta.protocols.match.output._protocols_match_output_)
unbound() (in TaskAwareScoreTypeFilter)	update_residue_for_packing() (in ElecDensAllAtomCenEnergy)	UpstreamResidueProcessor (in rosetta.protocols.match.upstream._protocols_match_upstream_)
unbound_score() (in DnaInterfacePacker)	update_residue_for_packing() (in ElecDensCenEnergy)	UpstreamResidueProcessorAP (in rosetta.protocols.match.upstream._protocols_match_upstream_)
unbound_struct() (in DGBindOptEData)	update_residue_for_packing() (in ElecDensEnergy)	UpstreamResidueProcessorCAP (in rosetta.protocols.match.upstream._protocols_match_upstream_)
UnboundRotamersOperation (in rosetta.core.pack.rotamer_set._core_pack_rotamer_set_)	update_residue_for_packing() (in FastDensEnergy)	UpstreamResTypeGeometry (in rosetta.protocols.match.upstream._protocols_match_upstream_)
UnboundRotamersOperationAP (in rosetta.core.pack.rotamer_set._core_pack_rotamer_set_)	update_residue_for_packing() (in PattersonCorrEnergy)	UpstreamResTypeGeometryAP (in rosetta.protocols.match.upstream._protocols_match_upstream_)
UnboundRotamersOperationCAP (in rosetta.core.pack.rotamer_set._core_pack_rotamer_set_)	update_residue_for_packing() (in ElecDensAtomwiseEnergy)	UpstreamResTypeGeometryCAP (in rosetta.protocols.match.upstream._protocols_match_upstream_)
unchecked (in StubStatus)	update_residue_for_packing() (in AnalyticEtableEnergy)	ur() (in PseudoBond)
unchecked (in rosetta.protocols.hotspot_hashing._protocols_hotspot_hashing_)	update_residue_for_packing() (in BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T)	ur_conn_id() (in PseudoBond)
unchecked (in rosetta.protocols.hotspot_hashing)	update_residue_for_packing() (in BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T)	ur_resconnid() (in PseudoBond)
UnconstrainedTorsionsMover (in rosetta.protocols.ligand_docking._protocols_ligand_docking_)	update_residue_for_packing() (in TableLookupEtableEnergy)	url (in rosetta.version')
UnconstrainedTorsionsMoverAP (in rosetta.protocols.ligand_docking._protocols_ligand_docking_)	update_residue_for_packing() (in FiberDiffractionEnergy)	URONIC_ACID (in rosetta)
UnconstrainedTorsionsMoverCAP (in rosetta.protocols.ligand_docking._protocols_ligand_docking_)	update_residue_for_packing() (in FiberDiffractionEnergyDens)	URONIC_ACID (in rosetta.core.chemical)
undefined_positions() (in Bridge)	update_residue_for_packing() (in ContextDependentGeometricSolEnergy)	URONIC_ACID (in ResidueProperty)
undefined_positions() (in BuildInstruction)	update_residue_for_packing() (in ContextIndependentGeometricSolEnergy)	URONIC_ACID (in rosetta.core.chemical._core_chemical_)
undefined_positions() (in BuildManager)	update_residue_for_packing() (in ExactOccludedHbondSolEnergy)	URONIC_ACID_VARIANT (in rosetta)
undefined_positions() (in ConnectRight)	update_residue_for_packing() (in OccludedHbondSolEnergy)	URONIC_ACID_VARIANT (in rosetta.core.chemical)
undefined_positions() (in GrowLeft)	update_residue_for_packing() (in OccludedHbondSolEnergy_onebody)	URONIC_ACID_VARIANT (in rosetta.core.chemical._core_chemical_)
undefined_positions() (in GrowRight)	update_residue_for_packing() (in HackAroEnergy)	URONIC_ACID_VARIANT (in VariantType)
undefined_positions() (in SegmentRebuild)	update_residue_for_packing() (in HBondEnergy)	urs_norm4() (in rosetta.numeric._numeric_)
undefined_positions() (in SegmentSwap)	update_residue_for_packing() (in DDPscore)	urs_Quat (in rosetta.numeric._numeric_)
unfinished_batches() (in ArchiveManager)	update_residue_for_packing() (in LoopCloseEnergy)	urs_QuatAP (in rosetta.numeric._numeric_)
UNFOLD (in rosetta.protocols.fldsgn.topology)	update_residue_for_packing() (in FaMPEnvEnergy)	urs_QuatCAP (in rosetta.numeric._numeric_)
UNFOLD (in SheetFoldType)	update_residue_for_packing() (in FaMPEnvSmoothEnergy)	urs_R2ang() (in rosetta.numeric._numeric_)
UNFOLD (in rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_)	update_residue_for_packing() (in FaMPSolvEnergy)	us_secmatch_hit_compare (in rosetta.protocols.match.downstream._protocols_match_downstream_)
unfolded (in ScoreType)	update_residue_for_packing() (in MPCbetaEnergy)	us_secmatch_hit_compareAP (in rosetta.protocols.match.downstream._protocols_match_downstream_)
unfolded (in rosetta.core.scoring._core_scoring_)	update_residue_for_packing() (in MPEnvEnergy)	us_secmatch_hit_compareCAP (in rosetta.protocols.match.downstream._protocols_match_downstream_)
unfolded (in rosetta.core.scoring)	update_residue_for_packing() (in MPLipoEnergy)	use_abego_bias() (in BluePrintBDR)
unfolded (in rosetta)	update_residue_for_packing() (in MPNonHelixPenalty)	use_cartesian() (in MinimizationRefiner)
unfolded_energies_type() (in EnergyMethodOptions)	update_residue_for_packing() (in MPPairEnergy)	use_coarse_vdw() (in ClassicRelax)
unfolded_energy_emap_vector() (in NestedEnergyTermPNatAAOptEPositionData)	update_residue_for_packing() (in MPTMProjPenalty)	use_coordinate_constraints() (in RNA_Minimizer)
unfolded_state_energy_calculator (in rosetta.protocols)	update_residue_for_packing() (in MPTerminiPenalty)	use_coordinate_constraints() (in StepWiseProteinMinimizer)
UnfoldedStateEnergy (in rosetta.core.scoring.methods._core_scoring_methods_)	update_residue_for_packing() (in BurialEnergy)	use_current_pose() (in JointSequenceOperation)
UnfoldedStateEnergyAP (in rosetta.core.scoring.methods._core_scoring_methods_)	update_residue_for_packing() (in CartesianBondedEnergy)	use_custom_task() (in DdgFilter)
UnfoldedStateEnergyCalculatorJobDistributor (in rosetta.protocols.unfolded_state_energy_calculator._protocols_unfolded_state_energy_calculator_)	update_residue_for_packing() (in CenHBEnergy)	use_custom_task() (in ddG)
UnfoldedStateEnergyCalculatorJobDistributorAP (in rosetta.protocols.unfolded_state_energy_calculator._protocols_unfolded_state_energy_calculator_)	update_residue_for_packing() (in CenPairEnergy)	use_defaults() (in PerturbBundleOptions)
UnfoldedStateEnergyCalculatorJobDistributorCAP (in rosetta.protocols.unfolded_state_energy_calculator._protocols_unfolded_state_energy_calculator_)	update_residue_for_packing() (in CenRotEnvEnergy)	use_degrees() (in MakeBundle)
UnfoldedStateEnergyCalculatorMover (in rosetta.protocols.unfolded_state_energy_calculator._protocols_unfolded_state_energy_calculator_)	update_residue_for_packing() (in CenRotPairEnergy)	use_degrees() (in PerturbBundle)
UnfoldedStateEnergyCalculatorMoverAP (in rosetta.protocols.unfolded_state_energy_calculator._protocols_unfolded_state_energy_calculator_)	update_residue_for_packing() (in ChainbreakEnergy)	use_different_build_points_for_each_geometric_constraint() (in MatcherTask)
UnfoldedStateEnergyCalculatorMoverCAP (in rosetta.protocols.unfolded_state_energy_calculator._protocols_unfolded_state_energy_calculator_)	update_residue_for_packing() (in ChemicalShiftAnisotropyEnergy)	use_distance_cst() (in AddConstraintsToCurrentConformationMover)
UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor (in rosetta.protocols.unfolded_state_energy_calculator._protocols_unfolded_state_energy_calculator_)	update_residue_for_packing() (in ContactOrderEnergy)	use_extended_intrares_energy_interface() (in CarbonHBondEnergy)
UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributorAP (in rosetta.protocols.unfolded_state_energy_calculator._protocols_unfolded_state_energy_calculator_)	update_residue_for_packing() (in ContextDependentLRTwoBodyEnergy)	use_extended_intrares_energy_interface() (in ConstraintsEnergy)
UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributorCAP (in rosetta.protocols.unfolded_state_energy_calculator._protocols_unfolded_state_energy_calculator_)	update_residue_for_packing() (in ContextDependentOneBodyEnergy)	use_extended_intrares_energy_interface() (in FullatomCustomPairDistanceEnergy)
UnfoldedStateEnergyCAP (in rosetta.core.scoring.methods._core_scoring_methods_)	update_residue_for_packing() (in ContextDependentTwoBodyEnergy)	use_extended_intrares_energy_interface() (in CentroidDisulfideEnergy)
UnfoldedStateEnergyCreator (in rosetta.core.scoring.methods._core_scoring_methods_)	update_residue_for_packing() (in ContextIndependentLRTwoBodyEnergy)	use_extended_intrares_energy_interface() (in DisulfideMatchingEnergy)
UnfoldedStateEnergyCreatorAP (in rosetta.core.scoring.methods._core_scoring_methods_)	update_residue_for_packing() (in ContextIndependentOneBodyEnergy)	use_extended_intrares_energy_interface() (in FullatomDisulfideEnergy)
UnfoldedStateEnergyCreatorCAP (in rosetta.core.scoring.methods._core_scoring_methods_)	update_residue_for_packing() (in ContextIndependentTwoBodyEnergy)	use_extended_intrares_energy_interface() (in DNATorsionEnergy)
UnfoldedStatePotential (in rosetta.core.scoring._core_scoring_)	update_residue_for_packing() (in CustomAtomPairEnergy)	use_extended_intrares_energy_interface() (in FA_ElecEnergy)
UnfoldedStatePotentialAP (in rosetta.core.scoring._core_scoring_)	update_residue_for_packing() (in D2H_SA_Energy)	use_extended_intrares_energy_interface() (in FA_ElecEnergyAroAll)
UnfoldedStatePotentialCAP (in rosetta.core.scoring._core_scoring_)	update_residue_for_packing() (in DNA_BaseEnergy)	use_extended_intrares_energy_interface() (in FA_ElecEnergyAroAro)
unfreeze() (in RigidBodyMover)	update_residue_for_packing() (in DipolarCouplingEnergy)	use_extended_intrares_energy_interface() (in FA_GrpElecEnergy)
ungapped_length() (in Sequence)	update_residue_for_packing() (in DirectReadoutEnergy)	use_extended_intrares_energy_interface() (in RNA_FA_ElecEnergy)
ungapped_sequence() (in Sequence)	update_residue_for_packing() (in DistanceChainbreakEnergy)	use_extended_intrares_energy_interface() (in ElecDensAllAtomCenEnergy)
Unhybridized (in HybridOrbitalType)	update_residue_for_packing() (in EnergyMethod)	use_extended_intrares_energy_interface() (in ElecDensCenEnergy)
Unhybridized (in GasteigerAtomTypeData)	update_residue_for_packing() (in EnvEnergy)	use_extended_intrares_energy_interface() (in ElecDensEnergy)
Uniform (in rosetta.protocols.ligand_docking)	update_residue_for_packing() (in EnvSmoothEnergy)	use_extended_intrares_energy_interface() (in FastDensEnergy)
Uniform (in Distribution)	update_residue_for_packing() (in Fa_MbenvEnergy)	use_extended_intrares_energy_interface() (in PattersonCorrEnergy)
Uniform (in rosetta.protocols.ligand_docking._protocols_ligand_docking_)	update_residue_for_packing() (in Fa_MbsolvEnergy)	use_extended_intrares_energy_interface() (in ElecDensAtomwiseEnergy)
uniform() (in RandomGenerator)	update_residue_for_packing() (in FreeDOF_Energy)	use_extended_intrares_energy_interface() (in AnalyticEtableEnergy)
uniform() (in rosetta.numeric.random._numeric_random_)	update_residue_for_packing() (in GaussianOverlapEnergy)	use_extended_intrares_energy_interface() (in BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T)
uniform() (in FragmentBiasAssigner)	update_residue_for_packing() (in GenBornEnergy)	use_extended_intrares_energy_interface() (in BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T)
uniform_dof_distribution() (in rosetta.protocols.simple_moves._protocols_simple_moves_)	update_residue_for_packing() (in GoapEnergy)	use_extended_intrares_energy_interface() (in TableLookupEtableEnergy)
uniform_modeler() (in MC_Comb)	update_residue_for_packing() (in HybridVDW_Energy)	use_extended_intrares_energy_interface() (in ContextDependentGeometricSolEnergy)
uniform_modeler() (in MC_OneTorsion)	update_residue_for_packing() (in IntermolEnergy)	use_extended_intrares_energy_interface() (in ContextIndependentGeometricSolEnergy)
uniform_modeler() (in MC_StepWiseSampler)	update_residue_for_packing() (in LK_BallEnergy)	use_extended_intrares_energy_interface() (in OccludedHbondSolEnergy)
uniform_modeler() (in RNA_MC_MultiSuite)	update_residue_for_packing() (in LK_PolarNonPolarEnergy)	use_extended_intrares_energy_interface() (in HackAroEnergy)
uniform_modeler() (in RNA_MC_Sugar)	update_residue_for_packing() (in LK_hack)	use_extended_intrares_energy_interface() (in HBondEnergy)
uniform_modeler() (in RNA_MC_Suite)	update_residue_for_packing() (in LinearChainbreakEnergy)	use_extended_intrares_energy_interface() (in DDPscore)
uniform_phipsi_from_allowed_rama() (in Ramachandran)	update_residue_for_packing() (in LongRangeTwoBodyEnergy)	use_extended_intrares_energy_interface() (in FaMPSolvEnergy)
uniform_RG (in rosetta.numeric.random._numeric_random_)	update_residue_for_packing() (in MMBondAngleEnergy)	use_extended_intrares_energy_interface() (in MPPairEnergy)
uniform_RGAP (in rosetta.numeric.random._numeric_random_)	update_residue_for_packing() (in MMBondLengthEnergy)	use_extended_intrares_energy_interface() (in CartesianBondedEnergy)
uniform_RGCAP (in rosetta.numeric.random._numeric_random_)	update_residue_for_packing() (in MMLJEnergyInter)	use_extended_intrares_energy_interface() (in CenHBEnergy)
UniformPerturber (in rosetta.protocols.kinematic_closure.perturbers._protocols_kinematic_closure_perturbers_)	update_residue_for_packing() (in MMLJEnergyIntra)	use_extended_intrares_energy_interface() (in CenPairEnergy)
UniformPerturberAP (in rosetta.protocols.kinematic_closure.perturbers._protocols_kinematic_closure_perturbers_)	update_residue_for_packing() (in MMTorsionEnergy)	use_extended_intrares_energy_interface() (in CenRotPairEnergy)
UniformPerturberCAP (in rosetta.protocols.kinematic_closure.perturbers._protocols_kinematic_closure_perturbers_)	update_residue_for_packing() (in MembraneCbetaEnergy)	use_extended_intrares_energy_interface() (in ContextDependentLRTwoBodyEnergy)
UniformRigidBodyCM (in rosetta.protocols.rigid._protocols_rigid_)	update_residue_for_packing() (in MembraneCenPairEnergy)	use_extended_intrares_energy_interface() (in ContextDependentTwoBodyEnergy)
UniformRigidBodyCMAP (in rosetta.protocols.rigid._protocols_rigid_)	update_residue_for_packing() (in MembraneEnvEnergy)	use_extended_intrares_energy_interface() (in ContextIndependentLRTwoBodyEnergy)
UniformRigidBodyCMCAP (in rosetta.protocols.rigid._protocols_rigid_)	update_residue_for_packing() (in MembraneEnvPenalties)	use_extended_intrares_energy_interface() (in ContextIndependentTwoBodyEnergy)
UniformRigidBodyCMCreator (in rosetta.protocols.rigid._protocols_rigid_)	update_residue_for_packing() (in MembraneEnvSmoothEnergy)	use_extended_intrares_energy_interface() (in CustomAtomPairEnergy)
UniformRigidBodyCMCreatorAP (in rosetta.protocols.rigid._protocols_rigid_)	update_residue_for_packing() (in MembraneLipo)	use_extended_intrares_energy_interface() (in DNA_BaseEnergy)
UniformRigidBodyCMCreatorCAP (in rosetta.protocols.rigid._protocols_rigid_)	update_residue_for_packing() (in MissingEnergy)	use_extended_intrares_energy_interface() (in Fa_MbsolvEnergy)
UniformRigidBodyMover (in rosetta.protocols.rigid._protocols_rigid_)	update_residue_for_packing() (in NMerPSSMEnergy)	use_extended_intrares_energy_interface() (in GaussianOverlapEnergy)
UniformRigidBodyMoverAP (in rosetta.protocols.rigid._protocols_rigid_)	update_residue_for_packing() (in NMerRefEnergy)	use_extended_intrares_energy_interface() (in GenBornEnergy)
UniformRigidBodyMoverCAP (in rosetta.protocols.rigid._protocols_rigid_)	update_residue_for_packing() (in NMerSVMEnergy)	use_extended_intrares_energy_interface() (in GoapEnergy)
UniformRigidBodyMoverCreator (in rosetta.protocols.rigid._protocols_rigid_)	update_residue_for_packing() (in OmegaTetherEnergy)	use_extended_intrares_energy_interface() (in HybridVDW_Energy)
UniformRigidBodyMoverCreatorAP (in rosetta.protocols.rigid._protocols_rigid_)	update_residue_for_packing() (in OneBodyEnergy)	use_extended_intrares_energy_interface() (in LK_BallEnergy)
UniformRigidBodyMoverCreatorCAP (in rosetta.protocols.rigid._protocols_rigid_)	update_residue_for_packing() (in OtherPoseEnergy)	use_extended_intrares_energy_interface() (in LK_PolarNonPolarEnergy)
UniformRotationMover (in rosetta.protocols.simple_moves._protocols_simple_moves_)	update_residue_for_packing() (in P_AA_Energy)	use_extended_intrares_energy_interface() (in LK_hack)
UniformRotationMoverAP (in rosetta.protocols.simple_moves._protocols_simple_moves_)	update_residue_for_packing() (in P_AA_pp_Energy)	use_extended_intrares_energy_interface() (in LongRangeTwoBodyEnergy)
UniformRotationMoverCAP (in rosetta.protocols.simple_moves._protocols_simple_moves_)	update_residue_for_packing() (in PackStatEnergy)	use_extended_intrares_energy_interface() (in MMBondAngleEnergy)
UniformRotationSampler (in rosetta.numeric._numeric_)	update_residue_for_packing() (in PairEnergy)	use_extended_intrares_energy_interface() (in MMBondLengthEnergy)
UniformRotationSamplerAP (in rosetta.numeric._numeric_)	update_residue_for_packing() (in PeptideBondEnergy)	use_extended_intrares_energy_interface() (in MMLJEnergyInter)
UniformRotationSamplerCAP (in rosetta.numeric._numeric_)	update_residue_for_packing() (in PoissonBoltzmannEnergy)	use_extended_intrares_energy_interface() (in MMLJEnergyIntra)
UniformSphereTransMover (in rosetta.protocols.rigid._protocols_rigid_)	update_residue_for_packing() (in ProClosureEnergy)	use_extended_intrares_energy_interface() (in MMTorsionEnergy)
UniformSphereTransMoverAP (in rosetta.protocols.rigid._protocols_rigid_)	update_residue_for_packing() (in ProQ_Energy)	use_extended_intrares_energy_interface() (in MembraneCenPairEnergy)
UniformSphereTransMoverCAP (in rosetta.protocols.rigid._protocols_rigid_)	update_residue_for_packing() (in RG_Energy_Fast)	use_extended_intrares_energy_interface() (in PairEnergy)
UniformTranslationMover (in rosetta.protocols.simple_moves._protocols_simple_moves_)	update_residue_for_packing() (in RG_LocalEnergy)	use_extended_intrares_energy_interface() (in PeptideBondEnergy)
UniformTranslationMoverAP (in rosetta.protocols.simple_moves._protocols_simple_moves_)	update_residue_for_packing() (in RMS_Energy)	use_extended_intrares_energy_interface() (in PoissonBoltzmannEnergy)
UniformTranslationMoverCAP (in rosetta.protocols.simple_moves._protocols_simple_moves_)	update_residue_for_packing() (in Rama2BOffsetEnergy)	use_extended_intrares_energy_interface() (in ProClosureEnergy)
unimplemented_method_error() (in ScoringScheme)	update_residue_for_packing() (in RamachandranEnergy)	use_extended_intrares_energy_interface() (in Rama2BOffsetEnergy)
union_interval() (in rosetta.protocols.forge.methods._protocols_forge_methods_)	update_residue_for_packing() (in RamachandranEnergy2B)	use_extended_intrares_energy_interface() (in RamachandranEnergy2B)
union_of_intervals_containing_undefined_positions() (in BuildManager)	update_residue_for_packing() (in ReferenceEnergy)	use_extended_intrares_energy_interface() (in ShortRangeTwoBodyEnergy)
UnionEdge (in rosetta.protocols.pockets._protocols_pockets_)	update_residue_for_packing() (in ReferenceEnergyNoncanonical)	use_extended_intrares_energy_interface() (in SmoothCenPairEnergy)
UnionEdgeAP (in rosetta.protocols.pockets._protocols_pockets_)	update_residue_for_packing() (in ResidualDipolarCouplingEnergy)	use_extended_intrares_energy_interface() (in SuckerEnergy)
UnionEdgeCAP (in rosetta.protocols.pockets._protocols_pockets_)	update_residue_for_packing() (in ResidualDipolarCouplingEnergy_Rohl)	use_extended_intrares_energy_interface() (in TwoBodyEnergy)
unique() (in Index)	update_residue_for_packing() (in SA_Energy)	use_extended_intrares_energy_interface() (in WaterAdductHBondEnergy)
unique_id() (in IRCollection)	update_residue_for_packing() (in SecondaryStructureEnergy)	use_extended_intrares_energy_interface() (in DFIRE_Energy)
UniqueConstraint (in rosetta.basic.database.schema_generator._basic_database_schema_generator_)	update_residue_for_packing() (in SequenceDependentRefEnergy)	use_extended_intrares_energy_interface() (in OrbitalsScore)
UniqueConstraintAP (in rosetta.basic.database.schema_generator._basic_database_schema_generator_)	update_residue_for_packing() (in ShortRangeTwoBodyEnergy)	use_extended_intrares_energy_interface() (in RNA_FullAtomStackingEnergy)
UniqueConstraintCAP (in rosetta.basic.database.schema_generator._basic_database_schema_generator_)	update_residue_for_packing() (in SmoothCenPairEnergy)	use_extended_intrares_energy_interface() (in RNA_JR_SuiteEnergy)
universal_main() (in rosetta.protocols.jobdist._protocols_jobdist_)	update_residue_for_packing() (in SmoothEnvEnergy)	use_extended_intrares_energy_interface() (in RNA_LJ_BaseEnergy)
UNK (in rosetta.protocols.frag_picker)	update_residue_for_packing() (in SuckerEnergy)	use_extended_intrares_energy_interface() (in RNA_Mg_Energy)
UNK (in ContactType)	update_residue_for_packing() (in SymmetricLigandEnergy)	use_extended_intrares_energy_interface() (in RNA_PairwiseLowResolutionEnergy)
UNK (in rosetta.protocols.frag_picker._protocols_frag_picker_)	update_residue_for_packing() (in TwoBodyEnergy)	use_extended_intrares_energy_interface() (in RNA_SuiteEnergy)
Unknown (in rosetta.protocols.antibody)	update_residue_for_packing() (in UnfoldedStateEnergy)	use_extended_intrares_energy_interface() (in RNA_TorsionEnergy)
Unknown (in H3BaseTypeEnum)	update_residue_for_packing() (in WaterAdductHBondEnergy)	use_extended_intrares_energy_interface() (in RNA_VDW_Energy)
unknown (in LightChainTypeEnum)	update_residue_for_packing() (in WaterAdductIntraEnergy)	use_extended_intrares_energy_interface() (in StackElecEnergy)
Unknown (in rosetta.protocols.antibody._protocols_antibody_)	update_residue_for_packing() (in WholeStructureEnergy)	use_extended_intrares_energy_interface() (in RNA_DataBackboneEnergy)
unknown (in rosetta.protocols.antibody._protocols_antibody_)	update_residue_for_packing() (in YHHPlanarityEnergy)	use_extended_intrares_energy_interface() (in symEnergy)
unknown (in rosetta.protocols.antibody)	update_residue_for_packing() (in pHEnergy)	use_extended_intrares_energy_interface() (in InterchainPairEnergy)
UNKNOWN (in rosetta.protocols.fldsgn.topology)	update_residue_for_packing() (in SugarBackboneEnergy)	use_extended_residue_energy_interface() (in DunbrackEnergy)
UNKNOWN (in SheetFoldType)	update_residue_for_packing() (in DFIRE_Energy)	use_extended_residue_energy_interface() (in CenRotDunEnergy)
UNKNOWN (in rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_)	update_residue_for_packing() (in NVscore)	use_extended_residue_energy_interface() (in HPatchEnergy)
unknown_effect (in perturber_effect)	update_residue_for_packing() (in OrbitalsScore)	use_extended_residue_energy_interface() (in SurfaceEnergy)
unknown_effect (in rosetta.protocols.generalized_kinematic_closure.perturber._protocols_generalized_kinematic_closure_perturber_)	update_residue_for_packing() (in HolesEnergy)	use_extended_residue_energy_interface() (in DNAChiEnergy)
unknown_effect (in rosetta.protocols.generalized_kinematic_closure.perturber)	update_residue_for_packing() (in HolesEnergyRes)	use_extended_residue_energy_interface() (in ExactOccludedHbondSolEnergy)
unknown_filter (in filter_type)	update_residue_for_packing() (in SurfEnergy)	use_extended_residue_energy_interface() (in OccludedHbondSolEnergy_onebody)
unknown_filter (in rosetta.protocols.generalized_kinematic_closure.filter._protocols_generalized_kinematic_closure_filter_)	update_residue_for_packing() (in SurfVolEnergy)	use_extended_residue_energy_interface() (in FaMPEnvEnergy)
unknown_filter (in rosetta.protocols.generalized_kinematic_closure.filter)	update_residue_for_packing() (in RG_Energy_RNA)	use_extended_residue_energy_interface() (in FaMPEnvSmoothEnergy)
UNKNOWN_HYBRID (in rosetta)	update_residue_for_packing() (in RNA_BulgeEnergy)	use_extended_residue_energy_interface() (in MPCbetaEnergy)
UNKNOWN_HYBRID (in rosetta.core.chemical)	update_residue_for_packing() (in RNA_FullAtomStackingEnergy)	use_extended_residue_energy_interface() (in MPEnvEnergy)
UNKNOWN_HYBRID (in Hybridization)	update_residue_for_packing() (in RNA_FullAtomVDW_BasePhosphate)	use_extended_residue_energy_interface() (in MPNonHelixPenalty)
UNKNOWN_HYBRID (in rosetta.core.chemical._core_chemical_)	update_residue_for_packing() (in RNA_JR_SuiteEnergy)	use_extended_residue_energy_interface() (in MPTerminiPenalty)
unknown_selector (in selector_type)	update_residue_for_packing() (in RNA_LJ_BaseEnergy)	use_extended_residue_energy_interface() (in BurialEnergy)
unknown_selector (in rosetta.protocols.generalized_kinematic_closure.selector._protocols_generalized_kinematic_closure_selector_)	update_residue_for_packing() (in RNA_Mg_Energy)	use_extended_residue_energy_interface() (in CenRotEnvEnergy)
unknown_selector (in rosetta.protocols.generalized_kinematic_closure.selector)	update_residue_for_packing() (in RNA_PairwiseLowResolutionEnergy)	use_extended_residue_energy_interface() (in ContextDependentOneBodyEnergy)
UnknownAromaticity (in rosetta)	update_residue_for_packing() (in RNA_SugarCloseEnergy)	use_extended_residue_energy_interface() (in ContextIndependentOneBodyEnergy)
UnknownAromaticity (in rosetta.core.chemical)	update_residue_for_packing() (in RNA_SuiteEnergy)	use_extended_residue_energy_interface() (in EnvEnergy)
UnknownAromaticity (in BondAromaticity)	update_residue_for_packing() (in RNA_TorsionEnergy)	use_extended_residue_energy_interface() (in EnvSmoothEnergy)
UnknownAromaticity (in rosetta.core.chemical._core_chemical_)	update_residue_for_packing() (in RNA_VDW_Energy)	use_extended_residue_energy_interface() (in Fa_MbenvEnergy)
UnknownBond (in rosetta)	update_residue_for_packing() (in StackElecEnergy)	use_extended_residue_energy_interface() (in FreeDOF_Energy)
UnknownBond (in rosetta.core.chemical)	update_residue_for_packing() (in RNA_ChemicalShiftEnergy)	use_extended_residue_energy_interface() (in MembraneCbetaEnergy)
UnknownBond (in BondName)	update_residue_for_packing() (in RNA_ChemicalMappingEnergy)	use_extended_residue_energy_interface() (in MembraneEnvEnergy)
UnknownBond (in rosetta.core.chemical._core_chemical_)	update_residue_for_packing() (in RNA_DataBackboneEnergy)	use_extended_residue_energy_interface() (in MembraneEnvSmoothEnergy)
UnknownBondOrder (in rosetta)	update_residue_for_packing() (in FastSAXSEnergy)	use_extended_residue_energy_interface() (in NMerPSSMEnergy)
UnknownBondOrder (in rosetta.core.chemical)	update_residue_for_packing() (in SAXSEnergy)	use_extended_residue_energy_interface() (in NMerRefEnergy)
UnknownBondOrder (in BondOrder)	update_residue_for_packing() (in symEnergy)	use_extended_residue_energy_interface() (in NMerSVMEnergy)
UnknownBondOrder (in rosetta.core.chemical._core_chemical_)	update_residue_for_packing() (in AACompositionEnergy)	use_extended_residue_energy_interface() (in OmegaTetherEnergy)
UnknownConjugability (in rosetta)	update_residue_for_packing() (in NatbiasSecondaryStructureEnergy)	use_extended_residue_energy_interface() (in OneBodyEnergy)
UnknownConjugability (in rosetta.core.chemical)	update_residue_for_packing() (in EnsembleEnergy)	use_extended_residue_energy_interface() (in P_AA_Energy)
UnknownConjugability (in BondConjugability)	update_residue_for_packing() (in InterchainEnvEnergy)	use_extended_residue_energy_interface() (in P_AA_pp_Energy)
UnknownConjugability (in rosetta.core.chemical._core_chemical_)	update_residue_for_packing() (in InterchainPairEnergy)	use_extended_residue_energy_interface() (in RamachandranEnergy)
UnknownIsometry (in rosetta)	update_residue_for_packing() (in ResidualDipolarCouplingEnergyRigidSegments)	use_extended_residue_energy_interface() (in ReferenceEnergy)
UnknownIsometry (in rosetta.core.chemical)	update_residue_for_packing() (in SpecialRotamerEnergy)	use_extended_residue_energy_interface() (in ReferenceEnergyNoncanonical)
UnknownIsometry (in BondIsometry)	update_residue_for_packing() (in PCS_Energy)	use_extended_residue_energy_interface() (in SequenceDependentRefEnergy)
UnknownIsometry (in rosetta.core.chemical._core_chemical_)	update_residue_for_packing() (in PcsEnergy)	use_extended_residue_energy_interface() (in SmoothEnvEnergy)
UnknownRingness (in rosetta)	update_residue_for_packing() (in PCS_Energy_Ts1)	use_extended_residue_energy_interface() (in SymmetricLigandEnergy)
UnknownRingness (in rosetta.core.chemical)	update_residue_for_packing() (in PCS_Energy_Ts2)	use_extended_residue_energy_interface() (in UnfoldedStateEnergy)
UnknownRingness (in BondRingness)	update_residue_for_packing() (in PCS_Energy_Ts3)	use_extended_residue_energy_interface() (in WaterAdductIntraEnergy)
UnknownRingness (in rosetta.core.chemical._core_chemical_)	update_residue_for_packing() (in PCS_Energy_Ts4)	use_extended_residue_energy_interface() (in YHHPlanarityEnergy)
unpaired_valence_electrons_sp() (in ElectronConfiguration)	update_residue_for_packing() (in PDDFEnergy)	use_extended_residue_energy_interface() (in pHEnergy)
UnrecognizedAtomFeatures (in rosetta.protocols.features._protocols_features_)	update_residue_intersection() (in PackerTask_)	use_extended_residue_energy_interface() (in SugarBackboneEnergy)
UnrecognizedAtomFeaturesAP (in rosetta.protocols.features._protocols_features_)	update_residue_links() (in ParametersSet)	use_extended_residue_energy_interface() (in NVscore)
UnrecognizedAtomFeaturesCAP (in rosetta.protocols.features._protocols_features_)	UPDATE_RESIDUE_NEIGHBORS (in rosetta.basic)	use_extended_residue_energy_interface() (in RNA_BulgeEnergy)
UnrecognizedAtomFeaturesCreator (in rosetta.protocols.features._protocols_features_)	UPDATE_RESIDUE_NEIGHBORS (in ProfTag)	use_extended_residue_energy_interface() (in RNA_FullAtomVDW_BasePhosphate)
UnrecognizedAtomFeaturesCreatorAP (in rosetta.protocols.features._protocols_features_)	UPDATE_RESIDUE_NEIGHBORS (in rosetta.basic._basic_)	use_extended_residue_energy_interface() (in RNA_SugarCloseEnergy)
UnrecognizedAtomFeaturesCreatorCAP (in rosetta.protocols.features._protocols_features_)	update_residue_neighbors() (in Pose)	use_extended_residue_energy_interface() (in AACompositionEnergy)
UnrecognizedAtomRecord (in rosetta.core.pose._core_pose_)	update_residue_neighbors() (in Energies)	use_extended_residue_energy_interface() (in InterchainEnvEnergy)
UnrecognizedAtomRecordAP (in rosetta.core.pose._core_pose_)	UPDATE_RESIDUE_TORSIONS (in rosetta.basic)	use_extended_residue_energy_interface() (in SpecialRotamerEnergy)
UnrecognizedAtomRecordCAP (in rosetta.core.pose._core_pose_)	UPDATE_RESIDUE_TORSIONS (in ProfTag)	use_extended_residue_pair_energy_interface() (in CarbonHBondEnergy)
unset_parent() (in HierarchicalDataMap)	UPDATE_RESIDUE_TORSIONS (in rosetta.basic._basic_)	use_extended_residue_pair_energy_interface() (in ConstraintsEnergy)
unsigned_periodic_range() (in rosetta.basic._basic_)	update_residue_union() (in PackerTask_)	use_extended_residue_pair_energy_interface() (in FullatomCustomPairDistanceEnergy)
up_coll_filt() (in MatchProcessor)	update_restraint() (in CartesianMD)	use_extended_residue_pair_energy_interface() (in CentroidDisulfideEnergy)
up_down_filt() (in MatchProcessor)	update_rna_base_base_interactions() (in RNA_LowResolutionPotential)	use_extended_residue_pair_energy_interface() (in DisulfideMatchingEnergy)
update() (in TMscoreStore)	update_rna_base_pair_list() (in RNA_LowResolutionPotential)	use_extended_residue_pair_energy_interface() (in FullatomDisulfideEnergy)
update() (in CentroidDisulfideEnergyContainer)	update_rna_centroid_info() (in RNA_LowResolutionPotential)	use_extended_residue_pair_energy_interface() (in DNATorsionEnergy)
update() (in DisulfideMatchingEnergyContainer)	update_rot_trans_mag() (in MultipleDomainMover)	use_extended_residue_pair_energy_interface() (in FA_ElecEnergy)
update() (in FullatomDisulfideEnergyContainer)	update_sampler_weights() (in WeightedFragmentSmoothTrialMover)	use_extended_residue_pair_energy_interface() (in FA_ElecEnergyAroAll)
update() (in LoopGraph)	update_sampler_weights() (in WeightedFragmentTrialMover)	use_extended_residue_pair_energy_interface() (in FA_ElecEnergyAroAro)
update() (in RNA_CentroidInfo)	update_score_multiply_factor() (in SymmetryInfo)	use_extended_residue_pair_energy_interface() (in FA_GrpElecEnergy)
update() (in BiasEnergy)	update_segments() (in BackrubSidechainMover)	use_extended_residue_pair_energy_interface() (in RNA_FA_ElecEnergy)
update() (in MC_Comb)	update_sequence() (in KinematicMover)	use_extended_residue_pair_energy_interface() (in ElecDensAllAtomCenEnergy)
update() (in MC_OneTorsion)	update_sequence_numbering() (in Residue)	use_extended_residue_pair_energy_interface() (in ElecDensCenEnergy)
update() (in MC_StepWiseSampler)	update_sequence_numbering() (in AtomID_Map_T_bool_T)	use_extended_residue_pair_energy_interface() (in ElecDensEnergy)
update() (in RNA_MC_MultiSuite)	update_sequence_numbering() (in AtomID_Map_T_core_id_AtomID_T)	use_extended_residue_pair_energy_interface() (in FastDensEnergy)
update() (in RNA_MC_Sugar)	update_sequence_numbering() (in AtomID_Map_T_double_T)	use_extended_residue_pair_energy_interface() (in PattersonCorrEnergy)
update() (in RNA_MC_Suite)	update_sequence_numbering() (in AtomID_Map_T_numeric_xyzVector_T_double_T__T)	use_extended_residue_pair_energy_interface() (in ElecDensAtomwiseEnergy)
update() (in GreedyKCenter)	update_sequence_numbering() (in NamedAtomID_Map_T_core_id_NamedAtomID_T)	use_extended_residue_pair_energy_interface() (in AnalyticEtableEnergy)
update() (in KCluster)	update_sequence_numbering() (in AtomTree)	use_extended_residue_pair_energy_interface() (in BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T)
update() (in KMedoid)	update_stub() (in Atom)	use_extended_residue_pair_energy_interface() (in BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T)
update() (in DbTrajectoryWriter)	update_stub() (in BondedAtom)	use_extended_residue_pair_energy_interface() (in TableLookupEtableEnergy)
update_actcoord() (in ResidueType)	update_stub() (in JumpAtom)	use_extended_residue_pair_energy_interface() (in ContextDependentGeometricSolEnergy)
update_actcoord() (in Conformation)	update_type() (in BackrubMover)	use_extended_residue_pair_energy_interface() (in ContextIndependentGeometricSolEnergy)
update_actcoord() (in Residue)	update_type() (in SidechainMover)	use_extended_residue_pair_energy_interface() (in OccludedHbondSolEnergy)
update_actcoord() (in Pose)	update_union() (in ResidueLevelTask_)	use_extended_residue_pair_energy_interface() (in HackAroEnergy)
update_actcoords() (in Conformation)	update_value_from_list() (in OptEVariableExpression)	use_extended_residue_pair_energy_interface() (in HBondEnergy)
update_actcoords() (in Pose)	update_VDW_screen_bin() (in RNA_VDW_BinChecker)	use_extended_residue_pair_energy_interface() (in DDPscore)
update_active_enmeths_for_residue() (in MinimizationNode)	update_X_Y_Z_all() (in PCS_data)	use_extended_residue_pair_energy_interface() (in FaMPSolvEnergy)
update_after_boltzmann() (in MetricRecorder)	update_X_Y_Z_all() (in PcsDataCenter)	use_extended_residue_pair_energy_interface() (in MPPairEnergy)
update_after_boltzmann() (in TrajectoryRecorder)	update_X_Y_Z_all() (in PCS_data_Ts1)	use_extended_residue_pair_energy_interface() (in CartesianBondedEnergy)
update_after_boltzmann() (in DOFHistogramRecorder)	update_X_Y_Z_all() (in PCS_data_Ts2)	use_extended_residue_pair_energy_interface() (in CenHBEnergy)
update_allow_sc_vectors() (in LoopMover_Refine_KIC)	update_X_Y_Z_all() (in PCS_data_Ts3)	use_extended_residue_pair_energy_interface() (in CenPairEnergy)
update_atom_information_based_on_occupancy() (in FileData)	update_X_Y_Z_all() (in PCS_data_Ts4)	use_extended_residue_pair_energy_interface() (in CenRotPairEnergy)
update_atom_map() (in rosetta.protocols.hybridization._protocols_hybridization_)	update_xyz_coords() (in Atom)	use_extended_residue_pair_energy_interface() (in ContextDependentLRTwoBodyEnergy)
update_base_stub_list_and_check_centroid_interaction() (in RNA_BaseCentroidChecker)	update_xyz_coords() (in Atom_)	use_extended_residue_pair_energy_interface() (in ContextDependentTwoBodyEnergy)
update_base_stub_list_and_check_that_terminal_res_are_unstacked() (in RNA_BaseCentroidChecker)	update_xyz_coords() (in BondedAtom)	use_extended_residue_pair_energy_interface() (in ContextIndependentLRTwoBodyEnergy)
update_center() (in SmallMol)	update_xyz_coords() (in JumpAtom)	use_extended_residue_pair_energy_interface() (in ContextIndependentTwoBodyEnergy)
update_centers() (in RNA_SuiteName)	updateCachedDensity() (in ElectronDensity)	use_extended_residue_pair_energy_interface() (in CustomAtomPairEnergy)
update_commutative() (in PackerTask)	updateChains() (in FlexPepDockingFlags)	use_extended_residue_pair_energy_interface() (in DNA_BaseEnergy)
update_commutative() (in PackerTask_)	updateChainsAndAnchors_fromParamsFile() (in FlexPepDockingFlags)	use_extended_residue_pair_energy_interface() (in Fa_MbsolvEnergy)
update_commutative() (in ResidueLevelTask_)	updateFcalc() (in PhenixInterface)	use_extended_residue_pair_energy_interface() (in GaussianOverlapEnergy)
update_conformation() (in UltraLightResidue)	updateSolventMask() (in PhenixInterface)	use_extended_residue_pair_energy_interface() (in GenBornEnergy)
update_connections_to_other_residue() (in Residue)	UpdateSolventMover (in rosetta.protocols.cryst._protocols_cryst_)	use_extended_residue_pair_energy_interface() (in GoapEnergy)
update_constraint_set_from_full_model_info() (in rosetta.core.pose.full_model_info._core_pose_full_model_info_)	UpdateSolventMoverAP (in rosetta.protocols.cryst._protocols_cryst_)	use_extended_residue_pair_energy_interface() (in HybridVDW_Energy)
update_counting_last_PDR() (in BBGaussianMover)	UpdateSolventMoverCAP (in rosetta.protocols.cryst._protocols_cryst_)	use_extended_residue_pair_energy_interface() (in LK_BallEnergy)
update_cumulative_distribution() (in WeightedSampler)	UpdateSolventMoverCreator (in rosetta.protocols.cryst._protocols_cryst_)	use_extended_residue_pair_energy_interface() (in LK_PolarNonPolarEnergy)
update_current_energy() (in SimpleEdge)	UpdateSolventMoverCreatorAP (in rosetta.protocols.cryst._protocols_cryst_)	use_extended_residue_pair_energy_interface() (in LK_hack)
update_derived_rna_data() (in RNA_ResidueType)	UpdateSolventMoverCreatorCAP (in rosetta.protocols.cryst._protocols_cryst_)	use_extended_residue_pair_energy_interface() (in LongRangeTwoBodyEnergy)
update_disulfides_from_full_model_info() (in rosetta.core.pose.full_model_info._core_pose_full_model_info_)	UpJumpSRFD (in rosetta.core.fragment._core_fragment_)	use_extended_residue_pair_energy_interface() (in MMBondAngleEnergy)
update_domain_map() (in Conformation)	UpJumpSRFDAP (in rosetta.core.fragment._core_fragment_)	use_extended_residue_pair_energy_interface() (in MMBondLengthEnergy)
update_domain_map() (in AtomTree)	UpJumpSRFDCAP (in rosetta.core.fragment._core_fragment_)	use_extended_residue_pair_energy_interface() (in MMLJEnergyInter)
update_domain_map() (in Atom)	upper() (in HyperRectangle)	use_extended_residue_pair_energy_interface() (in MMLJEnergyIntra)
update_domain_map() (in Atom_)	upper() (in Torsion)	use_extended_residue_pair_energy_interface() (in MMTorsionEnergy)
update_edge_label() (in FoldTree)	upper() (in DeltaFilter)	use_extended_residue_pair_energy_interface() (in MembraneCenPairEnergy)
update_edge_paired() (in RNA_DMS_LowResolutionPotential)	upper_atom_neighbors() (in NeighborList)	use_extended_residue_pair_energy_interface() (in PairEnergy)
update_energies_after_passive_change() (in SimpleNode)	upper_bound() (in PoissonBoltzmannPotential)	use_extended_residue_pair_energy_interface() (in PeptideBondEnergy)
update_energy() (in PyMolMover)	upper_bound() (in SOGFunc_Impl)	use_extended_residue_pair_energy_interface() (in PoissonBoltzmannEnergy)
update_entity_history() (in TopEntitySet)	upper_bound_score() (in SOGFunc_Impl)	use_extended_residue_pair_energy_interface() (in ProClosureEnergy)
update_fixed_domain_from_extra_minimize_jump_res() (in rosetta.protocols.stepwise.setup._protocols_stepwise_setup_)	upper_chain() (in RestrictToInterfaceVectorOperation)	use_extended_residue_pair_energy_interface() (in Rama2BOffsetEnergy)
update_fold_tree_at_virtual_sugars() (in StepWiseRNA_PoseSetup)	upper_connect() (in ResidueType)	use_extended_residue_pair_energy_interface() (in RamachandranEnergy2B)
update_from_pose() (in ContextGraph)	upper_connect() (in Residue)	use_extended_residue_pair_energy_interface() (in ShortRangeTwoBodyEnergy)
update_from_pose() (in TenANeighborGraph)	upper_connect_angle_params() (in ResidueCartBondedParameters)	use_extended_residue_pair_energy_interface() (in SmoothCenPairEnergy)
update_from_pose() (in TwelveANeighborGraph)	upper_connect_atom() (in ResidueType)	use_extended_residue_pair_energy_interface() (in SuckerEnergy)
update_full_model_info_from_pose() (in rosetta.core.pose.full_model_info._core_pose_full_model_info_)	upper_connect_atom() (in Residue)	use_extended_residue_pair_energy_interface() (in TwoBodyEnergy)
update_hydrogens() (in OopDPuckMinusMover)	upper_connect_id() (in ResidueType)	use_extended_residue_pair_energy_interface() (in WaterAdductHBondEnergy)
update_hydrogens() (in OopDPuckPlusMover)	upper_edge_list_begin() (in Node)	use_extended_residue_pair_energy_interface() (in DFIRE_Energy)
update_hydrogens() (in OopMover)	upper_edge_list_end() (in Node)	use_extended_residue_pair_energy_interface() (in OrbitalsScore)
update_hydrogens() (in OopPuckMinusMover)	upper_neighbor_id() (in DenseNeighborConstIterator)	use_extended_residue_pair_energy_interface() (in RNA_FullAtomStackingEnergy)
update_hydrogens() (in OopPuckPlusMover)	upper_neighbor_id() (in DenseNeighborIterator)	use_extended_residue_pair_energy_interface() (in RNA_JR_SuiteEnergy)
update_internal_coords() (in Atom)	upper_neighbor_id() (in OneToAllNeighborConstIterator)	use_extended_residue_pair_energy_interface() (in RNA_LJ_BaseEnergy)
update_internal_coords() (in Atom_)	upper_neighbor_id() (in OneToAllNeighborIterator)	use_extended_residue_pair_energy_interface() (in RNA_Mg_Energy)
update_internal_coords() (in BondedAtom)	upper_neighbor_id() (in PeptideBondedNeighborConstIterator)	use_extended_residue_pair_energy_interface() (in RNA_PairwiseLowResolutionEnergy)
update_internal_coords() (in JumpAtom)	upper_neighbor_id() (in PeptideBondedNeighborIterator)	use_extended_residue_pair_energy_interface() (in RNA_SuiteEnergy)
update_internal_energy_sums() (in DensePDNode)	upper_neighbor_id() (in ResidueNeighborConstIterator)	use_extended_residue_pair_energy_interface() (in RNA_TorsionEnergy)
update_internal_energy_sums() (in DoubleDensePDNode)	upper_neighbor_id() (in ResidueNeighborIterator)	use_extended_residue_pair_energy_interface() (in RNA_VDW_Energy)
update_internal_energy_sums() (in DoubleLazyNode)	upper_neighbor_id() (in CstResNeighbConstIterator)	use_extended_residue_pair_energy_interface() (in StackElecEnergy)
update_internal_energy_sums() (in FASTERNode)	upper_neighbor_id() (in CstResNeighbIterator)	use_extended_residue_pair_energy_interface() (in RNA_DataBackboneEnergy)
update_internal_energy_sums() (in LazyNode)	upper_neighbor_id() (in CentroidDisulfideEnergyContainer)	use_extended_residue_pair_energy_interface() (in symEnergy)
update_internal_energy_sums() (in LinearMemNode)	upper_neighbor_id() (in CentroidDisulfideNeighborConstIterator)	use_extended_residue_pair_energy_interface() (in InterchainPairEnergy)
update_internal_energy_sums() (in PDNode)	upper_neighbor_id() (in CentroidDisulfideNeighborIterator)	use_fragments() (in LoopBuilder)
update_internal_energy_sums() (in SymmLinearMemNode)	upper_neighbor_id() (in DisulfResNeighbConstIterator)	use_fullmer() (in BluePrintBDR)
update_internal_energy_sums() (in SymmMinimalistNode)	upper_neighbor_id() (in DisulfResNeighbIterator)	use_fullmer() (in BDR)
update_internal_energy_sums() (in FlexbbNode)	upper_neighbor_id() (in DisulfideMatchingEnergyContainer)	use_fullmer() (in VarLengthBuild)
update_intersection() (in ResidueLevelTask_)	upper_neighbor_id() (in DisulfideMatchingNeighborConstIterator)	use_green_packer() (in StepWiseBasicModelerOptions)
update_interval() (in PyMolMover)	upper_neighbor_id() (in DisulfideMatchingNeighborIterator)	use_hb_env_dep() (in HBondOptions)
update_jump_res() (in rosetta.protocols.stepwise.setup._protocols_stepwise_setup_)	upper_neighbor_id() (in FullatomDisulfideEnergyContainer)	use_hb_env_dep_DNA() (in HBondOptions)
update_library_NSGAII() (in MultiObjective)	upper_neighbor_iterator_begin() (in DenseEnergyContainer)	use_hierarchical_clustering() (in CanonicalSamplingMover)
update_loops() (in LoopGraph)	upper_neighbor_iterator_begin() (in LREnergyContainer)	use_incorrect_deriv() (in HBondDatabase)
update_loops_and_cycles() (in LoopGraph)	upper_neighbor_iterator_begin() (in OneToAllEnergyContainer)	use_input_for_ref() (in AtomTreeDiffJobOutputter)
update_matrix_A_all() (in PCS_data)	upper_neighbor_iterator_begin() (in PeptideBondedEnergyContainer)	USE_INPUT_SC (in rosetta.core.pack.task._core_pack_task_)
update_matrix_A_all() (in PcsDataCenter)	upper_neighbor_iterator_begin() (in CstEnergyContainer)	use_input_sc() (in MatcherTask)
update_matrix_A_all() (in PCS_data_Ts1)	upper_neighbor_iterator_begin() (in CentroidDisulfideEnergyContainer)	USE_INPUT_SCAP (in rosetta.core.pack.task._core_pack_task_)
update_matrix_A_all() (in PCS_data_Ts2)	upper_neighbor_iterator_begin() (in DisulfideMatchingEnergyContainer)	USE_INPUT_SCCAP (in rosetta.core.pack.task._core_pack_task_)
update_matrix_A_all() (in PCS_data_Ts3)	upper_neighbor_iterator_begin() (in FullatomDisulfideEnergyContainer)	use_interface() (in DnaInterfaceMinMover)
update_matrix_A_all() (in PCS_data_Ts4)	upper_neighbor_iterator_end() (in DenseEnergyContainer)	use_late_scoring_for_zeros() (in FragmentScoreManager)
update_matrix_A_all_for_cstyle() (in PcsDataCenter)	upper_neighbor_iterator_end() (in LREnergyContainer)	use_mean() (in ddGMover)
update_matrix_A_all_for_svd() (in PcsDataCenter)	upper_neighbor_iterator_end() (in OneToAllEnergyContainer)	use_min() (in ddGMover)
update_membrane_position() (in Conformation)	upper_neighbor_iterator_end() (in PeptideBondedEnergyContainer)	use_mover_status() (in SequenceMover)
update_movemap() (in SidechainMinMover)	upper_neighbor_iterator_end() (in CstEnergyContainer)	use_MPI_bcast() (in CanonicalSamplingMover)
update_movemap() (in SymSidechainMinMover)	upper_neighbor_iterator_end() (in CentroidDisulfideEnergyContainer)	use_MPI_sync_pools() (in CanonicalSamplingMover)
update_movemap_vectors() (in LoopMover_Refine_KIC)	upper_neighbor_iterator_end() (in DisulfideMatchingEnergyContainer)	use_multicool_annealer() (in OptH)
update_my_A_matrix() (in PCS_data_per_lanthanides)	upper_neighbor_iterator_end() (in FullatomDisulfideEnergyContainer)	use_natro() (in JointSequenceOperation)
update_my_A_matrix() (in PCS_data_per_lanthanides_Ts1)	UPPER_TERMINUS (in rosetta)	use_nblist() (in MinimizerOptions)
update_my_A_matrix() (in PCS_data_per_lanthanides_Ts2)	UPPER_TERMINUS (in rosetta.core.chemical)	use_nblist() (in Energies)
update_my_A_matrix() (in PCS_data_per_lanthanides_Ts3)	UPPER_TERMINUS (in ResidueProperty)	use_nblist_auto_update() (in Energies)
update_my_A_matrix() (in PCS_data_per_lanthanides_Ts4)	UPPER_TERMINUS (in rosetta.core.chemical._core_chemical_)	use_nbr() (in StartFrom)
update_my_A_matrix_for_cstyle() (in PcsDataLanthanide)	UPPER_TERMINUS_VARIANT (in rosetta)	use_nobias() (in NatbiasSecondaryStructureEnergy)
update_my_A_matrix_for_svd() (in PcsDataLanthanide)	UPPER_TERMINUS_VARIANT (in rosetta.core.chemical)	use_numbers() (in ResidueDecompositionByChainCalculator)
update_nmonomer_jumps() (in SymmetryInfo)	UPPER_TERMINUS_VARIANT (in rosetta.core.chemical._core_chemical_)	use_only_calpha() (in NcontactsCalculator)
update_noesy_filter_files() (in IterativeAbrelax)	UPPER_TERMINUS_VARIANT (in VariantType)	use_orientation_dep_rna_ch_o_bonds() (in CarbonHBondEnergy)
update_noesy_filter_files() (in IterativeBase)	upper_threshold() (in InterfacePackingFilter)	use_original_seq() (in LayerDesignOperation)
update_noesy_filter_files() (in IterativeCentroid)	upper_threshold() (in SymUnsatHbondFilter)	use_original_weights() (in EnergiesData)
update_noesy_filter_files() (in IterativeFullatom)	upper_threshold() (in DesignableResiduesFilter)	use_origseq_for_not_dsgned_layer() (in FlxbbDesign)
update_noncanonical_connection() (in Conformation)	upper_value() (in PerturbBundleOptions)	use_packer_instead_of_rotamer_trials() (in StepWiseBasicOptions)
update_one_body_energies() (in DensePDNode)	UpperEdgeGraph_T_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_T (in rosetta.core.conformation._core_conformation_)	use_phenix_geo() (in StepWiseRNA_ModelerOptions)
update_one_body_energies() (in DoubleDensePDNode)	UpperEdgeGraph_T_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_TAP (in rosetta.core.conformation._core_conformation_)	use_phenix_geo() (in RNA_HelixAssembler)
update_one_body_energies() (in FASTERNode)	UpperEdgeGraph_T_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_TCAP (in rosetta.core.conformation._core_conformation_)	use_phenix_geo() (in StepWiseMonteCarloOptions)
update_one_body_energies() (in InteractionGraphBase)	UPPERTERM_TRUNC (in rosetta)	use_pose_numbering (in LoopConfiguration)
update_one_body_energies() (in PDNode)	UPPERTERM_TRUNC (in rosetta.core.chemical)	use_pose_numbering (in rosetta.protocols.loops._protocols_loops_)
update_one_body_energy() (in DensePDNode)	UPPERTERM_TRUNC (in ResidueProperty)	use_pose_numbering (in rosetta.protocols.loops)
update_one_body_energy() (in DoubleDensePDNode)	UPPERTERM_TRUNC (in rosetta.core.chemical._core_chemical_)	use_pose_numbering (in rosetta)
update_one_body_energy() (in DoubleLazyNode)	UPPERTERM_TRUNC_VARIANT (in rosetta)	use_pose_sequence_as_native() (in ConservativeDesignOperation)
update_one_body_energy() (in FASTERNode)	UPPERTERM_TRUNC_VARIANT (in rosetta.core.chemical)	use_precomputed_library() (in StepWiseMonteCarloOptions)
update_one_body_energy() (in LazyNode)	UPPERTERM_TRUNC_VARIANT (in rosetta.core.chemical._core_chemical_)	use_prefiltering() (in LoopHashSampler)
update_one_body_energy() (in LinearMemNode)	UPPERTERM_TRUNC_VARIANT (in VariantType)	use_preset_task() (in DesignRepackMover)
update_one_body_energy() (in NodeBase)	upstream (in rosetta.protocols.match)	use_pssm_features() (in NMerSVMEnergy)
update_one_body_energy() (in OnTheFlyNode)	upstream_atom() (in Edge)	use_rama_2B() (in CCDLoopClosureMover)
update_one_body_energy() (in PDNode)	upstream_atom() (in FoldTree)	use_random_conformer() (in ConformerSwitchMover)
update_one_body_energy() (in SymmLinearMemNode)	upstream_builder() (in Matcher)	use_rattle() (in CartesianMD)
update_one_body_energy() (in SymmMinimalistNode)	upstream_combine() (in SequenceMapping)	use_residue_type_theta0() (in MMBondAngleResidueTypeParamSet)
update_one_body_energy() (in SymmOnTheFlyNode)	upstream_conf_id() (in Hit)	use_rt() (in ConnectRight)
update_one_body_energy() (in FlexbbNode)	upstream_conf_id() (in upstream_hit)	use_sequence_bias() (in BluePrintBDR)
update_one_body_energy() (in MinimalistFlexbbNode)	upstream_conformation_for_hit() (in UpstreamHitCacher)	use_sequence_bias() (in BDR)
update_one_body_energy() (in OTFFlexbbNode)	upstream_downstream_atom_collision_tolerance() (in MatcherTask)	use_sidechain_neighbors() (in SelectResiduesByLayer)
update_orbital_coords() (in Conformation)	upstream_downstream_residue_collision_score_cutoff() (in MatcherTask)	use_sp2_chi_penalty() (in HBondOptions)
update_orbital_coords() (in Residue)	upstream_downstream_residue_collision_Wfa_atr() (in MatcherTask)	user() (in FragmentBiasAssigner)
update_orbital_coords() (in Pose)	upstream_downstream_residue_collision_Wfa_rep() (in MatcherTask)	user_inputted_VDW_screen_pose() (in RNA_VDW_BinChecker)
update_packer_task() (in MSDMover)	upstream_downstream_residue_collision_Wfa_sol() (in MatcherTask)	user_options() (in Batch)
update_pdb_info_from_full_model_info() (in rosetta.core.pose.full_model_info._core_pose_full_model_info_)	upstream_hit (in rosetta.protocols.match._protocols_match_)	UserDefinedGroupDiscriminator (in rosetta.protocols.simple_moves._protocols_simple_moves_)
update_pdb_remarks() (in EnzConstraintParameters)	upstream_hitAP (in rosetta.protocols.match._protocols_match_)	UserDefinedGroupDiscriminatorAP (in rosetta.protocols.simple_moves._protocols_simple_moves_)
update_pdb_remarks_for_backbone_params() (in EnzConstraintIO)	upstream_hitCAP (in rosetta.protocols.match._protocols_match_)	UserDefinedGroupDiscriminatorCAP (in rosetta.protocols.simple_moves._protocols_simple_moves_)
update_pdblist_file() (in DockingEnsemble)	upstream_jump_residue() (in FoldTree)	useres1() (in ResPairMotifQuery)
update_polymeric_connection() (in Conformation)	upstream_jump_stub() (in Conformation)	useres1_ph() (in ResPairMotifQuery)
update_pose_and_cst_set_from_cst_string() (in FullModelParameters)	upstream_only() (in ClassicMatchAlgorithm)	useres1_po() (in ResPairMotifQuery)
update_pose_chains_from_pdb_chains() (in Pose)	upstream_only() (in DownstreamAlgorithm)	useres2() (in ResPairMotifQuery)
update_pose_fold_tree() (in rosetta.protocols.stepwise.setup._protocols_stepwise_setup_)	upstream_only() (in SecondaryMatcherToDownstreamResidue)	useres2_ph() (in ResPairMotifQuery)
update_pose_objects_from_full_model_info() (in rosetta.core.pose.full_model_info._core_pose_full_model_info_)	upstream_only() (in SecondaryMatcherToUpstreamResidue)	useres2_po() (in ResPairMotifQuery)
update_proposed_energy() (in SimpleEdge)	upstream_only() (in WriteUpstreamCoordinateKinemage)	USOGFunc (in rosetta.core.scoring.func._core_scoring_func_)
update_res_list_in_full_model_info_and_pdb_info() (in rosetta.core.pose.full_model_info._core_pose_full_model_info_)	upstream_only_geom_cst() (in MatcherTask)	USOGFuncAP (in rosetta.core.scoring.func._core_scoring_func_)
update_residue_commutative() (in PackerTask_)	upstream_pose() (in Matcher)	USOGFuncCAP (in rosetta.core.scoring.func._core_scoring_func_)
UPDATE_RESIDUE_COORDINATES (in rosetta.basic)	upstream_pose() (in MatcherTask)	util (in rosetta.core.pack.task.operation)
UPDATE_RESIDUE_COORDINATES (in ProfTag)	upstream_pose_build_resids_for_geometric_constraint() (in MatcherTask)	util (in rosetta.core)
UPDATE_RESIDUE_COORDINATES (in rosetta.basic._basic_)	upstream_pose_name() (in MatcherTask)	utilities (in rosetta.protocols.loop_modeling)
update_residue_for_packing() (in DunbrackEnergy)	upstream_res() (in MatchConstraintFileInfo)	utility (in rosetta)
update_residue_for_packing() (in CenRotDunEnergy)	upstream_resids_and_radii_defining_active_site() (in MatcherTask)	utility_vector1_boolAP (in rosetta.utility._utility_)
update_residue_for_packing() (in HPatchEnergy)	upstream_residue_collision_score_cutoff() (in MatcherTask)	utility_vector1_boolCAP (in rosetta.utility._utility_)