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O
O
(in
rosetta.protocols.comparative_modeling.features
)
OneToAllNeighborConstIterator
(in
rosetta.core.scoring._core_scoring_
)
OrbitalType
(in
rosetta.core.chemical.orbitals._core_chemical_orbitals_
)
O
(in
rosetta.protocols.comparative_modeling.features._protocols_comparative_modeling_features_
)
OneToAllNeighborConstIteratorAP
(in
rosetta.core.scoring._core_scoring_
)
OrbitalTypeAP
(in
rosetta.core.chemical.orbitals._core_chemical_orbitals_
)
O
(in
TorsionBin
)
OneToAllNeighborConstIteratorCAP
(in
rosetta.core.scoring._core_scoring_
)
OrbitalTypeCAP
(in
rosetta.core.chemical.orbitals._core_chemical_orbitals_
)
O()
(in
BB_Pos
)
OneToAllNeighborIterator
(in
rosetta.core.scoring._core_scoring_
)
OrbitalTypeMapper
(in
rosetta.core.chemical.orbitals._core_chemical_orbitals_
)
O()
(in
BB_Pos
)
OneToAllNeighborIteratorAP
(in
rosetta.core.scoring._core_scoring_
)
OrbitalTypeMapperAP
(in
rosetta.core.chemical.orbitals._core_chemical_orbitals_
)
O2H
(in
rosetta.core.chemical.rna
)
OneToAllNeighborIteratorCAP
(in
rosetta.core.scoring._core_scoring_
)
OrbitalTypeMapperCAP
(in
rosetta.core.chemical.orbitals._core_chemical_orbitals_
)
O2H
(in
rosetta.core.chemical.rna._core_chemical_rna_
)
only_enumerate_non_match_redundant_ligand_rotamers()
(in
MatcherTask
)
OrbitalTypeSet
(in
rosetta.core.chemical.orbitals._core_chemical_orbitals_
)
O2H
(in
RNA_Torsion
)
OnTheFlyEdge
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
OrbitalTypeSetAP
(in
rosetta.core.chemical.orbitals._core_chemical_orbitals_
)
O2M_MutateMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
OnTheFlyEdgeAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
OrbitalTypeSetCAP
(in
rosetta.core.chemical.orbitals._core_chemical_orbitals_
)
O2M_MutateMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
OnTheFlyEdgeCAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
OrbitalXYZCoords
(in
rosetta.core.conformation.orbitals._core_conformation_orbitals_
)
O2M_MutateMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
OnTheFlyInteractionGraph
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
OrbitalXYZCoordsAP
(in
rosetta.core.conformation.orbitals._core_conformation_orbitals_
)
O2PRIME
(in
rosetta.core.chemical.rna
)
OnTheFlyInteractionGraphAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
OrbitalXYZCoordsCAP
(in
rosetta.core.conformation.orbitals._core_conformation_orbitals_
)
O2PRIME
(in
BaseEdge
)
OnTheFlyInteractionGraphCAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
OrbOrbDist_cosAOD_energy()
(in
OrbitalsLookup
)
O2PRIME
(in
rosetta.core.chemical.rna._core_chemical_rna_
)
OnTheFlyNode
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
OrbOrbDist_cosDOA_energy()
(in
OrbitalsLookup
)
o2prime
(in
rosetta.protocols.stepwise.modeler.rna
)
OnTheFlyNodeAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
order()
(in
Bond
)
o2prime_index()
(in
RNA_ResidueType
)
OnTheFlyNodeCAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
order()
(in
rosetta.protocols.forge.methods._protocols_forge_methods_
)
o2prime_legacy_mode()
(in
StepWiseRNA_ModelerOptions
)
OOO
(in
rosetta.core._core_
)
order_by_energy()
(in
SilentFileData
)
o2prime_legacy_mode()
(in
StepWiseMonteCarloOptions
)
oop
(in
rosetta.protocols.ncbb
)
order_parameter()
(in
InteratomicVarianceMatrix
)
O2PRIME_PACK
(in
rosetta.protocols.stepwise.screener
)
oop
(in
rosetta.protocols.simple_moves
)
order_strand()
(in
Sheet
)
O2PRIME_PACK
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
OOP_POST
(in
rosetta
)
order_strands()
(in
Sheet
)
O2PRIME_PACK
(in
StepWiseScreenerType
)
OOP_POST
(in
rosetta.core.chemical
)
OrderCBC
(in
rosetta.core.scoring.packstat._core_scoring_packstat_
)
o2prime_trials()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
OOP_POST
(in
rosetta.core.chemical._core_chemical_
)
OrderCBCAP
(in
rosetta.core.scoring.packstat._core_scoring_packstat_
)
O2PrimePacker
(in
rosetta.protocols.stepwise.modeler.rna.o2prime._protocols_stepwise_modeler_rna_o2prime_
)
OOP_POST
(in
VariantType
)
OrderCBCCAP
(in
rosetta.core.scoring.packstat._core_scoring_packstat_
)
O2PrimePackerAP
(in
rosetta.protocols.stepwise.modeler.rna.o2prime._protocols_stepwise_modeler_rna_o2prime_
)
OOP_PRE
(in
rosetta
)
ordered_constrained_positions()
(in
EnzConstraintIO
)
O2PrimePackerCAP
(in
rosetta.protocols.stepwise.modeler.rna.o2prime._protocols_stepwise_modeler_rna_o2prime_
)
OOP_PRE
(in
rosetta.core.chemical
)
ordered_constrained_positions()
(in
EnzdesCstCache
)
O2PrimeScreener
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
OOP_PRE
(in
rosetta.core.chemical._core_chemical_
)
ORDERED_SEQUENTIAL
(in
rosetta.core.conformation.symmetry
)
O2PrimeScreenerAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
OOP_PRE
(in
VariantType
)
ORDERED_SEQUENTIAL
(in
rosetta.core.conformation.symmetry._core_conformation_symmetry_
)
O2PrimeScreenerCAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
OopCreatorMover
(in
rosetta.protocols.ncbb.oop._protocols_ncbb_oop_
)
ORDERED_SEQUENTIAL
(in
SlideType
)
o3prime_atom_index()
(in
RNA_ResidueType
)
OopCreatorMoverAP
(in
rosetta.protocols.ncbb.oop._protocols_ncbb_oop_
)
OrderedFragSet
(in
rosetta.core.fragment._core_fragment_
)
o4prime_atom_index()
(in
RNA_ResidueType
)
OopCreatorMoverCAP
(in
rosetta.protocols.ncbb.oop._protocols_ncbb_oop_
)
OrderedFragSetAP
(in
rosetta.core.fragment._core_fragment_
)
o5prime_atom_index()
(in
RNA_ResidueType
)
OopCreatorMoverCreator
(in
rosetta.protocols.ncbb.oop._protocols_ncbb_oop_
)
OrderedFragSetCAP
(in
rosetta.core.fragment._core_fragment_
)
O_atom_id()
(in
UpstreamResTypeGeometry
)
OopCreatorMoverCreatorAP
(in
rosetta.protocols.ncbb.oop._protocols_ncbb_oop_
)
OrderedFragSetIterator_
(in
rosetta.core.fragment._core_fragment_
)
O_p_sp2
(in
rosetta.core.chemical.orbitals
)
OopCreatorMoverCreatorCAP
(in
rosetta.protocols.ncbb.oop._protocols_ncbb_oop_
)
OrderedFragSetIterator_AP
(in
rosetta.core.fragment._core_fragment_
)
O_p_sp2
(in
rosetta.core.chemical.orbitals._core_chemical_orbitals_
)
OopDockDesignProtocol
(in
rosetta.protocols.ncbb.oop._protocols_ncbb_oop_
)
OrderedFragSetIterator_CAP
(in
rosetta.core.fragment._core_fragment_
)
O_p_sp2
(in
orbital_type_enum
)
OopDockDesignProtocolAP
(in
rosetta.protocols.ncbb.oop._protocols_ncbb_oop_
)
OrderedSequentialSymmetrySlider
(in
rosetta.protocols.simple_moves.symmetry._protocols_simple_moves_symmetry_
)
O_p_sp2
(in
OrbitalsStatistics
)
OopDockDesignProtocolCAP
(in
rosetta.protocols.ncbb.oop._protocols_ncbb_oop_
)
OrderedSequentialSymmetrySliderAP
(in
rosetta.protocols.simple_moves.symmetry._protocols_simple_moves_symmetry_
)
O_p_sp2
(in
orbital_type_name
)
OopDockDesignProtocolCreator
(in
rosetta.protocols.ncbb.oop._protocols_ncbb_oop_
)
OrderedSequentialSymmetrySliderCAP
(in
rosetta.protocols.simple_moves.symmetry._protocols_simple_moves_symmetry_
)
O_p_sp2_bb
(in
rosetta.core.chemical.orbitals
)
OopDockDesignProtocolCreatorAP
(in
rosetta.protocols.ncbb.oop._protocols_ncbb_oop_
)
OrExpression
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
O_p_sp2_bb
(in
rosetta.core.chemical.orbitals._core_chemical_orbitals_
)
OopDockDesignProtocolCreatorCAP
(in
rosetta.protocols.ncbb.oop._protocols_ncbb_oop_
)
OrExpressionAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
O_p_sp2_bb
(in
orbital_type_enum
)
OopDPuckMinusMover
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
OrExpressionCAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
O_p_sp3
(in
rosetta.core.chemical.orbitals
)
OopDPuckMinusMoverAP
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
orient()
(in
DimerPairing
)
O_p_sp3
(in
rosetta.core.chemical.orbitals._core_chemical_orbitals_
)
OopDPuckMinusMoverCAP
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
orient()
(in
HelixPairing
)
O_p_sp3
(in
orbital_type_enum
)
OopDPuckPlusMover
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
orient()
(in
SS_Base
)
O_p_sp3
(in
OrbitalsStatistics
)
OopDPuckPlusMoverAP
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
orient()
(in
StrandPairing
)
O_p_sp3
(in
orbital_type_name
)
OopDPuckPlusMoverCAP
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
orient_onto_residue()
(in
Residue
)
O_pi_sp2
(in
rosetta.core.chemical.orbitals
)
OopMover
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
orient_onto_residue_peptoid()
(in
Residue
)
O_pi_sp2
(in
rosetta.core.chemical.orbitals._core_chemical_orbitals_
)
OopMoverAP
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
orient_residue_for_ideal_bond()
(in
rosetta.core.conformation._core_conformation_
)
O_pi_sp2
(in
orbital_type_enum
)
OopMoverCAP
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
orient_rotamer_set_to_symmetric_partner()
(in
SymmetricRotamerSet_
)
O_pi_sp2
(in
OrbitalsStatistics
)
OopPatcher
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
orient_rotamer_set_to_symmetric_partner()
(in
SymmetricRotamerSets
)
O_pi_sp2
(in
orbital_type_name
)
OopPatcherAP
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
orient_strand()
(in
Sheet
)
O_pi_sp2_bb
(in
rosetta.core.chemical.orbitals
)
OopPatcherCAP
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
orient_strands()
(in
Sheet
)
O_pi_sp2_bb
(in
rosetta.core.chemical.orbitals._core_chemical_orbitals_
)
OopPuckMinusMover
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
Orientation()
(in
QuatSet
)
O_pi_sp2_bb
(in
orbital_type_enum
)
OopPuckMinusMoverAP
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
Orientation()
(in
Pairing
)
O_pos()
(in
ProteinBackboneBuildPoint
)
OopPuckMinusMoverCAP
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
orientations
(in
rosetta.basic.sampling
)
oatom1_oatom2_distance()
(in
LigandConformer
)
OopPuckPlusMover
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
origin()
(in
FingerprintBase
)
oatom1_oatom2_oatom3_angle()
(in
LigandConformer
)
OopPuckPlusMoverAP
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
original2modified()
(in
BuildManager
)
oatom2_oatom3_distance()
(in
LigandConformer
)
OopPuckPlusMoverCAP
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
original2modified_interval_endpoints()
(in
BuildManager
)
obey_ENDMDL()
(in
PDB_DReaderOptions
)
OopRandomPuckMover
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
original2modified_intervals()
(in
BuildManager
)
observe_after_metropolis()
(in
BackrubMover
)
OopRandomPuckMoverAP
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
original_deleted_positions()
(in
Bridge
)
observe_after_metropolis()
(in
BackrubSidechainMover
)
OopRandomPuckMoverCAP
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
original_deleted_positions()
(in
BuildInstruction
)
observe_after_metropolis()
(in
BiasEnergy
)
OopRandomSmallMover
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
original_deleted_positions()
(in
BuildManager
)
observe_after_metropolis()
(in
FixedTemperatureController
)
OopRandomSmallMoverAP
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
original_deleted_positions()
(in
ConnectRight
)
observe_after_metropolis()
(in
MetricRecorder
)
OopRandomSmallMoverCAP
(in
rosetta.protocols.simple_moves.oop._protocols_simple_moves_oop_
)
original_deleted_positions()
(in
GrowLeft
)
observe_after_metropolis()
(in
ParallelTempering
)
op()
(in
OperateOnCertainResidues
)
original_deleted_positions()
(in
GrowRight
)
observe_after_metropolis()
(in
ProgressBarObserver
)
op()
(in
OperateOnResidueSubset
)
original_deleted_positions()
(in
SegmentRebuild
)
observe_after_metropolis()
(in
SilentTrajectoryRecorder
)
op1_atom_index()
(in
RNA_ResidueType
)
original_deleted_positions()
(in
SegmentSwap
)
observe_after_metropolis()
(in
SimulatedTempering
)
op2_atom_index()
(in
RNA_ResidueType
)
original_end()
(in
GraftMoverBase
)
observe_after_metropolis()
(in
TemperatureController
)
open()
(in
rosetta.basic.database._basic_database_
)
original_fixed_positions()
(in
Bridge
)
observe_after_metropolis()
(in
TemperingBase
)
open()
(in
FileStream
)
original_fixed_positions()
(in
BuildInstruction
)
observe_after_metropolis()
(in
ThermodynamicMover
)
opening()
(in
DNABasepair
)
original_fixed_positions()
(in
ConnectRight
)
observe_after_metropolis()
(in
ThermodynamicObserver
)
operate_on_ex1()
(in
ResidueLevelTask
)
original_fixed_positions()
(in
GrowLeft
)
observe_after_metropolis()
(in
TrajectoryRecorder
)
operate_on_ex1()
(in
ResidueLevelTask_
)
original_fixed_positions()
(in
GrowRight
)
observe_after_metropolis()
(in
TrialCounterObserver
)
operate_on_ex2()
(in
ResidueLevelTask
)
original_fixed_positions()
(in
RelativeConnectRight
)
observe_after_metropolis()
(in
BalancedKicMover
)
operate_on_ex2()
(in
ResidueLevelTask_
)
original_fixed_positions()
(in
SegmentRebuild
)
observe_after_metropolis()
(in
RigidBodyDeterministicSpinMover
)
operate_on_ex3()
(in
ResidueLevelTask
)
original_fixed_positions()
(in
SegmentSwap
)
observe_after_metropolis()
(in
RigidBodyDofPerturbMover
)
operate_on_ex3()
(in
ResidueLevelTask_
)
original_i2p_deleted()
(in
BuildManager
)
observe_after_metropolis()
(in
RigidBodyDofRandomTransMover
)
operate_on_ex4()
(in
ResidueLevelTask
)
original_i2p_kept()
(in
BuildManager
)
observe_after_metropolis()
(in
RigidBodyDofRandomizeMover
)
operate_on_ex4()
(in
ResidueLevelTask_
)
original_insertion_point()
(in
OriginalBackboneBuildPoint
)
observe_after_metropolis()
(in
RigidBodyDofSeqPerturbMover
)
OperateOnCertainResidues
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
original_insertion_point()
(in
ScaffoldBuildPoint
)
observe_after_metropolis()
(in
RigidBodyDofSeqRandomizeMover
)
OperateOnCertainResiduesAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
original_interval()
(in
BuildInstruction
)
observe_after_metropolis()
(in
RigidBodyDofSeqTransMover
)
OperateOnCertainResiduesCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
original_interval_valid()
(in
Bridge
)
observe_after_metropolis()
(in
RigidBodyDofTransMover
)
OperateOnCertainResiduesCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
original_interval_valid()
(in
BuildInstruction
)
observe_after_metropolis()
(in
RigidBodyMover
)
OperateOnCertainResiduesCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
original_interval_valid()
(in
ConnectRight
)
observe_after_metropolis()
(in
RigidBodyPerturbMover
)
OperateOnCertainResiduesCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
original_interval_valid()
(in
GrowLeft
)
observe_after_metropolis()
(in
RigidBodyPerturbNoCenterMover
)
OperateOnResidueSubset
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
original_interval_valid()
(in
GrowRight
)
observe_after_metropolis()
(in
RigidBodyPerturbRandomJumpMover
)
OperateOnResidueSubsetAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
original_interval_valid()
(in
SegmentRebuild
)
observe_after_metropolis()
(in
RigidBodyRandomizeMover
)
OperateOnResidueSubsetCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
original_interval_valid()
(in
SegmentSwap
)
observe_after_metropolis()
(in
RigidBodySpinMover
)
OperateOnResidueSubsetCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
original_intervals_containing_deleted_positions()
(in
BuildManager
)
observe_after_metropolis()
(in
RigidBodyTransMover
)
OperateOnResidueSubsetCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
original_intervals_containing_kept_positions()
(in
BuildManager
)
observe_after_metropolis()
(in
UniformRigidBodyMover
)
OperateOnResidueSubsetCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
original_kept_positions()
(in
Bridge
)
observe_after_metropolis()
(in
UniformSphereTransMover
)
operation
(in
rosetta.core.pack.task
)
original_kept_positions()
(in
BuildInstruction
)
observe_after_metropolis()
(in
BBConRotMover
)
Operation
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
original_kept_positions()
(in
BuildManager
)
observe_after_metropolis()
(in
BBG8T3AMover
)
operation()
(in
Operator
)
original_kept_positions()
(in
ConnectRight
)
observe_after_metropolis()
(in
BBGaussianMover
)
Operator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
original_kept_positions()
(in
GrowLeft
)
observe_after_metropolis()
(in
BackboneMover
)
operator_filter()
(in
MultipleSigmoids
)
original_kept_positions()
(in
GrowRight
)
observe_after_metropolis()
(in
ShearMover
)
OperatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
original_kept_positions()
(in
SegmentRebuild
)
observe_after_metropolis()
(in
SmallMover
)
OperatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
original_kept_positions()
(in
SegmentSwap
)
observe_after_metropolis()
(in
JumpRotamerSidechainMover
)
OperatorFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
original_mutable_positions()
(in
Bridge
)
observe_after_metropolis()
(in
PerturbChiSidechainMover
)
OperatorFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
original_mutable_positions()
(in
BuildInstruction
)
observe_after_metropolis()
(in
PerturbRotamerSidechainMover
)
OperatorFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
original_mutable_positions()
(in
ConnectRight
)
observe_after_metropolis()
(in
SidechainMCMover
)
oprev_cprev_n_h_interres_torsion_params()
(in
ResidueCartBondedParameters
)
original_mutable_positions()
(in
GrowLeft
)
observe_after_metropolis()
(in
SidechainMover
)
OptCysHG
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
original_mutable_positions()
(in
GrowRight
)
observe_after_metropolis()
(in
SidechainMoverBase
)
OptCysHGAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
original_mutable_positions()
(in
SegmentRebuild
)
observer_cache()
(in
Pose
)
OptCysHGCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
original_mutable_positions()
(in
SegmentSwap
)
ObserverCache
(in
rosetta.core.pose.datacache._core_pose_datacache_
)
OptCysHGCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
original_pose_residue_is_in_residue_map()
(in
rosetta.protocols.generalized_kinematic_closure._protocols_generalized_kinematic_closure_
)
ObserverCacheAP
(in
rosetta.core.pose.datacache._core_pose_datacache_
)
OptCysHGCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
original_resid()
(in
OriginalBackboneBuildPoint
)
ObserverCacheCAP
(in
rosetta.core.pose.datacache._core_pose_datacache_
)
OptCysHGCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
original_sequence()
(in
VarLengthBuild
)
Obsolet_NamedAtomPairConstraint
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
optE_type_from_name()
(in
OptEPositionDataFactory
)
original_weights()
(in
DecomposeAndReweightEnergiesCalculator
)
Obsolet_NamedAtomPairConstraintAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
optE_type_name()
(in
OptEPositionDataFactory
)
OriginalBackboneBuildPoint
(in
rosetta.protocols.match.upstream._protocols_match_upstream_
)
Obsolet_NamedAtomPairConstraintCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
OptEData
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
OriginalBackboneBuildPointAP
(in
rosetta.protocols.match.upstream._protocols_match_upstream_
)
obsolete()
(in
PDBInfo
)
OptEDataAP
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
OriginalBackboneBuildPointCAP
(in
rosetta.protocols.match.upstream._protocols_match_upstream_
)
occ_sol_exact
(in
ScoreType
)
OptEDataCAP
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
ORNOT
(in
rosetta.protocols.filters
)
occ_sol_exact
(in
rosetta.core.scoring._core_scoring_
)
OptEMultifunc
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
ORNOT
(in
rosetta.protocols.filters._protocols_filters_
)
occ_sol_exact
(in
rosetta.core.scoring
)
OptEMultifuncAP
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
ORNOT
(in
boolean_operations
)
occ_sol_exact
(in
rosetta
)
OptEMultifuncCAP
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
ORNOT
(in
rosetta.protocols.toolbox.task_operations
)
occ_sol_fitted
(in
ScoreType
)
OptEMultifuncMPIMessages
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
ORNOT
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
occ_sol_fitted
(in
rosetta.core.scoring._core_scoring_
)
OptEPositionData
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
ORNOT
(in
boolean_operations
)
occ_sol_fitted
(in
rosetta.core.scoring
)
OptEPositionDataAP
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
OrResidueSelector
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
occ_sol_fitted
(in
rosetta
)
OptEPositionDataCAP
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
OrResidueSelectorAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
occ_sol_fitted_onebody
(in
ScoreType
)
OptEPositionDataFactory
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
OrResidueSelectorCAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
occ_sol_fitted_onebody
(in
rosetta.core.scoring._core_scoring_
)
OptEPositionDataFactoryAP
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
OrResidueSelectorCreator
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
occ_sol_fitted_onebody
(in
rosetta.core.scoring
)
OptEPositionDataFactoryCAP
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
OrResidueSelectorCreatorAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
occ_sol_fitted_onebody
(in
rosetta
)
OptEPositionDataType
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
OrResidueSelectorCreatorCAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
occ_space_bounding_box()
(in
MatcherTask
)
OptEVariableExpression
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
ortho_check()
(in
Jump
)
occ_space_hash()
(in
Matcher
)
OptEVariableExpressionAP
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
ortho_check()
(in
RT
)
OccFitParam
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
OptEVariableExpressionCAP
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
oshi
(in
atomitem
)
OccFitParam_amp
(in
rosetta.core.scoring.geometric_solvation
)
OptH
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
oshi
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
OccFitParam_amp
(in
OccFitParam
)
OptHAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
oshi
(in
rosetta.core.scoring.rna.chemical_shift
)
OccFitParam_amp
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
OptHCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
OStream
(in
rosetta.utility._utility_
)
OccFitParam_cos_angle_mu
(in
rosetta.core.scoring.geometric_solvation
)
OptHCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
ostream
(in
rosetta.utility._utility_
)
OccFitParam_cos_angle_mu
(in
OccFitParam
)
OptHCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
OStringStream
(in
rosetta.utility._utility_
)
OccFitParam_cos_angle_mu
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
OptHCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
otfedge_note_substitution_accepted()
(in
OTFFlexbbEdge
)
OccFitParam_dist_mu
(in
rosetta.core.scoring.geometric_solvation
)
optimal_connection_point()
(in
rosetta.protocols.protein_interface_design._protocols_protein_interface_design_
)
OTFFlexbbEdge
(in
rosetta.protocols.flexpack.interaction_graph._protocols_flexpack_interaction_graph_
)
OccFitParam_dist_mu
(in
OccFitParam
)
optimization
(in
rosetta.core
)
OTFFlexbbEdgeAP
(in
rosetta.protocols.flexpack.interaction_graph._protocols_flexpack_interaction_graph_
)
OccFitParam_dist_mu
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
optimization_loop()
(in
LocalRelax
)
OTFFlexbbEdgeCAP
(in
rosetta.protocols.flexpack.interaction_graph._protocols_flexpack_interaction_graph_
)
OccFitParam_max_sq_dist
(in
rosetta.core.scoring.geometric_solvation
)
optimize_angles()
(in
BranchAngleOptimizer
)
OTFFlexbbInteractionGraph
(in
rosetta.protocols.flexpack.interaction_graph._protocols_flexpack_interaction_graph_
)
OccFitParam_max_sq_dist
(in
OccFitParam
)
optimize_branch_angles()
(in
BackrubMover
)
OTFFlexbbInteractionGraphAP
(in
rosetta.protocols.flexpack.interaction_graph._protocols_flexpack_interaction_graph_
)
OccFitParam_max_sq_dist
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
optimize_foldtree()
(in
DesignRepackMover
)
OTFFlexbbInteractionGraphCAP
(in
rosetta.protocols.flexpack.interaction_graph._protocols_flexpack_interaction_graph_
)
OccFitParam_min_cos_angle
(in
rosetta.core.scoring.geometric_solvation
)
optimize_h()
(in
ResidueLevelTask
)
OTFFlexbbNode
(in
rosetta.protocols.flexpack.interaction_graph._protocols_flexpack_interaction_graph_
)
OccFitParam_min_cos_angle
(in
OccFitParam
)
optimize_h()
(in
ResidueLevelTask_
)
OTFFlexbbNodeAP
(in
rosetta.protocols.flexpack.interaction_graph._protocols_flexpack_interaction_graph_
)
OccFitParam_min_cos_angle
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
optimize_H_and_notify()
(in
rosetta.core.pack._core_pack_
)
OTFFlexbbNodeCAP
(in
rosetta.protocols.flexpack.interaction_graph._protocols_flexpack_interaction_graph_
)
OccFitParam_num_params
(in
rosetta.core.scoring.geometric_solvation
)
optimize_kurtosis()
(in
InteratomicVarianceMatrix
)
Other
(in
GasteigerAtomTypeData
)
OccFitParam_num_params
(in
OccFitParam
)
optimize_weights
(in
rosetta.protocols
)
Other
(in
TypeDifference
)
OccFitParam_num_params
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
optimizeH()
(in
rosetta.core.pack._core_pack_
)
other_atom()
(in
BondID
)
OccFitParam_twice_cos_angle_sigma_sq
(in
rosetta.core.scoring.geometric_solvation
)
optimizeSolventMask()
(in
PhenixInterface
)
other_atoms()
(in
SHOBuriedUnsatisfiedPolarsCalculator
)
OccFitParam_twice_cos_angle_sigma_sq
(in
OccFitParam
)
optimizeSolvParams()
(in
PhenixInterface
)
OTHER_DETAILS
(in
CompoundToken
)
OccFitParam_twice_cos_angle_sigma_sq
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
optimizeSolvParamsAndMask()
(in
PhenixInterface
)
OTHER_DETAILS
(in
HeaderInformation
)
OccFitParam_twice_dist_sigma_sq
(in
rosetta.core.scoring.geometric_solvation
)
OptimizeThreadingMover
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
other_energies()
(in
DecomposeAndReweightEnergiesCalculator
)
OccFitParam_twice_dist_sigma_sq
(in
OccFitParam
)
OptimizeThreadingMoverAP
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
other_helix()
(in
PerturbBundleOptions
)
OccFitParam_twice_dist_sigma_sq
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
OptimizeThreadingMoverCAP
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
other_neighbor_atom_indices()
(in
CentroidDisulfideEnergyContainer
)
OccludedHbondSolEnergy
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
OptimizeThreadingMoverCreator
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
other_neighbor_atom_indices()
(in
DisulfideMatchingEnergyContainer
)
OccludedHbondSolEnergy_onebody
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
OptimizeThreadingMoverCreatorAP
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
other_neighbor_atom_indices()
(in
FullatomDisulfideEnergyContainer
)
OccludedHbondSolEnergy_onebodyAP
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
OptimizeThreadingMoverCreatorCAP
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
other_neighbor_id()
(in
CentroidDisulfideEnergyContainer
)
OccludedHbondSolEnergy_onebodyCAP
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
optional_positive_intafteroption()
(in
rosetta.basic.options._basic_options_
)
other_neighbor_id()
(in
DisulfideMatchingEnergyContainer
)
OccludedHbondSolEnergy_onebodyCreator
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
options
(in
rosetta.basic
)
other_neighbor_id()
(in
FullatomDisulfideEnergyContainer
)
OccludedHbondSolEnergy_onebodyCreatorAP
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
options
(in
rosetta.protocols.stepwise.modeler
)
other_pose
(in
ScoreType
)
OccludedHbondSolEnergy_onebodyCreatorCAP
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
options
(in
rosetta.protocols.stepwise.monte_carlo
)
other_pose
(in
rosetta.core.scoring._core_scoring_
)
OccludedHbondSolEnergyAP
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
options
(in
rosetta.protocols.stepwise
)
other_pose
(in
rosetta.core.scoring
)
OccludedHbondSolEnergyCAP
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
options
(in
rosetta.utility
)
other_pose
(in
rosetta
)
OccludedHbondSolEnergyCreator
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
options()
(in
StepWiseModeler
)
other_pose()
(in
PDBOutput
)
OccludedHbondSolEnergyCreatorAP
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
options()
(in
StepWiseMonteCarlo
)
other_pose()
(in
DatabaseJobOutputter
)
OccludedHbondSolEnergyCreatorCAP
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
options_type()
(in
DatabaseSessionOptionsCreator
)
other_pose()
(in
AtomTreeDiffJobOutputter
)
occupancy()
(in
PDBInfo
)
options_type()
(in
ResourceOptionsCreator
)
other_pose()
(in
FileJobOutputter
)
occupied()
(in
Bool3DGrid
)
options_type()
(in
ResidueLoaderOptionsCreator
)
other_pose()
(in
JobOutputter
)
occupied()
(in
BumpGrid
)
options_type()
(in
SymmDataOptionsCreator
)
other_pose()
(in
NoOutputJobOutputter
)
occupied()
(in
ActiveSiteGrid
)
options_type()
(in
ImportPoseOptionsCreator
)
other_pose()
(in
PDBJobOutputter
)
OccupiedSpaceHash
(in
rosetta.protocols.match._protocols_match_
)
options_type()
(in
SilentFileOptionsCreator
)
other_pose()
(in
ScoreOnlyJobOutputter
)
OccupiedSpaceHashAP
(in
rosetta.protocols.match._protocols_match_
)
options_type()
(in
ElectronDensityOptionsCreator
)
other_pose()
(in
SilentFileJobOutputter
)
OccupiedSpaceHashCAP
(in
rosetta.protocols.match._protocols_match_
)
options_type()
(in
FiberDiffractionOptionsCreator
)
other_pose_list()
(in
FullModelInfo
)
occurrence_data()
(in
SequenceProfile
)
options_type()
(in
LoopHashLibraryOptionsCreator
)
other_struct_list()
(in
SilentStruct
)
OCTREE
(in
rosetta
)
options_type()
(in
LoopsFileOptionsCreator
)
OtherContextScoreFunction
(in
rosetta.protocols.flexpack._protocols_flexpack_
)
OCTREE
(in
rosetta.core.conformation
)
options_type()
(in
LipoFileOptionsCreator
)
OtherContextScoreFunctionAP
(in
rosetta.protocols.flexpack._protocols_flexpack_
)
OCTREE
(in
rosetta.core.conformation._core_conformation_
)
options_type()
(in
SpanFileOptionsCreator
)
OtherContextScoreFunctionCAP
(in
rosetta.protocols.flexpack._protocols_flexpack_
)
OCTREE
(in
Strategy
)
options_type()
(in
SurfaceVectorOptionsCreator
)
OtherPoseEnergy
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
Octree2D
(in
rosetta.core.scoring.packstat._core_scoring_packstat_
)
OR
(in
rosetta.protocols.filters
)
OtherPoseEnergyAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
Octree2DAP
(in
rosetta.core.scoring.packstat._core_scoring_packstat_
)
OR
(in
rosetta.protocols.filters._protocols_filters_
)
OtherPoseEnergyCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
Octree2DCAP
(in
rosetta.core.scoring.packstat._core_scoring_packstat_
)
OR
(in
boolean_operations
)
OtherPoseEnergyCreator
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
off_rotamer_pack()
(in
rosetta.core.pack._core_pack_
)
OR
(in
rosetta.protocols.toolbox.task_operations
)
OtherPoseEnergyCreatorAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
off_rotamer_pack()
(in
MinPackMover
)
OR
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
OtherPoseEnergyCreatorCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
off_rotamer_pack_optimize()
(in
rosetta.core.pack._core_pack_
)
OR
(in
boolean_operations
)
out_of_bounds()
(in
PoissonBoltzmannPotential
)
off_rotamer_pack_setup()
(in
rosetta.core.pack._core_pack_
)
or_adducts()
(in
PackerTask
)
out_path()
(in
StepWiseMonteCarlo
)
off_rotamer_pack_update_pose()
(in
rosetta.core.pack._core_pack_
)
or_adducts()
(in
PackerTask_
)
outbound()
(in
WorkUnitManager
)
offset()
(in
RDAT
)
or_adducts()
(in
ResidueLevelTask
)
outer_cycles()
(in
LoopMover_Refine_CCD
)
offset()
(in
Inputter
)
or_adducts()
(in
ResidueLevelTask_
)
outer_product()
(in
rosetta.numeric._numeric_
)
offset()
(in
Sigmoid
)
or_by_box_liberal()
(in
Bool3DGrid
)
output
(in
rosetta.protocols.match
)
OffsetPeriodicBoundFunc
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
or_by_sphere()
(in
BumpGrid
)
output()
(in
AlignmentCluster
)
OffsetPeriodicBoundFuncAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
or_by_sphere_conservative()
(in
Bool3DGrid
)
output_alternative_states()
(in
ProteinInterfaceMultiStateDesignMover
)
OffsetPeriodicBoundFuncCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
or_by_sphere_liberal()
(in
Bool3DGrid
)
output_bool_list()
(in
rosetta.protocols.stepwise.legacy.modeler.rna._protocols_stepwise_legacy_modeler_rna_'
)
OL_features
(in
rosetta.protocols.rotamer_recovery
)
or_by_spheres_conservative()
(in
Bool3DGrid
)
output_boolean()
(in
rosetta.core.pose.rna._core_pose_rna_
)
OL_features
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
or_double_lazy_ig()
(in
PackerTask
)
output_boolean()
(in
rosetta.protocols.stepwise.modeler._protocols_stepwise_modeler_
)
OL_features
(in
OutputLevel
)
or_double_lazy_ig()
(in
PackerTask_
)
output_callback()
(in
PyTracer
)
OL_full
(in
rosetta.protocols.rotamer_recovery
)
or_ex1()
(in
ResidueLevelTask
)
output_cluster_size()
(in
StepWiseBasicOptions
)
OL_full
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
or_ex1()
(in
ResidueLevelTask_
)
output_connectivity()
(in
Graph
)
OL_full
(in
OutputLevel
)
or_ex1_sample_level()
(in
ResidueLevelTask
)
output_connectivity()
(in
InteractionGraphBase
)
OL_none
(in
rosetta.protocols.rotamer_recovery
)
or_ex1_sample_level()
(in
ResidueLevelTask_
)
output_constraints_file()
(in
AddZincSiteConstraints
)
OL_none
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
or_ex1aro()
(in
ResidueLevelTask
)
output_copy_dofs()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
OL_none
(in
OutputLevel
)
or_ex1aro()
(in
ResidueLevelTask_
)
output_count()
(in
SidechainMetropolisHastingsMover
)
old_eval_atom_derivative()
(in
FullatomDisulfideEnergy
)
or_ex1aro_exposed()
(in
ResidueLevelTask
)
output_counts()
(in
StepWiseSampleAndScreen
)
old_eval_dof_derivative()
(in
OmegaTetherEnergy
)
or_ex1aro_exposed()
(in
ResidueLevelTask_
)
output_data()
(in
RDAT
)
old_rama()
(in
FragmentBiasAssigner
)
or_ex1aro_exposed_sample_level()
(in
ResidueLevelTask
)
output_data()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
old_seqpos()
(in
ResidueVicinityInfo
)
or_ex1aro_exposed_sample_level()
(in
ResidueLevelTask_
)
output_data_struct
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
OligomericAverageDegreeFilter
(in
rosetta.protocols.matdes._protocols_matdes_
)
or_ex1aro_sample_level()
(in
ResidueLevelTask
)
output_data_structAP
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
OligomericAverageDegreeFilterAP
(in
rosetta.protocols.matdes._protocols_matdes_
)
or_ex1aro_sample_level()
(in
ResidueLevelTask_
)
output_data_structCAP
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
OligomericAverageDegreeFilterCAP
(in
rosetta.protocols.matdes._protocols_matdes_
)
or_ex2()
(in
ResidueLevelTask
)
output_debug_structure()
(in
DoubleLayerKinematicAbinitio
)
OligomericAverageDegreeFilterCreator
(in
rosetta.protocols.matdes._protocols_matdes_
)
or_ex2()
(in
ResidueLevelTask_
)
output_debug_structure()
(in
FoldConstraints
)
OligomericAverageDegreeFilterCreatorAP
(in
rosetta.protocols.matdes._protocols_matdes_
)
or_ex2_sample_level()
(in
ResidueLevelTask
)
output_debug_structure()
(in
JumpingFoldConstraintsWrapper
)
OligomericAverageDegreeFilterCreatorCAP
(in
rosetta.protocols.matdes._protocols_matdes_
)
or_ex2_sample_level()
(in
ResidueLevelTask_
)
output_debug_structure()
(in
KinematicAbinitio
)
OMEGA
(in
rosetta
)
or_ex2aro()
(in
ResidueLevelTask
)
output_debug_structure()
(in
KinematicTaskControl
)
OMEGA
(in
rosetta.core.scoring
)
or_ex2aro()
(in
ResidueLevelTask_
)
output_debug_structure()
(in
LoopJumpFoldCst
)
OMEGA
(in
rosetta.core.scoring._core_scoring_
)
or_ex2aro_exposed()
(in
ResidueLevelTask
)
output_debug_structure()
(in
Protocol
)
OMEGA
(in
ProteinTorsion
)
or_ex2aro_exposed()
(in
ResidueLevelTask_
)
output_debug_structure()
(in
SlidingWindowLoopClosure
)
omega
(in
ScoreType
)
or_ex2aro_exposed_sample_level()
(in
ResidueLevelTask
)
output_decoy()
(in
PyJobDistributor
)
omega
(in
rosetta.core.scoring._core_scoring_
)
or_ex2aro_exposed_sample_level()
(in
ResidueLevelTask_
)
output_dimacs()
(in
Graph
)
omega
(in
rosetta.core.scoring
)
or_ex2aro_sample_level()
(in
ResidueLevelTask
)
output_dimacs()
(in
InteractionGraphBase
)
omega
(in
rosetta
)
or_ex2aro_sample_level()
(in
ResidueLevelTask_
)
output_extra_RMSDs()
(in
StepWiseWorkingParameters
)
omega()
(in
VallResidue
)
or_ex3()
(in
ResidueLevelTask
)
output_file_name()
(in
MetropolisHastingsMover
)
omega()
(in
DecoyStruct
)
or_ex3()
(in
ResidueLevelTask_
)
output_file_name()
(in
BasicJob
)
omega()
(in
Pose
)
or_ex3_sample_level()
(in
ResidueLevelTask
)
output_file_name()
(in
MatcherTask
)
omega()
(in
VallResidue
)
or_ex3_sample_level()
(in
ResidueLevelTask_
)
output_fold_tree_info()
(in
rosetta.protocols.stepwise.legacy.modeler.rna._protocols_stepwise_legacy_modeler_rna_'
)
omega()
(in
RMSVallData
)
or_ex4()
(in
ResidueLevelTask
)
output_fragments()
(in
FragmentPicker
)
omega()
(in
VallData
)
or_ex4()
(in
ResidueLevelTask_
)
output_hit()
(in
WriteUpstreamHitKinemage
)
omega()
(in
ClosureProblem
)
or_ex4_sample_level()
(in
ResidueLevelTask
)
output_id()
(in
HSSTripletFilter
)
omega()
(in
BackboneSegment
)
or_ex4_sample_level()
(in
ResidueLevelTask_
)
output_info_on_random_trials()
(in
StepWiseSampleAndScreen
)
omega()
(in
MinMover
)
or_exdna_sample_level()
(in
ResidueLevelTask
)
output_intermediate_pose()
(in
rosetta.protocols.jd2._protocols_jd2_
)
omega()
(in
MainChainTorsionSet
)
or_exdna_sample_level()
(in
ResidueLevelTask_
)
output_lores_silent_file()
(in
RNA_DeNovoProtocol
)
omega0()
(in
BundleGridSampler
)
or_fix_his_tautomer()
(in
PackerTask
)
output_matchres_only()
(in
MatcherTask
)
omega0()
(in
MakeBundleHelix
)
or_fix_his_tautomer()
(in
PackerTask_
)
output_minimized_pose_list()
(in
StepWiseBasicOptions
)
omega0()
(in
PerturbBundle
)
or_fix_his_tautomer()
(in
ResidueLevelTask
)
output_movemap()
(in
rosetta.protocols.stepwise.modeler._protocols_stepwise_modeler_
)
omega0()
(in
BundleParameters
)
or_fix_his_tautomer()
(in
ResidueLevelTask_
)
output_moves()
(in
StepWiseMoveSelector
)
omega0_copies_pitch_instead()
(in
PerturbBundleOptions
)
or_flip_HNQ()
(in
PackerTask
)
output_name()
(in
MetropolisHastingsMover
)
omega1()
(in
MakeBundleHelix
)
or_flip_HNQ()
(in
PackerTask_
)
output_name()
(in
PDBOutput
)
omega1()
(in
BundleParameters
)
or_flip_HNQ()
(in
ResidueLevelTask
)
output_name()
(in
DatabaseJobOutputter
)
omega2b_offset
(in
ScoreType
)
or_flip_HNQ()
(in
ResidueLevelTask_
)
output_name()
(in
AtomTreeDiffJobOutputter
)
omega2b_offset
(in
rosetta.core.scoring._core_scoring_
)
or_include_current()
(in
PackerTask
)
output_name()
(in
FileJobOutputter
)
omega2b_offset
(in
rosetta.core.scoring
)
or_include_current()
(in
PackerTask_
)
output_name()
(in
JobOutputter
)
omega2b_offset
(in
rosetta
)
or_include_current()
(in
ResidueLevelTask
)
output_name()
(in
NoOutputJobOutputter
)
omega_index()
(in
OmegaTether
)
or_include_current()
(in
ResidueLevelTask_
)
output_name()
(in
PDBJobOutputter
)
OmegaPerturber
(in
rosetta.protocols.kinematic_closure.perturbers._protocols_kinematic_closure_perturbers_
)
or_include_virtual_side_chain()
(in
ResidueLevelTask
)
output_name()
(in
ScoreOnlyJobOutputter
)
OmegaPerturberAP
(in
rosetta.protocols.kinematic_closure.perturbers._protocols_kinematic_closure_perturbers_
)
or_include_virtual_side_chain()
(in
ResidueLevelTask_
)
output_name()
(in
SilentFileJobOutputter
)
OmegaPerturberCAP
(in
rosetta.protocols.kinematic_closure.perturbers._protocols_kinematic_closure_perturbers_
)
or_lazy_ig()
(in
PackerTask
)
output_only_cluster_transitions()
(in
CanonicalSamplingMover
)
OmegaTether
(in
rosetta.core.scoring._core_scoring_
)
or_lazy_ig()
(in
PackerTask_
)
output_packstat()
(in
rosetta.protocols.vip._protocols_vip_
)
OmegaTetherAP
(in
rosetta.core.scoring._core_scoring_
)
or_linmem_ig()
(in
PackerTask
)
output_packstat_pdb()
(in
rosetta.core.scoring.packstat._core_scoring_packstat_
)
OmegaTetherCAP
(in
rosetta.core.scoring._core_scoring_
)
or_linmem_ig()
(in
PackerTask_
)
output_pair_size()
(in
rosetta.protocols.stepwise.legacy.modeler.rna._protocols_stepwise_legacy_modeler_rna_'
)
OmegaTetherEnergy
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
or_multi_cool_annealer()
(in
PackerTask
)
output_pdb()
(in
PoseBalls
)
OmegaTetherEnergyAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
or_multi_cool_annealer()
(in
PackerTask_
)
output_pose()
(in
MapHotspot
)
OmegaTetherEnergyCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
or_operate_on_ex1()
(in
ResidueLevelTask
)
output_pose_list()
(in
rosetta.protocols.stepwise.legacy.modeler.protein._protocols_stepwise_legacy_modeler_protein_
)
OmegaTetherEnergyCreator
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
or_operate_on_ex1()
(in
ResidueLevelTask_
)
output_rdat_to_file()
(in
RDAT
)
OmegaTetherEnergyCreatorAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
or_operate_on_ex2()
(in
ResidueLevelTask
)
output_repacked_poses()
(in
SetReturningPackRotamersMover
)
OmegaTetherEnergyCreatorCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
or_operate_on_ex2()
(in
ResidueLevelTask_
)
output_res_map()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
omg()
(in
Xfres
)
or_operate_on_ex3()
(in
ResidueLevelTask
)
output_residue()
(in
MolWriter
)
OMIT
(in
LayerOperationType
)
or_operate_on_ex3()
(in
ResidueLevelTask_
)
output_residue_pair_energies()
(in
ScoreCutoffFilter
)
OMIT
(in
LayerDesignOperation
)
or_operate_on_ex4()
(in
ResidueLevelTask
)
output_residue_struct()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
on_connection_change()
(in
PDBInfo
)
or_operate_on_ex4()
(in
ResidueLevelTask_
)
output_results()
(in
DnaInterfaceMultiStateDesign
)
on_connection_change()
(in
ConstraintSet
)
or_optimize_h()
(in
ResidueLevelTask
)
output_results()
(in
ProteinInterfaceMultiStateDesignMover
)
on_identity_change()
(in
PDBInfo
)
or_optimize_h()
(in
ResidueLevelTask_
)
output_scorefile()
(in
rosetta
)
on_length_change()
(in
PDBInfo
)
or_optimize_h_mode()
(in
PackerTask
)
output_scores()
(in
MatcherTask
)
on_length_change()
(in
ConstraintSet
)
or_optimize_h_mode()
(in
PackerTask_
)
output_seq_num_list()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
on_length_change()
(in
BuildInstruction
)
or_preserve_c_beta()
(in
PackerTask
)
output_silent()
(in
FragmentCandidate
)
on_new_fragments()
(in
ClassicFragmentMover
)
or_preserve_c_beta()
(in
PackerTask_
)
output_silent_file()
(in
StepWiseRNA_Clusterer
)
on_pose_conf_change()
(in
PoseMetricContainer
)
or_preserve_c_beta()
(in
ResidueLevelTask
)
output_silent_file()
(in
StepWiseLegacyClustererSilentBased
)
on_pose_destruction_change()
(in
PoseMetricContainer
)
or_preserve_c_beta()
(in
ResidueLevelTask_
)
output_silent_struct()
(in
rosetta.protocols.stepwise.legacy.modeler.protein._protocols_stepwise_legacy_modeler_protein_
)
on_pose_energy_change()
(in
PoseMetricContainer
)
or_with()
(in
Bool3DGrid
)
output_size_list()
(in
rosetta.protocols.stepwise.legacy.modeler.rna._protocols_stepwise_legacy_modeler_rna_'
)
on_residue_append()
(in
Bridge
)
or_with()
(in
BumpGrid
)
output_sqc_file()
(in
DesignContrast
)
on_residue_append()
(in
BuildInstruction
)
or_within_radius_of_backbone()
(in
ActiveSiteGrid
)
output_statistics()
(in
BackrubSidechainMover
)
on_residue_append()
(in
ConnectRight
)
or_within_radius_of_residue()
(in
ActiveSiteGrid
)
output_string_real_pairs_begin()
(in
Job
)
on_residue_append()
(in
GrowLeft
)
or_within_radius_of_sidechain()
(in
ActiveSiteGrid
)
output_string_real_pairs_end()
(in
Job
)
on_residue_append()
(in
GrowRight
)
orb_orb_rules()
(in
OrbitalsScore
)
output_string_string_pairs_begin()
(in
Job
)
on_residue_append()
(in
SegmentRebuild
)
OrbHdist_cosAOH_energy()
(in
OrbitalsLookup
)
output_string_string_pairs_end()
(in
Job
)
on_residue_append()
(in
SegmentSwap
)
OrbHdist_cosDHO_energy()
(in
OrbitalsLookup
)
output_strings_begin()
(in
Job
)
on_residue_delete()
(in
Bridge
)
Orbital
(in
rosetta.core.chemical._core_chemical_
)
output_strings_end()
(in
Job
)
on_residue_delete()
(in
BuildInstruction
)
orbital()
(in
ResidueType
)
output_tag()
(in
BasicJob
)
on_residue_delete()
(in
ConnectRight
)
orbital_enum()
(in
OrbitalType
)
output_title_text()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
on_residue_delete()
(in
GrowLeft
)
orbital_icoor_data()
(in
ResidueType
)
output_to_silent_file()
(in
RNA_DeNovoProtocol
)
on_residue_delete()
(in
GrowRight
)
orbital_index()
(in
ResidueType
)
output_to_silent_file()
(in
rosetta.protocols.stepwise.monte_carlo._protocols_stepwise_monte_carlo_
)
on_residue_delete()
(in
SegmentRebuild
)
orbital_name()
(in
OrbitalType
)
output_type()
(in
HSSTripletFilter
)
on_residue_delete()
(in
SegmentSwap
)
orbital_name()
(in
Residue
)
output_upstream_coordinates()
(in
WriteUpstreamHitKinemage
)
on_residue_prepend()
(in
Bridge
)
orbital_set_tag()
(in
ResidueLoaderOptions
)
output_writer()
(in
MatchProcessor
)
on_residue_prepend()
(in
BuildInstruction
)
orbital_type()
(in
ResidueType
)
output_writer_name()
(in
MatcherTask
)
on_residue_prepend()
(in
ConnectRight
)
orbital_type()
(in
Residue
)
OutputLevel
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
on_residue_prepend()
(in
GrowLeft
)
orbital_type_enum
(in
rosetta.core.chemical.orbitals._core_chemical_orbitals_
)
outputpose()
(in
JSON_RPC
)
on_residue_prepend()
(in
GrowRight
)
orbital_type_index()
(in
Orbital
)
outputter
(in
rosetta.protocols
)
on_residue_prepend()
(in
SegmentRebuild
)
orbital_type_index()
(in
OrbitalTypeSet
)
Outputter
(in
rosetta.protocols.outputter._protocols_outputter_
)
on_residue_prepend()
(in
SegmentSwap
)
orbital_type_index()
(in
Residue
)
OutputterAP
(in
rosetta.protocols.outputter._protocols_outputter_
)
One
(in
GasteigerAtomTypeData
)
orbital_type_name
(in
OrbitalsStatistics
)
OutputterCAP
(in
rosetta.protocols.outputter._protocols_outputter_
)
One
(in
PiContributionType
)
orbital_type_set()
(in
ChemicalManager
)
OutputWriter
(in
rosetta.protocols.match.output._protocols_match_output_
)
one()
(in
NumericTraits_T_double_T
)
orbital_type_set()
(in
ResidueTypeSet
)
OutputWriterAP
(in
rosetta.protocols.match.output._protocols_match_output_
)
one()
(in
NumericTraits_T_float_T
)
orbital_xyz()
(in
Residue
)
OutputWriterCAP
(in
rosetta.protocols.match.output._protocols_match_output_
)
one()
(in
NumericTraits_T_long_double_T
)
OrbitalAP
(in
rosetta.core.chemical._core_chemical_
)
overall_energy0()
(in
BranchCoef1
)
one_body_energies()
(in
FlexbbNode
)
OrbitalBond
(in
rosetta
)
overall_Ktheta()
(in
BranchCoef1
)
one_body_energy()
(in
SimpleNode
)
OrbitalBond
(in
rosetta.core.chemical
)
overall_params()
(in
BranchAngleOptimizer
)
one_letter()
(in
AnnotatedSequence
)
OrbitalBond
(in
BondName
)
overall_theta0()
(in
BranchCoef1
)
one_letter_sequence()
(in
SilentStruct
)
OrbitalBond
(in
rosetta.core.chemical._core_chemical_
)
overlap()
(in
Circle
)
one_letter_sequence()
(in
AnnotatedSequence
)
OrbitalBondOrder
(in
rosetta
)
overlap()
(in
AlignmentCluster
)
one_random_loop()
(in
Loops
)
OrbitalBondOrder
(in
rosetta.core.chemical
)
overlap1()
(in
ResPairMotifQuery
)
ONE_TORSION
(in
rosetta.protocols.stepwise.sampler
)
OrbitalBondOrder
(in
BondOrder
)
overlap2()
(in
ResPairMotifQuery
)
ONE_TORSION
(in
rosetta.protocols.stepwise.sampler._protocols_stepwise_sampler_
)
OrbitalBondOrder
(in
rosetta.core.chemical._core_chemical_
)
overlap_chainbreak
(in
ScoreType
)
ONE_TORSION
(in
StepWiseSamplerType
)
OrbitalCAP
(in
rosetta.core.chemical._core_chemical_
)
overlap_chainbreak
(in
rosetta.core.scoring._core_scoring_
)
ONE_VALUE
(in
rosetta.protocols.stepwise.sampler
)
orbitals
(in
rosetta.core.chemical
)
overlap_chainbreak
(in
rosetta.core.scoring
)
ONE_VALUE
(in
rosetta.protocols.stepwise.sampler._protocols_stepwise_sampler_
)
orbitals
(in
rosetta.core.conformation
)
overlap_chainbreak
(in
rosetta
)
ONE_VALUE
(in
StepWiseSamplerType
)
orbitals
(in
rosetta.core.scoring
)
overlap_chainbreak()
(in
rosetta.protocols.forge.methods._protocols_forge_methods_
)
ONE_VALUE_COMB
(in
rosetta.protocols.stepwise.sampler
)
orbitals_hpol_bb
(in
ScoreType
)
overlapping()
(in
HelixBundleFeatures
)
ONE_VALUE_COMB
(in
rosetta.protocols.stepwise.sampler._protocols_stepwise_sampler_
)
orbitals_hpol_bb
(in
rosetta.core.scoring._core_scoring_
)
overlapping_with_region()
(in
ConstantLengthFragSet
)
ONE_VALUE_COMB
(in
StepWiseSamplerType
)
orbitals_hpol_bb
(in
rosetta.core.scoring
)
overlapping_with_region()
(in
FragSet
)
onebody_energies()
(in
Energies
)
orbitals_hpol_bb
(in
rosetta
)
overlaps()
(in
RotamerDots
)
onebody_energies()
(in
DecomposeAndReweightEnergiesCalculator
)
OrbitalsFeatures
(in
rosetta.protocols.features._protocols_features_
)
overlaps()
(in
BumpGrid
)
OneBodyEnergy
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
OrbitalsFeaturesAP
(in
rosetta.protocols.features._protocols_features_
)
override_option_input()
(in
LigandMotifSearch
)
OneBodyEnergyAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
OrbitalsFeaturesCAP
(in
rosetta.protocols.features._protocols_features_
)
override_option_input()
(in
MotifSearch
)
OneBodyEnergyCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
OrbitalsFeaturesCreator
(in
rosetta.protocols.features._protocols_features_
)
overwrite()
(in
StoreCompoundTaskMover
)
OneGaussianScattering
(in
rosetta.core.scoring.electron_density._core_scoring_electron_density_
)
OrbitalsFeaturesCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
owner()
(in
EnvClaim
)
OneGaussianScattering
(in
rosetta.core.scoring.fiber_diffraction._core_scoring_fiber_diffraction_
)
OrbitalsFeaturesCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
owner()
(in
DofClaim
)
OneGaussianScatteringAP
(in
rosetta.core.scoring.electron_density._core_scoring_electron_density_
)
OrbitalsLookup
(in
rosetta.core.scoring.orbitals._core_scoring_orbitals_
)
owner_nodes_and_locations()
(in
InvrotCollector
)
OneGaussianScatteringAP
(in
rosetta.core.scoring.fiber_diffraction._core_scoring_fiber_diffraction_
)
OrbitalsLookupAP
(in
rosetta.core.scoring.orbitals._core_scoring_orbitals_
)
OXETOSE
(in
rosetta
)
OneGaussianScatteringCAP
(in
rosetta.core.scoring.electron_density._core_scoring_electron_density_
)
OrbitalsLookupCAP
(in
rosetta.core.scoring.orbitals._core_scoring_orbitals_
)
OXETOSE
(in
rosetta.core.chemical
)
OneGaussianScatteringCAP
(in
rosetta.core.scoring.fiber_diffraction._core_scoring_fiber_diffraction_
)
OrbitalsScore
(in
rosetta.core.scoring.orbitals._core_scoring_orbitals_
)
OXETOSE
(in
rosetta.core.chemical._core_chemical_
)
oneletter_code_from_aa()
(in
rosetta.core.chemical._core_chemical_
)
OrbitalsScoreAP
(in
rosetta.core.scoring.orbitals._core_scoring_orbitals_
)
OXETOSE
(in
ResidueProperty
)
oneletter_code_specifies_aa()
(in
rosetta.core.chemical._core_chemical_
)
OrbitalsScoreCAP
(in
rosetta.core.scoring.orbitals._core_scoring_orbitals_
)
OXIROSE
(in
rosetta
)
OnePerStruct
(in
ExecutionMode
)
OrbitalsScoreCreator
(in
rosetta.core.scoring.orbitals._core_scoring_orbitals_
)
OXIROSE
(in
rosetta.core.chemical
)
OnePerStruct
(in
PlaceProbeMover
)
OrbitalsScoreCreatorAP
(in
rosetta.core.scoring.orbitals._core_scoring_orbitals_
)
OXIROSE
(in
rosetta.core.chemical._core_chemical_
)
onError()
(in
rosetta.core.pack.task._core_pack_task_
)
OrbitalsScoreCreatorCAP
(in
rosetta.core.scoring.orbitals._core_scoring_orbitals_
)
OXIROSE
(in
ResidueProperty
)
OneToAllEnergyContainer
(in
rosetta.core.scoring._core_scoring_
)
OrbitalsStatistics
(in
rosetta.core.scoring.orbitals._core_scoring_orbitals_
)
OXY
(in
rosetta.protocols.match
)
OneToAllEnergyContainerAP
(in
rosetta.core.scoring._core_scoring_
)
OrbitalsStatisticsAP
(in
rosetta.core.scoring.orbitals._core_scoring_orbitals_
)
OXY
(in
rosetta.protocols.match._protocols_match_
)
OneToAllEnergyContainerCAP
(in
rosetta.core.scoring._core_scoring_
)
OrbitalsStatisticsCAP
(in
rosetta.core.scoring.orbitals._core_scoring_orbitals_
)
OXY
(in
ProbeRadius
)
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