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R
R()
(in
ResidualDipolarCoupling
)
reinitialize_for_new_input()
(in
UniformTranslationMover
)
ResidueConformationFeaturesAP
(in
rosetta.protocols.features._protocols_features_
)
r()
(in
Ball
)
reinitialize_for_new_input()
(in
VirtualRootMover
)
ResidueConformationFeaturesCAP
(in
rosetta.protocols.features._protocols_features_
)
r0()
(in
BundleGridSampler
)
reinitialize_for_new_input()
(in
ddG
)
ResidueConformationFeaturesCreator
(in
rosetta.protocols.features._protocols_features_
)
r0()
(in
MakeBundleHelix
)
reinitialize_for_new_input()
(in
AsymFoldandDockMoveRbJumpMover
)
ResidueConformationFeaturesCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
r0()
(in
PerturbBundle
)
reinitialize_for_new_input()
(in
AsymFoldandDockRbTrialMover
)
ResidueConformationFeaturesCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
r0()
(in
BundleParameters
)
reinitialize_for_new_input()
(in
InitializeByBins
)
ResidueConnection
(in
rosetta.core.chemical._core_chemical_
)
r1()
(in
MakeBundleHelix
)
reinitialize_for_new_input()
(in
PerturbByBins
)
ResidueConnectionAP
(in
rosetta.core.chemical._core_chemical_
)
r1()
(in
BundleParameters
)
reinitialize_for_new_input()
(in
ChiralMover
)
ResidueConnectionCAP
(in
rosetta.core.chemical._core_chemical_
)
r1_vect()
(in
MakeBundleHelix
)
reinitialize_for_new_input()
(in
HbsPatcher
)
ResidueConstraints
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
r1_vect()
(in
BundleParameters
)
reinitialize_for_new_input()
(in
OopDPuckMinusMover
)
ResidueConstraintsAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
R2quat()
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
reinitialize_for_new_input()
(in
OopDPuckPlusMover
)
ResidueConstraintsCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
rad2deg()
(in
NumericTraits_T_double_T
)
reinitialize_for_new_input()
(in
OopMover
)
ResidueContactScreener
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
rad2deg()
(in
NumericTraits_T_float_T
)
reinitialize_for_new_input()
(in
OopPatcher
)
ResidueContactScreenerAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
rad2deg()
(in
NumericTraits_T_long_double_T
)
reinitialize_for_new_input()
(in
OopPuckMinusMover
)
ResidueContactScreenerCAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
radial_bin_index()
(in
SixDCoordinateBinner
)
reinitialize_for_new_input()
(in
OopPuckPlusMover
)
ResidueCoordinateChangeList
(in
rosetta.core.kinematics._core_kinematics_
)
radial_count()
(in
LoopHashMap
)
reinitialize_for_new_input()
(in
OopRandomPuckMover
)
ResidueCoordinateChangeListAP
(in
rosetta.core.kinematics._core_kinematics_
)
radial_disp()
(in
GetRBDOFValues
)
reinitialize_for_new_input()
(in
OopRandomSmallMover
)
ResidueCoordinateChangeListCAP
(in
rosetta.core.kinematics._core_kinematics_
)
radial_lookup()
(in
LoopHashMap
)
reinitialize_for_new_input()
(in
RationalMonteCarlo
)
ResidueCountFilter
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
radial_lookup_withkey()
(in
LoopHashMap
)
reinitialize_for_new_input()
(in
JumpRotamerSidechainMover
)
ResidueCountFilterAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
radians_to_degrees()
(in
NumericTraits_T_double_T
)
reinitialize_for_new_input()
(in
PerturbChiSidechainMover
)
ResidueCountFilterCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
radians_to_degrees()
(in
NumericTraits_T_float_T
)
reinitialize_for_new_input()
(in
PerturbRotamerSidechainMover
)
ResidueCountFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
radians_to_degrees()
(in
NumericTraits_T_long_double_T
)
reinitialize_for_new_input()
(in
SetChiMover
)
ResidueCountFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
radius()
(in
Ball
)
reinitialize_for_new_input()
(in
SidechainMCMover
)
ResidueCountFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
radius()
(in
CavityBall
)
reinitialize_for_new_input()
(in
SidechainMover
)
ResidueDatabaseIO
(in
rosetta.core.chemical._core_chemical_
)
radius()
(in
Ball
)
reinitialize_for_new_input()
(in
SidechainMoverBase
)
ResidueDatabaseIOAP
(in
rosetta.core.chemical._core_chemical_
)
radius()
(in
HierarchicalLevel
)
reinitialize_for_new_input()
(in
DetectSymmetry
)
ResidueDatabaseIOCAP
(in
rosetta.core.chemical._core_chemical_
)
radius_for_attype()
(in
RotamerDots
)
reinitialize_for_new_input()
(in
ExtractAsymmetricPoseMover
)
ResidueDecompositionByChainCalculator
(in
rosetta.protocols.toolbox.pose_metric_calculators._protocols_toolbox_pose_metric_calculators_
)
RadiusOfGyrationFeatures
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
ExtractAsymmetricUnitMover
)
ResidueDecompositionByChainCalculatorAP
(in
rosetta.protocols.toolbox.pose_metric_calculators._protocols_toolbox_pose_metric_calculators_
)
RadiusOfGyrationFeaturesAP
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
FaSymDockingSlideTogether
)
ResidueDecompositionByChainCalculatorCAP
(in
rosetta.protocols.toolbox.pose_metric_calculators._protocols_toolbox_pose_metric_calculators_
)
RadiusOfGyrationFeaturesCAP
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
SetupForSymmetryMover
)
ResidueDecompositionCalculator
(in
rosetta.protocols.toolbox.pose_metric_calculators._protocols_toolbox_pose_metric_calculators_
)
RadiusOfGyrationFeaturesCreator
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
SetupNCSMover
)
ResidueDecompositionCalculatorAP
(in
rosetta.protocols.toolbox.pose_metric_calculators._protocols_toolbox_pose_metric_calculators_
)
RadiusOfGyrationFeaturesCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
SymDockingInitialPerturbation
)
ResidueDecompositionCalculatorCAP
(in
rosetta.protocols.toolbox.pose_metric_calculators._protocols_toolbox_pose_metric_calculators_
)
RadiusOfGyrationFeaturesCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
SymDockingSlideIntoContact
)
ResidueDistanceFilter
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
rama
(in
ScoreType
)
reinitialize_for_new_input()
(in
SymEnergyCutRotamerTrialsMover
)
ResidueDistanceFilterAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
rama
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_new_input()
(in
SymMinMover
)
ResidueDistanceFilterCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
rama
(in
rosetta.core.scoring
)
reinitialize_for_new_input()
(in
SymPackRotamersMover
)
ResidueDistanceFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
rama
(in
rosetta
)
reinitialize_for_new_input()
(in
SymRotamerTrialsMover
)
ResidueDistanceFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
rama()
(in
FragmentBiasAssigner
)
reinitialize_for_new_input()
(in
SymShakeStructureMover
)
ResidueDistanceFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
rama()
(in
CCDLoopClosureMover
)
reinitialize_for_new_input()
(in
SymmetricRMSMover
)
ResidueElement
(in
rosetta.protocols.environment.claims._protocols_environment_claims_
)
rama2b
(in
ScoreType
)
reinitialize_for_new_input()
(in
TaskAwareSymMinMover
)
ResidueElementAP
(in
rosetta.protocols.environment.claims._protocols_environment_claims_
)
rama2b
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_new_input()
(in
StepWiseProteinMinimizer
)
ResidueElementCAP
(in
rosetta.protocols.environment.claims._protocols_environment_claims_
)
rama2b
(in
rosetta.core.scoring
)
reinitialize_for_new_input()
(in
StepWiseProteinPoseSetup
)
ResidueFactory
(in
rosetta.core.conformation._core_conformation_
)
rama2b
(in
rosetta
)
reinitialize_for_new_input()
(in
StepWiseRNA_PoseSetup
)
ResidueFactoryAP
(in
rosetta.core.conformation._core_conformation_
)
rama2b_lr
(in
LongRangeEnergyType
)
reinitialize_for_new_input()
(in
StepWiseConnectionSampler
)
ResidueFactoryCAP
(in
rosetta.core.conformation._core_conformation_
)
rama2b_lr
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_new_input()
(in
StepWiseMinimizer
)
ResidueFeature
(in
rosetta.protocols.comparative_modeling.features._protocols_comparative_modeling_features_
)
rama2b_lr
(in
rosetta.core.scoring.methods
)
reinitialize_for_new_input()
(in
StepWiseModeler
)
ResidueFeatureAP
(in
rosetta.protocols.comparative_modeling.features._protocols_comparative_modeling_features_
)
rama2b_offset
(in
ScoreType
)
reinitialize_for_new_input()
(in
SideChainCopier
)
ResidueFeatureCAP
(in
rosetta.protocols.comparative_modeling.features._protocols_comparative_modeling_features_
)
rama2b_offset
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_new_input()
(in
StepWisePacker
)
ResidueFeatureFactory
(in
rosetta.protocols.comparative_modeling.features._protocols_comparative_modeling_features_
)
rama2b_offset
(in
rosetta.core.scoring
)
reinitialize_for_new_input()
(in
PolarHydrogenPacker
)
ResidueFeatureFactoryAP
(in
rosetta.protocols.comparative_modeling.features._protocols_comparative_modeling_features_
)
rama2b_offset
(in
rosetta
)
reinitialize_for_new_input()
(in
PrecomputedLibraryMover
)
ResidueFeatureFactoryCAP
(in
rosetta.protocols.comparative_modeling.features._protocols_comparative_modeling_features_
)
Rama2BOffset
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_new_input()
(in
StepWiseProteinBackboneSampler
)
ResidueFeatures
(in
rosetta.protocols.features._protocols_features_
)
Rama2BOffsetAP
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_new_input()
(in
StepWiseProteinCCD_Closer
)
ResidueFeaturesAP
(in
rosetta.protocols.features._protocols_features_
)
Rama2BOffsetCAP
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_new_input()
(in
StepWiseProteinCCD_MultiPoseCloser
)
ResidueFeaturesCAP
(in
rosetta.protocols.features._protocols_features_
)
Rama2BOffsetEnergy
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_new_input()
(in
StepWiseProteinKIC_LoopBridger
)
ResidueFeaturesCreator
(in
rosetta.protocols.features._protocols_features_
)
Rama2BOffsetEnergyAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_new_input()
(in
BulgeApplyMover
)
ResidueFeaturesCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
Rama2BOffsetEnergyCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_new_input()
(in
BulgeUnApplyMover
)
ResidueFeaturesCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
Rama2BOffsetEnergyCreator
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_new_input()
(in
RNA_ChainClosureChecker
)
ResidueGridScoresFeatures
(in
rosetta.protocols.features._protocols_features_
)
Rama2BOffsetEnergyCreatorAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_new_input()
(in
RNA_HelixAssembler
)
ResidueGridScoresFeaturesAP
(in
rosetta.protocols.features._protocols_features_
)
Rama2BOffsetEnergyCreatorCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_new_input()
(in
O2PrimePacker
)
ResidueGridScoresFeaturesCAP
(in
rosetta.protocols.features._protocols_features_
)
Rama2BOffsetTables
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_new_input()
(in
MultiPhosphateSampler
)
ResidueGridScoresFeaturesCreator
(in
rosetta.protocols.features._protocols_features_
)
Rama2bPerturber
(in
rosetta.protocols.kinematic_closure.perturbers._protocols_kinematic_closure_perturbers_
)
reinitialize_for_new_input()
(in
PhosphateMover
)
ResidueGridScoresFeaturesCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
Rama2bPerturberAP
(in
rosetta.protocols.kinematic_closure.perturbers._protocols_kinematic_closure_perturbers_
)
reinitialize_for_new_input()
(in
SugarInstantiateMover
)
ResidueGridScoresFeaturesCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
Rama2bPerturberCAP
(in
rosetta.protocols.kinematic_closure.perturbers._protocols_kinematic_closure_perturbers_
)
reinitialize_for_new_input()
(in
SugarVirtualizeMover
)
ResidueGroupIGEdgeUpweighter
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
rama_bin_probability_left()
(in
Ramachandran2B
)
reinitialize_for_new_input()
(in
VirtualSugarJustInTimeInstantiator
)
ResidueGroupIGEdgeUpweighterAP
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
rama_bin_probability_right()
(in
Ramachandran2B
)
reinitialize_for_new_input()
(in
VirtualSugarSampler
)
ResidueGroupIGEdgeUpweighterCAP
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
rama_delta()
(in
CCDLoopClosureMover
)
reinitialize_for_new_input()
(in
VirtualSugarSamplerFromStringList
)
ResidueHasProperty
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
rama_probability()
(in
Ramachandran
)
reinitialize_for_new_input()
(in
StepWiseMonteCarlo
)
ResidueHasPropertyAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
Ramachandran
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_new_input()
(in
AddMover
)
ResidueHasPropertyCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
Ramachandran2B
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_new_input()
(in
AddOrDeleteMover
)
ResidueHasPropertyCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
Ramachandran2BAP
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_new_input()
(in
DeleteMover
)
ResidueHasPropertyCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
Ramachandran2BCAP
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_new_input()
(in
FromScratchMover
)
ResidueHasPropertyCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
ramachandran_method
(in
EnergyMethods
)
reinitialize_for_new_input()
(in
ResampleMover
)
ResidueIdentifier
(in
rosetta.protocols.loops._protocols_loops_
)
ramachandran_method
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_new_input()
(in
StepWiseMasterMover
)
ResidueIEFilter
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
ramachandran_method
(in
rosetta.core.scoring.methods
)
reinitialize_for_new_input()
(in
RNA_AddDeleteMonteCarlo
)
ResidueIEFilterAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
RamachandranAP
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_new_input()
(in
RNA_O2PrimeMover
)
ResidueIEFilterCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
RamachandranCAP
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_new_input()
(in
RNA_TorsionMover
)
ResidueIEFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
RamachandranEnergy
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_new_input()
(in
JumpStepWiseSampler
)
ResidueIEFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
RamachandranEnergy2B
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_new_input()
(in
MC_Comb
)
ResidueIEFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
RamachandranEnergy2BAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_new_input()
(in
MC_OneTorsion
)
ResidueIndexDescription
(in
rosetta.protocols.loops._protocols_loops_
)
RamachandranEnergy2BCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_new_input()
(in
NoOpStepWiseSampler
)
ResidueIndexDescriptionAP
(in
rosetta.protocols.loops._protocols_loops_
)
RamachandranEnergy2BCreator
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_new_input()
(in
StepWiseSamplerAny
)
ResidueIndexDescriptionCAP
(in
rosetta.protocols.loops._protocols_loops_
)
RamachandranEnergy2BCreatorAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_new_input()
(in
StepWiseSamplerComb
)
ResidueIndexDescriptionFromFile
(in
rosetta.protocols.loops._protocols_loops_
)
RamachandranEnergy2BCreatorCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_new_input()
(in
StepWiseSamplerOneTorsion
)
ResidueIndexDescriptionFromFileAP
(in
rosetta.protocols.loops._protocols_loops_
)
RamachandranEnergyAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_new_input()
(in
StepWiseSamplerOneValue
)
ResidueIndexDescriptionFromFileCAP
(in
rosetta.protocols.loops._protocols_loops_
)
RamachandranEnergyCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_new_input()
(in
StepWiseSamplerOneValueComb
)
ResidueIndexIs
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RamachandranEnergyCreator
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_new_input()
(in
StepWiseSamplerSized
)
ResidueIndexIsAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RamachandranEnergyCreatorAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_new_input()
(in
StepWiseSamplerSizedAny
)
ResidueIndexIsCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RamachandranEnergyCreatorCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_new_input()
(in
StepWiseSamplerSizedComb
)
ResidueIndexIsCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RamachandranHash
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
CopyDofStepWiseSampler
)
ResidueIndexIsCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RamaCheck1B
(in
rosetta.protocols.loops.loop_closure.ccd._protocols_loops_loop_closure_ccd_
)
reinitialize_for_new_input()
(in
ResidueAlternativeStepWiseSampler
)
ResidueIndexIsCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RamaCheck1BAP
(in
rosetta.protocols.loops.loop_closure.ccd._protocols_loops_loop_closure_ccd_
)
reinitialize_for_new_input()
(in
ResidueAlternativeStepWiseSamplerComb
)
ResidueIndexIsnt
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RamaCheck1BCAP
(in
rosetta.protocols.loops.loop_closure.ccd._protocols_loops_loop_closure_ccd_
)
reinitialize_for_new_input()
(in
ResidueListStepWiseSampler
)
ResidueIndexIsntAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RamaCheck2B
(in
rosetta.protocols.loops.loop_closure.ccd._protocols_loops_loop_closure_ccd_
)
reinitialize_for_new_input()
(in
InputStreamStepWiseSampler
)
ResidueIndexIsntCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RamaCheck2BAP
(in
rosetta.protocols.loops.loop_closure.ccd._protocols_loops_loop_closure_ccd_
)
reinitialize_for_new_input()
(in
ProteinBetaAntiParallelStepWiseSampler
)
ResidueIndexIsntCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RamaCheck2BCAP
(in
rosetta.protocols.loops.loop_closure.ccd._protocols_loops_loop_closure_ccd_
)
reinitialize_for_new_input()
(in
ProteinFragmentStepWiseSampler
)
ResidueIndexIsntCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RamaCheckBase
(in
rosetta.protocols.loops.loop_closure.ccd._protocols_loops_loop_closure_ccd_
)
reinitialize_for_new_input()
(in
ProteinMainChainStepWiseSampler
)
ResidueIndexIsntCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RamaCheckBaseAP
(in
rosetta.protocols.loops.loop_closure.ccd._protocols_loops_loop_closure_ccd_
)
reinitialize_for_new_input()
(in
RigidBodyStepWiseSampler
)
ResidueIndexSelector
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
RamaCheckBaseCAP
(in
rosetta.protocols.loops.loop_closure.ccd._protocols_loops_loop_closure_ccd_
)
reinitialize_for_new_input()
(in
RigidBodyStepWiseSamplerWithResidueAlternatives
)
ResidueIndexSelectorAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
RamaE()
(in
Ramachandran2B
)
reinitialize_for_new_input()
(in
RigidBodyStepWiseSamplerWithResidueList
)
ResidueIndexSelectorCAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
RamaE_Lower()
(in
Ramachandran2B
)
reinitialize_for_new_input()
(in
RNA_ChiStepWiseSampler
)
ResidueIndexSelectorCreator
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
RamaE_Upper()
(in
Ramachandran2B
)
reinitialize_for_new_input()
(in
RNA_KIC_Sampler
)
ResidueIndexSelectorCreatorAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
RamaPerturber
(in
rosetta.protocols.kinematic_closure.perturbers._protocols_kinematic_closure_perturbers_
)
reinitialize_for_new_input()
(in
RNA_KinematicCloser
)
ResidueIndexSelectorCreatorCAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
RamaPerturberAP
(in
rosetta.protocols.kinematic_closure.perturbers._protocols_kinematic_closure_perturbers_
)
reinitialize_for_new_input()
(in
RNA_MC_MultiSuite
)
ResidueInformation
(in
rosetta.core.io.pdb._core_io_pdb_
)
RamaPerturberCAP
(in
rosetta.protocols.kinematic_closure.perturbers._protocols_kinematic_closure_perturbers_
)
reinitialize_for_new_input()
(in
RNA_MC_Sugar
)
ResidueInformationAP
(in
rosetta.core.io.pdb._core_io_pdb_
)
RamaScore
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
reinitialize_for_new_input()
(in
RNA_MC_Suite
)
ResidueInformationCAP
(in
rosetta.core.io.pdb._core_io_pdb_
)
RamaScoreAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
reinitialize_for_new_input()
(in
RNA_NucleosideStepWiseSampler
)
ResidueKinemageWriter
(in
rosetta.protocols.match.output._protocols_match_output_
)
RamaScoreCAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
reinitialize_for_new_input()
(in
RNA_SugarStepWiseSampler
)
ResidueKinemageWriterAP
(in
rosetta.protocols.match.output._protocols_match_output_
)
ramp_chainbreak()
(in
LoopClosure
)
reinitialize_for_new_input()
(in
RNA_SuiteStepWiseSampler
)
ResidueKinemageWriterCAP
(in
rosetta.protocols.match.output._protocols_match_output_
)
ramp_down_constraints()
(in
RelaxProtocolBase
)
reinitialize_for_new_input()
(in
StepWiseCSA_JobDistributor
)
ResidueKinWriter
(in
rosetta.core.conformation._core_conformation_
)
ramp_minpack_loop()
(in
rosetta.protocols.mpi_refinement._protocols_mpi_refinement_
)
reinitialize_for_new_input()
(in
StepWiseJobDistributor
)
ResidueKinWriterAP
(in
rosetta.core.conformation._core_conformation_
)
ramp_minpack_pose()
(in
rosetta.protocols.mpi_refinement._protocols_mpi_refinement_
)
reinitialize_for_new_input()
(in
StepWiseMonteCarloJobDistributor
)
ResidueKinWriterCAP
(in
rosetta.core.conformation._core_conformation_
)
RampingFunc
(in
rosetta.protocols.moves._protocols_moves_
)
reinitialize_for_new_input()
(in
CentroidRelaxMover
)
ResidueLacksProperty
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RampingFuncAP
(in
rosetta.protocols.moves._protocols_moves_
)
reinitialize_for_new_input()
(in
FullatomRelaxMover
)
ResidueLacksPropertyAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RampingFuncCAP
(in
rosetta.protocols.moves._protocols_moves_
)
reinitialize_for_new_input()
(in
SurfaceDockingProtocol
)
ResidueLacksPropertyCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RampingMover
(in
rosetta.protocols.moves._protocols_moves_
)
reinitialize_for_new_input()
(in
SurfaceOrientMover
)
ResidueLacksPropertyCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RampingMoverAP
(in
rosetta.protocols.moves._protocols_moves_
)
reinitialize_for_new_input()
(in
SymDockBaseProtocol
)
ResidueLacksPropertyCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RampingMoverCAP
(in
rosetta.protocols.moves._protocols_moves_
)
reinitialize_for_new_input()
(in
SymDockProtocol
)
ResidueLacksPropertyCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RampingMoverCreator
(in
rosetta.protocols.moves._protocols_moves_
)
reinitialize_for_new_input()
(in
SymDockingHiRes
)
ResidueLevelTask
(in
rosetta.core.pack.task._core_pack_task_
)
RampingMoverCreatorAP
(in
rosetta.protocols.moves._protocols_moves_
)
reinitialize_for_new_input()
(in
SymDockingLowRes
)
ResidueLevelTask_
(in
rosetta.core.pack.task._core_pack_task_
)
RampingMoverCreatorCAP
(in
rosetta.protocols.moves._protocols_moves_
)
reinitialize_for_new_input()
(in
SymFoldandDockMoveRbJumpMover
)
ResidueLevelTask_AP
(in
rosetta.core.pack.task._core_pack_task_
)
rand_sleep()
(in
rosetta.utility._utility_
)
reinitialize_for_new_input()
(in
SymFoldandDockRbTrialMover
)
ResidueLevelTask_CAP
(in
rosetta.core.pack.task._core_pack_task_
)
RANDOM
(in
rosetta.core.conformation.symmetry
)
reinitialize_for_new_input()
(in
SymFoldandDockSlideTrialMover
)
ResidueLevelTaskAP
(in
rosetta.core.pack.task._core_pack_task_
)
RANDOM
(in
rosetta.core.conformation.symmetry._core_conformation_symmetry_
)
reinitialize_for_new_input()
(in
SymInterfaceSidechainMinMover
)
ResidueLevelTaskCAP
(in
rosetta.core.pack.task._core_pack_task_
)
RANDOM
(in
SlideType
)
reinitialize_for_new_input()
(in
SymSidechainMinMover
)
ResidueListStepWiseSampler
(in
rosetta.protocols.stepwise.sampler.copy_dofs._protocols_stepwise_sampler_copy_dofs_
)
random
(in
rosetta.numeric
)
reinitialize_for_new_input()
(in
MPSymDockMover
)
ResidueListStepWiseSamplerAP
(in
rosetta.protocols.stepwise.sampler.copy_dofs._protocols_stepwise_sampler_copy_dofs_
)
random
(in
Direction
)
reinitialize_for_new_input()
(in
AlignPoseToInvrotTreeMover
)
ResidueListStepWiseSamplerCAP
(in
rosetta.protocols.stepwise.sampler.copy_dofs._protocols_stepwise_sampler_copy_dofs_
)
random
(in
rosetta.protocols.rigid._protocols_rigid_
)
reinitialize_for_new_input()
(in
StoreCombinedStoredTasksMover
)
ResidueLoader
(in
rosetta.core.chemical._core_chemical_
)
random
(in
rosetta.protocols.rigid
)
reinitialize_for_new_input()
(in
StoreCompoundTaskMover
)
ResidueLoaderAP
(in
rosetta.core.chemical._core_chemical_
)
random()
(in
JumpStepWiseSampler
)
reinitialize_for_new_input()
(in
StoreTaskMover
)
ResidueLoaderCAP
(in
rosetta.core.chemical._core_chemical_
)
random()
(in
MC_Comb
)
reinitialize_for_new_input()
(in
UnfoldedStateEnergyCalculatorMover
)
ResidueLoaderCreator
(in
rosetta.core.chemical._core_chemical_
)
random()
(in
MC_OneTorsion
)
reinitialize_mingraph_neighborhood_for_residue()
(in
rosetta.core.pack._core_pack_
)
ResidueLoaderCreatorAP
(in
rosetta.core.chemical._core_chemical_
)
random()
(in
NoOpStepWiseSampler
)
reinitialize_minnode_for_residue()
(in
ScoreFunction
)
ResidueLoaderCreatorCAP
(in
rosetta.core.chemical._core_chemical_
)
random()
(in
StepWiseSamplerAny
)
reject
(in
StubStatus
)
ResidueLoaderOptions
(in
rosetta.core.chemical._core_chemical_
)
random()
(in
StepWiseSamplerBase
)
reject
(in
rosetta.protocols.hotspot_hashing._protocols_hotspot_hashing_
)
ResidueLoaderOptionsAP
(in
rosetta.core.chemical._core_chemical_
)
random()
(in
StepWiseSamplerComb
)
reject
(in
rosetta.protocols.hotspot_hashing
)
ResidueLoaderOptionsCAP
(in
rosetta.core.chemical._core_chemical_
)
random()
(in
StepWiseSamplerOneTorsion
)
reject_change()
(in
SimpleInteractionGraph
)
ResidueLoaderOptionsCreator
(in
rosetta.core.chemical._core_chemical_
)
random()
(in
StepWiseSamplerOneValue
)
reject_change()
(in
SimpleNode
)
ResidueLoaderOptionsCreatorAP
(in
rosetta.core.chemical._core_chemical_
)
random()
(in
StepWiseSamplerOneValueComb
)
reject_mutant()
(in
AlterSpecDisruptionDriver
)
ResidueLoaderOptionsCreatorCAP
(in
rosetta.core.chemical._core_chemical_
)
random()
(in
StepWiseSamplerSized
)
reject_mutant()
(in
PointMutScanDriver
)
ResidueMatcher
(in
rosetta.core.conformation._core_conformation_
)
random()
(in
StepWiseSamplerSizedAny
)
reject_perturbation()
(in
FASTERInteractionGraph
)
ResidueMatcherAP
(in
rosetta.core.conformation._core_conformation_
)
random()
(in
StepWiseSamplerSizedComb
)
REJECTED
(in
ClaimRight
)
ResidueMatcherCAP
(in
rosetta.core.conformation._core_conformation_
)
random()
(in
CopyDofStepWiseSampler
)
REJECTED
(in
DofClaim
)
ResidueName3Is
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random()
(in
ResidueAlternativeStepWiseSampler
)
rel_deriv_dev()
(in
SimpleDerivCheckResult
)
ResidueName3IsAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random()
(in
ResidueAlternativeStepWiseSamplerComb
)
relative()
(in
XYZClaim
)
ResidueName3IsCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random()
(in
ResidueListStepWiseSampler
)
relative()
(in
FileName
)
ResidueName3IsCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random()
(in
InputStreamStepWiseSampler
)
relative()
(in
PathName
)
ResidueName3IsCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random()
(in
ProteinBetaAntiParallelStepWiseSampler
)
relative_pose_filter()
(in
MultipleSigmoids
)
ResidueName3IsCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random()
(in
ProteinFragmentStepWiseSampler
)
relative_pose_names()
(in
Operator
)
ResidueName3Isnt
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random()
(in
ProteinMainChainStepWiseSampler
)
relative_tmh_ori()
(in
MembraneTopology
)
ResidueName3IsntAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random()
(in
RigidBodyStepWiseSampler
)
RelativeConnectRight
(in
rosetta.protocols.forge.build._protocols_forge_build_'
)
ResidueName3IsntCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random()
(in
RigidBodyStepWiseSamplerWithResidueAlternatives
)
RelativeConnectRightAP
(in
rosetta.protocols.forge.build._protocols_forge_build_'
)
ResidueName3IsntCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random()
(in
RigidBodyStepWiseSamplerWithResidueList
)
RelativeConnectRightCAP
(in
rosetta.protocols.forge.build._protocols_forge_build_'
)
ResidueName3IsntCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random()
(in
RNA_ChiStepWiseSampler
)
RelativePoseFilter
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
ResidueName3IsntCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random()
(in
RNA_KIC_Sampler
)
RelativePoseFilterAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
ResidueNameSelector
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
random()
(in
RNA_KinematicCloser
)
RelativePoseFilterCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
ResidueNameSelectorAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
random()
(in
RNA_MC_MultiSuite
)
RelativePoseFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
ResidueNameSelectorCAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
random()
(in
RNA_MC_Sugar
)
RelativePoseFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
ResidueNameSelectorCreator
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
random()
(in
RNA_MC_Suite
)
RelativePoseFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
ResidueNameSelectorCreatorAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
random()
(in
RNA_NucleosideStepWiseSampler
)
RelativeSegmentFilter
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
ResidueNameSelectorCreatorCAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
random()
(in
RNA_SugarStepWiseSampler
)
RelativeSegmentFilterAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
ResidueNblistData
(in
rosetta.core.scoring._core_scoring_
)
random()
(in
RNA_SuiteStepWiseSampler
)
RelativeSegmentFilterCAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
ResidueNblistDataAP
(in
rosetta.core.scoring._core_scoring_
)
random_access()
(in
AddChainMover
)
RelativeSegmentFilterCreator
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
ResidueNblistDataCAP
(in
rosetta.core.scoring._core_scoring_
)
random_angle()
(in
BackrubMover
)
RelativeSegmentFilterCreatorAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
ResidueNeighborConstIterator
(in
rosetta.core.scoring._core_scoring_
)
random_basepair()
(in
DNAParameters
)
RelativeSegmentFilterCreatorCAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
ResidueNeighborConstIteratorAP
(in
rosetta.core.scoring._core_scoring_
)
random_basestep()
(in
DNAParameters
)
RelativeSequencePosition
(in
rosetta.protocols.forge.build._protocols_forge_build_'
)
ResidueNeighborConstIteratorCAP
(in
rosetta.core.scoring._core_scoring_
)
random_bin()
(in
BinTransitionCalculator
)
RelativeSequencePositionAP
(in
rosetta.protocols.forge.build._protocols_forge_build_'
)
ResidueNeighborIterator
(in
rosetta.core.scoring._core_scoring_
)
random_bin_based_on_prev_and_next()
(in
BinTransitionCalculator
)
RelativeSequencePositionCAP
(in
rosetta.protocols.forge.build._protocols_forge_build_'
)
ResidueNeighborIteratorAP
(in
rosetta.core.scoring._core_scoring_
)
random_bin_based_on_previous()
(in
BinTransitionCalculator
)
RELAX
(in
rosetta
)
ResidueNeighborIteratorCAP
(in
rosetta.core.scoring._core_scoring_
)
random_bin_i()
(in
BinTransitionData
)
RELAX
(in
rosetta.protocols.abinitio
)
ResidueNetwork
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
random_bin_iplus1()
(in
BinTransitionData
)
RELAX
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
ResidueNetworkAP
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
random_bin_iplus1_given_i()
(in
BinTransitionData
)
RELAX
(in
StageID
)
ResidueNetworkCAP
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
random_chunk
(in
AlignOption
)
relax
(in
MinTypeEnum
)
ResiduePairEvalType
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
random_chunk
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
relax
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
ResiduePairJump
(in
rosetta.protocols.jumping._protocols_jumping_
)
random_chunk
(in
rosetta.protocols.hybridization
)
relax
(in
rosetta.protocols.antibody.design
)
ResiduePairJumpAP
(in
rosetta.protocols.jumping._protocols_jumping_
)
random_chunk_insertion()
(in
RNA_ChunkLibrary
)
relax
(in
rosetta.protocols.membrane
)
ResiduePairJumpCAP
(in
rosetta.protocols.jumping._protocols_jumping_
)
random_connection()
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
relax
(in
rosetta.protocols
)
ResiduePairJumpSetup
(in
rosetta.protocols.jumping._protocols_jumping_
)
random_delay()
(in
rosetta.core.init._core_init_
)
relax()
(in
FASTERNode
)
ResiduePairJumpSetupAP
(in
rosetta.protocols.jumping._protocols_jumping_
)
random_drop_rate()
(in
ConstraintPreparer
)
relax()
(in
AbrelaxApplication
)
ResiduePairJumpSetupCAP
(in
rosetta.protocols.jumping._protocols_jumping_
)
random_entity()
(in
DiscreteRandomizer
)
relax()
(in
LoopRelaxMover
)
ResiduePairJumpSingle
(in
rosetta.protocols.jumping._protocols_jumping_
)
random_entity()
(in
EntityRandomizer
)
relax()
(in
LoopMoverFromCommandLine
)
ResiduePairJumpSingleAP
(in
rosetta.protocols.jumping._protocols_jumping_
)
random_entity()
(in
Mutate1Randomizer
)
relax_after_neighbors_perturbation()
(in
FASTERNode
)
ResiduePairJumpSingleCAP
(in
rosetta.protocols.jumping._protocols_jumping_
)
random_entity()
(in
PositionSpecificRandomizer
)
relax_bound()
(in
DdgFilter
)
ResiduePairNeighborList
(in
rosetta.core.scoring._core_scoring_
)
random_entry()
(in
PatchdockReader
)
relax_bound()
(in
ddG
)
ResiduePairNeighborListAP
(in
rosetta.core.scoring._core_scoring_
)
random_fragment_insertion()
(in
RNA_FragmentMover
)
relax_cdrs()
(in
AntibodyDesignModeler
)
ResiduePairNeighborListCAP
(in
rosetta.core.scoring._core_scoring_
)
random_jump_change()
(in
RNA_StructureParameters
)
relax_cdrs()
(in
AntibodyModeler
)
ResiduePairXYZ
(in
rosetta.core.scoring.func._core_scoring_func_
)
random_limit_groupsize()
(in
ClusterBase
)
relax_favorable_poses()
(in
VIP_Mover
)
ResiduePairXYZAP
(in
rosetta.core.scoring.func._core_scoring_func_
)
random_mainchain_torsions_from_bin()
(in
BinTransitionCalculator
)
relax_in_current_context()
(in
FASTERInteractionGraph
)
ResiduePairXYZCAP
(in
rosetta.core.scoring.func._core_scoring_func_
)
random_mainchain_torsions_from_bins()
(in
BinTransitionCalculator
)
relax_interface()
(in
AntibodyDesignModeler
)
ResiduePDBIndexIs
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_mainchain_torsions_using_adjacent_bins()
(in
BinTransitionCalculator
)
Relax_main()
(in
rosetta.protocols.relax._protocols_relax_
)
ResiduePDBIndexIsAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_mover()
(in
MetropolisHastingsMover
)
relax_mover()
(in
GreedyOptMutationMover
)
ResiduePDBIndexIsCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_mover()
(in
SidechainMetropolisHastingsMover
)
relax_mover()
(in
ParetoOptMutationMover
)
ResiduePDBIndexIsCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_normal()
(in
rosetta.numeric.random._numeric_random_
)
relax_mover()
(in
PointMutationCalculator
)
ResiduePDBIndexIsCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_perturbation()
(in
RNA_HelixAssembler
)
relax_mover()
(in
LoopHashMoverWrapper
)
ResiduePDBIndexIsCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_phipsi_from_rama()
(in
Ramachandran
)
relax_mover()
(in
MatDesGreedyOptMutationMover
)
ResiduePDBIndexIsnt
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_phipsi_from_rama_by_torsion_bin()
(in
Ramachandran
)
relax_mover()
(in
MatDesPointMutationCalculator
)
ResiduePDBIndexIsntAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_phipsi_from_rama_by_torsion_bin_left()
(in
Ramachandran2B
)
relax_mover()
(in
BindingStrainFilter
)
ResiduePDBIndexIsntCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_phipsi_from_rama_by_torsion_bin_right()
(in
Ramachandran2B
)
relax_mover()
(in
FilterScanFilter
)
ResiduePDBIndexIsntCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_phipsi_from_rama_left()
(in
Ramachandran2B
)
relax_mover()
(in
DdgFilter
)
ResiduePDBIndexIsntCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_phipsi_from_rama_right()
(in
Ramachandran2B
)
relax_mover()
(in
DeltaFilter
)
ResiduePDBIndexIsntCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_point()
(in
IntervalSet_T_double_T
)
relax_mover()
(in
RelativePoseFilter
)
ResiduePDBInfoHasLabel
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_range()
(in
RandomGenerator
)
relax_mover()
(in
ddG
)
ResiduePDBInfoHasLabelAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_range()
(in
rosetta.numeric.random._numeric_random_
)
relax_neighbors()
(in
FASTERNode
)
ResiduePDBInfoHasLabelCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_rotation()
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
relax_optimized_CDR_grafts()
(in
GraftMover
)
ResiduePDBInfoHasLabelCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_rotation()
(in
rosetta.numeric.random._numeric_random_
)
relax_pose()
(in
rosetta.protocols.relax._protocols_relax_
)
ResiduePDBInfoHasLabelCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_sample()
(in
WeightedSampler
)
relax_protocol()
(in
AbrelaxMover
)
ResiduePDBInfoHasLabelCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_selector
(in
rosetta.protocols.generalized_kinematic_closure.selector._protocols_generalized_kinematic_closure_selector_
)
relax_unbound()
(in
DeltaFilter
)
ResiduePDBInfoLacksLabel
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_selector
(in
selector_type
)
relaxmode()
(in
NormalModeRelaxMover
)
ResiduePDBInfoLacksLabelAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_selector
(in
rosetta.protocols.generalized_kinematic_closure.selector
)
RelaxProtocolBase
(in
rosetta.protocols.relax._protocols_relax_
)
ResiduePDBInfoLacksLabelCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RANDOM_SIDE
(in
rosetta.protocols.forge.build.SegmentInsertConnectionScheme
)
RelaxProtocolBaseAP
(in
rosetta.protocols.relax._protocols_relax_
)
ResiduePDBInfoLacksLabelCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RANDOM_SIDE
(in
Enum
)
RelaxProtocolBaseCAP
(in
rosetta.protocols.relax._protocols_relax_
)
ResiduePDBInfoLacksLabelCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RANDOM_SIDE
(in
rosetta.protocols.forge.build.SegmentInsertConnectionScheme._protocols_forge_build_SegmentInsertConnectionScheme_
)
RelaxScriptCommand
(in
rosetta.protocols.relax._protocols_relax_
)
ResiduePDBInfoLacksLabelCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
random_stub()
(in
HotspotStubSet
)
RelaxScriptCommandAP
(in
rosetta.protocols.relax._protocols_relax_
)
ResidueProbDesignOperation
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
random_torsion_move()
(in
RNA_TorsionMover
)
RelaxScriptCommandCAP
(in
rosetta.protocols.relax._protocols_relax_
)
ResidueProbDesignOperationAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
random_trans()
(in
Jump
)
release()
(in
TetherLigand
)
ResidueProbDesignOperationCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
random_tree_from_jump_points()
(in
FoldTree
)
release_buffers()
(in
ResidualDipolarCoupling
)
ResidueProperties
(in
rosetta.core.chemical._core_chemical_
)
random_unit_quaternion()
(in
rosetta.numeric.random._numeric_random_
)
release_file()
(in
MpiFileBuffer
)
ResiduePropertiesAP
(in
rosetta.core.chemical._core_chemical_
)
random_vector()
(in
rosetta.numeric.random._numeric_random_
)
relevant_downstream_atoms()
(in
MatcherTask
)
ResiduePropertiesCAP
(in
rosetta.core.chemical._core_chemical_
)
random_vector_spherical()
(in
rosetta.numeric.random._numeric_random_
)
remap()
(in
ResidueFeature
)
ResidueProperty
(in
rosetta.core.chemical._core_chemical_
)
random_vector_unit_cube()
(in
rosetta.numeric.random._numeric_random_
)
remap()
(in
RBSegment
)
residues()
(in
DunbrackConstraint
)
random_xform()
(in
rosetta.numeric.random._numeric_random_
)
remap_cis_omega_torsion_bins_to_trans()
(in
rosetta.core.conformation._core_conformation_
)
residues()
(in
RotamerConstraint
)
randomAngle()
(in
PocketGrid
)
remap_names_on_geometry()
(in
rosetta.core.io.pdb._core_io_pdb_
)
residues()
(in
AmbiguousConstraint
)
RandomConformerMover
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
remap_pdb_atom_names()
(in
ResidueType
)
residues()
(in
AmbiguousNMRConstraint
)
RandomConformerMoverAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
remap_rb_segments()
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
residues()
(in
AmbiguousNMRDistanceConstraint
)
RandomConformerMoverCAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
remap_resid()
(in
DunbrackConstraint
)
residues()
(in
AngleConstraint
)
RandomConformers
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
remap_resid()
(in
RotamerConstraint
)
residues()
(in
AtomPairConstraint
)
RandomConformersAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
remap_resid()
(in
AmbiguousConstraint
)
residues()
(in
BackboneStubConstraint
)
RandomConformersCAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
remap_resid()
(in
AmbiguousNMRConstraint
)
residues()
(in
BackboneStubLinearConstraint
)
RandomConformersCreator
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
remap_resid()
(in
AmbiguousNMRDistanceConstraint
)
residues()
(in
BigBinConstraint
)
RandomConformersCreatorAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
remap_resid()
(in
AngleConstraint
)
residues()
(in
ConstantConstraint
)
RandomConformersCreatorCAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
remap_resid()
(in
AtomPairConstraint
)
residues()
(in
Constraint
)
RandomGenerator
(in
rosetta.numeric.random._numeric_random_
)
remap_resid()
(in
BackboneStubConstraint
)
residues()
(in
CoordinateConstraint
)
RandomGeneratorAP
(in
rosetta.numeric.random._numeric_random_
)
remap_resid()
(in
BackboneStubLinearConstraint
)
residues()
(in
DihedralConstraint
)
RandomGeneratorCAP
(in
rosetta.numeric.random._numeric_random_
)
remap_resid()
(in
BigBinConstraint
)
residues()
(in
DihedralPairConstraint
)
randomize()
(in
ABEGOEval
)
remap_resid()
(in
ConstantConstraint
)
residues()
(in
DistancePairConstraint
)
randomize()
(in
EnergyEval
)
remap_resid()
(in
Constraint
)
residues()
(in
FabConstraint
)
randomize()
(in
IdentityEval
)
remap_resid()
(in
CoordinateConstraint
)
residues()
(in
KofNConstraint
)
randomize_alpha_backbone_by_rama
(in
perturber_effect
)
remap_resid()
(in
DihedralConstraint
)
residues()
(in
LocalCoordinateConstraint
)
randomize_alpha_backbone_by_rama
(in
rosetta.protocols.generalized_kinematic_closure.perturber._protocols_generalized_kinematic_closure_perturber_
)
remap_resid()
(in
DihedralPairConstraint
)
residues()
(in
MultiConstraint
)
randomize_alpha_backbone_by_rama
(in
rosetta.protocols.generalized_kinematic_closure.perturber
)
remap_resid()
(in
DistancePairConstraint
)
residues()
(in
NamedAngleConstraint
)
randomize_backbone_by_bins
(in
perturber_effect
)
remap_resid()
(in
FabConstraint
)
residues()
(in
NamedAtomPairConstraint
)
randomize_backbone_by_bins
(in
rosetta.protocols.generalized_kinematic_closure.perturber._protocols_generalized_kinematic_closure_perturber_
)
remap_resid()
(in
KofNConstraint
)
residues()
(in
NonResidueTypeConstraint
)
randomize_backbone_by_bins
(in
rosetta.protocols.generalized_kinematic_closure.perturber
)
remap_resid()
(in
LocalCoordinateConstraint
)
residues()
(in
ResidueTypeConstraint
)
randomize_dihedral
(in
perturber_effect
)
remap_resid()
(in
MultiConstraint
)
residues()
(in
ResidueTypeLinkingConstraint
)
randomize_dihedral
(in
rosetta.protocols.generalized_kinematic_closure.perturber._protocols_generalized_kinematic_closure_perturber_
)
remap_resid()
(in
NamedAngleConstraint
)
residues()
(in
SequenceProfileConstraint
)
randomize_dihedral
(in
rosetta.protocols.generalized_kinematic_closure.perturber
)
remap_resid()
(in
NamedAtomPairConstraint
)
residues()
(in
SiteConstraint
)
randomize_input_sequence()
(in
AnchoredDesignMover
)
remap_resid()
(in
NonResidueTypeConstraint
)
residues()
(in
SiteConstraintResidues
)
randomize_loop()
(in
LoopMover_SlidingWindow
)
remap_resid()
(in
ResidueTypeConstraint
)
residues()
(in
HolesParamsRes
)
randomize_loop()
(in
LoopMover_Perturb_QuickCCD
)
remap_resid()
(in
ResidueTypeLinkingConstraint
)
residues()
(in
AmbiguousMultiConstraint
)
randomize_loop_coords()
(in
MultiThreadingMover
)
remap_resid()
(in
SequenceProfileConstraint
)
residues()
(in
BindingSiteConstraint
)
randomize_loop_coords()
(in
ThreadingMover
)
remap_resid()
(in
SiteConstraint
)
residues()
(in
COMCoordinateConstraint
)
randomize_missing_coords()
(in
FileData
)
remap_resid()
(in
SiteConstraintResidues
)
residues()
(in
SequenceCoupling1BDConstraint
)
randomize_missing_coords()
(in
FileDataOptions
)
remap_resid()
(in
AmbiguousMultiConstraint
)
residues()
(in
SequenceCouplingConstraint
)
randomize_pose_rigid_bodies()
(in
MultipleDomainMover
)
remap_resid()
(in
BindingSiteConstraint
)
residues()
(in
ClosureProblem
)
randomize_selected_atoms()
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
remap_resid()
(in
COMCoordinateConstraint
)
residues()
(in
PocketConstraint
)
RandomMover
(in
rosetta.protocols.moves._protocols_moves_
)
remap_resid()
(in
SequenceCoupling1BDConstraint
)
residues()
(in
AddSidechainConstraintsToHotspots
)
RandomMoverAP
(in
rosetta.protocols.moves._protocols_moves_
)
remap_resid()
(in
SequenceCouplingConstraint
)
residues1()
(in
ShapeComplementarityFilter
)
RandomMoverCAP
(in
rosetta.protocols.moves._protocols_moves_
)
remap_resid()
(in
PocketConstraint
)
residues2()
(in
ShapeComplementarityFilter
)
RandomMoverCreator
(in
rosetta.protocols.moves._protocols_moves_
)
remap_resid()
(in
CovalentConnectionReplaceInfo
)
residues_adjacent_for_subunit_pair()
(in
SymmOnTheFlyEdge
)
RandomMoverCreatorAP
(in
rosetta.protocols.moves._protocols_moves_
)
remap_resid()
(in
EnzConstraintIO
)
residues_are_different()
(in
PDBOutput
)
RandomMoverCreatorCAP
(in
rosetta.protocols.moves._protocols_moves_
)
remap_resid()
(in
EnzConstraintParameters
)
residues_for_atom_name_remapping()
(in
FileDataOptions
)
RandomMutation
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
remap_resid()
(in
EnzCstTemplateRes
)
residues_for_entity_begin()
(in
EntityCorrespondence
)
RandomMutationAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
remap_resid()
(in
EnzCstTemplateResAtoms
)
residues_for_entity_end()
(in
EntityCorrespondence
)
RandomMutationCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
remap_resid()
(in
EnzCstTemplateResCache
)
residues_interact()
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
RandomMutationCreator
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
remap_resid()
(in
EnzdesCstCache
)
residues_moved_begin()
(in
ResidueCoordinateChangeList
)
RandomMutationCreatorAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
remap_resid()
(in
EnzdesCstParamCache
)
residues_moved_end()
(in
ResidueCoordinateChangeList
)
RandomMutationCreatorCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
remap_residue_level_tasks()
(in
PackerTask
)
residues_per_repeat()
(in
BackboneGridSampler
)
RandomOmegaFlipMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
remap_residue_level_tasks()
(in
PackerTask_
)
residues_per_repeat()
(in
BackboneGridSamplerHelper
)
RandomOmegaFlipMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
remap_residue_positions()
(in
ConstraintSet
)
residues_to_mutate()
(in
ddGMover
)
RandomOmegaFlipMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
remap_residues()
(in
EnzdesSeqRecoveryCache
)
ResidueScoresFeatures
(in
rosetta.protocols.features._protocols_features_
)
RandomOmegaFlipMoverCreator
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
remap_value()
(in
BaseCacheUnit
)
ResidueScoresFeaturesAP
(in
rosetta.protocols.features._protocols_features_
)
RandomOmegaFlipMoverCreatorAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
remapped_clone()
(in
DunbrackConstraint
)
ResidueScoresFeaturesCAP
(in
rosetta.protocols.features._protocols_features_
)
RandomOmegaFlipMoverCreatorCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
remapped_clone()
(in
RotamerConstraint
)
ResidueScoresFeaturesCreator
(in
rosetta.protocols.features._protocols_features_
)
RandomPositionRotationMover
(in
rosetta.protocols.membrane._protocols_membrane_
)
remapped_clone()
(in
AmbiguousConstraint
)
ResidueScoresFeaturesCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
RandomPositionRotationMoverAP
(in
rosetta.protocols.membrane._protocols_membrane_
)
remapped_clone()
(in
AmbiguousNMRConstraint
)
ResidueScoresFeaturesCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
RandomPositionRotationMoverCAP
(in
rosetta.protocols.membrane._protocols_membrane_
)
remapped_clone()
(in
AmbiguousNMRDistanceConstraint
)
ResidueSecondaryStructureFeatures
(in
rosetta.protocols.features._protocols_features_
)
RandomPositionTranslationMover
(in
rosetta.protocols.membrane._protocols_membrane_
)
remapped_clone()
(in
AngleConstraint
)
ResidueSecondaryStructureFeaturesAP
(in
rosetta.protocols.features._protocols_features_
)
RandomPositionTranslationMoverAP
(in
rosetta.protocols.membrane._protocols_membrane_
)
remapped_clone()
(in
AtomPairConstraint
)
ResidueSecondaryStructureFeaturesCAP
(in
rosetta.protocols.features._protocols_features_
)
RandomPositionTranslationMoverCAP
(in
rosetta.protocols.membrane._protocols_membrane_
)
remapped_clone()
(in
BackboneStubConstraint
)
ResidueSecondaryStructureFeaturesCreator
(in
rosetta.protocols.features._protocols_features_
)
RandomSheetBuilder
(in
rosetta.protocols.jumping._protocols_jumping_
)
remapped_clone()
(in
BackboneStubLinearConstraint
)
ResidueSecondaryStructureFeaturesCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
RandomSheetBuilderAP
(in
rosetta.protocols.jumping._protocols_jumping_
)
remapped_clone()
(in
BigBinConstraint
)
ResidueSecondaryStructureFeaturesCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
RandomSheetBuilderCAP
(in
rosetta.protocols.jumping._protocols_jumping_
)
remapped_clone()
(in
ConstantConstraint
)
ResidueSelector
(in
rosetta.core.chemical._core_chemical_
)
RandomSolutions
(in
rosetta.protocols.kinematic_closure.solution_pickers._protocols_kinematic_closure_solution_pickers_
)
remapped_clone()
(in
Constraint
)
ResidueSelector
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
RandomSolutionsAP
(in
rosetta.protocols.kinematic_closure.solution_pickers._protocols_kinematic_closure_solution_pickers_
)
remapped_clone()
(in
ConstraintSet
)
ResidueSelectorAP
(in
rosetta.core.chemical._core_chemical_
)
RandomSolutionsCAP
(in
rosetta.protocols.kinematic_closure.solution_pickers._protocols_kinematic_closure_solution_pickers_
)
remapped_clone()
(in
CoordinateConstraint
)
ResidueSelectorAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
RandomSymmetrySlider
(in
rosetta.protocols.simple_moves.symmetry._protocols_simple_moves_symmetry_
)
remapped_clone()
(in
DihedralConstraint
)
ResidueSelectorCAP
(in
rosetta.core.chemical._core_chemical_
)
RandomSymmetrySliderAP
(in
rosetta.protocols.simple_moves.symmetry._protocols_simple_moves_symmetry_
)
remapped_clone()
(in
DihedralPairConstraint
)
ResidueSelectorCAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
RandomSymmetrySliderCAP
(in
rosetta.protocols.simple_moves.symmetry._protocols_simple_moves_symmetry_
)
remapped_clone()
(in
DistancePairConstraint
)
ResidueSelectorCreator
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
RandomTorsionMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
remapped_clone()
(in
FabConstraint
)
ResidueSelectorCreatorAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
RandomTorsionMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
remapped_clone()
(in
KofNConstraint
)
ResidueSelectorCreatorCAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
RandomTorsionMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
remapped_clone()
(in
LocalCoordinateConstraint
)
ResidueSelectorFactory
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
RandomTorsionMoverCreator
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
remapped_clone()
(in
MultiConstraint
)
ResidueSelectorFactoryAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
RandomTorsionMoverCreatorAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
remapped_clone()
(in
NamedAngleConstraint
)
ResidueSelectorFactoryCAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
RandomTorsionMoverCreatorCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
remapped_clone()
(in
NamedAtomPairConstraint
)
ResidueSelectorLoader
(in
rosetta.protocols.jd2.parser._protocols_jd2_parser_
)
range()
(in
PairEPotential
)
remapped_clone()
(in
NonResidueTypeConstraint
)
ResidueSelectorLoaderAP
(in
rosetta.protocols.jd2.parser._protocols_jd2_parser_
)
range()
(in
MultiDimensionalHistogram
)
remapped_clone()
(in
ResidueTypeConstraint
)
ResidueSelectorLoaderCAP
(in
rosetta.protocols.jd2.parser._protocols_jd2_parser_
)
range()
(in
ConstraintedOptimizationWeightFunc
)
remapped_clone()
(in
ResidueTypeLinkingConstraint
)
ResidueSelectorLoaderCreator
(in
rosetta.protocols.jd2.parser._protocols_jd2_parser_
)
range()
(in
DDGBindOptEData
)
remapped_clone()
(in
SequenceProfileConstraint
)
ResidueSelectorLoaderCreatorAP
(in
rosetta.protocols.jd2.parser._protocols_jd2_parser_
)
range()
(in
DDGMutationOptEData
)
remapped_clone()
(in
SiteConstraint
)
ResidueSelectorLoaderCreatorCAP
(in
rosetta.protocols.jd2.parser._protocols_jd2_parser_
)
range()
(in
DGBindOptEData
)
remapped_clone()
(in
SiteConstraintResidues
)
ResidueSelectorSingle
(in
rosetta.core.chemical._core_chemical_
)
range()
(in
NestedEnergyTermDDGMutationOptEData
)
remapped_clone()
(in
IgnoreSubsetConstraintSet
)
ResidueSelectorSingleAP
(in
rosetta.core.chemical._core_chemical_
)
range()
(in
NestedEnergyTermPNatAAOptEPositionData
)
remapped_clone()
(in
AmbiguousMultiConstraint
)
ResidueSelectorSingleCAP
(in
rosetta.core.chemical._core_chemical_
)
range()
(in
OptEPositionData
)
remapped_clone()
(in
BindingSiteConstraint
)
ResidueSetChainEnergyFilter
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
range()
(in
PNatAAOptEPositionData
)
remapped_clone()
(in
COMCoordinateConstraint
)
ResidueSetChainEnergyFilterAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
range()
(in
PNatLigPoseOptEData
)
remapped_clone()
(in
MaxSeqSepConstraintSet
)
ResidueSetChainEnergyFilterCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
range()
(in
PNatRotOptEPositionData
)
remapped_clone()
(in
SequenceCoupling1BDConstraint
)
ResidueSetChainEnergyFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
range()
(in
PNatStructureOptEData
)
remapped_clone()
(in
SequenceCouplingConstraint
)
ResidueSetChainEnergyFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
range()
(in
PSSMOptEPositionData
)
remapped_clone()
(in
PocketConstraint
)
ResidueSetChainEnergyFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
range()
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
remark()
(in
Motif
)
ResiduesInInterfaceFilter
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
range()
(in
DeltaFilter
)
RemarkInfo
(in
rosetta.core.pose._core_pose_
)
ResiduesInInterfaceFilterAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
range1_lower()
(in
SymDof
)
RemarkInfoAP
(in
rosetta.core.pose._core_pose_
)
ResiduesInInterfaceFilterCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
range1_upper()
(in
SymDof
)
RemarkInfoCAP
(in
rosetta.core.pose._core_pose_
)
ResiduesInInterfaceFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
range2_is_bound()
(in
SymDof
)
Remarks
(in
rosetta.core.pose._core_pose_
)
ResiduesInInterfaceFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
range2_lower()
(in
SymDof
)
remarks()
(in
PDBInfo
)
ResiduesInInterfaceFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
range2_upper()
(in
SymDof
)
RemarksAP
(in
rosetta.core.pose._core_pose_
)
residueStubCentroid()
(in
StubGenerator
)
range_check()
(in
StrandPairing
)
RemarksCAP
(in
rosetta.core.pose._core_pose_
)
residueStubCentroidFrame()
(in
StubGenerator
)
RangeFilter
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
rematchResToPatterson()
(in
ElectronDensity
)
residueStubOrientFrame()
(in
StubGenerator
)
RangeFilterAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
remember_unrecognized_res()
(in
FileDataOptions
)
ResidueTorsionRestraints
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
RangeFilterCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
remember_unrecognized_water()
(in
FileDataOptions
)
ResidueTorsionRestraintsAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
RangeFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
remodel
(in
rosetta.protocols.forge
)
ResidueTorsionRestraintsCAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
RangeFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
remodel()
(in
LoopRelaxMover
)
ResidueTotalScoresFeatures
(in
rosetta.protocols.features._protocols_features_
)
RangeFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
remodel()
(in
LoopMoverFromCommandLine
)
ResidueTotalScoresFeaturesAP
(in
rosetta.protocols.features._protocols_features_
)
ranked_model()
(in
PairingStatistics
)
remodel_fold_tree_to_account_for_insertion()
(in
rosetta.core.kinematics._core_kinematics_
)
ResidueTotalScoresFeaturesCAP
(in
rosetta.protocols.features._protocols_features_
)
ranking_cenfilter()
(in
LoopHashDiversifier
)
remodel_generic_taskfactory()
(in
rosetta.protocols.forge.methods._protocols_forge_methods_
)
ResidueTotalScoresFeaturesCreator
(in
rosetta.protocols.features._protocols_features_
)
ranking_cenfilter()
(in
LoopHashMoverWrapper
)
RemodelConstraintGenerator
(in
rosetta.protocols.forge.remodel._protocols_forge_remodel_'
)
ResidueTotalScoresFeaturesCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
ranking_fafilter()
(in
LoopHashMoverWrapper
)
RemodelConstraintGeneratorAP
(in
rosetta.protocols.forge.remodel._protocols_forge_remodel_'
)
ResidueTotalScoresFeaturesCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
rate_threshold()
(in
SequenceRecoveryFilter
)
RemodelConstraintGeneratorCAP
(in
rosetta.protocols.forge.remodel._protocols_forge_remodel_'
)
ResidueType
(in
rosetta.core.chemical._core_chemical_
)
rate_threshold()
(in
MutationsFilter
)
RemodelEnzdesCstModuleAP
(in
rosetta.protocols.forge.remodel._protocols_forge_remodel_'
)
residueType()
(in
ResiduePairJumpSingle
)
ratio()
(in
DOF_DataPoint
)
RemodelEnzdesCstModuleCAP
(in
rosetta.protocols.forge.remodel._protocols_forge_remodel_'
)
ResidueTypeAP
(in
rosetta.core.chemical._core_chemical_
)
ratio()
(in
DerivCheckDataPoint
)
RemodelRotamerLinks
(in
rosetta.protocols.forge.remodel._protocols_forge_remodel_'
)
ResidueTypeCAP
(in
rosetta.core.chemical._core_chemical_
)
ratio_cutoff()
(in
FragQualCalculator
)
RemodelRotamerLinksAP
(in
rosetta.protocols.forge.remodel._protocols_forge_remodel_'
)
ResidueTypeConstraint
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
rational_mc
(in
rosetta.protocols.simple_moves
)
RemodelRotamerLinksCAP
(in
rosetta.protocols.forge.remodel._protocols_forge_remodel_'
)
ResidueTypeConstraintAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
RationalLoopComparator
(in
rosetta.protocols.loops._protocols_loops_
)
REMOVE
(in
CstAction
)
ResidueTypeConstraintCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
RationalLoopComparatorAP
(in
rosetta.protocols.loops._protocols_loops_
)
REMOVE
(in
rosetta.protocols.enzdes._protocols_enzdes_'
)
ResidueTypeConstraintMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
RationalLoopComparatorCAP
(in
rosetta.protocols.loops._protocols_loops_
)
remove()
(in
ParatopeEpitopeSiteConstraintMover
)
ResidueTypeConstraintMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
RationalMonteCarlo
(in
rosetta.protocols.simple_moves.rational_mc._protocols_simple_moves_rational_mc_
)
remove()
(in
ParatopeSiteConstraintMover
)
ResidueTypeConstraintMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
RationalMonteCarloAP
(in
rosetta.protocols.simple_moves.rational_mc._protocols_simple_moves_rational_mc_
)
remove()
(in
AddChainBreak
)
ResidueTypeConstraintMoverCreator
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
RationalMonteCarloCAP
(in
rosetta.protocols.simple_moves.rational_mc._protocols_simple_moves_rational_mc_
)
remove()
(in
CutClaim
)
ResidueTypeConstraintMoverCreatorAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
Rattle
(in
rosetta.protocols.md._protocols_md_
)
remove()
(in
JumpClaim
)
ResidueTypeConstraintMoverCreatorCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
RattleAP
(in
rosetta.protocols.md._protocols_md_
)
remove()
(in
LegacyRootClaim
)
ResidueTypeFilter
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RattleCAP
(in
rosetta.protocols.md._protocols_md_
)
remove_all_hotspot_constraints()
(in
HotspotStubSet
)
ResidueTypeFilterAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
raw_child_index()
(in
Atom
)
remove_all_variant_types()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
ResidueTypeFilterCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
raw_child_index()
(in
Atom_
)
remove_all_virtual_phosphates()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
ResidueTypeFilterCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
raw_data
(in
rosetta.core.io
)
remove_bad_inputs_from_job_list()
(in
FileSystemJobDistributor
)
ResidueTypeFilterCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
raw_get_nonjump_atom()
(in
Atom
)
remove_bad_inputs_from_job_list()
(in
MPIFileBufJobDistributor
)
ResidueTypeFilterCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
raw_get_nonjump_atom()
(in
Atom_
)
remove_bad_inputs_from_job_list()
(in
MPIWorkPartitionJobDistributor
)
ResidueTypeKinWriter
(in
rosetta.core.chemical._core_chemical_
)
raw_input_stub_atom0()
(in
Atom
)
remove_bad_inputs_from_job_list()
(in
MPIWorkPoolJobDistributor
)
ResidueTypeKinWriterAP
(in
rosetta.core.chemical._core_chemical_
)
raw_input_stub_atom0()
(in
Atom_
)
remove_calculator()
(in
CalculatorFactory
)
ResidueTypeKinWriterCAP
(in
rosetta.core.chemical._core_chemical_
)
raw_input_stub_atom1()
(in
Atom
)
remove_chain_break_variants()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
ResidueTypeLinkingConstraint
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
raw_input_stub_atom1()
(in
Atom_
)
remove_chainbreaks()
(in
JumpSample
)
ResidueTypeLinkingConstraintAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
raw_input_stub_atom2()
(in
Atom
)
remove_chainbreaks_according_to_jumps()
(in
rosetta.protocols.toolbox.pose_manipulation._protocols_toolbox_pose_manipulation_
)
ResidueTypeLinkingConstraintCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
raw_input_stub_atom2()
(in
Atom_
)
remove_constraint()
(in
Pose
)
ResidueTypeSet
(in
rosetta.core.chemical._core_chemical_
)
raw_input_stub_atom3()
(in
Atom
)
remove_constraint()
(in
ConstraintSet
)
ResidueTypeSetAP
(in
rosetta.core.chemical._core_chemical_
)
raw_input_stub_atom3()
(in
Atom_
)
remove_constraint()
(in
Constraints
)
ResidueTypeSetCAP
(in
rosetta.core.chemical._core_chemical_
)
raw_parent()
(in
Atom
)
remove_constraints()
(in
Pose
)
ResidueTypesFeatures
(in
rosetta.protocols.features._protocols_features_
)
raw_parent()
(in
Atom_
)
remove_constraints()
(in
ConstraintSet
)
ResidueTypesFeaturesAP
(in
rosetta.protocols.features._protocols_features_
)
raw_previous_child()
(in
Atom
)
remove_constraints_from_pose()
(in
EnzConstraintIO
)
ResidueTypesFeaturesCAP
(in
rosetta.protocols.features._protocols_features_
)
raw_previous_child()
(in
Atom_
)
remove_constraints_from_pose_for_block()
(in
EnzConstraintIO
)
ResidueTypesFeaturesCreator
(in
rosetta.protocols.features._protocols_features_
)
raw_previous_sibling()
(in
Atom
)
remove_constraints_of_type()
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
ResidueTypesFeaturesCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
raw_previous_sibling()
(in
Atom_
)
remove_coordinate_constraints_from_pose()
(in
rosetta.protocols.protein_interface_design._protocols_protein_interface_design_
)
ResidueTypesFeaturesCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
raw_stub_atom1()
(in
Atom
)
remove_covalent_connection_from_pose()
(in
CovalentConnectionReplaceInfo
)
ResidueVicinityInfo
(in
rosetta.protocols.forge.remodel._protocols_forge_remodel_'
)
raw_stub_atom1()
(in
BondedAtom
)
remove_covalent_connections_from_pose()
(in
EnzConstraintParameters
)
ResidueVicinityInfoAP
(in
rosetta.protocols.forge.remodel._protocols_forge_remodel_'
)
raw_stub_atom1()
(in
JumpAtom
)
remove_cut()
(in
rosetta.protocols.jumping._protocols_jumping_
)
ResidueVicinityInfoCAP
(in
rosetta.protocols.forge.remodel._protocols_forge_remodel_'
)
raw_stub_atom2()
(in
Atom
)
remove_cutpoint()
(in
rosetta.protocols.forge.methods._protocols_forge_methods_
)
ResidueXYZ
(in
rosetta.core.scoring.func._core_scoring_func_
)
raw_stub_atom2()
(in
BondedAtom
)
remove_cutpoint_closed()
(in
rosetta.protocols.farna._protocols_farna_
)
ResidueXYZAP
(in
rosetta.core.scoring.func._core_scoring_func_
)
raw_stub_atom2()
(in
JumpAtom
)
remove_cutpoint_variants()
(in
rosetta.core.util._core_util_
)
ResidueXYZCAP
(in
rosetta.core.scoring.func._core_scoring_func_
)
raw_stub_atom3()
(in
Atom
)
remove_cutpoint_variants()
(in
rosetta.protocols.forge.methods._protocols_forge_methods_
)
resindex()
(in
ResidueIndexDescription
)
raw_stub_atom3()
(in
BondedAtom
)
remove_cutpoint_variants()
(in
rosetta.protocols.loops._protocols_loops_
)
ResInteractions
(in
rosetta.protocols.toolbox.match_enzdes_util._protocols_toolbox_match_enzdes_util_
)
raw_stub_atom3()
(in
JumpAtom
)
remove_cutpoint_variants_for_ccd()
(in
rosetta.protocols.grafting._protocols_grafting_
)
ResInteractionsAP
(in
rosetta.protocols.toolbox.match_enzdes_util._protocols_toolbox_match_enzdes_util_
)
raw_unfolded_state_energymap()
(in
UnfoldedStatePotential
)
remove_cutpoints()
(in
rosetta.protocols.forge.methods._protocols_forge_methods_
)
ResInteractionsCAP
(in
rosetta.protocols.toolbox.match_enzdes_util._protocols_toolbox_match_enzdes_util_
)
RawFileData
(in
rosetta.core.io.raw_data._core_io_raw_data_
)
remove_cutpoints_closed()
(in
rosetta.protocols.farna._protocols_farna_
)
resize()
(in
DataCache_T_basic_datacache_CacheableData_T
)
RawFileDataAP
(in
rosetta.core.io.raw_data._core_io_raw_data_
)
remove_cycles()
(in
FoldTreeSketch
)
resize()
(in
vector1_AtomID
)
RawFileDataCAP
(in
rosetta.core.io.raw_data._core_io_raw_data_
)
remove_duplicate_phi_psi()
(in
NonPlaidFingerprint
)
resize()
(in
vector1_Pose
)
RawStruct
(in
rosetta.core.io.raw_data._core_io_raw_data_
)
remove_evaluation()
(in
EvaluatedArchive
)
resize()
(in
vector1_PoseOP
)
RawStructAP
(in
rosetta.core.io.raw_data._core_io_raw_data_
)
remove_favor_native_constraints()
(in
EnzdesCacheableObserver
)
resize()
(in
vector1_ScoreType
)
RawStructCAP
(in
rosetta.core.io.raw_data._core_io_raw_data_
)
remove_file()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
resize()
(in
vector1_pair_Real_Real
)
ray_distance_derivs
(in
rosetta.protocols.pockets._protocols_pockets_
)
remove_gapped_positions()
(in
SequenceAlignment
)
resize()
(in
vector1_pair_Real_string
)
ray_distance_derivsAP
(in
rosetta.protocols.pockets._protocols_pockets_
)
remove_highest_energy_member_of_each_group()
(in
ClusterBase
)
resize()
(in
vector1_pair_SSize_SSize
)
ray_distance_derivsCAP
(in
rosetta.protocols.pockets._protocols_pockets_
)
remove_hotspot_constraints_from_pose()
(in
rosetta.protocols.hotspot_hashing._protocols_hotspot_hashing_
)
resize()
(in
vector1_pair_SSize_string
)
RB1
(in
rosetta
)
remove_info()
(in
PDBOutput
)
resize()
(in
vector1_pair_Size_Real
)
RB1
(in
rosetta.core.id
)
remove_input_file()
(in
Inline_File_Provider
)
resize()
(in
vector1_pair_Size_Size
)
RB1
(in
DOF_Type
)
remove_invrots_clashing_with_parent_res()
(in
InvrotTreeNode
)
resize()
(in
vector1_pair_Size_SymDof
)
RB1
(in
rosetta.core.id._core_id_
)
remove_irrelevant_waters()
(in
LKB_ResidueInfo
)
resize()
(in
vector1_pair_Size_string
)
RB2
(in
rosetta
)
remove_last_filter()
(in
FilterCollection
)
resize()
(in
vector1_pair_char_pair_Size_Size
)
RB2
(in
rosetta.core.id
)
remove_ligand_canonical_residues()
(in
rosetta.core.pose._core_pose_
)
resize()
(in
vector1_pair_int_int
)
RB2
(in
DOF_Type
)
remove_lower_terminus_type_from_conformation_residue()
(in
rosetta.core.conformation._core_conformation_
)
resize()
(in
vector1_pair_int_string
)
RB2
(in
rosetta.core.id._core_id_
)
remove_lower_terminus_type_from_pose_residue()
(in
rosetta.core.pose._core_pose_
)
resize()
(in
vector1_pair_string_Real
)
RB3
(in
rosetta
)
remove_member()
(in
Cluster
)
resize()
(in
vector1_pair_string_SSize
)
RB3
(in
rosetta.core.id
)
remove_missing_density()
(in
rosetta.protocols.loops._protocols_loops_
)
resize()
(in
vector1_pair_string_Size
)
RB3
(in
DOF_Type
)
remove_non_protein_residues()
(in
rosetta.protocols.toolbox.pose_manipulation._protocols_toolbox_pose_manipulation_
)
resize()
(in
vector1_pair_string_int
)
RB3
(in
rosetta.core.id._core_id_
)
remove_nonbb_constraints()
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
resize()
(in
vector1_pair_string_string
)
RB4
(in
rosetta
)
remove_nonprotein_residues()
(in
rosetta.core.pose._core_pose_
)
resize()
(in
vector1_xyzVector_Real
)
RB4
(in
rosetta.core.id
)
remove_observer()
(in
PosePyObserver
)
resize()
(in
vector1_xyzVector_SSize
)
RB4
(in
DOF_Type
)
remove_other_pose_at_idx()
(in
FullModelInfo
)
resize()
(in
vector1_xyzVector_Size
)
RB4
(in
rosetta.core.id._core_id_
)
remove_output_observer()
(in
Job
)
resize()
(in
vector1_xyzVector_bool
)
RB5
(in
rosetta
)
remove_position_from_template_res()
(in
EnzConstraintIO
)
resize()
(in
vector1_xyzVector_char
)
RB5
(in
rosetta.core.id
)
remove_position_from_template_res_for_block()
(in
EnzConstraintIO
)
resize()
(in
vector1_xyzVector_float
)
RB5
(in
DOF_Type
)
remove_random_stubs_from_set()
(in
HotspotStubSet
)
resize()
(in
vector1_xyzVector_int
)
RB5
(in
rosetta.core.id._core_id_
)
remove_redundant()
(in
UniformRotationSampler
)
resize()
(in
vector1_xyzVector_uint
)
RB6
(in
rosetta
)
remove_remodel_constraints_from_pose()
(in
RemodelConstraintGenerator
)
resize()
(in
vector1_FragData
)
RB6
(in
rosetta.core.id
)
remove_residue_type()
(in
ResidueTypeSet
)
resize()
(in
vector1_FragDataOP
)
RB6
(in
DOF_Type
)
remove_seqpos()
(in
EnzCstTemplateResCache
)
resize()
(in
vector1_Frame
)
RB6
(in
rosetta.core.id._core_id_
)
remove_seqpos_from_template_res()
(in
EnzdesCstParamCache
)
resize()
(in
vector1_FrameOP
)
RB_DEFAULT
(in
rosetta.protocols.rbsegment_relax
)
remove_short_chunks()
(in
rosetta.protocols.loops._protocols_loops_
)
resize()
(in
AtomID_Map_T_bool_T
)
RB_DEFAULT
(in
RBSegmentType
)
remove_silent_file_if_it_exists()
(in
rosetta.protocols.stepwise.modeler._protocols_stepwise_modeler_
)
resize()
(in
AtomID_Map_T_core_id_AtomID_T
)
RB_DEFAULT
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
remove_singletons()
(in
ClusterBase
)
resize()
(in
AtomID_Map_T_double_T
)
rb_grid_rotamer_trials_atr_rep()
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
remove_singletons_and_update_pose_focus()
(in
DeleteMover
)
resize()
(in
AtomID_Map_T_numeric_xyzVector_T_double_T__T
)
rb_grid_score_atr_rep()
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
remove_small_gaps()
(in
rosetta.protocols.loops._protocols_loops_
)
resize()
(in
NamedAtomID_Map_T_core_id_NamedAtomID_T
)
RB_HELIX
(in
rosetta.protocols.rbsegment_relax
)
remove_stub()
(in
HotspotStubSet
)
resize()
(in
SequenceMapping
)
RB_HELIX
(in
RBSegmentType
)
remove_stubs_from_set()
(in
HotspotStubSet
)
resize()
(in
FragmentStore
)
RB_HELIX
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
remove_surface_waters()
(in
SimplePDB
)
resize()
(in
DecoyStruct
)
RB_JUMP
(in
Enum
)
remove_terminal_loops()
(in
Loops
)
resize()
(in
BinarySilentStruct
)
RB_JUMP
(in
CacheableDataType
)
remove_terminal_phosphates()
(in
rosetta.protocols.stepwise.modeler.rna.phosphate._protocols_stepwise_modeler_rna_phosphate_
)
resize()
(in
RNA_SilentStruct
)
rb_jump()
(in
RigidBodyMover
)
remove_trigger()
(in
GenericMonteCarloMover
)
resize()
(in
RotamerDotsCache
)
rb_jump()
(in
RotamerBoltzmannWeight
)
remove_trigger()
(in
RationalMonteCarlo
)
resize()
(in
RotamerCouplings
)
rb_jump()
(in
ddG
)
remove_upper_terminus_type_from_conformation_residue()
(in
rosetta.core.conformation._core_conformation_
)
resize()
(in
RotamerLinks
)
rb_jump()
(in
RestrictToInterface
)
remove_upper_terminus_type_from_pose_residue()
(in
rosetta.core.pose._core_pose_
)
resize()
(in
BB_Pos
)
RB_lt
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
remove_variant_type()
(in
ResidueType
)
resize()
(in
Helices
)
RB_ltAP
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
remove_variant_type_from_conformation_residue()
(in
rosetta.core.conformation._core_conformation_
)
resize()
(in
SS_Info
)
RB_ltCAP
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
remove_variant_type_from_pose_residue()
(in
rosetta.core.pose._core_pose_
)
resize()
(in
Strands
)
rb_minimizable()
(in
EnzCstTemplateRes
)
remove_variant_type_from_residue()
(in
rosetta.core.pose._core_pose_
)
resize()
(in
BasePartner
)
RB_SHEET
(in
rosetta.protocols.rbsegment_relax
)
remove_vector_exclude_residues()
(in
PCS_Energy_parameters_manager
)
resize()
(in
ElectronDensity
)
RB_SHEET
(in
RBSegmentType
)
remove_vector_exclude_residues()
(in
PCS_Energy_parameters_manager_Ts1
)
resize()
(in
RNA_FilteredBaseBaseInfo
)
RB_SHEET
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
remove_vector_exclude_residues()
(in
PCS_Energy_parameters_manager_Ts2
)
resize()
(in
RNA_RawBaseBaseInfo
)
RBResidueRange
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
remove_vector_exclude_residues()
(in
PCS_Energy_parameters_manager_Ts3
)
resize()
(in
vector1_numeric_geometry_hashing_Ball
)
RBResidueRangeAP
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
remove_vector_exclude_residues()
(in
PCS_Energy_parameters_manager_Ts4
)
resize()
(in
kiss_dct_state
)
RBResidueRangeCAP
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
remove_virtual_O2Prime_hydrogen()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
resize()
(in
kiss_fft_state
)
RBSegment
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
remove_virtual_residues()
(in
rosetta.core.pose._core_pose_
)
resize()
(in
kiss_fftnd_state
)
rbsegment_relax
(in
rosetta.protocols
)
remove_virtual_rna_residue_variant_type()
(in
rosetta.core.pose.rna._core_pose_rna_
)
resize()
(in
kiss_fftndr_state
)
RBSegmentAP
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
RemoveHybridization()
(in
PossibleAtomTypesForAtom
)
resize()
(in
kiss_fftr_state
)
RBSegmentCAP
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
RemoveNorCTermMPM
(in
rosetta.protocols.match._protocols_match_
)
resize()
(in
kiss_fftsplit_state
)
RBSegmentMover
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
RemoveNorCTermMPMAP
(in
rosetta.protocols.match._protocols_match_
)
resize()
(in
WeightedSampler
)
RBSegmentMoverAP
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
RemoveNorCTermMPMCAP
(in
rosetta.protocols.match._protocols_match_
)
resize()
(in
BB_Pos
)
RBSegmentMoverCAP
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
rename_atoms()
(in
rosetta.core.chemical._core_chemical_
)
resize()
(in
ABEGO_SS_Pool
)
RBSegmentRelax
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
rename_checkpoint_files()
(in
GeneticAlgorithm
)
resize()
(in
SecondaryStructurePool
)
RBSegmentRelaxAP
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
rename_checkpoint_files()
(in
GeneticAlgorithmBase
)
resize()
(in
TorsionFragmentLibrary
)
RBSegmentRelaxCAP
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
rename_energies()
(in
SilentStruct
)
resize()
(in
JumpSample
)
RBSegmentType
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
render()
(in
FoldTreeSketch
)
resize()
(in
LoopsFileData
)
rcl1
(in
atomitem
)
render_movemap()
(in
DofPassport
)
resize()
(in
BBGaussianMover
)
rcl1
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
renormalize_quota_pools()
(in
QuotaCollector
)
resize()
(in
std_vector_Real
)
rcl1
(in
rosetta.core.scoring.rna.chemical_shift
)
renormalize_weights()
(in
SOGFunc_Impl
)
resize()
(in
std_vector_SSize
)
rcl2
(in
atomitem
)
renumber_after_variant_changes()
(in
AllowInsert
)
resize()
(in
std_vector_Size
)
rcl2
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
renumber_all_decoys()
(in
SilentFileData
)
resize()
(in
std_vector_char
)
rcl2
(in
rosetta.core.scoring.rna.chemical_shift
)
renumber_decoys()
(in
SilentFilePoseInputStream
)
resize()
(in
std_vector_double
)
rcl3
(in
atomitem
)
renumber_jumps()
(in
FoldTree
)
resize()
(in
std_vector_float
)
rcl3
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
renumber_pdb()
(in
SaveResfileToDiskFilter
)
resize()
(in
std_vector_int
)
rcl3
(in
rosetta.core.scoring.rna.chemical_shift
)
renumber_pdbinfo_based_on_conf_chains()
(in
rosetta.core.pose._core_pose_
)
resize()
(in
std_vector_string
)
RDAT
(in
rosetta.core.io.rna._core_io_rna_
)
renumber_with_pdb_info()
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
resize()
(in
std_vector_uint
)
RDATAP
(in
rosetta.core.io.rna._core_io_rna_
)
reorder()
(in
FoldTree
)
resize()
(in
vec1_vec1_Real
)
RDATCAP
(in
rosetta.core.io.rna._core_io_rna_
)
reorder_foldtree_around_mobile_regions()
(in
LigandBaseProtocol
)
resize()
(in
vec1_vec1_SSize
)
RDC
(in
rosetta.core.scoring._core_scoring_
)
reorder_full_model_info_after_append()
(in
rosetta.core.pose.full_model_info._core_pose_full_model_info_
)
resize()
(in
vec1_vec1_Size
)
rdc
(in
ScoreType
)
reorder_full_model_info_after_delete()
(in
rosetta.core.pose.full_model_info._core_pose_full_model_info_
)
resize()
(in
vec1_vec1_bool
)
rdc
(in
rosetta.core.scoring._core_scoring_
)
reorder_full_model_info_after_prepend()
(in
rosetta.core.pose.full_model_info._core_pose_full_model_info_
)
resize()
(in
vec1_vec1_char
)
rdc
(in
rosetta.core.scoring
)
reorder_membrane_foldtree()
(in
rosetta.protocols.membrane.geometry._protocols_membrane_geometry_
)
resize()
(in
vec1_vec1_double
)
rdc
(in
rosetta
)
reorder_pose()
(in
rosetta.protocols.stepwise.setup._protocols_stepwise_setup_
)
resize()
(in
vec1_vec1_float
)
RDC_Evaluator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
reorder_spans()
(in
SpanningTopology
)
resize()
(in
vec1_vec1_int
)
RDC_EvaluatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
reorder_with_first_non_mobile_as_root()
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
resize()
(in
vec1_vec1_string
)
RDC_EvaluatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
reorient_extended_fibril()
(in
rosetta.protocols.fibril._protocols_fibril_
)
resize()
(in
vec1_vec1_uint
)
RDC_Rohl
(in
rosetta.core.scoring._core_scoring_
)
rep_weight()
(in
EtableEvaluator
)
resize()
(in
vector1_Real
)
rdc_rohl
(in
ScoreType
)
repack
(in
MinTypeEnum
)
resize()
(in
vector1_SSize
)
rdc_rohl
(in
rosetta.core.scoring._core_scoring_
)
repack
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
resize()
(in
vector1_Size
)
rdc_rohl
(in
rosetta.core.scoring
)
repack
(in
rosetta.protocols.antibody.design
)
resize()
(in
vector1_char
)
rdc_rohl
(in
rosetta
)
repack()
(in
BasicSimAnnealerRepacker
)
resize()
(in
vector1_double
)
RDC_RohlAP
(in
rosetta.core.scoring._core_scoring_
)
repack()
(in
DenseIGRepacker
)
resize()
(in
vector1_float
)
RDC_RohlCAP
(in
rosetta.core.scoring._core_scoring_
)
repack()
(in
DoubleDenseIGRepacker
)
resize()
(in
vector1_int
)
rdc_segments
(in
ScoreType
)
repack()
(in
FASTER_IG_Repacker
)
resize()
(in
vector1_string
)
rdc_segments
(in
rosetta.core.scoring._core_scoring_
)
repack()
(in
QuickRepacker
)
resize()
(in
vector1_uint
)
rdc_segments
(in
rosetta.core.scoring
)
repack()
(in
AlaScan
)
resize_asu()
(in
SymmetryInfo
)
rdc_segments
(in
rosetta
)
repack()
(in
DdgFilter
)
resize_atom_records()
(in
PDBInfo
)
RDC_TYPE
(in
RDC
)
repack()
(in
RotamerBoltzmannWeight
)
resize_bb_donor_acceptor_arrays()
(in
HBondSet
)
RDC_TYPE_CC
(in
RDC_TYPE
)
repack_antibody_interface()
(in
AntibodyDesignModeler
)
resize_bb_ids()
(in
RotData
)
RDC_TYPE_CC
(in
RDC
)
repack_antigen_ab_interface()
(in
AntibodyDesignModeler
)
resize_bbs()
(in
RotData
)
RDC_TYPE_CH
(in
RDC_TYPE
)
repack_antigen_interface()
(in
AntibodyDesignModeler
)
resize_espGrid_to_match_pocketGrid()
(in
ElectrostaticpotentialGrid
)
RDC_TYPE_CH
(in
RDC
)
repack_bound()
(in
DdgFilter
)
resize_residue_records()
(in
PDBInfo
)
RDC_TYPE_CHN
(in
RDC_TYPE
)
repack_bound()
(in
ddG
)
resize_semi_vectors()
(in
RotData
)
RDC_TYPE_CHN
(in
RDC
)
repack_cdrs()
(in
AntibodyDesignModeler
)
ResLvlTaskOperation
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RDC_TYPE_NC
(in
RDC_TYPE
)
repack_chain1()
(in
ProteinInterfaceDesignOperation
)
ResLvlTaskOperationAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RDC_TYPE_NC
(in
RDC
)
repack_chain2()
(in
ProteinInterfaceDesignOperation
)
ResLvlTaskOperationCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RDC_TYPE_NCA
(in
RDC_TYPE
)
repack_connection_and_residues_in_movemap()
(in
rosetta.protocols.grafting._protocols_grafting_
)
ResLvlTaskOperationCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RDC_TYPE_NCA
(in
RDC
)
repack_connection_and_residues_in_movemap_and_piece()
(in
rosetta.protocols.grafting._protocols_grafting_
)
ResLvlTaskOperationCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RDC_TYPE_NH
(in
RDC_TYPE
)
repack_connection_and_residues_in_movemap_and_piece_and_neighbors()
(in
rosetta.protocols.grafting._protocols_grafting_
)
ResLvlTaskOperationCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RDC_TYPE_NH
(in
RDC
)
repack_neighbors()
(in
LoopMover_Refine_CCD
)
ResLvlTaskOperationFactory
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RDCAP
(in
rosetta.core.scoring._core_scoring_
)
repack_period()
(in
LoopMover_Refine_CCD
)
ResLvlTaskOperationFactoryAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RDCCAP
(in
rosetta.core.scoring._core_scoring_
)
repack_query()
(in
MultiThreadingMover
)
ResLvlTaskOperationFactoryCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
RdcEvaluatorCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
repack_query()
(in
ThreadingMover
)
resname()
(in
ContactPartner
)
RdcEvaluatorCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
repack_shell()
(in
DesignAroundOperation
)
resname()
(in
BackboneGridSampler
)
RdcEvaluatorCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
repack_shell()
(in
RestrictToAlignedSegmentsOperation
)
resnum()
(in
Sequence
)
RDCScore
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
repack_to_matrix()
(in
CSTalosIO
)
resnum()
(in
PDBLandmark
)
RDCScoreAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
repackable_residues()
(in
rosetta.core.pack._core_pack_
)
resnum()
(in
ResidueFeature
)
RDCScoreCAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
repacking_radius()
(in
RotamerBoltzmannWeight
)
resnum()
(in
GeneralizedKICfilter
)
RdcSelectEvaluatorCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
repacking_residues()
(in
PackerTask
)
resnum()
(in
BluePrint
)
RdcSelectEvaluatorCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
repacking_residues()
(in
PackerTask_
)
resnum()
(in
Torsion
)
RdcSelectEvaluatorCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
RepackingRefiner
(in
rosetta.protocols.loop_modeling.refiners._protocols_loop_modeling_refiners_
)
resnum()
(in
AddChainBreak
)
RdcTargetEvaluatorCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
RepackingRefinerAP
(in
rosetta.protocols.loop_modeling.refiners._protocols_loop_modeling_refiners_
)
resnum()
(in
EnergyPerResidueFilter
)
RdcTargetEvaluatorCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
RepackingRefinerCAP
(in
rosetta.protocols.loop_modeling.refiners._protocols_loop_modeling_refiners_
)
resnum()
(in
NonSequentialNeighborsFilter
)
RdcTargetEvaluatorCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
RepackingRefinerCreator
(in
rosetta.protocols.loop_modeling.refiners._protocols_loop_modeling_refiners_
)
resnum()
(in
SetChiMover
)
rdf
(in
rosetta.protocols.ligand_docking
)
RepackingRefinerCreatorAP
(in
rosetta.protocols.loop_modeling.refiners._protocols_loop_modeling_refiners_
)
resnum_exists_in_set()
(in
ResidueProbDesignOperation
)
RDFBase
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepackingRefinerCreatorCAP
(in
rosetta.protocols.loop_modeling.refiners._protocols_loop_modeling_refiners_
)
resnum_map()
(in
BluePrint
)
RDFBaseAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepackMinimize
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
resnums()
(in
ResidueIEFilter
)
RDFBaseCAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepackMinimizeAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
resnums_allow_design()
(in
DesignAroundOperation
)
RDFBinaryHbondCreator
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepackMinimizeCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
ResolutionSwitcher
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
RDFBinaryHbondCreatorAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepackMinimizeCreator
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
ResolutionSwitcherAP
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
RDFBinaryHbondCreatorCAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepackMinimizeCreatorAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
ResolutionSwitcherCAP
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
RDFBinaryHbondFunction
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepackMinimizeCreatorCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
resolve_as_serialized_loop_from_pose()
(in
LoopFromFileData
)
RDFBinaryHbondFunctionAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepackSidechainsMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
resolve_as_serialized_loops()
(in
LoopsFileData
)
RDFBinaryHbondFunctionCAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepackSidechainsMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
resolve_db_partition()
(in
rosetta.basic.database._basic_database_
)
RDFBinaryOrbitalFunction
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepackSidechainsMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
resolve_index()
(in
ResidueIndexDescription
)
RDFBinaryOrbitalFunctionAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepackSidechainsMoverCreator
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
resolve_index()
(in
ResidueIndexDescriptionFromFile
)
RDFBinaryOrbitalFunctionCAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepackSidechainsMoverCreatorAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
resolve_jump()
(in
SequenceAnnotation
)
RDFBinaryOrbitalFunctionCreator
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepackSidechainsMoverCreatorCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
resolve_loop_indices()
(in
GuardedLoopsFromFile
)
RDFBinaryOrbitalFunctionCreatorAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepackTrial
(in
rosetta.protocols.loops.loop_mover.refine._protocols_loops_loop_mover_refine_
)
resolve_loop_indices_once()
(in
GuardedLoopsFromFile
)
RDFBinaryOrbitalFunctionCreatorCAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepackTrialAP
(in
rosetta.protocols.loops.loop_mover.refine._protocols_loops_loop_mover_refine_
)
resolve_loopfile_indices()
(in
LoopRelaxMover
)
RDFChargeCreator
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepackTrialCAP
(in
rosetta.protocols.loops.loop_mover.refine._protocols_loops_loop_mover_refine_
)
resolve_loops()
(in
LoopsFileData
)
RDFChargeCreatorAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepackTrialCreator
(in
rosetta.protocols.loops.loop_mover.refine._protocols_loops_loop_mover_refine_
)
resolve_seq()
(in
SequenceAnnotation
)
RDFChargeCreatorCAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepackTrialCreatorAP
(in
rosetta.protocols.loops.loop_mover.refine._protocols_loops_loop_mover_refine_
)
resolve_store_path()
(in
StructureStoreManager
)
RDFChargeFunction
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepackTrialCreatorCAP
(in
rosetta.protocols.loops.loop_mover.refine._protocols_loops_loop_mover_refine_
)
resolve_trie_vs_path()
(in
TrieCountPair1BC3
)
RDFChargeFunctionAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepeatMover
(in
rosetta.protocols.moves._protocols_moves_
)
resolve_trie_vs_path()
(in
TrieCountPair1BC4
)
RDFChargeFunctionCAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepeatMoverAP
(in
rosetta.protocols.moves._protocols_moves_
)
resolve_trie_vs_path()
(in
TrieCountPairAll
)
RDFElecCreator
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepeatMoverCAP
(in
rosetta.protocols.moves._protocols_moves_
)
resolve_trie_vs_path()
(in
TrieCountPairGeneric
)
RDFElecCreatorAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepeatParameterFilter
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
resolve_trie_vs_path()
(in
TrieCountPairNone
)
RDFElecCreatorCAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepeatParameterFilterAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
resolve_trie_vs_path()
(in
HBCountPairFunction
)
RDFElecFunction
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepeatParameterFilterCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
resolve_trie_vs_path()
(in
RotamerTrieBase
)
RDFElecFunctionAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepeatParameterFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
resolve_trie_vs_path()
(in
TrieCountPairBase
)
RDFElecFunctionCAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepeatParameterFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
resolve_trie_vs_trie()
(in
TrieCountPair1BC3
)
RDFEtableCreator
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepeatParameterFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
resolve_trie_vs_trie()
(in
TrieCountPair1BC4
)
RDFEtableCreatorAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepeatPropagationMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
resolve_trie_vs_trie()
(in
TrieCountPairAll
)
RDFEtableCreatorCAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepeatPropagationMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
resolve_trie_vs_trie()
(in
TrieCountPairGeneric
)
RDFEtableFunction
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepeatPropagationMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
resolve_trie_vs_trie()
(in
TrieCountPairNone
)
RDFEtableFunctionAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepeatPropagationMoverCreator
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
resolve_trie_vs_trie()
(in
HBCountPairFunction
)
RDFEtableFunctionCAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepeatPropagationMoverCreatorAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
resolve_trie_vs_trie()
(in
RotamerTrieBase
)
RDFFunctionCreator
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
RepeatPropagationMoverCreatorCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
resolve_trie_vs_trie()
(in
TrieCountPairBase
)
RDFFunctionCreatorAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
repeats()
(in
AlaScan
)
resolve_uncommitted_substitution()
(in
MinimalistFlexbbNode
)
RDFFunctionCreatorCAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
repeats()
(in
DdGScan
)
resolver()
(in
ProtectedConformation
)
RDFFunctionFactory
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
repeats()
(in
DdgFilter
)
resource_description()
(in
FallbackConfigurationCreator
)
RDFFunctionFactoryAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
repeats()
(in
ddG
)
resource_description()
(in
NativeFallbackConfigurationCreator
)
RDFFunctionFactoryCAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
repeats()
(in
PerturbByBins
)
resource_description()
(in
LoopsFileFallbackConfigurationCreator
)
RDFHbondCreator
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
replace()
(in
rosetta.protocols.forge.methods._protocols_forge_methods_
)
resource_description()
(in
SurfaceVectorFallbackConfigurationCreator
)
RDFHbondCreatorAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
replace_atom()
(in
Atom
)
resource_manager
(in
rosetta.basic
)
RDFHbondCreatorCAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
replace_atom()
(in
Atom_
)
ResourceConfiguration
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
RDFHbondFunction
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
replace_conformation_residue_copying_existing_coordinates()
(in
rosetta.core.conformation._core_conformation_
)
ResourceConfigurationAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
RDFHbondFunctionAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
replace_creator()
(in
ConstraintFactory
)
ResourceConfigurationCAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
RDFHbondFunctionCAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
replace_environment_variables()
(in
rosetta.utility._utility_
)
ResourceLoader
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
RDFOrbitalFunction
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
replace_in()
(in
rosetta.utility._utility_
)
ResourceLoaderAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
RDFOrbitalFunctionAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
replace_init()
(in
rosetta
)
ResourceLoaderCAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
RDFOrbitalFunctionCAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
replace_pose_residue_copying_existing_coordinates()
(in
rosetta.core.pose._core_pose_
)
ResourceLoaderCreator
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
RDFOrbitalFunctionCreator
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
replace_region()
(in
rosetta.protocols.grafting._protocols_grafting_
)
ResourceLoaderCreatorAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
RDFOrbitalFunctionCreatorAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
replace_res()
(in
PDBInfo
)
ResourceLoaderCreatorCAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
RDFOrbitalFunctionCreatorCAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
replace_res_remap_bfactors()
(in
PDBInfo
)
ResourceLoaderFactory
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
re_init()
(in
PcsEnergyParameterManager
)
replace_residue()
(in
Conformation
)
ResourceLoaderFactoryAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
re_init()
(in
PcsGridSearchParameterManager
)
replace_residue()
(in
SymmetricConformation
)
ResourceLoaderFactoryCAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
re_init()
(in
PcsInputCenterManager
)
replace_residue()
(in
Pose
)
ResourceLocator
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
reactivity()
(in
RDAT
)
replace_residue()
(in
ProtectedConformation
)
ResourceLocatorAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
reactivity_error()
(in
RDAT
)
replace_residue_in_atom_tree()
(in
rosetta.core.conformation._core_conformation_
)
ResourceLocatorCAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read()
(in
ElectronConfiguration
)
replace_residue_keeping_all_atom_positions()
(in
rosetta.protocols.toolbox.match_enzdes_util._protocols_toolbox_match_enzdes_util_
)
ResourceLocatorCreator
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read()
(in
Element
)
replace_residue_subtree()
(in
AtomTree
)
ResourceLocatorCreatorAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read()
(in
GasteigerAtomTypeData
)
replace_stub1()
(in
ICoorOrbitalData
)
ResourceLocatorCreatorCAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read()
(in
SymDof
)
replace_stub2()
(in
ICoorOrbitalData
)
ResourceLocatorFactory
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read()
(in
BBTorsionAndAnglesSRFD
)
replace_stub3()
(in
ICoorOrbitalData
)
ResourceLocatorFactoryAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read()
(in
DownJumpSRFD
)
replace_tree()
(in
AtomTree
)
ResourceLocatorFactoryCAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read()
(in
Frame
)
replaced_symmetric_foldtree_with_new_monomer()
(in
rosetta.core.conformation.symmetry._core_conformation_symmetry_
)
ResourceManager
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read()
(in
JumpingFrame
)
ReplaceRegionMover
(in
rosetta.protocols.grafting.simple_movers._protocols_grafting_simple_movers_
)
ResourceManagerAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read()
(in
NonContinuousFrame
)
ReplaceRegionMoverAP
(in
rosetta.protocols.grafting.simple_movers._protocols_grafting_simple_movers_
)
ResourceManagerCAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read()
(in
BUFFER
)
ReplaceRegionMoverCAP
(in
rosetta.protocols.grafting.simple_movers._protocols_grafting_simple_movers_
)
ResourceManagerCreator
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read()
(in
CSTalosIO
)
ReplaceRegionMoverCreator
(in
rosetta.protocols.grafting.simple_movers._protocols_grafting_simple_movers_
)
ResourceManagerCreatorAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read()
(in
JCouplingIO
)
ReplaceRegionMoverCreatorAP
(in
rosetta.protocols.grafting.simple_movers._protocols_grafting_simple_movers_
)
ResourceManagerCreatorCAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read()
(in
LAMBEGO_IO
)
ReplaceRegionMoverCreatorCAP
(in
rosetta.protocols.grafting.simple_movers._protocols_grafting_simple_movers_
)
ResourceManagerFactory
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read()
(in
PhiPsiTalosIO
)
replaces()
(in
Patch
)
ResourceManagerFactoryAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read()
(in
TorsionBinIO
)
ReplaceString()
(in
GenPharmacophore
)
ResourceManagerFactoryCAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read()
(in
ClusterBase
)
ReplicaExchangeMC
(in
rosetta.protocols.moves._protocols_moves_
)
ResourceOptions
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read()
(in
FoldandDockClaimer
)
ReplicaExchangeMCAP
(in
rosetta.protocols.moves._protocols_moves_
)
ResourceOptionsAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read()
(in
MembraneTopologyClaimer
)
ReplicaExchangeMCCAP
(in
rosetta.protocols.moves._protocols_moves_
)
ResourceOptionsCAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read()
(in
TopologyClaimer
)
ReplicateFilter
(in
rosetta.protocols.filters._protocols_filters_
)
ResourceOptionsCreator
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read()
(in
Tag
)
ReplicateFilterAP
(in
rosetta.protocols.filters._protocols_filters_
)
ResourceOptionsCreatorAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read_aa_encoding_matrix()
(in
NMerSVMEnergy
)
ReplicateFilterCAP
(in
rosetta.protocols.filters._protocols_filters_
)
ResourceOptionsCreatorCAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read_additional_pdb_data()
(in
rosetta.core.import_pose._core_import_pose_
)
ReplicateFilterCreator
(in
rosetta.protocols.filters._protocols_filters_
)
ResourceOptionsFactory
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read_alignment_file()
(in
rosetta.core.sequence._core_sequence_
)
ReplicateFilterCreatorAP
(in
rosetta.protocols.filters._protocols_filters_
)
ResourceOptionsFactoryAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read_all_alignments()
(in
rosetta.core.sequence._core_sequence_
)
ReplicateFilterCreatorCAP
(in
rosetta.protocols.filters._protocols_filters_
)
ResourceOptionsFactoryCAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read_all_poses()
(in
rosetta.core.import_pose._core_import_pose_
)
ReplicateTask
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
ResourceStream
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read_all_variables_from_input_file()
(in
DynamicAggregateFunction
)
ReplicateTaskAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
ResourceStreamAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read_aln()
(in
rosetta.core.sequence._core_sequence_
)
ReplicateTaskCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
ResourceStreamCAP
(in
rosetta.basic.resource_manager._basic_resource_manager_
)
read_anchorfile()
(in
Anchor
)
ReplicateTaskCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
ResPairMinimizationData
(in
rosetta.core.scoring._core_scoring_
)
read_and_store_fragments()
(in
H3PerturbCCD
)
ReplicateTaskCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
ResPairMinimizationDataAP
(in
rosetta.core.scoring._core_scoring_
)
read_and_store_fragments()
(in
AntibodyModeler
)
ReplicateTaskCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
ResPairMinimizationDataCAP
(in
rosetta.core.scoring._core_scoring_
)
read_binary()
(in
rosetta.core.io.serialization._core_io_serialization_
)
REPLONLY
(in
rosetta
)
ResPairMotif
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
read_binary()
(in
XformScore
)
REPLONLY
(in
rosetta.core.chemical
)
ResPairMotifAP
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
read_biounit()
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
REPLONLY
(in
rosetta.core.chemical._core_chemical_
)
ResPairMotifCAP
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
read_blueprint()
(in
BluePrint
)
REPLONLY
(in
VariantType
)
ResPairMotifMetaBinner
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
read_bond_file()
(in
GasteigerAtomTypeSet
)
Report
(in
rosetta.protocols.features._protocols_features_
)
ResPairMotifMetaBinnerAP
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
read_checkpoint()
(in
Entity
)
Report()
(in
Timer
)
ResPairMotifMetaBinnerCAP
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
read_checkpoint()
(in
GeneticAlgorithm
)
report()
(in
PeptideDeriverFilter
)
ResPairMotifQuery
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
read_checkpoint()
(in
GeneticAlgorithmBase
)
report()
(in
ExposedHydrophobicsFilter
)
ResPairMotifQueryAP
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
read_codes_and_roots_from_database_file()
(in
rosetta.core.chemical.carbohydrates._core_chemical_carbohydrates_
)
report()
(in
RotamerDNAHBondFilter
)
ResPairMotifQueryCAP
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
read_coef1()
(in
BranchAngleOptimizer
)
report()
(in
DockingHighResFilter
)
ResPairMotifs
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
read_coef1_default()
(in
BranchAngleOptimizer
)
report()
(in
DockingLowResFilter
)
ResPairMotifsAP
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
read_coef1_user()
(in
BranchAngleOptimizer
)
report()
(in
CalculatorFilter
)
ResPairMotifsCAP
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
read_coef2()
(in
BranchAngleOptimizer
)
report()
(in
CombinedFilter
)
respect_this_movemap()
(in
KinematicWrapper
)
read_coef2_default()
(in
BranchAngleOptimizer
)
report()
(in
CompoundFilter
)
respond_to_peripheral_hitlist_change()
(in
ClassicMatchAlgorithm
)
read_coef2_user()
(in
BranchAngleOptimizer
)
report()
(in
ContingentFilter
)
respond_to_peripheral_hitlist_change()
(in
DownstreamAlgorithm
)
read_comment_pdb()
(in
rosetta.core.pose._core_pose_
)
report()
(in
FalseFilter
)
respond_to_peripheral_hitlist_change()
(in
SecondaryMatcherToDownstreamResidue
)
read_conformers_from_database_file_for_ring_size()
(in
rosetta.core.chemical._core_chemical_
)
report()
(in
Filter
)
respond_to_peripheral_hitlist_change()
(in
SecondaryMatcherToUpstreamResidue
)
read_constraint()
(in
DunbrackConstraint
)
report()
(in
FilterCollection
)
respond_to_peripheral_hitlist_change()
(in
WriteUpstreamCoordinateKinemage
)
read_constraint()
(in
RotamerConstraint
)
report()
(in
IfThenFilter
)
respond_to_primary_hitlist_change()
(in
ClassicMatchAlgorithm
)
read_constraint()
(in
AmbiguousConstraint
)
report()
(in
MoveBeforeFilter
)
respond_to_primary_hitlist_change()
(in
DownstreamAlgorithm
)
read_constraint()
(in
AmbiguousNMRConstraint
)
report()
(in
ReplicateFilter
)
respond_to_primary_hitlist_change()
(in
SecondaryMatcherToDownstreamResidue
)
read_constraint()
(in
AmbiguousNMRDistanceConstraint
)
report()
(in
StochasticFilter
)
respond_to_primary_hitlist_change()
(in
SecondaryMatcherToUpstreamResidue
)
read_constraint()
(in
AngleConstraint
)
report()
(in
TimeFilter
)
respond_to_primary_hitlist_change()
(in
WriteUpstreamCoordinateKinemage
)
read_constraint()
(in
AtomPairConstraint
)
report()
(in
TrueFilter
)
ResRangePredicate
(in
rosetta.core.scoring._core_scoring_
)
read_constraint()
(in
BackboneStubConstraint
)
report()
(in
CoreDunbrackFilter
)
ResRangePredicateAP
(in
rosetta.core.scoring._core_scoring_
)
read_constraint()
(in
BackboneStubLinearConstraint
)
report()
(in
FragQualFilter
)
ResRangePredicateCAP
(in
rosetta.core.scoring._core_scoring_
)
read_constraint()
(in
BigBinConstraint
)
report()
(in
HSSTripletFilter
)
resSeq
(in
LoopConfiguration
)
read_constraint()
(in
ConstantConstraint
)
report()
(in
HelixKinkFilter
)
resSeq
(in
rosetta.protocols.loops._protocols_loops_
)
read_constraint()
(in
Constraint
)
report()
(in
HelixPairingFilter
)
resSeq
(in
rosetta.protocols.loops
)
read_constraint()
(in
CoordinateConstraint
)
report()
(in
InterlockingAromaFilter
)
resSeq
(in
rosetta
)
read_constraint()
(in
DihedralConstraint
)
report()
(in
NcontactsFilter
)
ResSingleMinimizationData
(in
rosetta.core.scoring._core_scoring_
)
read_constraint()
(in
DihedralPairConstraint
)
report()
(in
ParallelBetaPairingPreferenceFilter
)
ResSingleMinimizationDataAP
(in
rosetta.core.scoring._core_scoring_
)
read_constraint()
(in
DistancePairConstraint
)
report()
(in
SecondaryStructureCountFilter
)
ResSingleMinimizationDataCAP
(in
rosetta.core.scoring._core_scoring_
)
read_constraint()
(in
FabConstraint
)
report()
(in
SecondaryStructureFilter
)
rest_expression_token()
(in
ArithmeticASTRestExpression
)
read_constraint()
(in
KofNConstraint
)
report()
(in
SecondaryStructureHasResidueFilter
)
rest_term_token()
(in
ArithmeticASTRestTerm
)
read_constraint()
(in
LocalCoordinateConstraint
)
report()
(in
SheetTopologyFilter
)
restart()
(in
FileSystemJobDistributor
)
read_constraint()
(in
MultiConstraint
)
report()
(in
FragmentLookupFilter
)
restart()
(in
JobDistributor
)
read_constraint()
(in
NamedAngleConstraint
)
report()
(in
AtomCountFilter
)
restart_mode()
(in
VarLengthBuild
)
read_constraint()
(in
NamedAtomPairConstraint
)
report()
(in
ChainExistsFilter
)
restart_simulation()
(in
BiasEnergy
)
read_constraint()
(in
NonResidueTypeConstraint
)
report()
(in
CompleteConnectionsFilter
)
restart_simulation()
(in
DbTrajectoryRecorder
)
read_constraint()
(in
ResidueTypeConstraint
)
report()
(in
HBondAcceptorFilter
)
restart_simulation()
(in
FixedTemperatureController
)
read_constraint()
(in
ResidueTypeLinkingConstraint
)
report()
(in
HBondDonorFilter
)
restart_simulation()
(in
MetricRecorder
)
read_constraint()
(in
SequenceProfileConstraint
)
report()
(in
HeavyAtomFilter
)
restart_simulation()
(in
ParallelTempering
)
read_constraint()
(in
SiteConstraint
)
report()
(in
MolarMassFilter
)
restart_simulation()
(in
ProgressBarObserver
)
read_constraint()
(in
SiteConstraintResidues
)
report()
(in
MolecularMassFilter
)
restart_simulation()
(in
SilentTrajectoryRecorder
)
read_constraint()
(in
AmbiguousMultiConstraint
)
report()
(in
ClashCheckFilter
)
restart_simulation()
(in
SimulatedTempering
)
read_constraint()
(in
BindingSiteConstraint
)
report()
(in
GetRBDOFValues
)
restart_simulation()
(in
TemperatureController
)
read_constraint()
(in
COMCoordinateConstraint
)
report()
(in
InterfacePackingFilter
)
restart_simulation()
(in
TemperingBase
)
read_constraint()
(in
SequenceCoupling1BDConstraint
)
report()
(in
OligomericAverageDegreeFilter
)
restart_simulation()
(in
ThermodynamicObserver
)
read_constraint()
(in
SequenceCouplingConstraint
)
report()
(in
SymUnsatHbondFilter
)
restart_simulation()
(in
TrialCounterObserver
)
read_constraint()
(in
PocketConstraint
)
report()
(in
ReportSequenceDifferences
)
restore()
(in
ClosureProblem
)
read_constraints()
(in
ConstraintIO
)
report()
(in
AtomicContactCountFilter
)
restore_archive()
(in
ArchiveManager
)
read_constraints()
(in
Template
)
report()
(in
AverageDegreeFilter
)
restore_archive()
(in
BaseArchiveManager
)
read_constraints_new()
(in
ConstraintIO
)
report()
(in
BindingStrainFilter
)
restore_from_file()
(in
HedgeArchive
)
read_cst_file()
(in
FullModelParameters
)
report()
(in
BoltzmannFilter
)
restore_from_file()
(in
IterativeAbrelax
)
read_data()
(in
BBTorsionAndAnglesSRFD
)
report()
(in
ClashWithTargetFilter
)
restore_from_file()
(in
IterativeBase
)
read_data()
(in
BBTorsionSRFD
)
report()
(in
DesignableResiduesFilter
)
restore_from_file()
(in
IterativeCentroid
)
read_data()
(in
DownJumpSRFD
)
report()
(in
DisulfideFilter
)
restore_from_file()
(in
IterativeFullatom
)
read_data()
(in
FragmentIO
)
report()
(in
FNatFilter
)
restore_from_file()
(in
AbstractArchiveBase
)
read_data()
(in
IndependentBBTorsionSRFD
)
report()
(in
FilterScanFilter
)
restore_from_file()
(in
ArchiveBase
)
read_data()
(in
SecstructSRFD
)
report()
(in
HbondsToAtomFilter
)
restore_from_file()
(in
EvaluatedArchive
)
read_data()
(in
SingleResidueFragData
)
report()
(in
HbondsToResidueFilter
)
restore_from_file()
(in
NormalizedEvaluatedArchive
)
read_data()
(in
UpJumpSRFD
)
report()
(in
IRmsdFilter
)
restore_from_file()
(in
VarianceStatisticsArchive
)
read_data()
(in
DunbrackConstraint
)
report()
(in
InterfaceHolesFilter
)
restore_original_foldtree()
(in
FoldTreeHybridize
)
read_data()
(in
RotamerConstraint
)
report()
(in
LRmsdFilter
)
restore_pose_from_rbsegs()
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
read_data()
(in
AmbiguousConstraint
)
report()
(in
RelativeSegmentFilter
)
restore_residues()
(in
rosetta.protocols.forge.methods._protocols_forge_methods_
)
read_data()
(in
AmbiguousNMRConstraint
)
report()
(in
RmsdFilter
)
restore_status()
(in
HedgeArchive
)
read_data()
(in
AmbiguousNMRDistanceConstraint
)
report()
(in
RmsdSimpleFilter
)
restore_status()
(in
IterativeAbrelax
)
read_data()
(in
AngleConstraint
)
report()
(in
SSamountFilter
)
restore_status()
(in
IterativeBase
)
read_data()
(in
AtomPairConstraint
)
report()
(in
SequenceRecoveryFilter
)
restore_status()
(in
IterativeCentroid
)
read_data()
(in
BackboneStubConstraint
)
report()
(in
SpecificResiduesNearInterfaceFilter
)
restore_status()
(in
IterativeFullatom
)
read_data()
(in
BackboneStubLinearConstraint
)
report()
(in
StubScoreFilter
)
restore_status()
(in
ArchiveBase
)
read_data()
(in
BigBinConstraint
)
report()
(in
StubScoreLoopsFilter
)
restore_status()
(in
EvaluatedArchive
)
read_data()
(in
BoundFunc
)
report()
(in
Torsion
)
restore_status()
(in
NormalizedEvaluatedArchive
)
read_data()
(in
ConstantConstraint
)
report()
(in
AbinitioBaseFilter
)
restore_status()
(in
VarianceStatisticsArchive
)
read_data()
(in
Constraint
)
report()
(in
AlaScan
)
restoreState()
(in
RandomGenerator
)
read_data()
(in
CoordinateConstraint
)
report()
(in
AngleToVector
)
restoreState()
(in
mt19937_RG
)
read_data()
(in
DihedralConstraint
)
report()
(in
AtomicContactFilter
)
restoreState()
(in
standard_RG
)
read_data()
(in
DihedralPairConstraint
)
report()
(in
AtomicDistanceFilter
)
restoreState()
(in
uniform_RG
)
read_data()
(in
DistancePairConstraint
)
report()
(in
AveragePathLengthFilter
)
restrain_ligand_nbr_atom()
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
read_data()
(in
FabConstraint
)
report()
(in
BuriedUnsatHbondFilter
)
restrain_protein_Calphas()
(in
LigandBaseProtocol
)
read_data()
(in
KofNConstraint
)
report()
(in
COFilter
)
restrict_aatypes_for_selection()
(in
SelectResiduesByLayer
)
read_data()
(in
LocalCoordinateConstraint
)
report()
(in
ConservedPosMutationFilter
)
restrict_absent_canonical_aas()
(in
ResidueLevelTask
)
read_data()
(in
MultiConstraint
)
report()
(in
ConstraintScoreCutoffFilter
)
restrict_absent_canonical_aas()
(in
ResidueLevelTask_
)
read_data()
(in
NamedAngleConstraint
)
report()
(in
DdGScan
)
restrict_absent_nas()
(in
ResidueLevelTask
)
read_data()
(in
NamedAtomPairConstraint
)
report()
(in
DdgFilter
)
restrict_absent_nas()
(in
ResidueLevelTask_
)
read_data()
(in
NonResidueTypeConstraint
)
report()
(in
DeltaFilter
)
restrict_dna_rotamers()
(in
rosetta.protocols.dna._protocols_dna_
)
read_data()
(in
OffsetPeriodicBoundFunc
)
report()
(in
DisulfideEntropyFilter
)
restrict_identities()
(in
RestrictIdentitiesAtAlignedPositionsOperation
)
read_data()
(in
PeriodicBoundFunc
)
report()
(in
DomainInterfaceFilter
)
restrict_nonnative_canonical_aas()
(in
ResidueLevelTask
)
read_data()
(in
ResidueTypeConstraint
)
report()
(in
EnergyPerResidueFilter
)
restrict_nonnative_canonical_aas()
(in
ResidueLevelTask_
)
read_data()
(in
ResidueTypeLinkingConstraint
)
report()
(in
ExpiryFilter
)
restrict_only_design_to_loops()
(in
RestrictToLoops
)
read_data()
(in
SequenceProfileConstraint
)
report()
(in
FileExistFilter
)
restrict_sequence_profile()
(in
ProteinInterfaceMultiStateDesignMover
)
read_data()
(in
SiteConstraint
)
report()
(in
FileRemoveFilter
)
restrict_to_aligned_segments()
(in
SeqprofConsensusOperation
)
read_data()
(in
SiteConstraintResidues
)
report()
(in
GeometryFilter
)
restrict_to_nbrs()
(in
ddGMover
)
read_data()
(in
DistanceFunc
)
report()
(in
HolesFilter
)
restrict_to_protein_residues()
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
read_data()
(in
CBSG_Dihedral_Func
)
report()
(in
InterRepeatContactFilter
)
restrict_to_repacking()
(in
PackerTask
)
read_data()
(in
CB_Angle_Func
)
report()
(in
InterfaceBindingEnergyDensityFilter
)
restrict_to_repacking()
(in
PackerTask_
)
read_data()
(in
CaCbCbCa_Dihedral_Func
)
report()
(in
InterfaceSasaFilter
)
restrict_to_repacking()
(in
ResidueLevelTask
)
read_data()
(in
CaCbCb_Angle_Func
)
report()
(in
IntraRepeatContactFilter
)
restrict_to_repacking()
(in
ResidueLevelTask_
)
read_data()
(in
Cb_Distance_Func
)
report()
(in
LeastNativeLike9merFilter
)
restrict_to_repacking()
(in
DesignRepackMover
)
read_data()
(in
Cen_Distance_Func
)
report()
(in
MotifScoreFilter
)
restrict_to_residue()
(in
DisallowIfNonnative
)
read_data()
(in
NCaCaC_Dihedral_Func
)
report()
(in
MultipleSigmoids
)
restrict_to_residues()
(in
PackerTask
)
read_data()
(in
SGSG_Dihedral_Func
)
report()
(in
MutationsFilter
)
restrict_to_residues()
(in
PackerTask_
)
read_data()
(in
SG_Dist_Func
)
report()
(in
NMerPSSMEnergyFilter
)
restrict_to_single_sequence()
(in
rosetta.protocols.dna._protocols_dna_
)
read_data()
(in
AmberPeriodicFunc
)
report()
(in
NMerSVMEnergyFilter
)
RestrictAbsentCanonicalAAS
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_data()
(in
CharmmPeriodicFunc
)
report()
(in
NeighborTypeFilter
)
RestrictAbsentCanonicalAASAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_data()
(in
CircularGeneral1D_Func
)
report()
(in
NetChargeFilter
)
RestrictAbsentCanonicalAASCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_data()
(in
CircularHarmonicFunc
)
report()
(in
NonSequentialNeighborsFilter
)
RestrictAbsentCanonicalAASCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_data()
(in
CircularPowerFunc
)
report()
(in
Operator
)
RestrictAbsentCanonicalAASCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_data()
(in
CircularSigmoidalFunc
)
report()
(in
PDDFScoreFilter
)
RestrictAbsentCanonicalAASCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_data()
(in
CircularSplineFunc
)
report()
(in
PackStatFilter
)
RestrictAbsentCanonicalAASRLT
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_data()
(in
ConstantFunc
)
report()
(in
PackerNeighborGraphFilter
)
RestrictAbsentCanonicalAASRLTAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_data()
(in
CountViolFunc
)
report()
(in
PoseComment
)
RestrictAbsentCanonicalAASRLTCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_data()
(in
EtableFunc
)
report()
(in
PoseInfoFilter
)
RestrictAbsentCanonicalAASRLTCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_data()
(in
FadeFunc
)
report()
(in
RGFilter
)
RestrictAbsentCanonicalAASRLTCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_data()
(in
FlatHarmonicFunc
)
report()
(in
RangeFilter
)
RestrictAbsentCanonicalAASRLTCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_data()
(in
Func
)
report()
(in
RelativePoseFilter
)
RestrictByCalculatorsOperation
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
GaussianChainDoubleFunc
)
report()
(in
RepeatParameterFilter
)
RestrictByCalculatorsOperationAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
GaussianChainFunc
)
report()
(in
ReportFilter
)
RestrictByCalculatorsOperationCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
GaussianChainQuadrupleFunc
)
report()
(in
ResidueBurialFilter
)
RestrictByCalculatorsOperationCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
GaussianChainSingleFunc
)
report()
(in
ResidueCountFilter
)
RestrictByCalculatorsOperationCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
GaussianChainTripleFunc
)
report()
(in
ResidueDistanceFilter
)
RestrictByCalculatorsOperationCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
GaussianFunc
)
report()
(in
ResidueIEFilter
)
RestrictChainToRepackingOperation
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
HarmonicFunc
)
report()
(in
ResidueSetChainEnergyFilter
)
RestrictChainToRepackingOperationAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
IdentityFunc
)
report()
(in
ResiduesInInterfaceFilter
)
RestrictChainToRepackingOperationCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
KarplusFunc
)
report()
(in
RotamerBoltzmannWeight
)
RestrictChainToRepackingOperationCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
LinearPenaltyFunction
)
report()
(in
SAXSScoreFilter
)
RestrictChainToRepackingOperationCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
MinMultiHarmonicFunc
)
report()
(in
SSMotifFinder
)
RestrictChainToRepackingOperationCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
MixtureFunc
)
report()
(in
SavePoseConstraintToFileFilter
)
RestrictConservedLowDdgOperation
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
PeriodicFunc
)
report()
(in
SaveResfileToDiskFilter
)
RestrictConservedLowDdgOperationAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
SOGFunc
)
report()
(in
ScoreCutoffFilter
)
RestrictConservedLowDdgOperationCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
SOGFunc_Impl
)
report()
(in
ScoreTypeFilter
)
RestrictConservedLowDdgOperationCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
ScalarWeightedFunc
)
report()
(in
ShapeComplementarityFilter
)
RestrictConservedLowDdgOperationCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
SigmoidFunc
)
report()
(in
SheetFilter
)
RestrictConservedLowDdgOperationCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
SkipViolFunc
)
report()
(in
SidechainRmsdFilter
)
RestrictDesignToProteinDNAInterface
(in
rosetta.protocols.dna._protocols_dna_
)
read_data()
(in
SoedingFunc
)
report()
(in
Sigmoid
)
RestrictDesignToProteinDNAInterfaceAP
(in
rosetta.protocols.dna._protocols_dna_
)
read_data()
(in
SplineFunc
)
report()
(in
StemFinder
)
RestrictDesignToProteinDNAInterfaceCAP
(in
rosetta.protocols.dna._protocols_dna_
)
read_data()
(in
SquareWell2Func
)
report()
(in
SymmetricMotifFilter
)
RestrictDesignToProteinDNAInterfaceCreator
(in
rosetta.protocols.dna._protocols_dna_
)
read_data()
(in
SquareWellFunc
)
report()
(in
TaskAwareSASAFilter
)
RestrictDesignToProteinDNAInterfaceCreatorAP
(in
rosetta.protocols.dna._protocols_dna_
)
read_data()
(in
SumFunc
)
report()
(in
TaskAwareScoreTypeFilter
)
RestrictDesignToProteinDNAInterfaceCreatorCAP
(in
rosetta.protocols.dna._protocols_dna_
)
read_data()
(in
TopOutFunc
)
report()
(in
TerminusDistanceFilter
)
RestrictIdentitiesAtAlignedPositionsOperation
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
USOGFunc
)
report()
(in
TotalSasaFilter
)
RestrictIdentitiesAtAlignedPositionsOperationAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
ChemicalShiftScoringScheme
)
report_ab_H3_kink_metrics_features()
(in
AntibodyFeatures
)
RestrictIdentitiesAtAlignedPositionsOperationCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
CompassScoringScheme
)
report_ab_metrics_features()
(in
AntibodyFeatures
)
RestrictIdentitiesAtAlignedPositionsOperationCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
CompositeScoringScheme
)
report_adducts()
(in
ResidueType
)
RestrictIdentitiesAtAlignedPositionsOperationCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
DPScoringScheme
)
report_all()
(in
FilterScanFilter
)
RestrictIdentitiesAtAlignedPositionsOperationCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
L1ScoringScheme
)
report_all()
(in
ParsedProtocol
)
RestrictIdentitiesOperation
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
MatrixScoringScheme
)
report_all_interface_features()
(in
AntibodyFeatures
)
RestrictIdentitiesOperationAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
PairScoringScheme
)
report_all_interface_features()
(in
InterfaceFeatures
)
RestrictIdentitiesOperationCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
ProfSimScoringScheme
)
report_aln_components()
(in
AlignEvaluator
)
RestrictIdentitiesOperationCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
ScoringScheme
)
report_application_command()
(in
rosetta.core.init._core_init_
)
RestrictIdentitiesOperationCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
Sequence
)
report_as_silent()
(in
MDBase
)
RestrictIdentitiesOperationCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
SequenceAlignment
)
report_atom_pairs()
(in
AtomAtomPairFeatures
)
RestrictInterGroupVectorOperation
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
SimpleScoringScheme
)
report_atom_pairs()
(in
AtomInResidueAtomInResiduePairFeatures
)
RestrictInterGroupVectorOperationAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
KDPoint
)
report_batch_inconsistency()
(in
rosetta.protocols.jd2.archive._protocols_jd2_archive_
)
RestrictInterGroupVectorOperationCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
AmbiguousMultiConstraint
)
report_CA_rmsd()
(in
IdealizeMover
)
RestrictInterGroupVectorOperationCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
BindingSiteConstraint
)
report_call_order()
(in
ParsedProtocol
)
RestrictInterGroupVectorOperationCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
COMCoordinateConstraint
)
report_cdr_metrics_features()
(in
AntibodyFeatures
)
RestrictInterGroupVectorOperationCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
SequenceCoupling1BDConstraint
)
report_cdr_residue_features()
(in
AntibodyFeatures
)
RestrictNativeResiduesOperation
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
SequenceCouplingConstraint
)
report_cdr_residue_features_row()
(in
AntibodyFeatures
)
RestrictNativeResiduesOperationAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
HotspotStubSet
)
report_data()
(in
InterfaceAnalyzerMover
)
RestrictNativeResiduesOperationCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
PocketConstraint
)
report_ddG()
(in
ddG
)
RestrictNativeResiduesOperationCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
CstResInteractions
)
report_dev()
(in
StructAvrgMover
)
RestrictNativeResiduesOperationCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
GeomSampleInfo
)
report_diffs()
(in
DdGScan
)
RestrictNativeResiduesOperationCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
MatchConstraintFileInfo
)
report_features()
(in
AntibodyFeatures
)
RestrictNonSurfaceToRepackingOperation
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
MatchConstraintFileInfoList
)
report_features()
(in
CDRClusterFeatures
)
RestrictNonSurfaceToRepackingOperationAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data()
(in
ResInteractions
)
report_features()
(in
AtomAtomPairFeatures
)
RestrictNonSurfaceToRepackingOperationCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data_file()
(in
HolesParams
)
report_features()
(in
AtomInResidueAtomInResiduePairFeatures
)
RestrictNonSurfaceToRepackingOperationCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_data_file()
(in
HolesParamsRes
)
report_features()
(in
AtomTypesFeatures
)
RestrictNonSurfaceToRepackingOperationCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_database()
(in
BranchAngleOptimizer
)
report_features()
(in
BatchFeatures
)
RestrictNonSurfaceToRepackingOperationCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_db()
(in
BackboneDB
)
report_features()
(in
BetaTurnDetectionFeatures
)
RestrictOperationsBase
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_db()
(in
LoopHashMap
)
report_features()
(in
ChargeChargeFeatures
)
RestrictOperationsBaseAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
DunbrackConstraint
)
report_features()
(in
DdGFeatures
)
RestrictOperationsBaseCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
RotamerConstraint
)
report_features()
(in
FeaturesReporter
)
RestrictResiduesToRepackingOperation
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
AmbiguousConstraint
)
report_features()
(in
GeometricSolvationFeatures
)
RestrictResiduesToRepackingOperationAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
AmbiguousNMRConstraint
)
report_features()
(in
HBondFeatures
)
RestrictResiduesToRepackingOperationCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
AmbiguousNMRDistanceConstraint
)
report_features()
(in
HBondParameterFeatures
)
RestrictResiduesToRepackingOperationCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
AngleConstraint
)
report_features()
(in
HelixCapFeatures
)
RestrictResiduesToRepackingOperationCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
AtomPairConstraint
)
report_features()
(in
InterfaceFeatures
)
RestrictResiduesToRepackingOperationCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
BackboneStubConstraint
)
report_features()
(in
JobDataFeatures
)
RestrictResidueToRepacking
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_def()
(in
BackboneStubLinearConstraint
)
report_features()
(in
LoopAnchorFeatures
)
RestrictResidueToRepackingAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_def()
(in
BigBinConstraint
)
report_features()
(in
OrbitalsFeatures
)
RestrictResidueToRepackingCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_def()
(in
ConstantConstraint
)
report_features()
(in
PairFeatures
)
RestrictResidueToRepackingCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_def()
(in
Constraint
)
report_features()
(in
PdbDataFeatures
)
RestrictResidueToRepackingCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_def()
(in
CoordinateConstraint
)
report_features()
(in
PoseCommentsFeatures
)
RestrictResidueToRepackingCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_def()
(in
DihedralConstraint
)
report_features()
(in
PoseConformationFeatures
)
RestrictToAlignedSegmentsOperation
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
DihedralPairConstraint
)
report_features()
(in
ProteinBackboneAtomAtomPairFeatures
)
RestrictToAlignedSegmentsOperationAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
DistancePairConstraint
)
report_features()
(in
ProteinBackboneTorsionAngleFeatures
)
RestrictToAlignedSegmentsOperationCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
FabConstraint
)
report_features()
(in
ProteinBondGeometryFeatures
)
RestrictToAlignedSegmentsOperationCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
KofNConstraint
)
report_features()
(in
ProteinRMSDFeatures
)
RestrictToAlignedSegmentsOperationCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
LocalCoordinateConstraint
)
report_features()
(in
ProteinRMSDNoSuperpositionFeatures
)
RestrictToAlignedSegmentsOperationCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
MultiConstraint
)
report_features()
(in
ProteinResidueConformationFeatures
)
RestrictToCDRH3Loop
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
NamedAngleConstraint
)
report_features()
(in
ProtocolFeatures
)
RestrictToCDRH3LoopAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
NamedAtomPairConstraint
)
report_features()
(in
RadiusOfGyrationFeatures
)
RestrictToCDRH3LoopCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
NonResidueTypeConstraint
)
report_features()
(in
ReportToDB
)
RestrictToCDRH3LoopCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
ResidueTypeConstraint
)
report_features()
(in
ResidueBurialFeatures
)
RestrictToCDRH3LoopCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
ResidueTypeLinkingConstraint
)
report_features()
(in
ResidueConformationFeatures
)
RestrictToCDRH3LoopCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
SequenceProfileConstraint
)
report_features()
(in
ResidueFeatures
)
RestrictToCDRsAndNeighbors
(in
rosetta.protocols.antibody.task_operations._protocols_antibody_task_operations_
)
read_def()
(in
SiteConstraint
)
report_features()
(in
ResidueGridScoresFeatures
)
RestrictToCDRsAndNeighborsAP
(in
rosetta.protocols.antibody.task_operations._protocols_antibody_task_operations_
)
read_def()
(in
SiteConstraintResidues
)
report_features()
(in
ResidueScoresFeatures
)
RestrictToCDRsAndNeighborsCAP
(in
rosetta.protocols.antibody.task_operations._protocols_antibody_task_operations_
)
read_def()
(in
AmbiguousMultiConstraint
)
report_features()
(in
ResidueSecondaryStructureFeatures
)
RestrictToInterface
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
BindingSiteConstraint
)
report_features()
(in
ResidueTotalScoresFeatures
)
RestrictToInterfaceAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
COMCoordinateConstraint
)
report_features()
(in
ResidueTypesFeatures
)
RestrictToInterfaceCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
SequenceCoupling1BDConstraint
)
report_features()
(in
RotamerBoltzmannWeightFeatures
)
RestrictToInterfaceCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
SequenceCouplingConstraint
)
report_features()
(in
RotamerFeatures
)
RestrictToInterfaceCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_def()
(in
PocketConstraint
)
report_features()
(in
RotamerRecoveryFeatures
)
RestrictToInterfaceCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_depth()
(in
FragmentPicker
)
report_features()
(in
RuntimeFeatures
)
RestrictToInterfaceOperation
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_disulf_pairing_list()
(in
rosetta.protocols.jumping._protocols_jumping_
)
report_features()
(in
SaltBridgeFeatures
)
RestrictToInterfaceOperationAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_disulfide_database()
(in
DisulfideMatchingDatabase
)
report_features()
(in
ScoreFunctionFeatures
)
RestrictToInterfaceOperationCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_disulfides()
(in
FullModelParameters
)
report_features()
(in
ScoreTypeFeatures
)
RestrictToInterfaceOperationCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_DNA_rotlib()
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
report_features()
(in
ScreeningFeatures
)
RestrictToInterfaceOperationCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_dunbrack_library()
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
report_features()
(in
SecondaryStructureSegmentFeatures
)
RestrictToInterfaceOperationCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_eigvec_file()
(in
PCA
)
report_features()
(in
SmotifFeatures
)
RestrictToInterfaceVectorOperation
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_entities_checkpoint()
(in
GeneticAlgorithm
)
report_features()
(in
StructureFeatures
)
RestrictToInterfaceVectorOperationAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_entities_checkpoint()
(in
GeneticAlgorithmBase
)
report_features()
(in
StructureScoresFeatures
)
RestrictToInterfaceVectorOperationCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_enzyme_cstfile()
(in
EnzConstraintIO
)
report_features()
(in
TaskOperationFeatures
)
RestrictToInterfaceVectorOperationCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_fasta_file()
(in
rosetta.core.sequence._core_sequence_
)
report_features()
(in
TotalScoreFeatures
)
RestrictToInterfaceVectorOperationCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_fasta_file_return_str()
(in
rosetta.core.sequence._core_sequence_
)
report_features()
(in
TrajectoryMapFeatures
)
RestrictToInterfaceVectorOperationCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_fasta_file_str()
(in
rosetta.core.sequence._core_sequence_
)
report_features()
(in
UnrecognizedAtomFeatures
)
RestrictToLoops
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_file()
(in
AtomTypeSet
)
report_features()
(in
WaterFeatures
)
RestrictToLoopsAndNeighbors
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_file()
(in
ElementSet
)
report_features()
(in
ConcurrencyTest
)
RestrictToLoopsAndNeighborsAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_file()
(in
IdealBondLengthSet
)
report_features()
(in
HelixBundleFeatures
)
RestrictToLoopsAndNeighborsCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_file()
(in
MMAtomTypeSet
)
report_features()
(in
SandwichFeatures
)
RestrictToLoopsAndNeighborsCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_file()
(in
Patch
)
report_features()
(in
StrandBundleFeatures
)
RestrictToLoopsAndNeighborsCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_file()
(in
GasteigerAtomTypeSet
)
report_filter_name()
(in
ReportFilter
)
RestrictToLoopsAndNeighborsCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_file()
(in
OrbitalTypeSet
)
report_filters_to_job()
(in
ParsedProtocol
)
RestrictToLoopsAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_file()
(in
AtomTreeDiff
)
report_filters_to_pose()
(in
ParsedProtocol
)
RestrictToLoopsCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_file()
(in
SilentFileData
)
report_gdt_components()
(in
Align_RmsdEvaluator
)
RestrictToLoopsCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_file()
(in
RMSVallData
)
report_gdt_components()
(in
RmsdEvaluator
)
RestrictToLoopsCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_file()
(in
TorsionFragmentLibrary
)
report_haro_orbital_interactions()
(in
OrbitalsFeatures
)
RestrictToLoopsCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_file()
(in
VallData
)
report_heading_directions_of_all_AA_in_a_strand()
(in
rosetta.protocols.features.strand_assembly._protocols_features_strand_assembly_
)
RestrictToMoveMapChiOperation
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_file()
(in
JumpSelector
)
report_hpol_orbital_interactions()
(in
OrbitalsFeatures
)
RestrictToMoveMapChiOperationAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_file()
(in
JumpSetup
)
report_interface_features()
(in
AntibodyFeatures
)
RestrictToMoveMapChiOperationCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_file()
(in
ResiduePairJumpSetup
)
report_interface_features()
(in
InterfaceFeatures
)
RestrictToNeighborhoodOperation
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_files()
(in
ResidueTypeSet
)
report_interface_residue_features()
(in
AntibodyFeatures
)
RestrictToNeighborhoodOperationAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_fold_tree()
(in
ImportPoseOptions
)
report_interface_residue_features()
(in
InterfaceFeatures
)
RestrictToNeighborhoodOperationCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_fold_tree_from_file()
(in
rosetta.protocols.backrub._protocols_backrub_
)
report_interface_side_features()
(in
AntibodyFeatures
)
RestrictToNeighborhoodOperationCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_fragment_candidates()
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
report_interface_side_features()
(in
InterfaceFeatures
)
RestrictToNeighborhoodOperationCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_fragment_file()
(in
ConstantLengthFragSet
)
report_interres_angles()
(in
ProteinBondGeometryFeatures
)
RestrictToNeighborhoodOperationCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_fragment_stream()
(in
ConstantLengthFragSet
)
report_interres_lengths()
(in
ProteinBondGeometryFeatures
)
RestrictToRepacking
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_from_binary()
(in
SingleResidueDunbrackLibrary
)
report_intrares_angles()
(in
ProteinBondGeometryFeatures
)
RestrictToRepackingAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_from_binary()
(in
SingleResiduePeptoidLibrary
)
report_intrares_lengths()
(in
ProteinBondGeometryFeatures
)
RestrictToRepackingCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_from_binary_chk()
(in
SequenceProfile
)
report_intrares_torsions()
(in
ProteinBondGeometryFeatures
)
RestrictToRepackingCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_from_binary_file()
(in
ConstraintedOptimizationWeightFunc
)
report_parameter_features()
(in
HBondDatabase
)
RestrictToRepackingCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_from_binary_file()
(in
DDGBindOptEData
)
report_parameter_features_schema_to_db()
(in
HBondDatabase
)
RestrictToRepackingCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_from_binary_file()
(in
DDGMutationOptEData
)
report_predicted_features()
(in
RRReporterSQLite
)
RestrictToRepackingRLT
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_from_binary_file()
(in
DGBindOptEData
)
report_property()
(in
PosePropertyReporter
)
RestrictToRepackingRLTAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_from_binary_file()
(in
NestedEnergyTermDDGMutationOptEData
)
report_residue_pairs()
(in
PairFeatures
)
RestrictToRepackingRLTCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_from_binary_file()
(in
NestedEnergyTermPNatAAOptEPositionData
)
report_rotamer_recovery()
(in
PerNativeRRReporterHuman
)
RestrictToRepackingRLTCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_from_binary_file()
(in
OptEData
)
report_rotamer_recovery()
(in
RRReporter
)
RestrictToRepackingRLTCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_from_binary_file()
(in
OptEPositionData
)
report_rotamer_recovery()
(in
RRReporterHuman
)
RestrictToRepackingRLTCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_from_binary_file()
(in
PNatAAOptEPositionData
)
report_rotamer_recovery()
(in
RRReporterSQLite
)
RestrictToTerminiOperation
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_from_binary_file()
(in
PNatLigPoseOptEData
)
report_rotamer_recovery()
(in
RRReporterSimple
)
RestrictToTerminiOperationAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_from_binary_file()
(in
PNatRotOptEPositionData
)
report_rotamer_recovery_features()
(in
RRReporterSQLite
)
RestrictToTerminiOperationCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_from_binary_file()
(in
PNatStructureOptEData
)
report_rotamer_recovery_full()
(in
RRReporterSQLite
)
RestrictToTerminiOperationCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_from_binary_file()
(in
PSSMOptEPositionData
)
report_silent()
(in
MDBase
)
RestrictToTerminiOperationCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_from_checkpoint()
(in
SequenceProfile
)
report_sm()
(in
PeptideDeriverFilter
)
RestrictToTerminiOperationCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_from_cmd_line()
(in
SilentStructStore
)
report_sm()
(in
ExposedHydrophobicsFilter
)
RestrictYSDesign
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_from_database()
(in
MatrixScoringScheme
)
report_sm()
(in
DockingHighResFilter
)
RestrictYSDesignAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_from_file()
(in
SecondaryStructure
)
report_sm()
(in
DockingLowResFilter
)
RestrictYSDesignCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_from_file()
(in
SingleResidueCenrotLibrary
)
report_sm()
(in
CalculatorFilter
)
RestrictYSDesignCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_from_file()
(in
ChemicalShiftScoringScheme
)
report_sm()
(in
CombinedFilter
)
RestrictYSDesignCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_from_file()
(in
ChemicalShiftSequence
)
report_sm()
(in
CompoundFilter
)
RestrictYSDesignCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
read_from_file()
(in
CompassScoringScheme
)
report_sm()
(in
ContingentFilter
)
restype()
(in
ClassicMatchAlgorithm
)
read_from_file()
(in
CompositeScoringScheme
)
report_sm()
(in
FalseFilter
)
restype()
(in
TargetRotamerCoords
)
read_from_file()
(in
CompositeSequence
)
report_sm()
(in
Filter
)
restype()
(in
BuildSet
)
read_from_file()
(in
DPScoringScheme
)
report_sm()
(in
IfThenFilter
)
restype()
(in
ProteinUpstreamBuilder
)
read_from_file()
(in
L1ScoringScheme
)
report_sm()
(in
MoveBeforeFilter
)
restype()
(in
UpstreamBuilder
)
read_from_file()
(in
MatrixScoringScheme
)
report_sm()
(in
ReplicateFilter
)
restype_atomno()
(in
TargetRotamerCoords
)
read_from_file()
(in
PairScoringScheme
)
report_sm()
(in
StochasticFilter
)
restype_for_rotblock()
(in
ContinuousRotamerSet
)
read_from_file()
(in
ProfSimScoringScheme
)
report_sm()
(in
TimeFilter
)
restype_geometry()
(in
BuildSet
)
read_from_file()
(in
ScoringScheme
)
report_sm()
(in
TrueFilter
)
restype_id_2_collision_check_id()
(in
LigandConformer
)
read_from_file()
(in
Sequence
)
report_sm()
(in
CoreDunbrackFilter
)
restype_index()
(in
ResidueAtomTreeCollectionMomento
)
read_from_file()
(in
SequenceAlignment
)
report_sm()
(in
FragQualFilter
)
restype_name1()
(in
Motif
)
read_from_file()
(in
SequenceCoupling
)
report_sm()
(in
HSSTripletFilter
)
restype_name2()
(in
Motif
)
read_from_file()
(in
SequenceProfile
)
report_sm()
(in
HelixKinkFilter
)
ResTypeFragmentMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
read_from_file()
(in
SimpleScoringScheme
)
report_sm()
(in
HelixPairingFilter
)
ResTypeFragmentMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
read_from_file()
(in
DisulfPairingLibrary
)
report_sm()
(in
InterlockingAromaFilter
)
ResTypeFragmentMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
read_from_file()
(in
PairingLibrary
)
report_sm()
(in
NcontactsFilter
)
ResTypeSequence_lt
(in
rosetta.protocols.dna._protocols_dna_
)
read_from_file()
(in
ConstraintedOptimizationWeightFunc
)
report_sm()
(in
ParallelBetaPairingPreferenceFilter
)
ResTypeSequence_ltAP
(in
rosetta.protocols.dna._protocols_dna_
)
read_from_file()
(in
DDGBindOptEData
)
report_sm()
(in
SecondaryStructureCountFilter
)
ResTypeSequence_ltCAP
(in
rosetta.protocols.dna._protocols_dna_
)
read_from_file()
(in
DDGMutationOptEData
)
report_sm()
(in
SecondaryStructureFilter
)
result()
(in
EnvClaimBroker
)
read_from_file()
(in
DGBindOptEData
)
report_sm()
(in
SecondaryStructureHasResidueFilter
)
result_query_string()
(in
DatabaseEntryWorkUnit
)
read_from_file()
(in
NestedEnergyTermDDGMutationOptEData
)
report_sm()
(in
SheetTopologyFilter
)
retain_top()
(in
rosetta.core.fragment._core_fragment_
)
read_from_file()
(in
NestedEnergyTermPNatAAOptEPositionData
)
report_sm()
(in
FragmentLookupFilter
)
retrieve()
(in
HotspotStubSet
)
read_from_file()
(in
OptEData
)
report_sm()
(in
AtomCountFilter
)
retrieve_base_partner_from_pose()
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
read_from_file()
(in
OptEPositionData
)
report_sm()
(in
ChainExistsFilter
)
retrieve_calculator()
(in
CalculatorFactory
)
read_from_file()
(in
PNatAAOptEPositionData
)
report_sm()
(in
CompleteConnectionsFilter
)
retrieve_centroid_scatter_from_pose()
(in
rosetta.core.scoring.fiber_diffraction._core_scoring_fiber_diffraction_
)
read_from_file()
(in
PNatLigPoseOptEData
)
report_sm()
(in
HBondAcceptorFilter
)
retrieve_CSA_from_pose()
(in
rosetta.core.scoring._core_scoring_
)
read_from_file()
(in
PNatRotOptEPositionData
)
report_sm()
(in
HBondDonorFilter
)
retrieve_DC_from_pose()
(in
rosetta.core.scoring._core_scoring_
)
read_from_file()
(in
PNatStructureOptEData
)
report_sm()
(in
HeavyAtomFilter
)
retrieve_energy()
(in
DenseNeighborConstIterator
)
read_from_file()
(in
PSSMOptEPositionData
)
report_sm()
(in
MolarMassFilter
)
retrieve_energy()
(in
DenseNeighborIterator
)
read_from_file()
(in
SilentStructStore
)
report_sm()
(in
MolecularMassFilter
)
retrieve_energy()
(in
OneToAllNeighborConstIterator
)
read_from_file_no_filters()
(in
PairingLibrary
)
report_sm()
(in
ClashCheckFilter
)
retrieve_energy()
(in
OneToAllNeighborIterator
)
read_from_pose()
(in
BackboneSegment
)
report_sm()
(in
GetRBDOFValues
)
retrieve_energy()
(in
PeptideBondedNeighborConstIterator
)
read_from_stream()
(in
SilentStructStore
)
report_sm()
(in
InterfacePackingFilter
)
retrieve_energy()
(in
PeptideBondedNeighborIterator
)
read_from_string()
(in
SilentStructStore
)
report_sm()
(in
OligomericAverageDegreeFilter
)
retrieve_energy()
(in
ResidueNeighborConstIterator
)
read_Gaussian_parameters_from_database_file()
(in
rosetta.core.scoring.carbohydrates._core_scoring_carbohydrates_
)
report_sm()
(in
SymUnsatHbondFilter
)
retrieve_energy()
(in
ResidueNeighborIterator
)
read_general_aln()
(in
rosetta.core.sequence._core_sequence_
)
report_sm()
(in
AtomicContactCountFilter
)
retrieve_energy()
(in
CstResNeighbConstIterator
)
read_general_aln_file()
(in
rosetta.core.sequence._core_sequence_
)
report_sm()
(in
AverageDegreeFilter
)
retrieve_energy()
(in
CstResNeighbIterator
)
read_generations_checkpoint()
(in
GeneticAlgorithm
)
report_sm()
(in
BindingStrainFilter
)
retrieve_energy()
(in
CentroidDisulfideEnergyContainer
)
read_generations_checkpoint()
(in
GeneticAlgorithmBase
)
report_sm()
(in
BoltzmannFilter
)
retrieve_energy()
(in
CentroidDisulfideNeighborConstIterator
)
read_grishin_aln_file()
(in
rosetta.core.sequence._core_sequence_
)
report_sm()
(in
ClashWithTargetFilter
)
retrieve_energy()
(in
CentroidDisulfideNeighborIterator
)
read_H3_cter_fragment()
(in
H3CterInsert
)
report_sm()
(in
DesignableResiduesFilter
)
retrieve_energy()
(in
DisulfResNeighbConstIterator
)
read_H3_cter_fragment()
(in
rosetta.protocols.antibody_legacy._protocols_antibody_legacy_
)
report_sm()
(in
DisulfideFilter
)
retrieve_energy()
(in
DisulfResNeighbIterator
)
read_homologs()
(in
BackboneDB
)
report_sm()
(in
FNatFilter
)
retrieve_energy()
(in
DisulfideMatchingEnergyContainer
)
read_in_and_set_disulfides()
(in
DisulfideFile
)
report_sm()
(in
FilterScanFilter
)
retrieve_energy()
(in
DisulfideMatchingNeighborConstIterator
)
read_in_spanfile()
(in
MembraneTopology
)
report_sm()
(in
HbondsToAtomFilter
)
retrieve_energy()
(in
DisulfideMatchingNeighborIterator
)
read_in_structures()
(in
PointMutScanDriver
)
report_sm()
(in
HbondsToResidueFilter
)
retrieve_energy()
(in
FullatomDisulfideEnergyContainer
)
read_individual_constraint_new()
(in
ConstraintIO
)
report_sm()
(in
IRmsdFilter
)
retrieve_fa_scatter_from_pose()
(in
rosetta.core.scoring.fiber_diffraction._core_scoring_fiber_diffraction_
)
read_info_file()
(in
Batch
)
report_sm()
(in
InterfaceHolesFilter
)
retrieve_RDC_from_pose()
(in
rosetta.core.scoring._core_scoring_
)
read_jumps_from_file()
(in
RNA_JumpLibrary
)
report_sm()
(in
LRmsdFilter
)
retrieve_RDC_ROHL_from_pose()
(in
rosetta.core.scoring._core_scoring_
)
read_legacydb()
(in
BackboneDB
)
report_sm()
(in
RelativeSegmentFilter
)
retrieve_RDC_segments_from_pose()
(in
rosetta.protocols.scoring._protocols_scoring_
)
read_legacydb()
(in
LoopHashMap
)
report_sm()
(in
RmsdFilter
)
retrieve_relevant_poses_for_entity()
(in
DaemonSet
)
read_link_records()
(in
PDB_DReaderOptions
)
report_sm()
(in
RmsdSimpleFilter
)
retrieve_residue_num_of_rkde()
(in
rosetta.protocols.features.strand_assembly._protocols_features_strand_assembly_
)
read_list_of_residues()
(in
ResidueTypeSet
)
report_sm()
(in
SSamountFilter
)
retrieve_tensor_from_svd()
(in
PcsDataLanthanide
)
read_loop_file()
(in
JSONFormattedLoopsFileReader
)
report_sm()
(in
SequenceRecoveryFilter
)
RetrieveStoredTaskOperation
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_loop_file()
(in
LoopsFileIO
)
report_sm()
(in
SpecificResiduesNearInterfaceFilter
)
RetrieveStoredTaskOperationAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_loop_file_stream()
(in
LoopsFileIO
)
report_sm()
(in
StubScoreFilter
)
RetrieveStoredTaskOperationCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_loop_fragments()
(in
rosetta.protocols.loops._protocols_loops_
)
report_sm()
(in
StubScoreLoopsFilter
)
RetrieveStoredTaskOperationCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_loops_file()
(in
EnzdesLoopsFile
)
report_sm()
(in
Torsion
)
RetrieveStoredTaskOperationCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_loops_file_block()
(in
EnzdesLoopInfo
)
report_sm()
(in
AbinitioBaseFilter
)
RetrieveStoredTaskOperationCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
read_loops_options()
(in
Loops
)
report_sm()
(in
AlaScan
)
return_centroid()
(in
ClassicAbinitio
)
read_mArray()
(in
rosetta.utility.json_spirit._utility_json_spirit_
)
report_sm()
(in
AngleToVector
)
return_centroid()
(in
DoubleLayerKinematicAbinitio
)
read_metric_value()
(in
rosetta.basic._basic_
)
report_sm()
(in
AtomicContactFilter
)
return_centroid()
(in
FoldConstraints
)
read_minor_helix_params()
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
report_sm()
(in
AtomicDistanceFilter
)
return_centroid()
(in
JumpingFoldConstraintsWrapper
)
read_mObject()
(in
rosetta.utility.json_spirit._utility_json_spirit_
)
report_sm()
(in
AveragePathLengthFilter
)
return_centroid()
(in
KinematicAbinitio
)
read_motifs_binary()
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
report_sm()
(in
BuriedUnsatHbondFilter
)
return_centroid()
(in
KinematicTaskControl
)
read_mover_weight()
(in
TopologyClaimer
)
report_sm()
(in
COFilter
)
return_centroid()
(in
LoopJumpFoldCst
)
read_nmer_pssm()
(in
NMerPSSMEnergy
)
report_sm()
(in
ConservedPosMutationFilter
)
return_centroid()
(in
MembraneAbinitio
)
read_nmer_pssm_list()
(in
NMerPSSMEnergy
)
report_sm()
(in
ConstraintScoreCutoffFilter
)
return_centroid()
(in
Protocol
)
read_nmer_svm()
(in
NMerSVMEnergy
)
report_sm()
(in
DdGScan
)
return_combine_history()
(in
CombinePoseMover
)
read_nmer_svm_list()
(in
NMerSVMEnergy
)
report_sm()
(in
DdgFilter
)
return_file_callback()
(in
Inline_File_Provider_Hook
)
read_options()
(in
SingleResidueDunbrackLibrary
)
report_sm()
(in
DeltaFilter
)
return_key()
(in
LoopHashMap
)
read_options()
(in
SingleResiduePeptoidLibrary
)
report_sm()
(in
DisulfideEntropyFilter
)
return_lowest_poses_in_clusters()
(in
ClusterBase
)
read_options()
(in
Anchor
)
report_sm()
(in
DomainInterfaceFilter
)
return_nearest_residue()
(in
rosetta.core.conformation.symmetry._core_conformation_symmetry_
)
read_options()
(in
AnchorMoversData
)
report_sm()
(in
EnergyPerResidueFilter
)
return_nearest_residue()
(in
rosetta.core.pose._core_pose_
)
read_options()
(in
AnchoredDesignMover
)
report_sm()
(in
ExpiryFilter
)
return_nearest_residue()
(in
rosetta.protocols.membrane.geometry._protocols_membrane_geometry_
)
read_options()
(in
AnchoredPerturbMover
)
report_sm()
(in
FileExistFilter
)
return_pseudo_hits()
(in
WriteUpstreamCoordinateKinemage
)
read_options()
(in
AnchoredRefineMover
)
report_sm()
(in
FileRemoveFilter
)
return_region()
(in
rosetta.protocols.grafting._protocols_grafting_
)
read_options()
(in
FlxbbDesign
)
report_sm()
(in
GeometryFilter
)
return_silent()
(in
CombinePoseMover
)
read_options()
(in
ConstraintSetMover
)
report_sm()
(in
HolesFilter
)
return_top_poses_in_clusters()
(in
ClusterBase
)
read_pairing_list()
(in
rosetta.core.scoring.dssp._core_scoring_dssp_
)
report_sm()
(in
InterRepeatContactFilter
)
ReturnSidechainMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
read_pairings()
(in
Templates
)
report_sm()
(in
InterfaceBindingEnergyDensityFilter
)
ReturnSidechainMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
read_params()
(in
EnzCstTemplateRes
)
report_sm()
(in
InterfaceSasaFilter
)
ReturnSidechainMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
read_patchdock()
(in
PatchdockReader
)
report_sm()
(in
IntraRepeatContactFilter
)
retype_is_aromatic()
(in
rosetta.core.chemical._core_chemical_
)
read_patchdock_entry()
(in
PatchdockReader
)
report_sm()
(in
LeastNativeLike9merFilter
)
revamp_weight_by_burial()
(in
PoissonBoltzmannEnergy
)
read_pdb_header()
(in
PDB_DReaderOptions
)
report_sm()
(in
MotifScoreFilter
)
reverse()
(in
BondID
)
read_pose()
(in
AtomTreeDiff
)
report_sm()
(in
MultipleSigmoids
)
reverse()
(in
SequenceMapping
)
read_pose()
(in
TMalign
)
report_sm()
(in
MutationsFilter
)
reverse()
(in
Jump
)
read_pose_numbered_loops_file()
(in
PoseNumberedLoopFileReader
)
report_sm()
(in
NMerPSSMEnergyFilter
)
reverse()
(in
RT
)
read_poses()
(in
PatchdockReader
)
report_sm()
(in
NMerSVMEnergyFilter
)
reverse()
(in
Pairing
)
read_potential()
(in
DFIRE_Potential
)
report_sm()
(in
NeighborTypeFilter
)
reverse_in_place()
(in
ResPairMotif
)
read_probabilities_or_die()
(in
rosetta.numeric._numeric_
)
report_sm()
(in
NetChargeFilter
)
reverse_in_place_unsafe()
(in
ResPairMotif
)
read_psipred_ss2()
(in
SecondaryStructure
)
report_sm()
(in
NonSequentialNeighborsFilter
)
reverse_move()
(in
StepWiseMoveSelector
)
read_psipred_ss2()
(in
FragmentPicker
)
report_sm()
(in
Operator
)
reverse_score_filter()
(in
SilentFileData
)
read_psipred_ss2_file()
(in
rosetta.core.pose._core_pose_
)
report_sm()
(in
PDDFScoreFilter
)
reversed()
(in
BondID
)
read_RBSegment_file()
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
report_sm()
(in
PackStatFilter
)
reversed()
(in
Jump
)
read_rdat_file()
(in
RDAT
)
report_sm()
(in
PackerNeighborGraphFilter
)
reversed()
(in
ResPairMotif
)
read_RDC_file()
(in
ResidualDipolarCoupling
)
report_sm()
(in
PoseComment
)
reversed()
(in
HelicalFragment
)
read_RDC_file()
(in
ResidualDipolarCoupling_Rohl
)
report_sm()
(in
PoseInfoFilter
)
reversion_scan()
(in
DnaInterfacePacker
)
read_residuetype_from_database()
(in
ResidueDatabaseIO
)
report_sm()
(in
RGFilter
)
Revert
(in
rosetta.protocols.protein_interface_design._protocols_protein_interface_design_
)
read_resource_locators_tags()
(in
JD2ResourceManager
)
report_sm()
(in
RangeFilter
)
revert_to_pre_talaris_2013_defaults()
(in
rosetta.core.init._core_init_
)
read_resource_options_tags()
(in
JD2ResourceManager
)
report_sm()
(in
RelativePoseFilter
)
RevertAP
(in
rosetta.protocols.protein_interface_design._protocols_protein_interface_design_
)
read_resources_tags()
(in
JD2ResourceManager
)
report_sm()
(in
RepeatParameterFilter
)
RevertCAP
(in
rosetta.protocols.protein_interface_design._protocols_protein_interface_design_
)
read_score_headers()
(in
SilentStruct
)
report_sm()
(in
ReportFilter
)
revise_root_and_moving_res()
(in
rosetta.protocols.stepwise.modeler._protocols_stepwise_modeler_
)
read_sequence()
(in
SilentStruct
)
report_sm()
(in
ResidueBurialFilter
)
revise_root_and_moving_res_list()
(in
rosetta.protocols.stepwise.modeler._protocols_stepwise_modeler_
)
read_silent_struct()
(in
SymmetryInfo
)
report_sm()
(in
ResidueCountFilter
)
revision_id()
(in
ConstraintSet
)
read_spine_x()
(in
FragmentPicker
)
report_sm()
(in
ResidueDistanceFilter
)
revision_id()
(in
OccupiedSpaceHash
)
read_ss2()
(in
rosetta.protocols.mpi_refinement._protocols_mpi_refinement_
)
report_sm()
(in
ResidueIEFilter
)
revoke_all_access()
(in
DofPassport
)
read_ss_file()
(in
FragmentPicker
)
report_sm()
(in
ResidueSetChainEnergyFilter
)
reweighters_begin()
(in
IGEdgeReweightContainer
)
read_ss_files()
(in
FragmentPicker
)
report_sm()
(in
ResiduesInInterfaceFilter
)
reweighters_end()
(in
IGEdgeReweightContainer
)
read_std_frags_from_cmd()
(in
rosetta.core.fragment._core_fragment_
)
report_sm()
(in
RotamerBoltzmannWeight
)
RFd_like
(in
rosetta.protocols.fldsgn.topology
)
read_stream()
(in
SilentFileData
)
report_sm()
(in
SAXSScoreFilter
)
RFd_like
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
read_structures()
(in
HedgeArchive
)
report_sm()
(in
SSMotifFinder
)
RFd_like
(in
SheetFoldType
)
read_structures()
(in
IterativeAbrelax
)
report_sm()
(in
SavePoseConstraintToFileFilter
)
RG
(in
rosetta.basic
)
read_structures()
(in
IterativeBase
)
report_sm()
(in
SaveResfileToDiskFilter
)
RG
(in
ProfTag
)
read_structures()
(in
IterativeCentroid
)
report_sm()
(in
ScoreCutoffFilter
)
RG
(in
rosetta.basic._basic_
)
read_structures()
(in
IterativeFullatom
)
report_sm()
(in
ScoreTypeFilter
)
rg
(in
ScoreType
)
read_structures()
(in
AbstractArchiveBase
)
report_sm()
(in
ShapeComplementarityFilter
)
rg
(in
rosetta.core.scoring._core_scoring_
)
read_structures()
(in
ArchiveBase
)
report_sm()
(in
SheetFilter
)
rg
(in
rosetta.core.scoring
)
read_structures()
(in
EvaluatedArchive
)
report_sm()
(in
SidechainRmsdFilter
)
rg
(in
rosetta
)
read_structures()
(in
NormalizedEvaluatedArchive
)
report_sm()
(in
Sigmoid
)
rg()
(in
rosetta.numeric.random._numeric_random_
)
read_structures()
(in
VarianceStatisticsArchive
)
report_sm()
(in
StemFinder
)
rg()
(in
SymmetrySlider
)
read_symmetry_data_from_file()
(in
SymmData
)
report_sm()
(in
SymmetricMotifFilter
)
RG_Energy_Fast
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
read_symmetry_data_from_stream()
(in
SymmData
)
report_sm()
(in
TaskAwareSASAFilter
)
RG_Energy_FastAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
read_tags_fast()
(in
RawFileData
)
report_sm()
(in
TaskAwareScoreTypeFilter
)
RG_Energy_FastCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
read_tags_fast()
(in
SilentFileData
)
report_sm()
(in
TerminusDistanceFilter
)
RG_Energy_FastCreator
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
read_talos_ss()
(in
SecondaryStructure
)
report_sm()
(in
TotalSasaFilter
)
RG_Energy_FastCreatorAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
read_talos_ss()
(in
FragmentPicker
)
report_string()
(in
ReportFilter
)
RG_Energy_FastCreatorCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
read_topology_file()
(in
rosetta.core.chemical._core_chemical_
)
report_structure_features()
(in
ReportToDB
)
RG_Energy_RNA
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
read_undefined_coef1()
(in
BranchAngleOptimizer
)
report_subvalues()
(in
Operator
)
RG_Energy_RNAAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
read_undefined_coef2()
(in
BranchAngleOptimizer
)
report_symmetry()
(in
AlaScan
)
RG_Energy_RNACAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
read_vall()
(in
FragmentPicker
)
ReportAP
(in
rosetta.protocols.features._protocols_features_
)
RG_Energy_RNACreator
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
read_vall_torsions()
(in
FullAtomRNA_Fragments
)
ReportCAP
(in
rosetta.protocols.features._protocols_features_
)
RG_Energy_RNACreatorAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
read_xfrag_binary()
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
ReportEffectivePKA
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
RG_Energy_RNACreatorCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
read_xfres_binary()
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
ReportEffectivePKAAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
RG_LOCAL
(in
rosetta.basic
)
ReadFromFileOrDie()
(in
rosetta.utility._utility_
)
ReportEffectivePKACAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
RG_LOCAL
(in
ProfTag
)
readMRCandResize()
(in
ElectronDensity
)
ReportEffectivePKACreator
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
RG_LOCAL
(in
rosetta.basic._basic_
)
readMRCandResize()
(in
ElectronDensityAtomwise
)
ReportEffectivePKACreatorAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
rg_local
(in
ScoreType
)
ReadResfile
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
ReportEffectivePKACreatorCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
rg_local
(in
rosetta.core.scoring._core_scoring_
)
ReadResfileAndObeyLengthEvents
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
ReportFilter
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
rg_local
(in
rosetta.core.scoring
)
ReadResfileAndObeyLengthEventsAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
ReportFilterAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
rg_local
(in
rosetta
)
ReadResfileAndObeyLengthEventsCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
ReportFilterCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
RG_LOCAL_MINDATA
(in
Enum
)
ReadResfileAndObeyLengthEventsCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
ReportFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
RG_LOCAL_MINDATA
(in
CacheableDataType
)
ReadResfileAndObeyLengthEventsCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
ReportFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
RG_Local_MinData
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
ReadResfileAndObeyLengthEventsCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
ReportFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
RG_Local_MinDataAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
ReadResfileAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
ReportFSC
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
RG_Local_MinDataCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
ReadResfileCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
ReportFSCAP
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
RG_LocalEnergy
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
ReadResfileCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
ReportFSCCAP
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
RG_LocalEnergyAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
ReadResfileCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
ReportFSCCreator
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
RG_LocalEnergyCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
ReadResfileCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
ReportFSCCreatorAP
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
RG_LocalEnergyCreator
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
ReadResfileFromDB
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
ReportFSCCreatorCAP
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
RG_LocalEnergyCreatorAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
ReadResfileFromDBAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
ReportPSSMDifferences
(in
rosetta.protocols.protein_interface_design._protocols_protein_interface_design_
)
RG_LocalEnergyCreatorCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
ReadResfileFromDBCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
ReportPSSMDifferencesAP
(in
rosetta.protocols.protein_interface_design._protocols_protein_interface_design_
)
RG_MINDATA
(in
Enum
)
ReadResfileFromDBCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
ReportPSSMDifferencesCAP
(in
rosetta.protocols.protein_interface_design._protocols_protein_interface_design_
)
RG_MINDATA
(in
CacheableDataType
)
ReadResfileFromDBCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
ReportSequenceDifferences
(in
rosetta.protocols.protein_interface_design._protocols_protein_interface_design_
)
RG_MinData
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
ReadResfileFromDBCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
ReportSequenceDifferencesAP
(in
rosetta.protocols.protein_interface_design._protocols_protein_interface_design_
)
RG_MinDataAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
readValueOrDie()
(in
rosetta.core.scoring.func._core_scoring_func_
)
ReportSequenceDifferencesCAP
(in
rosetta.protocols.protein_interface_design._protocols_protein_interface_design_
)
RG_MinDataCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
ready()
(in
BuildInstruction
)
ReportToDB
(in
rosetta.protocols.features._protocols_features_
)
rgb_to_hsv()
(in
rosetta.numeric._numeric_
)
ready_for_batch()
(in
IterativeAbrelax
)
ReportToDBAP
(in
rosetta.protocols.features._protocols_features_
)
RGFilter
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
ready_for_batch()
(in
IterativeBase
)
ReportToDBCAP
(in
rosetta.protocols.features._protocols_features_
)
RGFilterAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
ready_for_batch()
(in
IterativeCentroid
)
ReportToDBCreator
(in
rosetta.protocols.features._protocols_features_
)
RGFilterCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
ready_for_batch()
(in
IterativeFullatom
)
ReportToDBCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
rgg()
(in
rosetta.numeric.linear_algebra._numeric_linear_algebra_
)
ready_for_nonideal_scoring()
(in
ScoreFunction
)
ReportToDBCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
rgstr_shift()
(in
StrandPairing
)
ready_to_align()
(in
StepWiseProteinPoseSetup
)
representative_downstream_algorithm()
(in
Matcher
)
rho()
(in
HolesParamsRes
)
real2afteroption()
(in
rosetta.basic.options._basic_options_
)
representative_group_matches()
(in
CloudPDBWriter
)
rho()
(in
PackingScore
)
real3afteroption()
(in
rosetta.basic.options._basic_options_
)
representative_seqpos()
(in
ResidueAlternativeSet
)
right()
(in
ClusteringTreeNode
)
realafteroption()
(in
rosetta.basic.options._basic_options_
)
representative_seqpos()
(in
ResidueAlternativeStepWiseSampler
)
right()
(in
DofClaim
)
RealAngleToShort()
(in
rosetta.protocols.loophash._protocols_loophash_
)
repulsive
(in
AtomPairEnergy
)
right_cdf()
(in
Ramachandran2B
)
RealFilter
(in
rosetta.core.chemical._core_chemical_
)
repulsive_ramp()
(in
AntibodyModeler
)
right_cdf_for_torsion_bin()
(in
Ramachandran2B
)
RealFilterAP
(in
rosetta.core.chemical._core_chemical_
)
RepulsiveOnlyMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
right_child()
(in
KDNode
)
RealFilterCAP
(in
rosetta.core.chemical._core_chemical_
)
RepulsiveOnlyMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
right_multiply_by()
(in
Quaternion_Real
)
reassign_atoms_for_intra_residue_stubs()
(in
FoldTree
)
RepulsiveOnlyMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
right_multiply_by()
(in
Quaternion_double
)
rebuild_bulge_mode()
(in
StepWiseWorkingParameters
)
request()
(in
DbMoverMessageListener
)
right_multiply_by()
(in
Quaternion_float
)
rebuild_bulge_mode()
(in
StepWiseMonteCarloOptions
)
request()
(in
MessageListener
)
right_multiply_by_inverse_of()
(in
Quaternion_Real
)
rebuild_disulfide()
(in
rosetta.core.util._core_util_
)
request_by_name()
(in
QuaternionGridManager
)
right_multiply_by_inverse_of()
(in
Quaternion_double
)
rebuild_filter()
(in
LoopRelaxMover
)
request_by_radius()
(in
QuaternionGridManager
)
right_multiply_by_inverse_of()
(in
Quaternion_float
)
rebuild_loops_until_closed()
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
request_by_size()
(in
QuaternionGridManager
)
RIGHT_PAREN
(in
rosetta.numeric.expression_parser
)
rebuild_pdb2pose()
(in
PDBInfo
)
request_data_from_head_node()
(in
rosetta.basic.message_listening._basic_message_listening_
)
RIGHT_PAREN
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
rebuild_polymer_bond_dependent_atoms()
(in
Conformation
)
request_file()
(in
Inline_File_Provider_Hook
)
RIGHT_PAREN
(in
TokenType
)
rebuild_polymer_bond_dependent_atoms()
(in
ProtectedConformation
)
request_fold_tree()
(in
KicMover
)
right_stub_atoms()
(in
ConnectRight
)
rebuild_polymer_bond_dependent_atoms_this_residue_only()
(in
Conformation
)
request_fold_tree()
(in
LoopBuilder
)
rigid
(in
rosetta.protocols
)
rebuild_residue_connection_dependent_atoms()
(in
Conformation
)
request_fold_tree()
(in
LoopModeler
)
rigid_body
(in
rosetta.protocols.stepwise.modeler.rna
)
recalculate_rmsd_and_output_silent_file()
(in
StepWiseRNA_Clusterer
)
request_fold_tree()
(in
LoopMover
)
RIGID_BODY
(in
rosetta.protocols.stepwise.sampler
)
recalculate_transforms()
(in
SymmetricConformation
)
request_fold_tree()
(in
LoopProtocol
)
RIGID_BODY
(in
rosetta.protocols.stepwise.sampler._protocols_stepwise_sampler_
)
recalculate_z_coordinate()
(in
EllipsoidalRandomizationMover
)
request_fold_tree()
(in
MinimizationRefiner
)
RIGID_BODY
(in
StepWiseSamplerType
)
receive()
(in
DbMoverMessageListener
)
request_fold_tree()
(in
RepackingRefiner
)
rigid_body
(in
rosetta.protocols.stepwise.sampler
)
receive()
(in
MessageListener
)
request_fold_tree()
(in
RotamerTrialsRefiner
)
rigid_body
(in
rosetta.protocols.toolbox
)
receive_char_from_node()
(in
SimulateMPI
)
request_fold_tree()
(in
LegacyKicSampler
)
rigid_body_rotamer()
(in
RigidBodyStepWiseSamplerWithResidueAlternatives
)
receive_char_from_node()
(in
rosetta.utility._utility_
)
request_fold_tree()
(in
AcceptanceCheck
)
rigid_body_rotamer()
(in
RigidBodyStepWiseSamplerWithResidueList
)
receive_double_from_node()
(in
SimulateMPI
)
request_fold_tree()
(in
LoopFilter
)
rigid_body_trial()
(in
DockingLowRes
)
receive_double_from_node()
(in
rosetta.utility._utility_
)
request_fold_tree()
(in
LoopMoverGroup
)
rigid_body_trial()
(in
SymDockingLowRes
)
receive_doubles_from_node()
(in
SimulateMPI
)
request_fold_tree()
(in
PrepareForCentroid
)
RIGID_BODY_WITH_RESIDUE_ALTERNATIVES
(in
rosetta.protocols.stepwise.sampler
)
receive_doubles_from_node()
(in
rosetta.utility._utility_
)
request_fold_tree()
(in
PrepareForFullatom
)
RIGID_BODY_WITH_RESIDUE_ALTERNATIVES
(in
rosetta.protocols.stepwise.sampler._protocols_stepwise_sampler_
)
receive_integer_from_anyone()
(in
SimulateMPI
)
REQUEST_MESSAGE_TAG
(in
rosetta.protocols.jd2
)
RIGID_BODY_WITH_RESIDUE_ALTERNATIVES
(in
StepWiseSamplerType
)
receive_integer_from_anyone()
(in
rosetta.utility._utility_
)
REQUEST_MESSAGE_TAG
(in
rosetta.protocols.jd2._protocols_jd2_
)
RIGID_BODY_WITH_RESIDUE_LIST
(in
rosetta.protocols.stepwise.sampler
)
receive_integer_from_node()
(in
SimulateMPI
)
REQUEST_MESSAGE_TAG
(in
mpi_tags
)
RIGID_BODY_WITH_RESIDUE_LIST
(in
rosetta.protocols.stepwise.sampler._protocols_stepwise_sampler_
)
receive_integer_from_node()
(in
rosetta.utility._utility_
)
REQUEST_SYMMETRIZE_BY_INTERSECTION
(in
rosetta
)
RIGID_BODY_WITH_RESIDUE_LIST
(in
StepWiseSamplerType
)
receive_integers_from_node()
(in
SimulateMPI
)
REQUEST_SYMMETRIZE_BY_INTERSECTION
(in
rosetta.core.pack.task
)
RIGID_CORE_RESAMPLING
(in
IterationStage
)
receive_integers_from_node()
(in
rosetta.utility._utility_
)
REQUEST_SYMMETRIZE_BY_INTERSECTION
(in
PackerTaskSymmetryStatus
)
RIGID_CORE_RESAMPLING
(in
IterativeBase
)
receive_message()
(in
FoldandDockClaimer
)
REQUEST_SYMMETRIZE_BY_INTERSECTION
(in
rosetta.core.pack.task._core_pack_task_
)
RigidBodyDeterministicSpinMover
(in
rosetta.protocols.rigid._protocols_rigid_
)
receive_message()
(in
MembraneTopologyClaimer
)
request_symmetrize_by_intersection()
(in
PackerTask
)
RigidBodyDeterministicSpinMoverAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
receive_message()
(in
TopologyClaimer
)
request_symmetrize_by_intersection()
(in
PackerTask_
)
RigidBodyDeterministicSpinMoverCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
RECEIVE_MESSAGE_TAG
(in
rosetta.protocols.jd2
)
REQUEST_SYMMETRIZE_BY_UNION
(in
rosetta
)
RigidBodyDofPerturbMover
(in
rosetta.protocols.rigid._protocols_rigid_
)
RECEIVE_MESSAGE_TAG
(in
rosetta.protocols.jd2._protocols_jd2_
)
REQUEST_SYMMETRIZE_BY_UNION
(in
rosetta.core.pack.task
)
RigidBodyDofPerturbMoverAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
RECEIVE_MESSAGE_TAG
(in
mpi_tags
)
REQUEST_SYMMETRIZE_BY_UNION
(in
PackerTaskSymmetryStatus
)
RigidBodyDofPerturbMoverCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
receive_observers_from()
(in
Conformation
)
REQUEST_SYMMETRIZE_BY_UNION
(in
rosetta.core.pack.task._core_pack_task_
)
RigidBodyDofRandomizeMover
(in
rosetta.protocols.rigid._protocols_rigid_
)
receive_string_from_node()
(in
SimulateMPI
)
request_symmetrize_by_union()
(in
PackerTask
)
RigidBodyDofRandomizeMoverAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
receive_string_from_node()
(in
rosetta.utility._utility_
)
request_symmetrize_by_union()
(in
PackerTask_
)
RigidBodyDofRandomizeMoverCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
recent_history_queue
(in
rosetta.utility._utility_
)
require_all_target_residue_atom_coordinates()
(in
AtomAngleSecMatchRPE
)
RigidBodyDofRandomTransMover
(in
rosetta.protocols.rigid._protocols_rigid_
)
recent_history_queueAP
(in
rosetta.utility._utility_
)
require_all_target_residue_atom_coordinates()
(in
AtomDihedralSecMatchRPE
)
RigidBodyDofRandomTransMoverAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
recent_history_queueCAP
(in
rosetta.utility._utility_
)
require_all_target_residue_atom_coordinates()
(in
AtomDistanceSecMatchRPE
)
RigidBodyDofRandomTransMoverCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
recent_score()
(in
PDDFScoreFilter
)
require_all_target_residue_atom_coordinates()
(in
AtomGeometrySecMatchRPE
)
RigidBodyDofSeqPerturbMover
(in
rosetta.protocols.rigid._protocols_rigid_
)
recent_score()
(in
SAXSScoreFilter
)
require_all_target_residue_atom_coordinates()
(in
GeometrySecMatchRPE
)
RigidBodyDofSeqPerturbMoverAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
recenter()
(in
rosetta.core.conformation.symmetry._core_conformation_symmetry_
)
require_all_target_residue_atom_coordinates()
(in
ScoringSecMatchRPE
)
RigidBodyDofSeqPerturbMoverCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
recenter()
(in
PocketGrid
)
require_all_target_residue_atom_coordinates()
(in
SecMatchResiduePairEvaluator
)
RigidBodyDofSeqRandomizeMover
(in
rosetta.protocols.rigid._protocols_rigid_
)
receptor_chain()
(in
FlexPepDockingFlags
)
require_atom_to_reside_in_active_site()
(in
DownstreamBuilder
)
RigidBodyDofSeqRandomizeMoverAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
receptor_first_res()
(in
FlexPepDockingFlags
)
require_atom_to_reside_in_active_site()
(in
LigandConformerBuilder
)
RigidBodyDofSeqRandomizeMoverCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
receptor_last_res()
(in
FlexPepDockingFlags
)
require_atom_to_reside_in_active_site()
(in
RigidLigandBuilder
)
RigidBodyDofSeqTransMover
(in
rosetta.protocols.rigid._protocols_rigid_
)
receptor_nres()
(in
FlexPepDockingFlags
)
require_candidate_residue_atoms_to_lie_near_target_atom()
(in
AtomAngleSecMatchRPE
)
RigidBodyDofSeqTransMoverAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
reciprocalSpaceFilter()
(in
ElectronDensity
)
require_candidate_residue_atoms_to_lie_near_target_atom()
(in
AtomDihedralSecMatchRPE
)
RigidBodyDofSeqTransMoverCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
recompute_and_print()
(in
SHOBuriedUnsatisfiedPolarsCalculator
)
require_candidate_residue_atoms_to_lie_near_target_atom()
(in
AtomDistanceSecMatchRPE
)
RigidBodyDofTransMover
(in
rosetta.protocols.rigid._protocols_rigid_
)
RecomputeDensityMapMover
(in
rosetta.protocols.cryst._protocols_cryst_
)
require_candidate_residue_atoms_to_lie_near_target_atom()
(in
AtomGeometrySecMatchRPE
)
RigidBodyDofTransMoverAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
RecomputeDensityMapMoverAP
(in
rosetta.protocols.cryst._protocols_cryst_
)
require_candidate_residue_atoms_to_lie_near_target_atom()
(in
GeometrySecMatchRPE
)
RigidBodyDofTransMoverCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
RecomputeDensityMapMoverCAP
(in
rosetta.protocols.cryst._protocols_cryst_
)
require_candidate_residue_atoms_to_lie_near_target_atom()
(in
ScoringSecMatchRPE
)
RigidBodyInfo
(in
rosetta.protocols.docking._protocols_docking_
)
RecomputeDensityMapMoverCreator
(in
rosetta.protocols.cryst._protocols_cryst_
)
require_candidate_residue_atoms_to_lie_near_target_atom()
(in
SecMatchResiduePairEvaluator
)
RigidBodyInfoAP
(in
rosetta.protocols.docking._protocols_docking_
)
RecomputeDensityMapMoverCreatorAP
(in
rosetta.protocols.cryst._protocols_cryst_
)
require_context_graph()
(in
Energies
)
RigidBodyInfoCAP
(in
rosetta.protocols.docking._protocols_docking_
)
RecomputeDensityMapMoverCreatorCAP
(in
rosetta.protocols.cryst._protocols_cryst_
)
require_final()
(in
ResidueType
)
RigidBodyMotionMover
(in
rosetta.protocols.rigid._protocols_rigid_
)
record()
(in
MultiDimensionalHistogram
)
require_mm_bend()
(in
BackrubMover
)
RigidBodyMotionMoverAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
record_annealer_trajectory()
(in
FixbbSimAnnealer
)
require_mm_bend()
(in
BackrubSidechainMover
)
RigidBodyMotionMoverCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
record_helix_sasas()
(in
HelixBundleFeatures
)
require_target_atom_coordinate()
(in
AtomAngleSecMatchRPE
)
RigidBodyMoveBaseRSO
(in
rosetta.protocols.toolbox.rotamer_set_operations._protocols_toolbox_rotamer_set_operations_
)
record_match()
(in
CloudPDBWriter
)
require_target_atom_coordinate()
(in
AtomDihedralSecMatchRPE
)
RigidBodyMoveBaseRSOAP
(in
rosetta.protocols.toolbox.rotamer_set_operations._protocols_toolbox_rotamer_set_operations_
)
record_match()
(in
OutputWriter
)
require_target_atom_coordinate()
(in
AtomDistanceSecMatchRPE
)
RigidBodyMoveBaseRSOCAP
(in
rosetta.protocols.toolbox.rotamer_set_operations._protocols_toolbox_rotamer_set_operations_
)
record_match()
(in
PDBWriter
)
require_target_atom_coordinate()
(in
AtomGeometrySecMatchRPE
)
RigidBodyMover
(in
rosetta.protocols.rigid._protocols_rigid_
)
record_match()
(in
PoseMatchOutputWriter
)
require_target_atom_coordinate()
(in
GeometrySecMatchRPE
)
RigidBodyMoverAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
record_match()
(in
WriteKinemageOutputter
)
require_target_atom_coordinate()
(in
ScoringSecMatchRPE
)
RigidBodyMoverCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
record_statistics()
(in
BackrubSidechainMover
)
require_target_atom_coordinate()
(in
SecMatchResiduePairEvaluator
)
RigidBodyMoveRSO
(in
rosetta.protocols.toolbox.rotamer_set_operations._protocols_toolbox_rotamer_set_operations_
)
recover_checkpoint()
(in
MembraneAbinitio
)
required_separation_distance()
(in
BumpGrid
)
RigidBodyMoveRSOAP
(in
rosetta.protocols.toolbox.rotamer_set_operations._protocols_toolbox_rotamer_set_operations_
)
recover_checkpoint()
(in
CheckPointer
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
DunbrackEnergy
)
RigidBodyMoveRSOCAP
(in
rosetta.protocols.toolbox.rotamer_set_operations._protocols_toolbox_rotamer_set_operations_
)
recover_conformer_sidechains()
(in
DockingEnsemble
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
CenRotDunEnergy
)
RigidBodyPerturbMover
(in
rosetta.protocols.rigid._protocols_rigid_
)
recover_hit()
(in
ProteinUpstreamBuilder
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
HPatchEnergy
)
RigidBodyPerturbMoverAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
recover_hit()
(in
UpstreamBuilder
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
SurfaceEnergy
)
RigidBodyPerturbMoverCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
recover_hits()
(in
ProteinUpstreamBuilder
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
CarbonHBondEnergy
)
RigidBodyPerturbNoCenterMover
(in
rosetta.protocols.rigid._protocols_rigid_
)
recover_hits()
(in
UpstreamBuilder
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
ConstraintsEnergy
)
RigidBodyPerturbNoCenterMoverAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
recover_low()
(in
RigidSearchMover
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
FullatomCustomPairDistanceEnergy
)
RigidBodyPerturbNoCenterMoverCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
recover_low()
(in
DualMonteCarlo
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
CentroidDisulfideEnergy
)
RigidBodyPerturbNoCenterMoverCreator
(in
rosetta.protocols.rigid._protocols_rigid_
)
recover_low()
(in
MonteCarlo
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
DisulfideMatchingEnergy
)
RigidBodyPerturbNoCenterMoverCreatorAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
recover_low()
(in
GenericMonteCarloMover
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
FullatomDisulfideEnergy
)
RigidBodyPerturbNoCenterMoverCreatorCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
recover_low()
(in
MonteCarloRecover
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
DNAChiEnergy
)
RigidBodyPerturbRandomJumpMover
(in
rosetta.protocols.rigid._protocols_rigid_
)
recover_low()
(in
RationalMonteCarlo
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
DNATorsionEnergy
)
RigidBodyPerturbRandomJumpMoverAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
recover_low()
(in
StepWiseMonteCarloOptions
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
FA_ElecEnergy
)
RigidBodyPerturbRandomJumpMoverCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
recover_original_on_failure()
(in
VarLengthBuild
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
FA_ElecEnergyAroAll
)
RigidBodyRandomizeMover
(in
rosetta.protocols.rigid._protocols_rigid_
)
recover_relevant_poses_for_entity()
(in
MultistateFitnessFunction
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
FA_ElecEnergyAroAro
)
RigidBodyRandomizeMoverAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
recover_sidechains()
(in
SymDockProtocol
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
FA_GrpElecEnergy
)
RigidBodyRandomizeMoverCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
RecoverSideChainsMover
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
RNA_FA_ElecEnergy
)
RigidBodyRandomTMHMoverAP
(in
rosetta.protocols.topology_broker._protocols_topology_broker_'
)
RecoverSideChainsMoverAP
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
ElecDensAllAtomCenEnergy
)
RigidBodyRandomTMHMoverCAP
(in
rosetta.protocols.topology_broker._protocols_topology_broker_'
)
RecoverSideChainsMoverCAP
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
ElecDensCenEnergy
)
RigidBodySilentStruct
(in
rosetta.core.io.silent._core_io_silent_
)
recovery_rate()
(in
RRReporter
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
ElecDensEnergy
)
RigidBodySilentStructAP
(in
rosetta.core.io.silent._core_io_silent_
)
recovery_rate()
(in
RRReporterHuman
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
FastDensEnergy
)
RigidBodySilentStructCAP
(in
rosetta.core.io.silent._core_io_silent_
)
recovery_rate()
(in
RRReporterSQLite
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
PattersonCorrEnergy
)
RigidBodySilentStructCreator
(in
rosetta.core.io.silent._core_io_silent_
)
recovery_rate()
(in
RRReporterSimple
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
ElecDensAtomwiseEnergy
)
RigidBodySilentStructCreatorAP
(in
rosetta.core.io.silent._core_io_silent_
)
recovery_rate()
(in
RotamerRecovery
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
AnalyticEtableEnergy
)
RigidBodySilentStructCreatorCAP
(in
rosetta.core.io.silent._core_io_silent_
)
recreate_pose_for_entity()
(in
PackDaemon
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T
)
RigidBodySpinMover
(in
rosetta.protocols.rigid._protocols_rigid_
)
redefine_begin_end()
(in
StrandPairing
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T
)
RigidBodySpinMoverAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
redefine_chi()
(in
ResidueType
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
TableLookupEtableEnergy
)
RigidBodySpinMoverCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
RedefineChi
(in
rosetta.core.chemical._core_chemical_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
ContextDependentGeometricSolEnergy
)
RigidBodyStepWiseSampler
(in
rosetta.protocols.stepwise.sampler.rigid_body._protocols_stepwise_sampler_rigid_body_
)
RedefineChiAP
(in
rosetta.core.chemical._core_chemical_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
ContextIndependentGeometricSolEnergy
)
RigidBodyStepWiseSamplerAP
(in
rosetta.protocols.stepwise.sampler.rigid_body._protocols_stepwise_sampler_rigid_body_
)
RedefineChiCAP
(in
rosetta.core.chemical._core_chemical_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
ExactOccludedHbondSolEnergy
)
RigidBodyStepWiseSamplerCAP
(in
rosetta.protocols.stepwise.sampler.rigid_body._protocols_stepwise_sampler_rigid_body_
)
redesign_loop_neighborhood()
(in
BDR
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
OccludedHbondSolEnergy
)
RigidBodyStepWiseSamplerValueRange
(in
rosetta.protocols.stepwise.sampler.rigid_body._protocols_stepwise_sampler_rigid_body_
)
redo()
(in
SameStrand
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
OccludedHbondSolEnergy_onebody
)
RigidBodyStepWiseSamplerValueRangeAP
(in
rosetta.protocols.stepwise.sampler.rigid_body._protocols_stepwise_sampler_rigid_body_
)
reduce
(in
SasaRadii
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
HackAroEnergy
)
RigidBodyStepWiseSamplerValueRangeCAP
(in
rosetta.protocols.stepwise.sampler.rigid_body._protocols_stepwise_sampler_rigid_body_
)
reduce
(in
rosetta.core.scoring.sasa._core_scoring_sasa_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
HBondEnergy
)
RigidBodyStepWiseSamplerWithResidueAlternatives
(in
rosetta.protocols.stepwise.sampler.rigid_body._protocols_stepwise_sampler_rigid_body_
)
reduce
(in
rosetta.core.scoring.sasa
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
DDPscore
)
RigidBodyStepWiseSamplerWithResidueAlternativesAP
(in
rosetta.protocols.stepwise.sampler.rigid_body._protocols_stepwise_sampler_rigid_body_
)
reduce_fa_rep()
(in
SymShakeStructureMover
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
FaMPEnvEnergy
)
RigidBodyStepWiseSamplerWithResidueAlternativesCAP
(in
rosetta.protocols.stepwise.sampler.rigid_body._protocols_stepwise_sampler_rigid_body_
)
Reduced_Jdipolar()
(in
RDC
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
FaMPEnvSmoothEnergy
)
RigidBodyStepWiseSamplerWithResidueList
(in
rosetta.protocols.stepwise.sampler.rigid_body._protocols_stepwise_sampler_rigid_body_
)
Reduced_Jdipolar()
(in
RDC_Rohl
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
FaMPSolvEnergy
)
RigidBodyStepWiseSamplerWithResidueListAP
(in
rosetta.protocols.stepwise.sampler.rigid_body._protocols_stepwise_sampler_rigid_body_
)
ref
(in
ScoreType
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
MPCbetaEnergy
)
RigidBodyStepWiseSamplerWithResidueListCAP
(in
rosetta.protocols.stepwise.sampler.rigid_body._protocols_stepwise_sampler_rigid_body_
)
ref
(in
rosetta.core.scoring._core_scoring_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
MPEnvEnergy
)
RigidBodyTransMover
(in
rosetta.protocols.rigid._protocols_rigid_
)
ref
(in
rosetta.core.scoring
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
MPNonHelixPenalty
)
RigidBodyTransMoverAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
ref
(in
rosetta
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
MPPairEnergy
)
RigidBodyTransMoverCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
ref_baseline()
(in
DeltaFilter
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
MPTerminiPenalty
)
RigidBodyTransMoverCreator
(in
rosetta.protocols.rigid._protocols_rigid_
)
ref_nc
(in
ScoreType
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
BurialEnergy
)
RigidBodyTransMoverCreatorAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
ref_nc
(in
rosetta.core.scoring._core_scoring_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
CartesianBondedEnergy
)
RigidBodyTransMoverCreatorCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
ref_nc
(in
rosetta.core.scoring
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
CenHBEnergy
)
RigidChunkCM
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
ref_nc
(in
rosetta
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
CenPairEnergy
)
RigidChunkCMAP
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
ref_pKa()
(in
IonizableResidue
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
CenRotEnvEnergy
)
RigidChunkCMCAP
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
ref_pose()
(in
DecoySetEvaluation
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
CenRotPairEnergy
)
RigidChunkCMCreator
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
ref_pose_for()
(in
AtomTreeDiff
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
ContextDependentLRTwoBodyEnergy
)
RigidChunkCMCreatorAP
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
ref_start_struct()
(in
FlexPepDockingFlags
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
ContextDependentOneBodyEnergy
)
RigidChunkCMCreatorCAP
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
reference_conformation()
(in
DofPassport
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
ContextDependentTwoBodyEnergy
)
RigidLigandBuilder
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
reference_e_method
(in
EnergyMethods
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
ContextIndependentLRTwoBodyEnergy
)
RigidLigandBuilderAP
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
reference_e_method
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
ContextIndependentOneBodyEnergy
)
RigidLigandBuilderCAP
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
reference_e_method
(in
rosetta.core.scoring.methods
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
ContextIndependentTwoBodyEnergy
)
RigidScore
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
reference_pose()
(in
DnaInterfacePacker
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
CustomAtomPairEnergy
)
RigidScoreAP
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
reference_pose()
(in
PDBOutput
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
DNA_BaseEnergy
)
RigidScoreCAP
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
reference_pose()
(in
RestrictDesignToProteinDNAInterface
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
EnvEnergy
)
RigidSearchMover
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
reference_pose()
(in
ProteinRMSDFeatures
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
EnvSmoothEnergy
)
RigidSearchMoverAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
reference_pose()
(in
ProteinRMSDNoSuperpositionFeatures
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
Fa_MbenvEnergy
)
RigidSearchMoverCAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
reference_pose()
(in
MatDesGreedyOptMutationMover
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
Fa_MbsolvEnergy
)
ring_conformer()
(in
Residue
)
reference_pose()
(in
MatDesPointMutationCalculator
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
FreeDOF_Energy
)
ring_conformer_set()
(in
ResidueType
)
reference_pose()
(in
SymUnsatHbondFilter
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
GaussianOverlapEnergy
)
ring_current_coeff()
(in
RNA_CS_residue_parameters
)
reference_pose()
(in
RmsdFilter
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
GenBornEnergy
)
ring_current_effect()
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
reference_pose()
(in
SequenceRecoveryFilter
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
GoapEnergy
)
ring_height()
(in
RNA_CS_residue_parameters
)
reference_pose()
(in
MutationsFilter
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
HybridVDW_Energy
)
RING_HYBRID
(in
rosetta
)
reference_pose()
(in
RestrictNativeResiduesOperation
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
LK_BallEnergy
)
RING_HYBRID
(in
rosetta.core.chemical
)
reference_pose()
(in
SelectByDeltaScoreOperation
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
LK_PolarNonPolarEnergy
)
RING_HYBRID
(in
Hybridization
)
reference_pose_from_options()
(in
ProteinRMSDNoSuperpositionFeatures
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
LK_hack
)
RING_HYBRID
(in
rosetta.core.chemical._core_chemical_
)
reference_res()
(in
RigidBodyStepWiseSampler
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
LongRangeTwoBodyEnergy
)
ring_intensity()
(in
RNA_CS_residue_parameters
)
reference_structure()
(in
RRProtocolReferenceStructure
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
MMBondAngleEnergy
)
ring_pos()
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
reference_stub()
(in
RigidBodyStepWiseSampler
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
MMBondLengthEnergy
)
ring_radius()
(in
RNA_CS_residue_parameters
)
reference_xyz_consistency_check()
(in
RNA_VDW_BinChecker
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
MMLJEnergyInter
)
ring_size()
(in
RingConformerSet
)
ReferenceEnergy
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
MMLJEnergyIntra
)
ring_size()
(in
CarbohydrateInfo
)
ReferenceEnergyAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
MMTorsionEnergy
)
RingConformationMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
ReferenceEnergyCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
MembraneCbetaEnergy
)
RingConformationMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
ReferenceEnergyCreator
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
MembraneCenPairEnergy
)
RingConformationMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
ReferenceEnergyCreatorAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
MembraneEnvEnergy
)
RingConformationMoverCreator
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
ReferenceEnergyCreatorCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
MembraneEnvSmoothEnergy
)
RingConformationMoverCreatorAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
ReferenceEnergyNoncanonical
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
NMerPSSMEnergy
)
RingConformationMoverCreatorCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
ReferenceEnergyNoncanonicalAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
NMerRefEnergy
)
RingConformer
(in
rosetta.core.chemical._core_chemical_
)
ReferenceEnergyNoncanonicalCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
NMerSVMEnergy
)
RingConformerAP
(in
rosetta.core.chemical._core_chemical_
)
ReferenceEnergyNoncanonicalCreator
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
OmegaTetherEnergy
)
RingConformerCAP
(in
rosetta.core.chemical._core_chemical_
)
ReferenceEnergyNoncanonicalCreatorAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
OneBodyEnergy
)
RingConformerManager
(in
rosetta.core.chemical._core_chemical_
)
ReferenceEnergyNoncanonicalCreatorCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
P_AA_Energy
)
RingConformerManagerAP
(in
rosetta.core.chemical._core_chemical_
)
refine
(in
rosetta.protocols.loops.loop_mover
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
P_AA_pp_Energy
)
RingConformerManagerCAP
(in
rosetta.core.chemical._core_chemical_
)
refine()
(in
LoopRelaxMover
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
PairEnergy
)
RingConformerSet
(in
rosetta.core.chemical._core_chemical_
)
refine()
(in
LoopMoverFromCommandLine
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
PeptideBondEnergy
)
RingConformerSetAP
(in
rosetta.core.chemical._core_chemical_
)
refine()
(in
LoopRemodel
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
PoissonBoltzmannEnergy
)
RingConformerSetCAP
(in
rosetta.core.chemical._core_chemical_
)
RefineBetaBarrel
(in
rosetta.protocols.antibody._protocols_antibody_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
ProClosureEnergy
)
RingData
(in
rosetta.protocols.sparta._protocols_sparta_
)
RefineBetaBarrelAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
Rama2BOffsetEnergy
)
RingDataAP
(in
rosetta.protocols.sparta._protocols_sparta_
)
RefineBetaBarrelCAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
RamachandranEnergy
)
RingDataCAP
(in
rosetta.protocols.sparta._protocols_sparta_
)
RefineOneCDRLoop
(in
rosetta.protocols.antibody._protocols_antibody_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
RamachandranEnergy2B
)
ringness()
(in
Bond
)
RefineOneCDRLoopAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
ReferenceEnergy
)
rings()
(in
ResidueType
)
RefineOneCDRLoopCAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
ReferenceEnergyNoncanonical
)
rise()
(in
DNABasestep
)
RefineOneCDRLoopCentroid
(in
rosetta.protocols.antibody._protocols_antibody_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
SequenceDependentRefEnergy
)
RM_BB
(in
rosetta.core.scoring.motif
)
RefineOneCDRLoopCentroidAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
ShortRangeTwoBodyEnergy
)
RM_BB
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
RefineOneCDRLoopCentroidCAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
SmoothCenPairEnergy
)
RM_BB
(in
RM_Type
)
refiners
(in
rosetta.protocols.loop_modeling
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
SmoothEnvEnergy
)
RM_PH
(in
rosetta.core.scoring.motif
)
refresh_bbstub_constraints()
(in
PlacementMinimizationMover
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
SuckerEnergy
)
RM_PH
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
refresh_coordinate_constraints()
(in
PlaceSimultaneouslyMover
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
SymmetricLigandEnergy
)
RM_PH
(in
RM_Type
)
refresh_normalmode()
(in
NormalModeRelaxMover
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
TwoBodyEnergy
)
RM_PO
(in
rosetta.core.scoring.motif
)
refx()
(in
AngleToVector
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
UnfoldedStateEnergy
)
RM_PO
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
refy()
(in
AngleToVector
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
WaterAdductHBondEnergy
)
RM_PO
(in
RM_Type
)
refz()
(in
AngleToVector
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
WaterAdductIntraEnergy
)
RM_SC
(in
rosetta.core.scoring.motif
)
region()
(in
ConstantLengthFragSet
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
YHHPlanarityEnergy
)
RM_SC
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
region()
(in
FragSet
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
pHEnergy
)
RM_SC
(in
RM_Type
)
region()
(in
FragSetCollection
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
SugarBackboneEnergy
)
rm_seq_label()
(in
SequenceAnnotation
)
region()
(in
OrderedFragSet
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
DFIRE_Energy
)
RM_Type
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
region()
(in
DeleteRegionMover
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
NVscore
)
RM_Type_NONE
(in
rosetta.core.scoring.motif
)
region()
(in
KeepRegionMover
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
OrbitalsScore
)
RM_Type_NONE
(in
RM_Type
)
region1()
(in
RegionalConnections
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
RNA_BulgeEnergy
)
RM_Type_NONE
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
region2()
(in
RegionalConnections
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
RNA_FullAtomStackingEnergy
)
rm_virt_phosphate()
(in
StepWiseRNA_ModelerOptions
)
region_all()
(in
FragSet
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
RNA_FullAtomVDW_BasePhosphate
)
rms
(in
ScoreType
)
region_simple()
(in
FragSet
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
RNA_JR_SuiteEnergy
)
rms
(in
rosetta.core.scoring._core_scoring_
)
RegionalConnections
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
RNA_LJ_BaseEnergy
)
rms
(in
rosetta.core.scoring
)
RegionalConnectionsAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
RNA_Mg_Energy
)
rms
(in
rosetta
)
RegionalConnectionsCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
RNA_PairwiseLowResolutionEnergy
)
rms()
(in
SingleStructureData
)
register_calculator()
(in
CalculatorFactory
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
RNA_SugarCloseEnergy
)
rms_at_all_corresponding_atoms()
(in
rosetta.core.scoring._core_scoring_
)
register_factory_prototypes()
(in
RosettaScriptsParser
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
RNA_SuiteEnergy
)
rms_at_corresponding_atoms()
(in
rosetta.core.scoring._core_scoring_
)
register_ff()
(in
FormFactorManager
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
RNA_TorsionEnergy
)
rms_at_corresponding_atoms_no_super()
(in
rosetta.core.scoring._core_scoring_
)
register_mover()
(in
Environment
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
RNA_VDW_Energy
)
rms_at_corresponding_heavy_atoms()
(in
rosetta.core.scoring._core_scoring_
)
register_mover()
(in
MoverList
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
StackElecEnergy
)
RMS_Energy
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
register_options()
(in
AbrelaxApplication
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
RNA_DataBackboneEnergy
)
RMS_EnergyAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
register_options()
(in
ClassicAbinitio
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
symEnergy
)
RMS_EnergyCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
register_options()
(in
ConstraintFragmentSampler
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
AACompositionEnergy
)
RMS_EnergyCreator
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
register_options()
(in
FoldConstraints
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
InterchainEnvEnergy
)
RMS_EnergyCreatorAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
register_options()
(in
FragmentSampler
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
InterchainPairEnergy
)
RMS_EnergyCreatorCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
register_options()
(in
IterativeAbrelax
)
requires_a_setup_for_derivatives_for_residue_opportunity()
(in
SpecialRotamerEnergy
)
rms_error_with_noise()
(in
rosetta.core.import_pose.atom_tree_diffs._core_import_pose_atom_tree_diffs_
)
register_options()
(in
IterativeBase
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
CarbonHBondEnergy
)
rms_pose_list()
(in
StepWiseLegacyClusterer
)
register_options()
(in
IterativeFullatom
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
ConstraintsEnergy
)
rms_wrapper()
(in
rosetta.numeric.model_quality._numeric_model_quality_
)
register_options()
(in
KinematicAbinitio
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
FullatomCustomPairDistanceEnergy
)
rms_wrapper_slow_and_correct()
(in
rosetta.numeric.model_quality._numeric_model_quality_
)
register_options()
(in
MembraneAbinitio
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
CentroidDisulfideEnergy
)
rmsd()
(in
FragmentRmsd
)
register_options()
(in
PairingStatistics
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
DisulfideMatchingEnergy
)
rmsd()
(in
PlaidFingerprint
)
register_options()
(in
Protocol
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
FullatomDisulfideEnergy
)
rmsd()
(in
SSMotifFinder
)
register_options()
(in
Template
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
DNATorsionEnergy
)
rmsd()
(in
StemFinder
)
register_options()
(in
Templates
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
FA_ElecEnergy
)
rmsd()
(in
StepWisePoseAligner
)
register_options()
(in
AntibodyModelerProtocol
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
FA_ElecEnergyAroAll
)
rmsd()
(in
DecoySetEvaluation
)
register_options()
(in
GraftCDRLoopsProtocol
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
FA_ElecEnergyAroAro
)
rmsd_cutoff()
(in
FragQualCalculator
)
register_options()
(in
CanonicalSamplingMover
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
FA_GrpElecEnergy
)
rmsd_cutoff_1()
(in
LigandMotifSearch
)
register_options()
(in
HamiltonianExchange
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
RNA_FA_ElecEnergy
)
rmsd_cutoff_1()
(in
MotifSearch
)
register_options()
(in
ParallelTempering
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
ElecDensAllAtomCenEnergy
)
rmsd_cutoff_2()
(in
LigandMotifSearch
)
register_options()
(in
SilentTrajectoryRecorder
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
ElecDensCenEnergy
)
rmsd_cutoff_2()
(in
MotifSearch
)
register_options()
(in
SimulatedTempering
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
ElecDensEnergy
)
rmsd_over_alignment_atoms()
(in
StepWisePoseAligner
)
register_options()
(in
TemperingBase
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
FastDensEnergy
)
rmsd_over_residue_list()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
register_options()
(in
TrajectoryRecorder
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
PattersonCorrEnergy
)
rmsd_screen()
(in
StepWiseBasicOptions
)
register_options()
(in
AlignRmsdTargetEvaluatorCreator
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
ElecDensAtomwiseEnergy
)
RmsData
(in
rosetta.numeric.model_quality._numeric_model_quality_
)
register_options()
(in
CombinedConstraintEvaluatorCreator
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
AnalyticEtableEnergy
)
RmsDataAP
(in
rosetta.numeric.model_quality._numeric_model_quality_
)
register_options()
(in
ConstraintEvaluatorCreator
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T
)
RmsDataCAP
(in
rosetta.numeric.model_quality._numeric_model_quality_
)
register_options()
(in
DockTaskFactory
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T
)
RmsdEvaluator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
register_options()
(in
DockingInitialPerturbation
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
TableLookupEtableEnergy
)
RmsdEvaluatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
register_options()
(in
DockingProtocol
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
ContextDependentGeometricSolEnergy
)
RmsdEvaluatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
register_options()
(in
TemperedDocking
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
ContextIndependentGeometricSolEnergy
)
RmsdEvaluatorCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
register_options()
(in
rosetta.protocols.evaluation._protocols_evaluation_
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
OccludedHbondSolEnergy
)
RmsdEvaluatorCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
register_options()
(in
DatabaseJobInputter
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
HackAroEnergy
)
RmsdEvaluatorCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
register_options()
(in
DatabaseJobOutputter
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
HBondEnergy
)
RmsdFilter
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
register_options()
(in
ReportToDB
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
DDPscore
)
RmsdFilterAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
register_options()
(in
TrajectoryReportToDB
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
FaMPSolvEnergy
)
RmsdFilterCAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
register_options()
(in
FlxbbDesign
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
MPPairEnergy
)
RmsdFilterCreator
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
register_options()
(in
NonlocalFrags
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
CartesianBondedEnergy
)
RmsdFilterCreatorAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
register_options()
(in
rosetta.protocols.jd2._protocols_jd2_
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
CenHBEnergy
)
RmsdFilterCreatorCAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
register_options()
(in
ArchiveBase
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
CenPairEnergy
)
RmsdSimpleFilter
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
register_options()
(in
ArchiveManager
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
CenRotPairEnergy
)
RmsdSimpleFilterAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
register_options()
(in
EvaluatedArchive
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
ContextDependentLRTwoBodyEnergy
)
RmsdSimpleFilterCAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
register_options()
(in
NormalizedEvaluatedArchive
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
ContextDependentTwoBodyEnergy
)
RmsdSimpleFilterCreator
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
register_options()
(in
CCDLoopClosureMover
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
ContextIndependentLRTwoBodyEnergy
)
RmsdSimpleFilterCreatorAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
register_options()
(in
FASelectSlidingWindowLoopClosure
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
ContextIndependentTwoBodyEnergy
)
RmsdSimpleFilterCreatorCAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
register_options()
(in
RamaCheckBase
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
CustomAtomPairEnergy
)
RmsdTargetEvaluatorCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
register_options()
(in
WidthFirstSlidingWindowLoopClosure
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
DNA_BaseEnergy
)
RmsdTargetEvaluatorCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
register_options()
(in
LoopRefineInnerCycle
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
Fa_MbsolvEnergy
)
RmsdTargetEvaluatorCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
register_options()
(in
LoopRefineInnerCycleContainer
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
GaussianOverlapEnergy
)
rmsf()
(in
DecoySetEvaluation
)
register_options()
(in
RepackTrial
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
GenBornEnergy
)
rmsfitca2()
(in
rosetta.numeric.model_quality._numeric_model_quality_
)
register_options()
(in
SmallMinCCDTrial
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
GoapEnergy
)
rmsfitca3()
(in
rosetta.numeric.model_quality._numeric_model_quality_
)
register_options()
(in
Mover
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
HybridVDW_Energy
)
RMSVallData
(in
rosetta.protocols.frags._protocols_frags_
)
register_options()
(in
ClassicRelax
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
LK_BallEnergy
)
RMSVallDataAP
(in
rosetta.protocols.frags._protocols_frags_
)
register_options()
(in
RelaxProtocolBase
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
LK_PolarNonPolarEnergy
)
RMSVallDataCAP
(in
rosetta.protocols.frags._protocols_frags_
)
register_options()
(in
RotamerRecovery
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
LK_hack
)
RMSwrapper()
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
register_options()
(in
RotamerRecoveryMover
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
LongRangeTwoBodyEnergy
)
RNA
(in
rosetta
)
register_options()
(in
CamShiftEvaluatorCreator
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
MMBondAngleEnergy
)
RNA
(in
rosetta.core.chemical
)
register_options()
(in
ContactMapEvaluatorCreator
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
MMBondLengthEnergy
)
RNA
(in
rosetta.core.chemical._core_chemical_
)
register_options()
(in
ExtraScoreEvaluatorCreator
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
MMLJEnergyInter
)
RNA
(in
ResidueProperty
)
register_options()
(in
JScoreEvaluatorCreator
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
MMLJEnergyIntra
)
rna
(in
rosetta.core.chemical
)
register_options()
(in
JumpNrEvaluatorCreator
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
MMTorsionEnergy
)
rna
(in
rosetta.core.io
)
register_options()
(in
NativeEvaluatorCreator
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
MembraneCenPairEnergy
)
rna
(in
rosetta.core.pack.task
)
register_options()
(in
PalesEvaluatorCreator
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
PairEnergy
)
rna
(in
rosetta.core.pose
)
register_options()
(in
PoolEvaluatorCreator
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
PeptideBondEnergy
)
rna
(in
rosetta.core.scoring
)
register_options()
(in
PredictedBurialFnEvaluatorCreator
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
PoissonBoltzmannEnergy
)
rna
(in
rosetta.protocols.stepwise.legacy.modeler
)
register_options()
(in
RdcEvaluatorCreator
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
ProClosureEnergy
)
rna
(in
rosetta.protocols.stepwise.modeler
)
register_options()
(in
RdcSelectEvaluatorCreator
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
Rama2BOffsetEnergy
)
rna
(in
rosetta.protocols.stepwise.monte_carlo
)
register_options()
(in
RdcTargetEvaluatorCreator
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
RamachandranEnergy2B
)
rna
(in
rosetta.protocols.stepwise.sampler
)
register_options()
(in
RmsdEvaluatorCreator
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
ShortRangeTwoBodyEnergy
)
rna()
(in
ImportPoseOptions
)
register_options()
(in
RmsdTargetEvaluatorCreator
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
SmoothCenPairEnergy
)
RNA_AddDeleteMonteCarlo
(in
rosetta.protocols.stepwise.monte_carlo.rna._protocols_stepwise_monte_carlo_rna_
)
register_options()
(in
StructureSimilarityEvaluatorCreator
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
SuckerEnergy
)
RNA_AddDeleteMonteCarloAP
(in
rosetta.protocols.stepwise.monte_carlo.rna._protocols_stepwise_monte_carlo_rna_
)
register_options()
(in
ConstraintSetMover
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
TwoBodyEnergy
)
RNA_AddDeleteMonteCarloCAP
(in
rosetta.protocols.stepwise.monte_carlo.rna._protocols_stepwise_monte_carlo_rna_
)
register_options()
(in
RingConformationMover
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
WaterAdductHBondEnergy
)
RNA_ANTI_CHI
(in
rosetta.core.pose.full_model_info
)
register_options()
(in
ScoreMover
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
DFIRE_Energy
)
RNA_ANTI_CHI
(in
FullModelParameterType
)
register_options()
(in
ChemicalShiftEvaluatorCreator
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
OrbitalsScore
)
RNA_ANTI_CHI
(in
rosetta.core.pose.full_model_info._core_pose_full_model_info_
)
register_options()
(in
Sparta
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
RNA_FullAtomStackingEnergy
)
rna_anti_chi_res()
(in
FullModelInfo
)
register_options()
(in
SymDockProtocol
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
RNA_JR_SuiteEnergy
)
RNA_AtomVDW
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
register_options()
(in
DecoySetEvaluation
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
RNA_LJ_BaseEnergy
)
RNA_AtomVDWAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
register_options_broker()
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
RNA_Mg_Energy
)
RNA_AtomVDWCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
register_options_universal_main()
(in
rosetta.protocols.jobdist._protocols_jobdist_
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
RNA_PairwiseLowResolutionEnergy
)
RNA_AtrRepChecker
(in
rosetta.protocols.stepwise.modeler.rna.checker._protocols_stepwise_modeler_rna_checker_
)
register_score_maker()
(in
FragmentScoreManager
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
RNA_SuiteEnergy
)
RNA_AtrRepCheckerAP
(in
rosetta.protocols.stepwise.modeler.rna.checker._protocols_stepwise_modeler_rna_checker_
)
register_variable_expression()
(in
WrapperOptEMultifunc
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
RNA_TorsionEnergy
)
RNA_AtrRepCheckerCAP
(in
rosetta.protocols.stepwise.modeler.rna.checker._protocols_stepwise_modeler_rna_checker_
)
register_work_unit()
(in
WorkUnitList
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
RNA_VDW_Energy
)
rna_backbone_backbone
(in
ScoreType
)
register_work_units()
(in
WorkUnitManager
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
StackElecEnergy
)
rna_backbone_backbone
(in
rosetta.core.scoring._core_scoring_
)
reindex_residues()
(in
VallSection
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
RNA_DataBackboneEnergy
)
rna_backbone_backbone
(in
rosetta.core.scoring
)
reindex_sections()
(in
VallLibrary
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
symEnergy
)
rna_backbone_backbone
(in
rosetta
)
reinitialize_active_energy_methods()
(in
MinimizationEdge
)
requires_a_setup_for_derivatives_for_residue_pair_opportunity()
(in
InterchainPairEnergy
)
rna_backbone_backbone_pair_energy()
(in
RNA_LowResolutionPotential
)
reinitialize_CCD_torsions()
(in
StepWiseRNA_ModelerOptions
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
DunbrackEnergy
)
RNA_base_atoms()
(in
RNA_ResidueType
)
reinitialize_for_each_job()
(in
RotamerDumpMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
CenRotDunEnergy
)
rna_base_axis
(in
ScoreType
)
reinitialize_for_each_job()
(in
AbrelaxMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
HPatchEnergy
)
rna_base_axis
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
ClassicAbinitio
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
SurfaceEnergy
)
rna_base_axis
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
ConstraintFragmentSampler
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
CarbonHBondEnergy
)
rna_base_axis
(in
rosetta
)
reinitialize_for_each_job()
(in
DomainAssembly
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
ConstraintsEnergy
)
rna_base_axis_pairwise
(in
ScoreType
)
reinitialize_for_each_job()
(in
DoubleLayerKinematicAbinitio
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
FullatomCustomPairDistanceEnergy
)
rna_base_axis_pairwise
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
FoldConstraints
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
CentroidDisulfideEnergy
)
rna_base_axis_pairwise
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
FragmentSampler
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
DisulfideMatchingEnergy
)
rna_base_axis_pairwise
(in
rosetta
)
reinitialize_for_each_job()
(in
JumpingFoldConstraintsWrapper
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
FullatomDisulfideEnergy
)
rna_base_backbone
(in
ScoreType
)
reinitialize_for_each_job()
(in
KinematicAbinitio
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
DNAChiEnergy
)
rna_base_backbone
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
KinematicTaskControl
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
DNATorsionEnergy
)
rna_base_backbone
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
LoopJumpFoldCst
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
FA_ElecEnergy
)
rna_base_backbone
(in
rosetta
)
reinitialize_for_each_job()
(in
MembraneAbinitio
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
FA_ElecEnergyAroAll
)
rna_base_backbone_pair_energy()
(in
RNA_LowResolutionPotential
)
reinitialize_for_each_job()
(in
Protocol
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
FA_ElecEnergyAroAro
)
rna_base_pair
(in
ScoreType
)
reinitialize_for_each_job()
(in
ResolutionSwitcher
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
FA_GrpElecEnergy
)
rna_base_pair
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
AbscriptLoopCloserCM
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
RNA_FA_ElecEnergy
)
rna_base_pair
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
AbscriptMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
ElecDensAllAtomCenEnergy
)
rna_base_pair
(in
rosetta
)
reinitialize_for_each_job()
(in
AbscriptStageMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
ElecDensCenEnergy
)
rna_base_pair_pairwise
(in
ScoreType
)
reinitialize_for_each_job()
(in
ConstraintPreparer
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
ElecDensEnergy
)
rna_base_pair_pairwise
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
FragmentCM
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
FastDensEnergy
)
rna_base_pair_pairwise
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
FragmentJumpCM
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
PattersonCorrEnergy
)
rna_base_pair_pairwise
(in
rosetta
)
reinitialize_for_each_job()
(in
RigidChunkCM
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
ElecDensAtomwiseEnergy
)
rna_base_stack
(in
ScoreType
)
reinitialize_for_each_job()
(in
StagePreparer
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
AnalyticEtableEnergy
)
rna_base_stack
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
StructPerturberCM
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T
)
rna_base_stack
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
InterfaceAnalyzerMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T
)
rna_base_stack
(in
rosetta
)
reinitialize_for_each_job()
(in
LoopAnalyzerMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
TableLookupEtableEnergy
)
rna_base_stack_axis
(in
ScoreType
)
reinitialize_for_each_job()
(in
PackStatMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
ContextDependentGeometricSolEnergy
)
rna_base_stack_axis
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
AnchoredDesignMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
ContextIndependentGeometricSolEnergy
)
rna_base_stack_axis
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
AnchoredPerturbMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
ExactOccludedHbondSolEnergy
)
rna_base_stack_axis
(in
rosetta
)
reinitialize_for_each_job()
(in
AnchoredRefineMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
OccludedHbondSolEnergy
)
rna_base_stack_axis_pairwise
(in
ScoreType
)
reinitialize_for_each_job()
(in
AntibodyModelerProtocol
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
OccludedHbondSolEnergy_onebody
)
rna_base_stack_axis_pairwise
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
CDRsMinPackMin
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
HackAroEnergy
)
rna_base_stack_axis_pairwise
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
CloseOneCDRLoop
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
HBondEnergy
)
rna_base_stack_axis_pairwise
(in
rosetta
)
reinitialize_for_each_job()
(in
GraftCDRLoopsProtocol
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
DDPscore
)
rna_base_stack_pairwise
(in
ScoreType
)
reinitialize_for_each_job()
(in
GraftOneCDRLoop
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
FaMPEnvEnergy
)
rna_base_stack_pairwise
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
GraftedStemOptimizer
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
FaMPEnvSmoothEnergy
)
rna_base_stack_pairwise
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
H3CterInsert
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
FaMPSolvEnergy
)
rna_base_stack_pairwise
(in
rosetta
)
reinitialize_for_each_job()
(in
H3PerturbCCD
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
MPCbetaEnergy
)
rna_base_stagger
(in
ScoreType
)
reinitialize_for_each_job()
(in
H3RefineCCD
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
MPEnvEnergy
)
rna_base_stagger
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
LHRepulsiveRamp
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
MPNonHelixPenalty
)
rna_base_stagger
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
ModelCDRH3
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
MPPairEnergy
)
rna_base_stagger
(in
rosetta
)
reinitialize_for_each_job()
(in
RefineBetaBarrel
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
MPTerminiPenalty
)
rna_base_stagger_pairwise
(in
ScoreType
)
reinitialize_for_each_job()
(in
RefineOneCDRLoop
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
BurialEnergy
)
rna_base_stagger_pairwise
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
RefineOneCDRLoopCentroid
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
CartesianBondedEnergy
)
rna_base_stagger_pairwise
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
CDRDihedralConstraintMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
CenHBEnergy
)
rna_base_stagger_pairwise
(in
rosetta
)
reinitialize_for_each_job()
(in
ParatopeEpitopeSiteConstraintMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
CenPairEnergy
)
RNA_BaseCentroidChecker
(in
rosetta.protocols.stepwise.modeler.rna.checker._protocols_stepwise_modeler_rna_checker_
)
reinitialize_for_each_job()
(in
ParatopeSiteConstraintMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
CenRotEnvEnergy
)
RNA_BaseCentroidCheckerAP
(in
rosetta.protocols.stepwise.modeler.rna.checker._protocols_stepwise_modeler_rna_checker_
)
reinitialize_for_each_job()
(in
AntibodyDesignMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
CenRotPairEnergy
)
RNA_BaseCentroidCheckerCAP
(in
rosetta.protocols.stepwise.modeler.rna.checker._protocols_stepwise_modeler_rna_checker_
)
reinitialize_for_each_job()
(in
AntibodyDesignProtocol
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
ContextDependentLRTwoBodyEnergy
)
rna_bond_geometry
(in
ScoreType
)
reinitialize_for_each_job()
(in
MutateFrameworkForCluster
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
ContextDependentOneBodyEnergy
)
rna_bond_geometry
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
AntibodyModeler
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
ContextDependentTwoBodyEnergy
)
rna_bond_geometry
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
CDRH3Modeler
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
ContextIndependentLRTwoBodyEnergy
)
rna_bond_geometry
(in
rosetta
)
reinitialize_for_each_job()
(in
CloseOneMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
ContextIndependentOneBodyEnergy
)
rna_bond_geometry_energy()
(in
ConstraintEdge
)
reinitialize_for_each_job()
(in
GraftMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
ContextIndependentTwoBodyEnergy
)
RNA_BULGE
(in
rosetta.core.pose.full_model_info
)
reinitialize_for_each_job()
(in
GraftOneMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
CustomAtomPairEnergy
)
RNA_BULGE
(in
FullModelParameterType
)
reinitialize_for_each_job()
(in
LoopRlxMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
DNA_BaseEnergy
)
RNA_BULGE
(in
rosetta.core.pose.full_model_info._core_pose_full_model_info_
)
reinitialize_for_each_job()
(in
BackrubMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
EnvEnergy
)
rna_bulge
(in
ScoreType
)
reinitialize_for_each_job()
(in
BackrubProtocol
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
EnvSmoothEnergy
)
rna_bulge
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
BackrubSidechainMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
Fa_MbenvEnergy
)
rna_bulge
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
CanonicalSamplingMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
Fa_MbsolvEnergy
)
rna_bulge
(in
rosetta
)
reinitialize_for_each_job()
(in
FixedTemperatureController
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
FreeDOF_Energy
)
rna_bulge_res()
(in
FullModelInfo
)
reinitialize_for_each_job()
(in
MetricRecorder
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
GaussianOverlapEnergy
)
RNA_BulgeEnergy
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
MetropolisHastingsMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
GenBornEnergy
)
RNA_BulgeEnergyAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
ParallelTempering
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
GoapEnergy
)
RNA_BulgeEnergyCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
ProgressBarObserver
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
HybridVDW_Energy
)
RNA_BulgeEnergyCreator
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
SidechainMetropolisHastingsMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
LK_BallEnergy
)
RNA_BulgeEnergyCreatorAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
SimulatedTempering
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
LK_PolarNonPolarEnergy
)
RNA_BulgeEnergyCreatorCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
TemperatureController
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
LK_hack
)
rna_centroid_info()
(in
RNA_ScoringInfo
)
reinitialize_for_each_job()
(in
TemperingBase
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
LongRangeTwoBodyEnergy
)
RNA_CentroidInfo
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
ThermodynamicMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
MMBondAngleEnergy
)
RNA_CentroidInfoAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
ThermodynamicObserver
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
MMBondLengthEnergy
)
RNA_CentroidInfoCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
TrialCounterObserver
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
MMLJEnergyInter
)
RNA_CHAIN_CLOSABLE_GEOMETRY
(in
rosetta.protocols.stepwise.screener
)
reinitialize_for_each_job()
(in
AssignToClustersMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
MMLJEnergyIntra
)
RNA_CHAIN_CLOSABLE_GEOMETRY
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
reinitialize_for_each_job()
(in
ClusterBase
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
MMTorsionEnergy
)
RNA_CHAIN_CLOSABLE_GEOMETRY
(in
StepWiseScreenerType
)
reinitialize_for_each_job()
(in
ClusterPhilStyle
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
MembraneCbetaEnergy
)
RNA_CHAIN_CLOSABLE_GEOMETRY_RESIDUE_BASED
(in
rosetta.protocols.stepwise.screener
)
reinitialize_for_each_job()
(in
ClusterPhilStyle_Loop
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
MembraneCenPairEnergy
)
RNA_CHAIN_CLOSABLE_GEOMETRY_RESIDUE_BASED
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
reinitialize_for_each_job()
(in
ClusterPhilStyle_PoseReporter
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
MembraneEnvEnergy
)
RNA_CHAIN_CLOSABLE_GEOMETRY_RESIDUE_BASED
(in
StepWiseScreenerType
)
reinitialize_for_each_job()
(in
EnsembleConstraints
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
MembraneEnvSmoothEnergy
)
RNA_CHAIN_CLOSABLE_GEOMETRY_STUB_BASED
(in
rosetta.protocols.stepwise.screener
)
reinitialize_for_each_job()
(in
EnsembleConstraints_Simple
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
NMerPSSMEnergy
)
RNA_CHAIN_CLOSABLE_GEOMETRY_STUB_BASED
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
reinitialize_for_each_job()
(in
GatherPosesMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
NMerRefEnergy
)
RNA_CHAIN_CLOSABLE_GEOMETRY_STUB_BASED
(in
StepWiseScreenerType
)
reinitialize_for_each_job()
(in
CoarseRNA_LoopCloser
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
NMerSVMEnergy
)
RNA_CHAIN_CLOSURE
(in
rosetta.protocols.stepwise.screener
)
reinitialize_for_each_job()
(in
ExtraThreadingMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
OmegaTetherEnergy
)
RNA_CHAIN_CLOSURE
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
reinitialize_for_each_job()
(in
LoopRelaxMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
OneBodyEnergy
)
RNA_CHAIN_CLOSURE
(in
StepWiseScreenerType
)
reinitialize_for_each_job()
(in
LoopRelaxThreadingMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
P_AA_Energy
)
RNA_ChainClosableGeometryChecker
(in
rosetta.protocols.stepwise.modeler.rna.checker._protocols_stepwise_modeler_rna_checker_
)
reinitialize_for_each_job()
(in
MultiThreadingMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
P_AA_pp_Energy
)
RNA_ChainClosableGeometryCheckerAP
(in
rosetta.protocols.stepwise.modeler.rna.checker._protocols_stepwise_modeler_rna_checker_
)
reinitialize_for_each_job()
(in
PartialThreadingMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
PairEnergy
)
RNA_ChainClosableGeometryCheckerCAP
(in
rosetta.protocols.stepwise.modeler.rna.checker._protocols_stepwise_modeler_rna_checker_
)
reinitialize_for_each_job()
(in
RecoverSideChainsMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
PeptideBondEnergy
)
RNA_ChainClosableGeometryResidueBasedScreener
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
reinitialize_for_each_job()
(in
StealLigandMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
PoissonBoltzmannEnergy
)
RNA_ChainClosableGeometryResidueBasedScreenerAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
reinitialize_for_each_job()
(in
StealSideChainsMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
ProClosureEnergy
)
RNA_ChainClosableGeometryResidueBasedScreenerCAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
reinitialize_for_each_job()
(in
ThreadingMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
Rama2BOffsetEnergy
)
RNA_ChainClosableGeometryScreener
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
reinitialize_for_each_job()
(in
ContactMap
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
RamachandranEnergy
)
RNA_ChainClosableGeometryScreenerAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
reinitialize_for_each_job()
(in
FitBfactorsMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
RamachandranEnergy2B
)
RNA_ChainClosableGeometryScreenerCAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
reinitialize_for_each_job()
(in
LoadDensityMapMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
ReferenceEnergy
)
RNA_ChainClosableGeometryStubBasedScreener
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
reinitialize_for_each_job()
(in
RecomputeDensityMapMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
ReferenceEnergyNoncanonical
)
RNA_ChainClosableGeometryStubBasedScreenerAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
reinitialize_for_each_job()
(in
SetCrystWeightMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
SequenceDependentRefEnergy
)
RNA_ChainClosableGeometryStubBasedScreenerCAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
reinitialize_for_each_job()
(in
SetRefinementOptionsMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
ShortRangeTwoBodyEnergy
)
RNA_ChainClosureChecker
(in
rosetta.protocols.stepwise.modeler.rna.checker._protocols_stepwise_modeler_rna_checker_
)
reinitialize_for_each_job()
(in
TagPoseWithRefinementStatsMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
SmoothCenPairEnergy
)
RNA_ChainClosureCheckerAP
(in
rosetta.protocols.stepwise.modeler.rna.checker._protocols_stepwise_modeler_rna_checker_
)
reinitialize_for_each_job()
(in
UpdateSolventMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
SmoothEnvEnergy
)
RNA_ChainClosureCheckerCAP
(in
rosetta.protocols.stepwise.modeler.rna.checker._protocols_stepwise_modeler_rna_checker_
)
reinitialize_for_each_job()
(in
CreateAngleConstraint
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
SuckerEnergy
)
RNA_ChainClosureScreener
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
reinitialize_for_each_job()
(in
CreateDistanceConstraint
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
SymmetricLigandEnergy
)
RNA_ChainClosureScreenerAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
reinitialize_for_each_job()
(in
CreateTorsionConstraint
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
TwoBodyEnergy
)
RNA_ChainClosureScreenerCAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
reinitialize_for_each_job()
(in
DeclareBond
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
UnfoldedStateEnergy
)
rna_chem_map
(in
ScoreType
)
reinitialize_for_each_job()
(in
PeptideStubMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
WaterAdductHBondEnergy
)
rna_chem_map
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
ddGMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
WaterAdductIntraEnergy
)
rna_chem_map
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
GreedyOptMutationMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
YHHPlanarityEnergy
)
rna_chem_map
(in
rosetta
)
reinitialize_for_each_job()
(in
ParetoOptMutationMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
pHEnergy
)
rna_chem_map_lores
(in
ScoreType
)
reinitialize_for_each_job()
(in
DesignProteinBackboneAroundDNA
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
SugarBackboneEnergy
)
rna_chem_map_lores
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
DnaInterfaceMinMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
DFIRE_Energy
)
rna_chem_map_lores
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
DnaInterfaceMultiStateDesign
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
NVscore
)
rna_chem_map_lores
(in
rosetta
)
reinitialize_for_each_job()
(in
DnaInterfacePacker
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
OrbitalsScore
)
rna_chem_shift
(in
ScoreType
)
reinitialize_for_each_job()
(in
SeparateDnaFromNonDna
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
RNA_BulgeEnergy
)
rna_chem_shift
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
ConformerSwitchMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
RNA_FullAtomStackingEnergy
)
rna_chem_shift
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
DockMCMCycle
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
RNA_FullAtomVDW_BasePhosphate
)
rna_chem_shift
(in
rosetta
)
reinitialize_for_each_job()
(in
DockMCMProtocol
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
RNA_JR_SuiteEnergy
)
RNA_ChemicalMappingEnergy
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
DockMinMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
RNA_LJ_BaseEnergy
)
RNA_ChemicalMappingEnergyAP
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
DockSetupMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
RNA_Mg_Energy
)
RNA_ChemicalMappingEnergyCAP
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
DockingEnsemblePrepackProtocol
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
RNA_PairwiseLowResolutionEnergy
)
RNA_ChemicalMappingEnergyCreator
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
DockingHighRes
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
RNA_SugarCloseEnergy
)
RNA_ChemicalMappingEnergyCreatorAP
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
DockingHighResLegacy
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
RNA_SuiteEnergy
)
RNA_ChemicalMappingEnergyCreatorCAP
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
DockingInitialPerturbation
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
RNA_TorsionEnergy
)
RNA_ChemicalShiftEnergy
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
reinitialize_for_each_job()
(in
DockingLowRes
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
RNA_VDW_Energy
)
RNA_ChemicalShiftEnergyAP
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
reinitialize_for_each_job()
(in
DockingLowResEnsemble
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
StackElecEnergy
)
RNA_ChemicalShiftEnergyCAP
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
reinitialize_for_each_job()
(in
DockingPrepackProtocol
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
RNA_DataBackboneEnergy
)
RNA_ChemicalShiftEnergyCreator
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
reinitialize_for_each_job()
(in
DockingProtocol
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
symEnergy
)
RNA_ChemicalShiftEnergyCreatorAP
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
reinitialize_for_each_job()
(in
DockingSlideIntoContact
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
AACompositionEnergy
)
RNA_ChemicalShiftEnergyCreatorCAP
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
reinitialize_for_each_job()
(in
EllipsoidalRandomizationMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
InterchainEnvEnergy
)
RNA_ChemicalShiftPotential
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
reinitialize_for_each_job()
(in
FaDockingSlideIntoContact
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
InterchainPairEnergy
)
RNA_ChemicalShiftPotentialAP
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
reinitialize_for_each_job()
(in
InterfaceSidechainMinMover
)
requires_a_setup_for_scoring_for_residue_opportunity()
(in
SpecialRotamerEnergy
)
RNA_ChemicalShiftPotentialCAP
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
reinitialize_for_each_job()
(in
SidechainMinMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
CarbonHBondEnergy
)
RNA_CHI
(in
rosetta.protocols.stepwise.sampler
)
reinitialize_for_each_job()
(in
TemperedDocking
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
ConstraintsEnergy
)
RNA_CHI
(in
rosetta.protocols.stepwise.sampler._protocols_stepwise_sampler_
)
reinitialize_for_each_job()
(in
MPDockingMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
FullatomCustomPairDistanceEnergy
)
RNA_CHI
(in
StepWiseSamplerType
)
reinitialize_for_each_job()
(in
MPDockingSetupMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
CentroidDisulfideEnergy
)
RNA_ChiStepWiseSampler
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
SaneDockingProtocol
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
DisulfideMatchingEnergy
)
RNA_ChiStepWiseSamplerAP
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
AddAssemblyConstraints
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
FullatomDisulfideEnergy
)
RNA_ChiStepWiseSamplerCAP
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
AssembleLinkerMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
DNATorsionEnergy
)
RNA_ChunkLibrary
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
CombineChainsMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
FA_ElecEnergy
)
RNA_ChunkLibraryAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
PostDockAssemblyScorer
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
FA_ElecEnergyAroAll
)
RNA_ChunkLibraryCAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
BfactorFittingMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
FA_ElecEnergyAroAro
)
RNA_CS_parameters
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
reinitialize_for_each_job()
(in
DensityMorphingMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
FA_GrpElecEnergy
)
RNA_CS_parametersAP
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
reinitialize_for_each_job()
(in
ReportFSC
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
RNA_FA_ElecEnergy
)
RNA_CS_parametersCAP
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
reinitialize_for_each_job()
(in
ScaleMapIntensities
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
ElecDensAllAtomCenEnergy
)
RNA_CS_residue_parameters
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
reinitialize_for_each_job()
(in
SetupForDensityScoringMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
ElecDensCenEnergy
)
RNA_CS_residue_parametersAP
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
reinitialize_for_each_job()
(in
ClientMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
ElecDensEnergy
)
RNA_CS_residue_parametersCAP
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
reinitialize_for_each_job()
(in
CoMTrackerCM
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
FastDensEnergy
)
rna_data()
(in
RNA_DataInfo
)
reinitialize_for_each_job()
(in
EnvMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
PattersonCorrEnergy
)
rna_data_backbone
(in
ScoreType
)
reinitialize_for_each_job()
(in
ScriptCM
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
ElecDensAtomwiseEnergy
)
rna_data_backbone
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
MultipleDomainMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
AnalyticEtableEnergy
)
rna_data_backbone
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
RNA_DeNovoProtocol
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T
)
rna_data_backbone
(in
rosetta
)
reinitialize_for_each_job()
(in
RNA_FragmentMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T
)
rna_data_base
(in
ScoreType
)
reinitialize_for_each_job()
(in
RNA_LoopCloser
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
TableLookupEtableEnergy
)
rna_data_base
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
RNA_Minimizer
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
ContextDependentGeometricSolEnergy
)
rna_data_base
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
RNA_Relaxer
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
ContextIndependentGeometricSolEnergy
)
rna_data_base
(in
rosetta
)
reinitialize_for_each_job()
(in
ReportToDB
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
OccludedHbondSolEnergy
)
rna_data_info()
(in
RNA_ScoringInfo
)
reinitialize_for_each_job()
(in
TrajectoryReportToDB
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
HackAroEnergy
)
RNA_DataBackboneEnergy
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
SetupForFibrilMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
HBondEnergy
)
RNA_DataBackboneEnergyAP
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
BluePrintBDR
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
DDPscore
)
RNA_DataBackboneEnergyCAP
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
CircularPermutation
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
FaMPSolvEnergy
)
RNA_DataBackboneEnergyCreator
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
MatchResiduesMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
MPPairEnergy
)
RNA_DataBackboneEnergyCreatorAP
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
SheetConstraintsRCG
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
CartesianBondedEnergy
)
RNA_DataBackboneEnergyCreatorCAP
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
SetAACompositionPotential
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
CenHBEnergy
)
RNA_DataInfo
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
SetSecStructEnergies
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
CenPairEnergy
)
RNA_DataInfoAP
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
FlexPacker
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
CenRotPairEnergy
)
RNA_DataInfoCAP
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
FlexPepDockingAbInitio
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
ContextDependentLRTwoBodyEnergy
)
RNA_DataReader
(in
rosetta.core.io.rna._core_io_rna_
)
reinitialize_for_each_job()
(in
FlexPepDockingLowRes
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
ContextDependentTwoBodyEnergy
)
RNA_DataReaderAP
(in
rosetta.core.io.rna._core_io_rna_
)
reinitialize_for_each_job()
(in
FlexPepDockingProtocol
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
ContextIndependentLRTwoBodyEnergy
)
RNA_DataReaderCAP
(in
rosetta.core.io.rna._core_io_rna_
)
reinitialize_for_each_job()
(in
FloppyTailMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
ContextIndependentTwoBodyEnergy
)
RNA_Datum
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
FlxbbDesign
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
CustomAtomPairEnergy
)
RNA_DatumAP
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
FlxbbDesignPack
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
DNA_BaseEnergy
)
RNA_DatumCAP
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
InterlockAroma
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
Fa_MbsolvEnergy
)
RNA_DeNovoProtocol
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
BDR
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
GaussianOverlapEnergy
)
RNA_DeNovoProtocolAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
VarLengthBuild
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
GenBornEnergy
)
RNA_DeNovoProtocolCAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
RemodelConstraintGenerator
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
GoapEnergy
)
RNA_DMS_LowResolutionPotential
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
NonlocalFrags
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
HybridVDW_Energy
)
RNA_DMS_LowResolutionPotentialAP
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
TorsionFragmentMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
LK_BallEnergy
)
RNA_DMS_LowResolutionPotentialCAP
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
GeneralizedKIC
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
LK_PolarNonPolarEnergy
)
RNA_DMS_Potential
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
AnchoredGraftMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
LK_hack
)
RNA_DMS_PotentialAP
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
CCDEndsGraftMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
LongRangeTwoBodyEnergy
)
RNA_DMS_PotentialCAP
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
GraftMoverBase
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
MMBondAngleEnergy
)
RNA_EnergyMethodOptions
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
DeleteRegionMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
MMBondLengthEnergy
)
RNA_EnergyMethodOptionsAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
InsertPoseIntoPoseMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
MMLJEnergyInter
)
RNA_EnergyMethodOptionsCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
KeepRegionMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
MMLJEnergyIntra
)
rna_fa_atr_base
(in
ScoreType
)
reinitialize_for_each_job()
(in
ReplaceRegionMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
MMTorsionEnergy
)
rna_fa_atr_base
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
BackboneGridSampler
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
MembraneCenPairEnergy
)
rna_fa_atr_base
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
BundleGridSampler
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
PairEnergy
)
rna_fa_atr_base
(in
rosetta
)
reinitialize_for_each_job()
(in
FitSimpleHelix
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
PeptideBondEnergy
)
rna_fa_elec_one_way()
(in
RNA_FA_ElecEnergy
)
reinitialize_for_each_job()
(in
MakeBundle
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
PoissonBoltzmannEnergy
)
RNA_FA_ElecEnergy
(in
rosetta.core.scoring.elec._core_scoring_elec_
)
reinitialize_for_each_job()
(in
MakeBundleHelix
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
ProClosureEnergy
)
RNA_FA_ElecEnergyAP
(in
rosetta.core.scoring.elec._core_scoring_elec_
)
reinitialize_for_each_job()
(in
PerturbBundle
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
Rama2BOffsetEnergy
)
RNA_FA_ElecEnergyCAP
(in
rosetta.core.scoring.elec._core_scoring_elec_
)
reinitialize_for_each_job()
(in
PerturbBundleHelix
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
RamachandranEnergy2B
)
RNA_FA_ElecEnergyCreator
(in
rosetta.core.scoring.elec._core_scoring_elec_
)
reinitialize_for_each_job()
(in
BackboneTorsionPerturbation
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
ShortRangeTwoBodyEnergy
)
RNA_FA_ElecEnergyCreatorAP
(in
rosetta.core.scoring.elec._core_scoring_elec_
)
reinitialize_for_each_job()
(in
BackboneTorsionSampler
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
SmoothCenPairEnergy
)
RNA_FA_ElecEnergyCreatorCAP
(in
rosetta.core.scoring.elec._core_scoring_elec_
)
reinitialize_for_each_job()
(in
CartesianHybridize
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
SuckerEnergy
)
rna_fa_rep_base
(in
ScoreType
)
reinitialize_for_each_job()
(in
CartesianSampler
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
TwoBodyEnergy
)
rna_fa_rep_base
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
ChunkTrialMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
WaterAdductHBondEnergy
)
rna_fa_rep_base
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
DomainAssembly
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
DFIRE_Energy
)
rna_fa_rep_base
(in
rosetta
)
reinitialize_for_each_job()
(in
FoldTreeHybridize
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
OrbitalsScore
)
rna_filtered_base_base_info()
(in
RNA_ScoringInfo
)
reinitialize_for_each_job()
(in
HybridizeProtocol
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
RNA_FullAtomStackingEnergy
)
RNA_FilteredBaseBaseInfo
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
InsertChunkMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
RNA_JR_SuiteEnergy
)
RNA_FilteredBaseBaseInfoAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
MRMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
RNA_LJ_BaseEnergy
)
RNA_FilteredBaseBaseInfoCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
WeightedFragmentSmoothTrialMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
RNA_Mg_Energy
)
RNA_FittedTorsionInfo
(in
rosetta.core.chemical.rna._core_chemical_rna_
)
reinitialize_for_each_job()
(in
WeightedFragmentTrialMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
RNA_PairwiseLowResolutionEnergy
)
RNA_FittedTorsionInfoAP
(in
rosetta.core.chemical.rna._core_chemical_rna_
)
reinitialize_for_each_job()
(in
IdealizeMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
RNA_SuiteEnergy
)
RNA_FittedTorsionInfoCAP
(in
rosetta.core.chemical.rna._core_chemical_rna_
)
reinitialize_for_each_job()
(in
BalancedKicMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
RNA_TorsionEnergy
)
RNA_FragmentMover
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
KicMover
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
RNA_VDW_Energy
)
RNA_FragmentMoverAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
AddHydrogen
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
StackElecEnergy
)
RNA_FragmentMoverCAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
AddHydrogens
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
RNA_DataBackboneEnergy
)
RNA_Fragments
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
CompoundTranslate
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
symEnergy
)
RNA_FragmentsAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
ComputeLigandRDF
)
requires_a_setup_for_scoring_for_residue_pair_opportunity()
(in
InterchainPairEnergy
)
RNA_FragmentsCAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
FinalMinimizer
)
requires_actcoord()
(in
ResidueType
)
RNA_FullAtomStackingEnergy
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
GrowLigand
)
requires_actcoord()
(in
Residue
)
RNA_FullAtomStackingEnergyAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
HighResDocker
)
requires_context_graph()
(in
ScoreFunctionInfo
)
RNA_FullAtomStackingEnergyCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
InterfaceScoreCalculator
)
requires_pose()
(in
FixedTemperatureController
)
RNA_FullAtomStackingEnergyCreator
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
LigandDesign
)
requires_pose()
(in
MetricRecorder
)
RNA_FullAtomStackingEnergyCreatorAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
MinimizeBackbone
)
requires_pose()
(in
ParallelTempering
)
RNA_FullAtomStackingEnergyCreatorCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
MinimizeLigand
)
requires_pose()
(in
ProgressBarObserver
)
RNA_FullAtomVDW_BasePhosphate
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
RandomConformerMover
)
requires_pose()
(in
SimulatedTempering
)
RNA_FullAtomVDW_BasePhosphateAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
RandomConformers
)
requires_pose()
(in
TemperatureController
)
RNA_FullAtomVDW_BasePhosphateCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
RigidSearchMover
)
requires_pose()
(in
TemperingBase
)
RNA_FullAtomVDW_BasePhosphateCreator
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
Rotate
)
requires_pose()
(in
ThermodynamicObserver
)
RNA_FullAtomVDW_BasePhosphateCreatorAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
Rotates
)
requires_pose()
(in
TrialCounterObserver
)
RNA_FullAtomVDW_BasePhosphateCreatorCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
SlideTogether
)
reroot()
(in
rosetta.protocols.stepwise.modeler._protocols_stepwise_modeler_
)
RNA_HelixAssembler
(in
rosetta.protocols.stepwise.modeler.rna.helix._protocols_stepwise_modeler_rna_helix_
)
reinitialize_for_each_job()
(in
StartFrom
)
reroot_based_on_full_model_info()
(in
rosetta.protocols.stepwise.modeler._protocols_stepwise_modeler_
)
RNA_HelixAssemblerAP
(in
rosetta.protocols.stepwise.modeler.rna.helix._protocols_stepwise_modeler_rna_helix_
)
reinitialize_for_each_job()
(in
TetherLigand
)
reroot_restype()
(in
rosetta.core.chemical._core_chemical_
)
RNA_HelixAssemblerCAP
(in
rosetta.protocols.stepwise.modeler.rna.helix._protocols_stepwise_modeler_rna_helix_
)
reinitialize_for_each_job()
(in
Transform
)
res()
(in
RDC_Rohl
)
RNA_IdealCoord
(in
rosetta.core.pose.rna._core_pose_rna_
)
reinitialize_for_each_job()
(in
Translate
)
res()
(in
BigBinConstraint
)
RNA_IdealCoordAP
(in
rosetta.core.pose.rna._core_pose_rna_
)
reinitialize_for_each_job()
(in
UnconstrainedTorsionsMover
)
res1()
(in
CSA
)
RNA_IdealCoordCAP
(in
rosetta.core.pose.rna._core_pose_rna_
)
reinitialize_for_each_job()
(in
WriteLigandMolFile
)
res1()
(in
DC
)
rna_jr_suite
(in
ScoreType
)
reinitialize_for_each_job()
(in
LoopBuildMover
)
res1()
(in
RDC
)
rna_jr_suite
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
LoopmodelWrapper
)
res1()
(in
DimerPairing
)
rna_jr_suite
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
LoopBuilder
)
res1_atom1_index()
(in
Motif
)
rna_jr_suite
(in
rosetta
)
reinitialize_for_each_job()
(in
LoopModeler
)
res1_atom1_int()
(in
Motif
)
RNA_JR_SuiteEnergy
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
LoopMover
)
res1_atom1_name()
(in
Motif
)
RNA_JR_SuiteEnergyAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
LoopProtocol
)
res1_atom2_index()
(in
Motif
)
RNA_JR_SuiteEnergyCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
MinimizationRefiner
)
res1_atom2_int()
(in
Motif
)
RNA_JR_SuiteEnergyCreator
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
RepackingRefiner
)
res1_atom2_name()
(in
Motif
)
RNA_JR_SuiteEnergyCreatorAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
RotamerTrialsRefiner
)
res1_atom3_index()
(in
Motif
)
RNA_JR_SuiteEnergyCreatorCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
LegacyKicSampler
)
res1_atom3_int()
(in
Motif
)
RNA_JumpLibrary
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
AcceptanceCheck
)
res1_atom3_name()
(in
Motif
)
RNA_JumpLibraryAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
LoopFilter
)
res2()
(in
CSA
)
RNA_JumpLibraryCAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
LoopMoverGroup
)
res2()
(in
DC
)
RNA_KIC
(in
rosetta.protocols.stepwise.sampler
)
reinitialize_for_each_job()
(in
PrepareForCentroid
)
res2()
(in
RDC
)
RNA_KIC
(in
rosetta.protocols.stepwise.sampler._protocols_stepwise_sampler_
)
reinitialize_for_each_job()
(in
PrepareForFullatom
)
res2()
(in
DimerPairing
)
RNA_KIC
(in
StepWiseSamplerType
)
reinitialize_for_each_job()
(in
FastGapMover
)
res2_atom1_index()
(in
Motif
)
RNA_KIC_Sampler
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
LoopHashDiversifier
)
res2_atom1_int()
(in
Motif
)
RNA_KIC_SamplerAP
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
LoopHashLibrary
)
res2_atom1_name()
(in
Motif
)
RNA_KIC_SamplerCAP
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
LoopHashMoverWrapper
)
res2_atom2_index()
(in
Motif
)
RNA_KINEMATIC_CLOSER
(in
rosetta.protocols.stepwise.sampler
)
reinitialize_for_each_job()
(in
LoopHashRelaxProtocol
)
res2_atom2_int()
(in
Motif
)
RNA_KINEMATIC_CLOSER
(in
rosetta.protocols.stepwise.sampler._protocols_stepwise_sampler_
)
reinitialize_for_each_job()
(in
Mover_LoopHashRefine
)
res2_atom2_name()
(in
Motif
)
RNA_KINEMATIC_CLOSER
(in
StepWiseSamplerType
)
reinitialize_for_each_job()
(in
FoldTreeFromLoops
)
res2_atom3_index()
(in
Motif
)
RNA_KinematicCloser
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
CCDLoopClosureMover
)
res2_atom3_int()
(in
Motif
)
RNA_KinematicCloserAP
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
FASelectSlidingWindowLoopClosure
)
res2_atom3_name()
(in
Motif
)
RNA_KinematicCloserCAP
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
SlidingWindowLoopClosure
)
res3()
(in
CSA
)
RNA_LJ_BaseEnergy
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
WidthFirstSlidingWindowLoopClosure
)
res_anchor()
(in
Rose
)
RNA_LJ_BaseEnergyAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
KinematicMover
)
res_for_rotamer()
(in
FixbbRotamerSets
)
RNA_LJ_BaseEnergyCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
KinematicWrapper
)
res_for_rotamer()
(in
RotamerSets
)
RNA_LJ_BaseEnergyCreator
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
LoopCM
)
res_for_rotamer()
(in
RotamerSetsBase
)
RNA_LJ_BaseEnergyCreatorAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
LoopRefineInnerCycle
)
res_for_rotamer()
(in
RotamerSubsets
)
RNA_LJ_BaseEnergyCreatorCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
LoopRefineInnerCycleContainer
)
res_for_rotamer()
(in
FlexbbRotamerSets
)
RNA_LoopCloser
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
RepackTrial
)
res_haslabel()
(in
PDBInfo
)
RNA_LoopCloserAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
ShearMinCCDTrial
)
res_ids()
(in
RestrictIdentitiesAtAlignedPositionsOperation
)
RNA_LoopCloserCAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
SmallMinCCDTrial
)
res_interactions()
(in
EnzdesLoopInfo
)
RNA_LowResolutionPotential
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
MakeRotLibMover
)
res_labels()
(in
SimplePDB
)
RNA_LowResolutionPotentialAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
MatcherMover
)
res_links()
(in
FindConsensusSequence
)
RNA_LowResolutionPotentialCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
ExtractSubposeMover
)
res_links()
(in
MSDMover
)
RNA_MC_MULTI_SUITE
(in
rosetta.protocols.stepwise.sampler
)
reinitialize_for_each_job()
(in
MatDesGreedyOptMutationMover
)
res_list()
(in
FullModelInfo
)
RNA_MC_MULTI_SUITE
(in
rosetta.protocols.stepwise.sampler._protocols_stepwise_sampler_
)
reinitialize_for_each_job()
(in
SchemePlaceMotifsMover
)
res_map()
(in
ResidueAlternativeSet
)
RNA_MC_MULTI_SUITE
(in
StepWiseSamplerType
)
reinitialize_for_each_job()
(in
SymDofMover
)
res_min_data()
(in
MinimizationNode
)
RNA_MC_MultiSuite
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
CartesianMD
)
res_moved()
(in
Energies
)
RNA_MC_MultiSuiteAP
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
MDBase
)
res_name()
(in
UnrecognizedAtomRecord
)
RNA_MC_MultiSuiteCAP
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
MedalExchangeMover
)
res_name()
(in
PoseBalls
)
RNA_MC_SUGAR
(in
rosetta.protocols.stepwise.sampler
)
reinitialize_for_each_job()
(in
MedalMover
)
res_name()
(in
MutateResidue
)
RNA_MC_SUGAR
(in
rosetta.protocols.stepwise.sampler._protocols_stepwise_sampler_
)
reinitialize_for_each_job()
(in
AddMPLigandMover
)
res_name1()
(in
ReportPSSMDifferences
)
RNA_MC_SUGAR
(in
StepWiseSamplerType
)
reinitialize_for_each_job()
(in
AddMembraneMover
)
res_name1()
(in
ReportSequenceDifferences
)
RNA_MC_Sugar
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
FlipMover
)
res_name2()
(in
ReportSequenceDifferences
)
RNA_MC_SugarAP
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
MembranePositionFromTopologyMover
)
res_num()
(in
UnrecognizedAtomRecord
)
RNA_MC_SugarCAP
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
RandomPositionRotationMover
)
res_num()
(in
PoseBalls
)
RNA_MC_SUITE
(in
rosetta.protocols.stepwise.sampler
)
reinitialize_for_each_job()
(in
RandomPositionTranslationMover
)
res_num()
(in
PoseBallsLite
)
RNA_MC_SUITE
(in
rosetta.protocols.stepwise.sampler._protocols_stepwise_sampler_
)
reinitialize_for_each_job()
(in
RotationMover
)
res_pair_min_data()
(in
MinimizationEdge
)
RNA_MC_SUITE
(in
StepWiseSamplerType
)
reinitialize_for_each_job()
(in
SetMembraneCenterMover
)
res_part_of_flexsegment()
(in
FlexbbRotamerSets
)
RNA_MC_Suite
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
SetMembraneNormalMover
)
res_res_geometric_sol_one_way()
(in
GeometricSolEnergyEvaluator
)
RNA_MC_SuiteAP
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
SetMembranePositionMover
)
res_res_min_distance()
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
RNA_MC_SuiteCAP
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
TransformIntoMembraneMover
)
res_res_weight()
(in
IGEdgeReweightContainer
)
rna_mg
(in
ScoreType
)
reinitialize_for_each_job()
(in
TranslationMover
)
res_rmsd()
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
rna_mg
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
TranslationRotationMover
)
res_type_constraint
(in
ScoreType
)
rna_mg
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
SymmetricAddMembraneMover
)
res_type_constraint
(in
rosetta.core.scoring._core_scoring_
)
rna_mg
(in
rosetta
)
reinitialize_for_each_job()
(in
VisualizeEmbeddingMover
)
res_type_constraint
(in
rosetta.core.scoring
)
RNA_Mg_Energy
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
VisualizeMembraneMover
)
res_type_constraint
(in
rosetta
)
RNA_Mg_EnergyAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
ZincHeterodimerMover
)
res_type_linking_constraint
(in
ScoreType
)
RNA_Mg_EnergyCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
MotifGraftMover
)
res_type_linking_constraint
(in
rosetta.core.scoring._core_scoring_
)
RNA_Mg_EnergyCreator
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
MotifDnaPacker
)
res_type_linking_constraint
(in
rosetta.core.scoring
)
RNA_Mg_EnergyCreatorAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
CompositionMover
)
res_type_linking_constraint
(in
rosetta
)
RNA_Mg_EnergyCreatorCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
CycleMover
)
res_type_linking_constraint_energy()
(in
ConstraintEdge
)
rna_mg_indirect
(in
ScoreType
)
reinitialize_for_each_job()
(in
CyclicMover
)
res_types()
(in
ResidueCountFilter
)
rna_mg_indirect
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
DsspMover
)
resA()
(in
CstResInteractions
)
rna_mg_indirect
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
FilterMover
)
resA()
(in
EnzConstraintParameters
)
rna_mg_indirect
(in
rosetta
)
reinitialize_for_each_job()
(in
FilterReporterMover
)
RESAMPLE
(in
rosetta.protocols.stepwise.monte_carlo.mover
)
RNA_Mg_KnowledgeBasedPotential
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
IfMover
)
RESAMPLE
(in
MoveType
)
RNA_Mg_KnowledgeBasedPotentialAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
IteratedConvergenceMover
)
RESAMPLE
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
RNA_Mg_KnowledgeBasedPotentialCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
JumpOutMover
)
RESAMPLE_INTERNAL_LOCAL
(in
rosetta.protocols.stepwise.monte_carlo.mover
)
rna_mg_rep
(in
ScoreType
)
reinitialize_for_each_job()
(in
MCShowMover
)
RESAMPLE_INTERNAL_LOCAL
(in
MoveType
)
rna_mg_rep
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
MonteCarloUtil
)
RESAMPLE_INTERNAL_LOCAL
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
rna_mg_rep
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
MoveMapMover
)
ResampleMover
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
rna_mg_rep
(in
rosetta
)
reinitialize_for_each_job()
(in
Mover
)
ResampleMoverAP
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
RNA_Minimizer
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
MoverApplyingMover
)
ResampleMoverCAP
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
RNA_MinimizerAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
MoverContainer
)
resatom_and_func_struct
(in
rosetta.core.scoring.custom_pair_distance._core_scoring_custom_pair_distance_
)
RNA_MinimizerCAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
MoverForPoseList
)
resatom_and_func_structAP
(in
rosetta.core.scoring.custom_pair_distance._core_scoring_custom_pair_distance_
)
RNA_NORTH_SUGAR
(in
rosetta.core.pose.full_model_info
)
reinitialize_for_each_job()
(in
NullMover
)
resatom_and_func_structCAP
(in
rosetta.core.scoring.custom_pair_distance._core_scoring_custom_pair_distance_
)
RNA_NORTH_SUGAR
(in
FullModelParameterType
)
reinitialize_for_each_job()
(in
PDBDumpMover
)
resB()
(in
EnzConstraintParameters
)
RNA_NORTH_SUGAR
(in
rosetta.core.pose.full_model_info._core_pose_full_model_info_
)
reinitialize_for_each_job()
(in
ProfilerMover
)
rescale()
(in
SequenceProfile
)
RNA_NUCLEOSIDE
(in
rosetta.protocols.stepwise.sampler
)
reinitialize_for_each_job()
(in
PyMolMover
)
rescale()
(in
Thermostat
)
RNA_NUCLEOSIDE
(in
rosetta.protocols.stepwise.sampler._protocols_stepwise_sampler_
)
reinitialize_for_each_job()
(in
RampingMover
)
rescale_fastscoring_temp_bins()
(in
ElectronDensity
)
RNA_NUCLEOSIDE
(in
StepWiseSamplerType
)
reinitialize_for_each_job()
(in
RandomMover
)
rescale_scorefxn()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
RNA_NucleosideStepWiseSampler
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
RepeatMover
)
ResConnID
(in
rosetta.core.chemical._core_chemical_
)
RNA_NucleosideStepWiseSamplerAP
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
SequenceMover
)
ResConnIDAP
(in
rosetta.core.chemical._core_chemical_
)
RNA_NucleosideStepWiseSamplerCAP
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
StructureRestrictor
)
ResConnIDCAP
(in
rosetta.core.chemical._core_chemical_
)
RNA_O2PrimeMover
(in
rosetta.protocols.stepwise.monte_carlo.rna._protocols_stepwise_monte_carlo_rna_
)
reinitialize_for_each_job()
(in
TrialMover
)
rescore()
(in
HedgeArchive
)
RNA_O2PrimeMoverAP
(in
rosetta.protocols.stepwise.monte_carlo.rna._protocols_stepwise_monte_carlo_rna_
)
reinitialize_for_each_job()
(in
VectorPoseMover
)
rescore()
(in
IterativeAbrelax
)
RNA_O2PrimeMoverCAP
(in
rosetta.protocols.stepwise.monte_carlo.rna._protocols_stepwise_monte_carlo_rna_
)
reinitialize_for_each_job()
(in
WhileMover
)
rescore()
(in
IterativeBase
)
rna_options()
(in
EnergyMethodOptions
)
reinitialize_for_each_job()
(in
StructAvrgMover
)
rescore()
(in
IterativeCentroid
)
RNA_Pairing
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
NcbbDockDesignProtocol
)
rescore()
(in
IterativeFullatom
)
RNA_PairingAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
OopCreatorMover
)
rescore()
(in
HotspotStubSet
)
RNA_PairingCAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
OopDockDesignProtocol
)
rescore()
(in
EvaluatedArchive
)
RNA_PairingTemplate
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
CartesianNormalModeMover
)
rescore()
(in
NormalizedEvaluatedArchive
)
RNA_PairingTemplateAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
NormalModeMinimizer
)
rescore()
(in
VarianceStatisticsArchive
)
RNA_PairingTemplateCAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
NormalModeRelaxMover
)
rescore_all_decoys()
(in
WorkUnit_BatchRelax_and_PostRescore
)
RNA_PairwiseLowResolutionEnergy
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
TorsionNormalModeMover
)
reserve()
(in
vector1_AtomID
)
RNA_PairwiseLowResolutionEnergyAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
SetupPoissonBoltzmannPotential
)
reserve()
(in
vector1_Pose
)
RNA_PairwiseLowResolutionEnergyCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
AddChainBreak
)
reserve()
(in
vector1_PoseOP
)
RNA_PairwiseLowResolutionEnergyCreator
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
AddSidechainConstraintsToHotspots
)
reserve()
(in
vector1_ScoreType
)
RNA_PairwiseLowResolutionEnergyCreatorAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
BackrubDDMover
)
reserve()
(in
vector1_pair_Real_Real
)
RNA_PairwiseLowResolutionEnergyCreatorCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
BestHotspotCstMover
)
reserve()
(in
vector1_pair_Real_string
)
rna_raw_base_base_info()
(in
RNA_ScoringInfo
)
reinitialize_for_each_job()
(in
BuildAlaPose
)
reserve()
(in
vector1_pair_SSize_SSize
)
RNA_RawBaseBaseInfo
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
DesignMinimizeHbonds
)
reserve()
(in
vector1_pair_SSize_string
)
RNA_RawBaseBaseInfoAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
DisulfideMover
)
reserve()
(in
vector1_pair_Size_Real
)
RNA_RawBaseBaseInfoCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
DockAndRetrieveSidechains
)
reserve()
(in
vector1_pair_Size_Size
)
rna_reactivities()
(in
RNA_DataInfo
)
reinitialize_for_each_job()
(in
DockWithHotspotMover
)
reserve()
(in
vector1_pair_Size_SymDof
)
RNA_Reactivity
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
FavorNativeResiduePreCycle
)
reserve()
(in
vector1_pair_Size_string
)
RNA_ReactivityAP
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
FavorNonNativeResiduePreCycle
)
reserve()
(in
vector1_pair_char_pair_Size_Size
)
RNA_ReactivityCAP
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
HotspotDisjointedFoldTreeMover
)
reserve()
(in
vector1_pair_int_int
)
RNA_ReactivityType
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
reinitialize_for_each_job()
(in
HotspotHasherMover
)
reserve()
(in
vector1_pair_int_string
)
RNA_Relaxer
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
InterfaceRecapitulationMover
)
reserve()
(in
vector1_pair_string_Real
)
RNA_RelaxerAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
LoopFinder
)
reserve()
(in
vector1_pair_string_SSize
)
RNA_RelaxerCAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
LoopLengthChange
)
reserve()
(in
vector1_pair_string_Size
)
rna_repulsive
(in
ScoreType
)
reinitialize_for_each_job()
(in
LoopMoverFromCommandLine
)
reserve()
(in
vector1_pair_string_int
)
rna_repulsive
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
LoopOver
)
reserve()
(in
vector1_pair_string_string
)
rna_repulsive
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
LoopRemodel
)
reserve()
(in
vector1_xyzVector_Real
)
rna_repulsive
(in
rosetta
)
reinitialize_for_each_job()
(in
MapHotspot
)
reserve()
(in
vector1_xyzVector_SSize
)
rna_repulsive_pair_energy()
(in
RNA_LowResolutionPotential
)
reinitialize_for_each_job()
(in
PatchdockTransform
)
reserve()
(in
vector1_xyzVector_Size
)
RNA_ResidueLevelTask
(in
rosetta.core.pack.task.rna._core_pack_task_rna_
)
reinitialize_for_each_job()
(in
PeptideStapleDesignMover
)
reserve()
(in
vector1_xyzVector_bool
)
RNA_ResidueLevelTaskAP
(in
rosetta.core.pack.task.rna._core_pack_task_rna_
)
reinitialize_for_each_job()
(in
PlaceOnLoop
)
reserve()
(in
vector1_xyzVector_char
)
RNA_ResidueLevelTaskCAP
(in
rosetta.core.pack.task.rna._core_pack_task_rna_
)
reinitialize_for_each_job()
(in
PlaceSimultaneouslyMover
)
reserve()
(in
vector1_xyzVector_float
)
RNA_ResidueType
(in
rosetta.core.chemical.rna._core_chemical_rna_
)
reinitialize_for_each_job()
(in
PlaceStubMover
)
reserve()
(in
vector1_xyzVector_int
)
RNA_ResidueTypeAP
(in
rosetta.core.chemical.rna._core_chemical_rna_
)
reinitialize_for_each_job()
(in
PlacementAuctionMover
)
reserve()
(in
vector1_xyzVector_uint
)
RNA_ResidueTypeCAP
(in
rosetta.core.chemical.rna._core_chemical_rna_
)
reinitialize_for_each_job()
(in
PlacementMinimizationMover
)
reserve()
(in
vector1_FragData
)
rna_rg
(in
ScoreType
)
reinitialize_for_each_job()
(in
PrepackMover
)
reserve()
(in
vector1_FragDataOP
)
rna_rg
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
ProteinInterfaceMultiStateDesignMover
)
reserve()
(in
vector1_Frame
)
rna_rg
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
RandomMutation
)
reserve()
(in
vector1_FrameOP
)
rna_rg
(in
rosetta
)
reinitialize_for_each_job()
(in
RepackMinimize
)
reserve()
(in
VallLibrary
)
RNA_SAMPLE_SUGAR
(in
rosetta.core.pose.full_model_info
)
reinitialize_for_each_job()
(in
SaveAndRetrieveSidechains
)
reserve()
(in
VallSection
)
RNA_SAMPLE_SUGAR
(in
FullModelParameterType
)
reinitialize_for_each_job()
(in
SetAtomTree
)
reserve()
(in
vector1_numeric_geometry_hashing_Ball
)
RNA_SAMPLE_SUGAR
(in
rosetta.core.pose.full_model_info._core_pose_full_model_info_
)
reinitialize_for_each_job()
(in
SetTemperatureFactor
)
reserve()
(in
DecoySetEvaluation
)
rna_sample_sugar_res()
(in
FullModelInfo
)
reinitialize_for_each_job()
(in
SetupHotspotConstraintsLoopsMover
)
reserve()
(in
std_vector_Real
)
RNA_SCORING_INFO
(in
Enum
)
reinitialize_for_each_job()
(in
SetupHotspotConstraintsMover
)
reserve()
(in
std_vector_SSize
)
RNA_SCORING_INFO
(in
CacheableDataType
)
reinitialize_for_each_job()
(in
ShoveResidueMover
)
reserve()
(in
std_vector_Size
)
rna_scoring_info_from_pose()
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
SpinMover
)
reserve()
(in
std_vector_char
)
RNA_ScoringInfo
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
SubroutineMover
)
reserve()
(in
std_vector_double
)
RNA_ScoringInfoAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
TaskAwareCsts
)
reserve()
(in
std_vector_float
)
RNA_ScoringInfoCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
TopologyBrokerMover
)
reserve()
(in
std_vector_int
)
RNA_SECSTRUCT_INFO
(in
Enum
)
reinitialize_for_each_job()
(in
TryRotamers
)
reserve()
(in
std_vector_string
)
RNA_SECSTRUCT_INFO
(in
CacheableDataType
)
reinitialize_for_each_job()
(in
VLB
)
reserve()
(in
std_vector_uint
)
RNA_SecStructInfo
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
AutoRBMover
)
reserve()
(in
vec1_vec1_Real
)
RNA_SecStructInfoAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
FragInsertAndAlignMover
)
reserve()
(in
vec1_vec1_SSize
)
RNA_SecStructInfoCAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
GaussianRBSegmentMover
)
reserve()
(in
vec1_vec1_Size
)
RNA_SilentStruct
(in
rosetta.core.io.silent._core_io_silent_
)
reinitialize_for_each_job()
(in
HelicalGaussianMover
)
reserve()
(in
vec1_vec1_bool
)
RNA_SilentStructAP
(in
rosetta.core.io.silent._core_io_silent_
)
reinitialize_for_each_job()
(in
IdealizeHelicesMover
)
reserve()
(in
vec1_vec1_char
)
RNA_SilentStructCAP
(in
rosetta.core.io.silent._core_io_silent_
)
reinitialize_for_each_job()
(in
MakeStarTopologyMover
)
reserve()
(in
vec1_vec1_double
)
RNA_SilentStructCreator
(in
rosetta.core.io.silent._core_io_silent_
)
reinitialize_for_each_job()
(in
OptimizeThreadingMover
)
reserve()
(in
vec1_vec1_float
)
RNA_SilentStructCreatorAP
(in
rosetta.core.io.silent._core_io_silent_
)
reinitialize_for_each_job()
(in
RBSegmentMover
)
reserve()
(in
vec1_vec1_int
)
RNA_SilentStructCreatorCAP
(in
rosetta.core.io.silent._core_io_silent_
)
reinitialize_for_each_job()
(in
RBSegmentRelax
)
reserve()
(in
vec1_vec1_string
)
RNA_SOUTH_SUGAR
(in
rosetta.core.pose.full_model_info
)
reinitialize_for_each_job()
(in
SequenceShiftMover
)
reserve()
(in
vec1_vec1_uint
)
RNA_SOUTH_SUGAR
(in
FullModelParameterType
)
reinitialize_for_each_job()
(in
StrandTwistingMover
)
reserve()
(in
vector1_Real
)
RNA_SOUTH_SUGAR
(in
rosetta.core.pose.full_model_info._core_pose_full_model_info_
)
reinitialize_for_each_job()
(in
AtomCoordinateCstMover
)
reserve()
(in
vector1_SSize
)
RNA_StructureParameters
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
CentroidRelax
)
reserve()
(in
vector1_Size
)
RNA_StructureParametersAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
ClassicRelax
)
reserve()
(in
vector1_char
)
RNA_StructureParametersCAP
(in
rosetta.protocols.farna._protocols_farna_
)
reinitialize_for_each_job()
(in
FastRelax
)
reserve()
(in
vector1_double
)
RNA_SUGAR
(in
rosetta.protocols.stepwise.sampler
)
reinitialize_for_each_job()
(in
LocalRelax
)
reserve()
(in
vector1_float
)
RNA_SUGAR
(in
rosetta.protocols.stepwise.sampler._protocols_stepwise_sampler_
)
reinitialize_for_each_job()
(in
MiniRelax
)
reserve()
(in
vector1_int
)
RNA_SUGAR
(in
StepWiseSamplerType
)
reinitialize_for_each_job()
(in
RelaxProtocolBase
)
reserve()
(in
vector1_string
)
rna_sugar_close
(in
ScoreType
)
reinitialize_for_each_job()
(in
MPFastRelaxMover
)
reserve()
(in
vector1_uint
)
rna_sugar_close
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
MembraneCenterPerturbationMover
)
reserve_buffers()
(in
ResidualDipolarCoupling
)
rna_sugar_close
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
MembraneNormalPerturbationMover
)
reserve_destination_size()
(in
subset_mapping
)
rna_sugar_close
(in
rosetta
)
reinitialize_for_each_job()
(in
MovePoseToMembraneCenterMover
)
reservoir_sample_accept_prob()
(in
rosetta.numeric.random._numeric_random_
)
RNA_SugarCloseEnergy
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
RigidBodyDeterministicSpinMover
)
RESET
(in
rosetta.core.pack.task._core_pack_task_
)
RNA_SugarCloseEnergyAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
RigidBodyDofPerturbMover
)
Reset()
(in
Timer
)
RNA_SugarCloseEnergyCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
RigidBodyDofRandomTransMover
)
reset()
(in
ExtendedPoseInputStream
)
RNA_SugarCloseEnergyCreator
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
RigidBodyDofRandomizeMover
)
reset()
(in
LazySilentFilePoseInputStream
)
RNA_SugarCloseEnergyCreatorAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
RigidBodyDofSeqPerturbMover
)
reset()
(in
MetaPoseInputStream
)
RNA_SugarCloseEnergyCreatorCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
RigidBodyDofSeqRandomizeMover
)
reset()
(in
PDBPoseInputStream
)
RNA_SugarStepWiseSampler
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
RigidBodyDofSeqTransMover
)
reset()
(in
PoseInputStream
)
RNA_SugarStepWiseSamplerAP
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
RigidBodyDofTransMover
)
reset()
(in
SilentFilePoseInputStream
)
RNA_SugarStepWiseSamplerCAP
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
RigidBodyMotionMover
)
reset()
(in
Jump
)
rna_suite
(in
ScoreType
)
reinitialize_for_each_job()
(in
RigidBodyMover
)
reset()
(in
RT
)
rna_suite
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
RigidBodyPerturbMover
)
reset()
(in
CartesianMinimizerMap
)
rna_suite
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
RigidBodyPerturbNoCenterMover
)
reset()
(in
MinimizerMap
)
RNA_SUITE
(in
rosetta.protocols.stepwise.sampler
)
reinitialize_for_each_job()
(in
RigidBodyPerturbRandomJumpMover
)
reset()
(in
BumpSelector
)
RNA_SUITE
(in
rosetta.protocols.stepwise.sampler._protocols_stepwise_sampler_
)
reinitialize_for_each_job()
(in
RigidBodyRandomizeMover
)
reset()
(in
ScoreFunction
)
RNA_SUITE
(in
StepWiseSamplerType
)
reinitialize_for_each_job()
(in
RigidBodySpinMover
)
reset()
(in
ResPairMotif
)
rna_suite
(in
rosetta
)
reinitialize_for_each_job()
(in
RigidBodyTransMover
)
reset()
(in
AreaAccumulator
)
rna_suite_lr
(in
LongRangeEnergyType
)
reinitialize_for_each_job()
(in
RollMover
)
Reset()
(in
MolecularSurfaceCalculator
)
rna_suite_lr
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
reinitialize_for_each_job()
(in
RotateJumpAxisMover
)
Reset()
(in
ShapeComplementarityCalculator
)
rna_suite_lr
(in
rosetta.core.scoring.methods
)
reinitialize_for_each_job()
(in
UniformRigidBodyCM
)
reset()
(in
BiasedMonteCarlo
)
RNA_SuiteAssignment
(in
rosetta.core.pose.rna._core_pose_rna_
)
reinitialize_for_each_job()
(in
UniformRigidBodyMover
)
reset()
(in
MetricRecorder
)
RNA_SuiteAssignmentAP
(in
rosetta.core.pose.rna._core_pose_rna_
)
reinitialize_for_each_job()
(in
UniformSphereTransMover
)
reset()
(in
MultiTemperatureTrialCounter
)
RNA_SuiteAssignmentCAP
(in
rosetta.core.pose.rna._core_pose_rna_
)
reinitialize_for_each_job()
(in
WholeBodyRotationMover
)
reset()
(in
PDBTrajectoryRecorder
)
RNA_SuiteEnergy
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
WholeBodyTranslationMover
)
reset()
(in
TrajectoryRecorder
)
RNA_SuiteEnergyAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
AdditionalOutputWrapper
)
reset()
(in
Timer
)
RNA_SuiteEnergyCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
MultipleOutputWrapper
)
reset()
(in
ContactMap
)
RNA_SuiteEnergyCreator
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
MultiplePoseMover
)
reset()
(in
TimeEvaluator
)
RNA_SuiteEnergyCreatorAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
ParsedProtocol
)
reset()
(in
FilterStructs
)
RNA_SuiteEnergyCreatorCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
SavePoseMover
)
reset()
(in
FilterStructs_Packstat
)
RNA_SuiteInfo
(in
rosetta.core.pose.rna._core_pose_rna_
)
reinitialize_for_each_job()
(in
RotamerRecoveryMover
)
reset()
(in
FilterStructs_TotalCharge
)
RNA_SuiteInfoAP
(in
rosetta.core.pose.rna._core_pose_rna_
)
reinitialize_for_each_job()
(in
CAcstGenerator
)
reset()
(in
BackboneGridSamplerHelper
)
RNA_SuiteInfoCAP
(in
rosetta.core.pose.rna._core_pose_rna_
)
reinitialize_for_each_job()
(in
CloseFold
)
reset()
(in
BundleGridSamplerHelper
)
RNA_SuiteName
(in
rosetta.core.pose.rna._core_pose_rna_
)
reinitialize_for_each_job()
(in
CoordinateCst
)
reset()
(in
HybridizeFoldtreeDynamic
)
RNA_SuiteNameAP
(in
rosetta.core.pose.rna._core_pose_rna_
)
reinitialize_for_each_job()
(in
DefineMovableLoops
)
reset()
(in
LimitHitsPerRotamerFilter
)
RNA_SuiteNameCAP
(in
rosetta.core.pose.rna._core_pose_rna_
)
reinitialize_for_each_job()
(in
GrowPeptides
)
reset()
(in
MatchGrouper
)
RNA_SuitePotential
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
SeedFoldTree
)
reset()
(in
SameChiBinComboGrouper
)
RNA_SuitePotentialAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
SeedSetupMover
)
reset()
(in
SameRotamerComboGrouper
)
RNA_SuitePotentialCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
SegmentHybridizer
)
reset()
(in
SameSequenceAndDSPositionGrouper
)
RNA_SuiteStepWiseSampler
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
SwapSegment
)
reset()
(in
SameSequenceGrouper
)
RNA_SuiteStepWiseSamplerAP
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
EvaluatedTrialMover
)
reset()
(in
StateAccumulatingMatchFilter
)
RNA_SuiteStepWiseSamplerCAP
(in
rosetta.protocols.stepwise.sampler.rna._protocols_stepwise_sampler_rna_
)
reinitialize_for_each_job()
(in
AddCavitiesMover
)
reset()
(in
DualMonteCarlo
)
RNA_SYN_CHI
(in
rosetta.core.pose.full_model_info
)
reinitialize_for_each_job()
(in
AddChainMover
)
reset()
(in
MonteCarlo
)
RNA_SYN_CHI
(in
FullModelParameterType
)
reinitialize_for_each_job()
(in
AddConstraintsToCurrentConformationMover
)
reset()
(in
ReplicaExchangeMC
)
RNA_SYN_CHI
(in
rosetta.core.pose.full_model_info._core_pose_full_model_info_
)
reinitialize_for_each_job()
(in
AddJobPairData
)
reset()
(in
TrialCounter
)
rna_syn_chi_res()
(in
FullModelInfo
)
reinitialize_for_each_job()
(in
AlignChainMover
)
reset()
(in
GridSearchIterator
)
rna_task()
(in
ResidueLevelTask
)
reinitialize_for_each_job()
(in
BBConRotMover
)
reset()
(in
GridSearchIteratorCA
)
RNA_TERMINAL
(in
rosetta.core.pose.full_model_info
)
reinitialize_for_each_job()
(in
BBG8T3AMover
)
reset()
(in
GridSearchIterator_Ts1
)
RNA_TERMINAL
(in
FullModelParameterType
)
reinitialize_for_each_job()
(in
BBGaussianMover
)
reset()
(in
GridSearchIterator_Ts2
)
RNA_TERMINAL
(in
rosetta.core.pose.full_model_info._core_pose_full_model_info_
)
reinitialize_for_each_job()
(in
BackboneMover
)
reset()
(in
GridSearchIterator_Ts3
)
rna_terminal_res()
(in
FullModelInfo
)
reinitialize_for_each_job()
(in
BoltzmannRotamerMover
)
reset()
(in
GridSearchIterator_Ts4
)
RNA_Torsion
(in
rosetta.core.chemical.rna._core_chemical_rna_
)
reinitialize_for_each_job()
(in
ChainSplitMover
)
reset()
(in
GenericMonteCarloMover
)
rna_torsion
(in
ScoreType
)
reinitialize_for_each_job()
(in
ChangeAndResetFoldTreeMover
)
reset()
(in
RationalMonteCarlo
)
rna_torsion
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
ClearConstraintsMover
)
reset()
(in
StepWiseSampleAndScreen
)
rna_torsion
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
CombinePoseMover
)
reset()
(in
StepWiseMasterPacker
)
rna_torsion
(in
rosetta
)
reinitialize_for_each_job()
(in
ConsensusDesignMover
)
reset()
(in
StepWisePacker
)
rna_torsion_sc
(in
ScoreType
)
reinitialize_for_each_job()
(in
ConstrainToIdealMover
)
reset()
(in
InputStreamWithResidueInfo
)
rna_torsion_sc
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
ConstraintSetMover
)
reset()
(in
MultiPhosphateSampler
)
rna_torsion_sc
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
ContingentAcceptMover
)
reset()
(in
JumpStepWiseSampler
)
rna_torsion_sc
(in
rosetta
)
reinitialize_for_each_job()
(in
CopyDofMover
)
reset()
(in
MC_Comb
)
RNA_TorsionEnergy
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
CoupledMover
)
reset()
(in
MC_OneTorsion
)
RNA_TorsionEnergyAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
CutChainMover
)
reset()
(in
NoOpStepWiseSampler
)
RNA_TorsionEnergyCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
CyclizationMover
)
reset()
(in
StepWiseSamplerAny
)
RNA_TorsionEnergyCreator
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
DME_FilterMover
)
reset()
(in
StepWiseSamplerBase
)
RNA_TorsionEnergyCreatorAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
DeleteChainsMover
)
reset()
(in
StepWiseSamplerComb
)
RNA_TorsionEnergyCreatorCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
DesignRepackMover
)
reset()
(in
StepWiseSamplerOneTorsion
)
RNA_TorsionMover
(in
rosetta.protocols.stepwise.monte_carlo.rna._protocols_stepwise_monte_carlo_rna_
)
reinitialize_for_each_job()
(in
DisulfideInsertionMover
)
reset()
(in
StepWiseSamplerOneValue
)
RNA_TorsionMoverAP
(in
rosetta.protocols.stepwise.monte_carlo.rna._protocols_stepwise_monte_carlo_rna_
)
reinitialize_for_each_job()
(in
DumpPdb
)
reset()
(in
StepWiseSamplerOneValueComb
)
RNA_TorsionMoverCAP
(in
rosetta.protocols.stepwise.monte_carlo.rna._protocols_stepwise_monte_carlo_rna_
)
reinitialize_for_each_job()
(in
EnergyCutRotamerTrialsMinMover
)
reset()
(in
StepWiseSamplerSized
)
RNA_TorsionPotential
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
EnergyCutRotamerTrialsMover
)
reset()
(in
StepWiseSamplerSizedAny
)
RNA_TorsionPotentialAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
ExtendedPoseMover
)
reset()
(in
StepWiseSamplerSizedComb
)
RNA_TorsionPotentialCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
FavorSequenceProfile
)
reset()
(in
CopyDofStepWiseSampler
)
RNA_TorsionScreener
(in
rosetta.protocols.stepwise.sampler.screener._protocols_stepwise_sampler_screener_
)
reinitialize_for_each_job()
(in
FavorSymmetricSequence
)
reset()
(in
ResidueAlternativeStepWiseSampler
)
RNA_TorsionScreenerAP
(in
rosetta.protocols.stepwise.sampler.screener._protocols_stepwise_sampler_screener_
)
reinitialize_for_each_job()
(in
FindConsensusSequence
)
reset()
(in
ResidueAlternativeStepWiseSamplerComb
)
RNA_TorsionScreenerCAP
(in
rosetta.protocols.stepwise.sampler.screener._protocols_stepwise_sampler_screener_
)
reinitialize_for_each_job()
(in
ForceDisulfidesMover
)
reset()
(in
ResidueListStepWiseSampler
)
RNA_type()
(in
ResidueType
)
reinitialize_for_each_job()
(in
GenericMonteCarloMover
)
reset()
(in
InputStreamStepWiseSampler
)
RNA_type()
(in
Residue
)
reinitialize_for_each_job()
(in
GreenPacker
)
reset()
(in
ProteinBetaAntiParallelStepWiseSampler
)
rna_update_last_controlling_chi()
(in
RNA_ResidueType
)
reinitialize_for_each_job()
(in
LoadPDBMover
)
reset()
(in
ProteinFragmentStepWiseSampler
)
rna_vdw
(in
ScoreType
)
reinitialize_for_each_job()
(in
LoadUnboundRotMover
)
reset()
(in
ProteinMainChainStepWiseSampler
)
rna_vdw
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_each_job()
(in
MSDMover
)
reset()
(in
RigidBodyStepWiseSampler
)
rna_vdw
(in
rosetta.core.scoring
)
reinitialize_for_each_job()
(in
MakePolyXMover
)
reset()
(in
RigidBodyStepWiseSamplerWithResidueAlternatives
)
rna_vdw
(in
rosetta
)
reinitialize_for_each_job()
(in
MembraneTopology
)
reset()
(in
RigidBodyStepWiseSamplerWithResidueList
)
RNA_VDW_BinChecker
(in
rosetta.protocols.stepwise.modeler.rna.checker._protocols_stepwise_modeler_rna_checker_
)
reinitialize_for_each_job()
(in
MinMover
)
reset()
(in
RNA_ChiStepWiseSampler
)
RNA_VDW_BinCheckerAP
(in
rosetta.protocols.stepwise.modeler.rna.checker._protocols_stepwise_modeler_rna_checker_
)
reinitialize_for_each_job()
(in
MinPackMover
)
reset()
(in
RNA_KIC_Sampler
)
RNA_VDW_BinCheckerCAP
(in
rosetta.protocols.stepwise.modeler.rna.checker._protocols_stepwise_modeler_rna_checker_
)
reinitialize_for_each_job()
(in
MissingDensityToJumpMover
)
reset()
(in
RNA_KinematicCloser
)
RNA_VDW_Energy
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
ModifyVariantTypeMover
)
reset()
(in
RNA_MC_MultiSuite
)
RNA_VDW_EnergyAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
MonteCarloRecover
)
reset()
(in
RNA_MC_Sugar
)
RNA_VDW_EnergyCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
MonteCarloReset
)
reset()
(in
RNA_MC_Suite
)
RNA_VDW_EnergyCreator
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
MonteCarloTest
)
reset()
(in
RNA_NucleosideStepWiseSampler
)
RNA_VDW_EnergyCreatorAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
MutateResidue
)
reset()
(in
RNA_SugarStepWiseSampler
)
RNA_VDW_EnergyCreatorCAP
(in
rosetta.core.scoring.rna._core_scoring_rna_
)
reinitialize_for_each_job()
(in
O2M_MutateMover
)
reset()
(in
RNA_SuiteStepWiseSampler
)
RNAseH
(in
rosetta.protocols.fldsgn.topology
)
reinitialize_for_each_job()
(in
PDBReloadMover
)
reset()
(in
StepWiseScreener
)
RNAseH
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
reinitialize_for_each_job()
(in
PSSM2BfactorMover
)
reset_3d_projection()
(in
OccupiedSpaceHash
)
RNAseH
(in
SheetFoldType
)
reinitialize_for_each_job()
(in
PackRotamersMover
)
reset_accept_counter()
(in
ArchiveBase
)
roc_curve()
(in
RocCurve
)
reinitialize_for_each_job()
(in
PackRotamersMoverLazy
)
reset_accounting()
(in
BuildInstruction
)
RocCurve
(in
rosetta.numeric._numeric_
)
reinitialize_for_each_job()
(in
PeptideStapleMover
)
reset_accounting()
(in
BuildManager
)
RocCurveAP
(in
rosetta.numeric._numeric_
)
reinitialize_for_each_job()
(in
PeriodicBoxMover
)
reset_all_flags()
(in
ClusteringTreeNode
)
RocCurveCAP
(in
rosetta.numeric._numeric_
)
reinitialize_for_each_job()
(in
ProlineFixMover
)
reset_allowed_scoring()
(in
MembraneTopology
)
RocPoint
(in
rosetta.numeric._numeric_
)
reinitialize_for_each_job()
(in
RandomOmegaFlipMover
)
reset_alternate_states_for_uncommited_substitution()
(in
FlexbbEdge
)
RocPointAP
(in
rosetta.numeric._numeric_
)
reinitialize_for_each_job()
(in
RandomTorsionMover
)
reset_and_initialize_data()
(in
BackboneGridSampler
)
RocPointCAP
(in
rosetta.numeric._numeric_
)
reinitialize_for_each_job()
(in
RepackSidechainsMover
)
reset_arrays_danger_expert_only()
(in
LKB_ResidueInfo
)
RocStatus
(in
rosetta.numeric._numeric_
)
reinitialize_for_each_job()
(in
RepeatPropagationMover
)
reset_baseline()
(in
MultipleSigmoids
)
roll()
(in
DNABasestep
)
reinitialize_for_each_job()
(in
ReportEffectivePKA
)
reset_baseline()
(in
Operator
)
rolling_score()
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
reinitialize_for_each_job()
(in
RepulsiveOnlyMover
)
reset_baseline()
(in
Sigmoid
)
RollMover
(in
rosetta.protocols.rigid._protocols_rigid_
)
reinitialize_for_each_job()
(in
ResetBaselineMover
)
reset_baselines()
(in
GenericMonteCarloMover
)
RollMoverAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
reinitialize_for_each_job()
(in
ResidueTypeConstraintMover
)
reset_chain_endings()
(in
Conformation
)
RollMoverCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
reinitialize_for_each_job()
(in
ReturnSidechainMover
)
reset_chain_endings()
(in
ProtectedConformation
)
RollMoverCreator
(in
rosetta.protocols.rigid._protocols_rigid_
)
reinitialize_for_each_job()
(in
RingConformationMover
)
reset_count()
(in
Contact
)
RollMoverCreatorAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
reinitialize_for_each_job()
(in
RotamerTrialsMinMover
)
reset_counters()
(in
MonteCarlo
)
RollMoverCreatorCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
reinitialize_for_each_job()
(in
RotamerTrialsMover
)
reset_counts()
(in
MultiDimensionalHistogram
)
root()
(in
AtomTree
)
reinitialize_for_each_job()
(in
RotamerizeMover
)
reset_coval()
(in
heap
)
root()
(in
FoldTree
)
reinitialize_for_each_job()
(in
SaneMinMover
)
reset_cycle_index()
(in
DockMCMCycle
)
root()
(in
KDTree
)
reinitialize_for_each_job()
(in
ScoreMover
)
reset_cycle_index()
(in
CycleMover
)
root()
(in
ResiduePairJumpSetup
)
reinitialize_for_each_job()
(in
SequenceProfileMover
)
reset_delta_filter_baselines()
(in
MatDesGreedyOptMutationMover
)
root1()
(in
Polynomial_1d
)
reinitialize_for_each_job()
(in
SetReturningPackRotamersMover
)
reset_delta_omega1()
(in
BundleParameters
)
root2()
(in
Polynomial_1d
)
reinitialize_for_each_job()
(in
SetTorsion
)
reset_delta_z1()
(in
BundleParameters
)
root_atom()
(in
ResidueType
)
reinitialize_for_each_job()
(in
ShakeStructureMover
)
reset_edge_list_iterator_for_node()
(in
InteractionGraphBase
)
root_expression()
(in
SurrogateVariableExpression
)
reinitialize_for_each_job()
(in
ShearMover
)
reset_energy_methods()
(in
ScoreFunction
)
rootj()
(in
rosetta.core.scoring.fiber_diffraction._core_scoring_fiber_diffraction_
)
reinitialize_for_each_job()
(in
ShortBackrubMover
)
reset_eval_count()
(in
func_1d
)
Rose
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
reinitialize_for_each_job()
(in
SmallMover
)
reset_filters()
(in
CombinedFilter
)
RoseAP
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
reinitialize_for_each_job()
(in
SuperimposeMover
)
reset_filters()
(in
CompoundFilter
)
RoseCAP
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
reinitialize_for_each_job()
(in
SwitchChainOrderMover
)
reset_filters()
(in
MatchProcessor
)
rosetta
reinitialize_for_each_job()
(in
SwitchResidueTypeSetMover
)
reset_from_interface()
(in
DnaInterfaceMinMover
)
rosetta_database_from_env()
(in
rosetta
)
reinitialize_for_each_job()
(in
TailsScoreMover
)
reset_from_ref()
(in
PcsTensor
)
rosetta_recharge_fullatom()
(in
rosetta.core.chemical._core_chemical_
)
reinitialize_for_each_job()
(in
TaskAwareMinMover
)
reset_grouper()
(in
MatchConsolidator
)
rosetta_retype_fullatom()
(in
rosetta.core.chemical._core_chemical_
)
reinitialize_for_each_job()
(in
TorsionDOFMover
)
reset_jump_rb_deltas()
(in
MinimizerMap
)
rosetta_scripts
(in
rosetta.protocols
)
reinitialize_for_each_job()
(in
TorsionSetMover
)
reset_jump_rb_deltas()
(in
SymMinimizerMap
)
RosettaScriptsParser
(in
rosetta.protocols.rosetta_scripts._protocols_rosetta_scripts_
)
reinitialize_for_each_job()
(in
Tumble
)
reset_mode()
(in
BundleGridSampler
)
RosettaScriptsParserAP
(in
rosetta.protocols.rosetta_scripts._protocols_rosetta_scripts_
)
reinitialize_for_each_job()
(in
UniformRotationMover
)
reset_move_data()
(in
Conformation
)
RosettaScriptsParserCAP
(in
rosetta.protocols.rosetta_scripts._protocols_rosetta_scripts_
)
reinitialize_for_each_job()
(in
UniformTranslationMover
)
reset_move_data()
(in
ProtectedConformation
)
RosettaScriptWrapper
(in
rosetta.protocols.jd2
)
reinitialize_for_each_job()
(in
VirtualRootMover
)
reset_mover_data()
(in
PeptideStubMover
)
RosI
(in
rosetta.protocols.fldsgn.topology
)
reinitialize_for_each_job()
(in
ddG
)
reset_nblist()
(in
Energies
)
RosI
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
reinitialize_for_each_job()
(in
AsymFoldandDockMoveRbJumpMover
)
reset_num_connections()
(in
RegionalConnections
)
RosI
(in
SheetFoldType
)
reinitialize_for_each_job()
(in
AsymFoldandDockRbTrialMover
)
reset_option_input()
(in
LigandMotifSearch
)
RosO
(in
rosetta.protocols.fldsgn.topology
)
reinitialize_for_each_job()
(in
InitializeByBins
)
reset_option_input()
(in
MotifSearch
)
RosO
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
reinitialize_for_each_job()
(in
PerturbByBins
)
reset_pose()
(in
MakeBundle
)
RosO
(in
SheetFoldType
)
reinitialize_for_each_job()
(in
ChiralMover
)
reset_pose()
(in
MakeBundleHelix
)
rot()
(in
xyzTransform_T_double_T
)
reinitialize_for_each_job()
(in
HbsPatcher
)
reset_r1()
(in
BundleParameters
)
rot()
(in
xyzTransform_T_float_T
)
reinitialize_for_each_job()
(in
OopDPuckMinusMover
)
reset_recovery()
(in
RRReporter
)
rot1
(in
dofType
)
reinitialize_for_each_job()
(in
OopDPuckPlusMover
)
reset_recovery()
(in
RRReporterHuman
)
rot1
(in
rosetta.protocols.jumping._protocols_jumping_
)
reinitialize_for_each_job()
(in
OopMover
)
reset_recovery()
(in
RRReporterSQLite
)
rot1
(in
rosetta.protocols.jumping
)
reinitialize_for_each_job()
(in
OopPatcher
)
reset_recovery()
(in
RRReporterSimple
)
rot2
(in
dofType
)
reinitialize_for_each_job()
(in
OopPuckMinusMover
)
reset_recovery()
(in
RotamerRecovery
)
rot2
(in
rosetta.protocols.jumping._protocols_jumping_
)
reinitialize_for_each_job()
(in
OopPuckPlusMover
)
reset_relaxed()
(in
FASTERNode
)
rot2
(in
rosetta.protocols.jumping
)
reinitialize_for_each_job()
(in
OopRandomPuckMover
)
reset_relaxed_for_neighbors()
(in
FASTERNode
)
rot_center()
(in
RigidBodyMover
)
reinitialize_for_each_job()
(in
OopRandomSmallMover
)
reset_res_moved()
(in
Energies
)
rot_center()
(in
RigidBodyPerturbMover
)
reinitialize_for_each_job()
(in
RationalMonteCarlo
)
reset_residue_list()
(in
Parameters
)
rot_center()
(in
RigidBodySpinMover
)
reinitialize_for_each_job()
(in
JumpRotamerSidechainMover
)
reset_residue_list()
(in
BundleParameters
)
rot_deg()
(in
xyzTransform_T_double_T
)
reinitialize_for_each_job()
(in
PerturbChiSidechainMover
)
reset_rpe_calculations_count()
(in
OnTheFlyInteractionGraph
)
rot_deg()
(in
xyzTransform_T_float_T
)
reinitialize_for_each_job()
(in
PerturbRotamerSidechainMover
)
reset_rpe_calculations_count()
(in
SymmOnTheFlyInteractionGraph
)
rot_level()
(in
LigandMotifSearch
)
reinitialize_for_each_job()
(in
SetChiMover
)
reset_sample_index()
(in
MutationSetDesignOperation
)
rot_level()
(in
MotifSearch
)
reinitialize_for_each_job()
(in
SidechainMCMover
)
reset_scorefxn()
(in
MonteCarlo
)
rot_magnitude()
(in
RigidBodyDofPerturbMover
)
reinitialize_for_each_job()
(in
SidechainMover
)
reset_state_energies()
(in
LinearMemEdge
)
rot_magnitude()
(in
RigidBodyDofSeqPerturbMover
)
reinitialize_for_each_job()
(in
SidechainMoverBase
)
reset_state_energies()
(in
SymmLinearMemEdge
)
rot_magnitude()
(in
RigidBodyPerturbMover
)
reinitialize_for_each_job()
(in
DetectSymmetry
)
reset_statistics()
(in
BackrubSidechainMover
)
rot_magnitude()
(in
RigidBodyPerturbNoCenterMover
)
reinitialize_for_each_job()
(in
ExtractAsymmetricPoseMover
)
reset_status()
(in
Mover
)
rot_number()
(in
PNatAAOptERotamerData
)
reinitialize_for_each_job()
(in
ExtractAsymmetricUnitMover
)
reset_structure_moved()
(in
Conformation
)
rot_pose()
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
reinitialize_for_each_job()
(in
FaSymDockingSlideTogether
)
reset_surf()
(in
PoseBalls
)
rot_sample_from_name()
(in
rosetta.core.pack.task._core_pack_task_
)
reinitialize_for_each_job()
(in
SetupForSymmetryMover
)
reset_surface_residue_information()
(in
SurfaceEnergies
)
rot_sets()
(in
PackDaemon
)
reinitialize_for_each_job()
(in
SetupNCSMover
)
reset_task_factory()
(in
AntibodyDesignModeler
)
rot_well()
(in
DunbrackRotamerSampleData
)
reinitialize_for_each_job()
(in
SymDockingInitialPerturbation
)
reset_tensor()
(in
PCS_tensor
)
rotAlign2DPose()
(in
ElectronDensity
)
reinitialize_for_each_job()
(in
SymDockingSlideIntoContact
)
reset_tensor()
(in
PcsTensor
)
rotamer()
(in
RotamerSetBase
)
reinitialize_for_each_job()
(in
SymEnergyCutRotamerTrialsMover
)
reset_tensor()
(in
PCS_tensor_Ts1
)
rotamer()
(in
InvRotamerDots
)
reinitialize_for_each_job()
(in
SymMinMover
)
reset_tensor()
(in
PCS_tensor_Ts2
)
rotamer()
(in
RotamerDots
)
reinitialize_for_each_job()
(in
SymPackRotamersMover
)
reset_tensor()
(in
PCS_tensor_Ts3
)
rotamer()
(in
FixbbRotamerSets
)
reinitialize_for_each_job()
(in
SymRotamerTrialsMover
)
reset_tensor()
(in
PCS_tensor_Ts4
)
rotamer()
(in
RotamerSet
)
reinitialize_for_each_job()
(in
SymShakeStructureMover
)
reset_tmh_insert()
(in
MembraneTopology
)
rotamer()
(in
RotamerSet_
)
reinitialize_for_each_job()
(in
SymmetricRMSMover
)
reset_to_original_pose()
(in
MultiPhosphateSampler
)
rotamer()
(in
RotamerSets
)
reinitialize_for_each_job()
(in
TaskAwareSymMinMover
)
reset_unique_id()
(in
IRCollection
)
rotamer()
(in
RotamerSetsBase
)
reinitialize_for_each_job()
(in
StepWiseProteinMinimizer
)
reset_x()
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
rotamer()
(in
RotamerSubset
)
reinitialize_for_each_job()
(in
StepWiseProteinPoseSetup
)
RESETAP
(in
rosetta.core.pack.task._core_pack_task_
)
rotamer()
(in
RotamerSubsets
)
reinitialize_for_each_job()
(in
StepWiseRNA_PoseSetup
)
ResetBaselineMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
rotamer()
(in
SymmetricRotamerSet_
)
reinitialize_for_each_job()
(in
StepWiseConnectionSampler
)
ResetBaselineMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
rotamer()
(in
OTFFlexbbNode
)
reinitialize_for_each_job()
(in
StepWiseMinimizer
)
ResetBaselineMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
rotamer()
(in
FlexbbRotamerSet
)
reinitialize_for_each_job()
(in
StepWiseModeler
)
ResetBaselineMoverCreator
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
rotamer()
(in
FlexbbRotamerSets
)
reinitialize_for_each_job()
(in
SideChainCopier
)
ResetBaselineMoverCreatorAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
rotamer_aa()
(in
ResidueType
)
reinitialize_for_each_job()
(in
StepWisePacker
)
ResetBaselineMoverCreatorCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
rotamer_couplings()
(in
PackerTask
)
reinitialize_for_each_job()
(in
PolarHydrogenPacker
)
RESETCAP
(in
rosetta.core.pack.task._core_pack_task_
)
rotamer_couplings()
(in
PackerTask_
)
reinitialize_for_each_job()
(in
PrecomputedLibraryMover
)
resfile()
(in
DesignTask
)
rotamer_couplings_exist()
(in
PackerTask
)
reinitialize_for_each_job()
(in
StepWiseProteinBackboneSampler
)
resfile()
(in
BDR
)
rotamer_couplings_exist()
(in
PackerTask_
)
reinitialize_for_each_job()
(in
StepWiseProteinCCD_Closer
)
resfile_at()
(in
FindConsensusSequence
)
rotamer_data_begin()
(in
PNatAAOptEPositionData
)
reinitialize_for_each_job()
(in
StepWiseProteinCCD_MultiPoseCloser
)
resfile_commands()
(in
ReadResfileAndObeyLengthEvents
)
rotamer_data_begin()
(in
PNatRotOptEPositionData
)
reinitialize_for_each_job()
(in
StepWiseProteinKIC_LoopBridger
)
resfile_general_property()
(in
FilterScanFilter
)
rotamer_data_end()
(in
PNatAAOptEPositionData
)
reinitialize_for_each_job()
(in
BulgeApplyMover
)
resfile_general_property()
(in
SaveResfileToDiskFilter
)
rotamer_data_end()
(in
PNatRotOptEPositionData
)
reinitialize_for_each_job()
(in
BulgeUnApplyMover
)
resfile_name()
(in
FilterScanFilter
)
rotamer_energy()
(in
RotamerLibrary
)
reinitialize_for_each_job()
(in
RNA_ChainClosureChecker
)
resfile_name()
(in
SaveResfileToDiskFilter
)
rotamer_energy()
(in
SingleLigandRotamerLibrary
)
reinitialize_for_each_job()
(in
RNA_HelixAssembler
)
resfile_prefix()
(in
SaveResfileToDiskFilter
)
rotamer_energy()
(in
SingleResidueRotamerLibrary
)
reinitialize_for_each_job()
(in
O2PrimePacker
)
resfile_suffix()
(in
SaveResfileToDiskFilter
)
rotamer_energy()
(in
SingleResidueCenrotLibrary
)
reinitialize_for_each_job()
(in
MultiPhosphateSampler
)
ResfileCommand
(in
rosetta.core.pack.task._core_pack_task_
)
rotamer_energy_deriv()
(in
RotamerLibrary
)
reinitialize_for_each_job()
(in
PhosphateMover
)
ResfileCommandAP
(in
rosetta.core.pack.task._core_pack_task_
)
rotamer_energy_deriv()
(in
SingleLigandRotamerLibrary
)
reinitialize_for_each_job()
(in
SugarInstantiateMover
)
ResfileCommandCAP
(in
rosetta.core.pack.task._core_pack_task_
)
rotamer_energy_deriv()
(in
SingleResidueRotamerLibrary
)
reinitialize_for_each_job()
(in
SugarVirtualizeMover
)
ResfileContents
(in
rosetta.core.pack.task._core_pack_task_
)
rotamer_energy_deriv()
(in
SingleResidueCenrotLibrary
)
reinitialize_for_each_job()
(in
VirtualSugarJustInTimeInstantiator
)
ResfileContentsAP
(in
rosetta.core.pack.task._core_pack_task_
)
rotamer_for_moltenres()
(in
FixbbRotamerSets
)
reinitialize_for_each_job()
(in
VirtualSugarSampler
)
ResfileContentsCAP
(in
rosetta.core.pack.task._core_pack_task_
)
rotamer_for_moltenres()
(in
RotamerSets
)
reinitialize_for_each_job()
(in
VirtualSugarSamplerFromStringList
)
ResFileOutputter
(in
rosetta.protocols.outputter._protocols_outputter_
)
rotamer_for_moltenres()
(in
RotamerSetsBase
)
reinitialize_for_each_job()
(in
StepWiseMonteCarlo
)
ResFileOutputterAP
(in
rosetta.protocols.outputter._protocols_outputter_
)
rotamer_for_moltenres()
(in
RotamerSubsets
)
reinitialize_for_each_job()
(in
AddMover
)
ResFileOutputterCAP
(in
rosetta.protocols.outputter._protocols_outputter_
)
rotamer_for_moltenres()
(in
FlexbbRotamerSets
)
reinitialize_for_each_job()
(in
AddOrDeleteMover
)
ResfileReaderException
(in
rosetta.core.pack.task._core_pack_task_
)
rotamer_for_residue()
(in
FlexbbRotamerSets
)
reinitialize_for_each_job()
(in
DeleteMover
)
ResfileReaderExceptionAP
(in
rosetta.core.pack.task._core_pack_task_
)
rotamer_from_chi()
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
reinitialize_for_each_job()
(in
FromScratchMover
)
ResfileReaderExceptionCAP
(in
rosetta.core.pack.task._core_pack_task_
)
rotamer_from_chi_02()
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
reinitialize_for_each_job()
(in
ResampleMover
)
resfiles()
(in
FindConsensusSequence
)
rotamer_index()
(in
PNatRotOptERotamerData
)
reinitialize_for_each_job()
(in
StepWiseMasterMover
)
resfiles()
(in
MSDMover
)
rotamer_is_glycine()
(in
OTFFlexbbNode
)
reinitialize_for_each_job()
(in
RNA_AddDeleteMonteCarlo
)
ResFilter
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
rotamer_is_proline()
(in
OTFFlexbbNode
)
reinitialize_for_each_job()
(in
RNA_O2PrimeMover
)
ResFilterAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
rotamer_library()
(in
SidechainMover
)
reinitialize_for_each_job()
(in
RNA_TorsionMover
)
ResFilterCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
rotamer_library()
(in
SidechainMoverBase
)
reinitialize_for_each_job()
(in
JumpStepWiseSampler
)
ResFilterComposition
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
rotamer_links()
(in
PackerTask
)
reinitialize_for_each_job()
(in
MC_Comb
)
ResFilterCompositionAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
rotamer_links()
(in
PackerTask_
)
reinitialize_for_each_job()
(in
MC_OneTorsion
)
ResFilterCompositionCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
rotamer_links_exist()
(in
PackerTask
)
reinitialize_for_each_job()
(in
NoOpStepWiseSampler
)
ResFilterCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
rotamer_links_exist()
(in
PackerTask_
)
reinitialize_for_each_job()
(in
StepWiseSamplerAny
)
ResFilterCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
rotamer_operations()
(in
ResidueLevelTask
)
reinitialize_for_each_job()
(in
StepWiseSamplerComb
)
ResFilterCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
rotamer_operations()
(in
ResidueLevelTask_
)
reinitialize_for_each_job()
(in
StepWiseSamplerOneTorsion
)
ResFilterFactory
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
rotamer_recovery
(in
rosetta.protocols
)
reinitialize_for_each_job()
(in
StepWiseSamplerOneValue
)
ResFilterFactoryAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
rotamer_ref()
(in
RotamerSetBase
)
reinitialize_for_each_job()
(in
StepWiseSamplerOneValueComb
)
ResFilterFactoryCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
rotamer_ref()
(in
RotamerSet
)
reinitialize_for_each_job()
(in
StepWiseSamplerSized
)
resi()
(in
VallResidue
)
rotamer_ref()
(in
RotamerSet_
)
reinitialize_for_each_job()
(in
StepWiseSamplerSizedAny
)
resi()
(in
Ball
)
rotamer_ref()
(in
RotamerSubset
)
reinitialize_for_each_job()
(in
StepWiseSamplerSizedComb
)
resi()
(in
xyzStripeHash
)
rotamer_ref()
(in
SymmetricRotamerSet_
)
reinitialize_for_each_job()
(in
CopyDofStepWiseSampler
)
resi()
(in
VallResidue
)
rotamer_ref()
(in
FlexbbRotamerSet
)
reinitialize_for_each_job()
(in
ResidueAlternativeStepWiseSampler
)
resi1()
(in
ResPairMotif
)
rotamer_set
(in
rosetta.core.pack
)
reinitialize_for_each_job()
(in
ResidueAlternativeStepWiseSamplerComb
)
resi2()
(in
ResPairMotif
)
rotamer_set
(in
rosetta.protocols.flexpack
)
reinitialize_for_each_job()
(in
ResidueListStepWiseSampler
)
ResId
(in
rosetta.protocols.moves._protocols_moves_
)
rotamer_set()
(in
TryRotamers
)
reinitialize_for_each_job()
(in
InputStreamStepWiseSampler
)
resid()
(in
ResConnID
)
rotamer_set_contains_rotamer()
(in
AddGood2BPairEnergyRotamers
)
reinitialize_for_each_job()
(in
ProteinBetaAntiParallelStepWiseSampler
)
resid()
(in
RotamerSetBase
)
rotamer_set_for_moltenres()
(in
ContinuousRotamerSets
)
reinitialize_for_each_job()
(in
ProteinFragmentStepWiseSampler
)
resid()
(in
ResidueInformation
)
rotamer_set_for_moltenresidue()
(in
FixbbRotamerSets
)
reinitialize_for_each_job()
(in
ProteinMainChainStepWiseSampler
)
resid()
(in
ContinuousRotamerSet
)
rotamer_set_for_moltenresidue()
(in
RotamerSets
)
reinitialize_for_each_job()
(in
RigidBodyStepWiseSampler
)
resid()
(in
RotamerSet
)
rotamer_set_for_moltenresidue()
(in
RotamerSubsets
)
reinitialize_for_each_job()
(in
RigidBodyStepWiseSamplerWithResidueAlternatives
)
resid()
(in
RotamerSet_
)
rotamer_set_for_res()
(in
ContinuousRotamerSets
)
reinitialize_for_each_job()
(in
RigidBodyStepWiseSamplerWithResidueList
)
resid()
(in
RotamerSubset
)
rotamer_set_for_residue()
(in
FixbbRotamerSets
)
reinitialize_for_each_job()
(in
RNA_ChiStepWiseSampler
)
resid()
(in
SymmetricRotamerSet_
)
rotamer_set_for_residue()
(in
RotamerSets
)
reinitialize_for_each_job()
(in
RNA_KIC_Sampler
)
resid()
(in
RotamerExplosion
)
rotamer_set_for_residue()
(in
RotamerSubsets
)
reinitialize_for_each_job()
(in
RNA_KinematicCloser
)
resid()
(in
AmbiguousNMRDistanceConstraint
)
rotamer_set_operation_begin()
(in
ResidueLevelTask
)
reinitialize_for_each_job()
(in
RNA_MC_MultiSuite
)
resid()
(in
FlexbbRotamerSet
)
rotamer_set_operation_begin()
(in
ResidueLevelTask_
)
reinitialize_for_each_job()
(in
RNA_MC_Sugar
)
resid()
(in
SelectResiduesWithinChainOperation
)
rotamer_set_operation_end()
(in
ResidueLevelTask
)
reinitialize_for_each_job()
(in
RNA_MC_Suite
)
resid_2_moltenres()
(in
FixbbRotamerSets
)
rotamer_set_operation_end()
(in
ResidueLevelTask_
)
reinitialize_for_each_job()
(in
RNA_NucleosideStepWiseSampler
)
resid_2_moltenres()
(in
RotamerSets
)
rotamer_set_operations
(in
rosetta.protocols.toolbox
)
reinitialize_for_each_job()
(in
RNA_SugarStepWiseSampler
)
resid_2_moltenres()
(in
RotamerSetsBase
)
rotamer_sets()
(in
PackRotamersMover
)
reinitialize_for_each_job()
(in
RNA_SuiteStepWiseSampler
)
resid_2_moltenres()
(in
RotamerSubsets
)
rotamer_sets()
(in
RotamerizeMover
)
reinitialize_for_each_job()
(in
StepWiseCSA_JobDistributor
)
resid_2_moltenres()
(in
FlexbbRotamerSets
)
ROTAMER_TRIALS
(in
rosetta.basic
)
reinitialize_for_each_job()
(in
StepWiseJobDistributor
)
resid_2_moltenres_vector()
(in
FixbbRotamerSets
)
ROTAMER_TRIALS
(in
ProfTag
)
reinitialize_for_each_job()
(in
StepWiseMonteCarloJobDistributor
)
resid_2_moltenres_vector()
(in
RotamerSets
)
ROTAMER_TRIALS
(in
rosetta.basic._basic_
)
reinitialize_for_each_job()
(in
CentroidRelaxMover
)
resid_2_moltenresid()
(in
ContinuousRotamerSets
)
rotamer_trials()
(in
rosetta.core.pack._core_pack_
)
reinitialize_for_each_job()
(in
FullatomRelaxMover
)
resid_for_entry()
(in
CPDataCorrespondence
)
RotamerAssigningAnnealer
(in
rosetta.core.pack.annealer._core_pack_annealer_
)
reinitialize_for_each_job()
(in
SurfaceDockingProtocol
)
ResIdAP
(in
rosetta.protocols.moves._protocols_moves_
)
RotamerAssigningAnnealerAP
(in
rosetta.core.pack.annealer._core_pack_annealer_
)
reinitialize_for_each_job()
(in
SurfaceOrientMover
)
ResIdCAP
(in
rosetta.protocols.moves._protocols_moves_
)
RotamerAssigningAnnealerCAP
(in
rosetta.core.pack.annealer._core_pack_annealer_
)
reinitialize_for_each_job()
(in
SymDockBaseProtocol
)
RESIDUAL_DIPOLAR_COUPLING_DATA
(in
Enum
)
RotamerBoltzCalculator
(in
rosetta.protocols.toolbox.pose_metric_calculators._protocols_toolbox_pose_metric_calculators_
)
reinitialize_for_each_job()
(in
SymDockProtocol
)
RESIDUAL_DIPOLAR_COUPLING_DATA
(in
CacheableDataType
)
RotamerBoltzCalculatorAP
(in
rosetta.protocols.toolbox.pose_metric_calculators._protocols_toolbox_pose_metric_calculators_
)
reinitialize_for_each_job()
(in
SymDockingHiRes
)
RESIDUAL_DIPOLAR_COUPLING_DATA_ROHL
(in
Enum
)
RotamerBoltzCalculatorCAP
(in
rosetta.protocols.toolbox.pose_metric_calculators._protocols_toolbox_pose_metric_calculators_
)
reinitialize_for_each_job()
(in
SymDockingLowRes
)
RESIDUAL_DIPOLAR_COUPLING_DATA_ROHL
(in
CacheableDataType
)
RotamerBoltzmannWeight
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
reinitialize_for_each_job()
(in
SymFoldandDockMoveRbJumpMover
)
RESIDUAL_DIPOLAR_COUPLING_SEGMENTS_DATA
(in
Enum
)
RotamerBoltzmannWeightAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
reinitialize_for_each_job()
(in
SymFoldandDockRbTrialMover
)
RESIDUAL_DIPOLAR_COUPLING_SEGMENTS_DATA
(in
CacheableDataType
)
RotamerBoltzmannWeightCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
reinitialize_for_each_job()
(in
SymFoldandDockSlideTrialMover
)
ResidualDipolarCoupling
(in
rosetta.core.scoring._core_scoring_
)
RotamerBoltzmannWeightFeatures
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_each_job()
(in
SymInterfaceSidechainMinMover
)
ResidualDipolarCoupling_Rohl
(in
rosetta.core.scoring._core_scoring_
)
RotamerBoltzmannWeightFeaturesAP
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_each_job()
(in
SymSidechainMinMover
)
ResidualDipolarCoupling_RohlAP
(in
rosetta.core.scoring._core_scoring_
)
RotamerBoltzmannWeightFeaturesCAP
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_each_job()
(in
MPSymDockMover
)
ResidualDipolarCoupling_RohlCAP
(in
rosetta.core.scoring._core_scoring_
)
RotamerBoltzmannWeightFeaturesCreator
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_each_job()
(in
AlignPoseToInvrotTreeMover
)
ResidualDipolarCouplingAP
(in
rosetta.core.scoring._core_scoring_
)
RotamerBoltzmannWeightFeaturesCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_each_job()
(in
StoreCombinedStoredTasksMover
)
ResidualDipolarCouplingCAP
(in
rosetta.core.scoring._core_scoring_
)
RotamerBoltzmannWeightFeaturesCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_each_job()
(in
StoreCompoundTaskMover
)
ResidualDipolarCouplingEnergy
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
RotamerBoltzmannWeightFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
reinitialize_for_each_job()
(in
StoreTaskMover
)
ResidualDipolarCouplingEnergy_Rohl
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
RotamerBoltzmannWeightFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
reinitialize_for_each_job()
(in
UnfoldedStateEnergyCalculatorMover
)
ResidualDipolarCouplingEnergy_RohlAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
RotamerBoltzmannWeightFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
reinitialize_for_new_input()
(in
RotamerDumpMover
)
ResidualDipolarCouplingEnergy_RohlCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
RotamerBuildingData
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
reinitialize_for_new_input()
(in
AbrelaxMover
)
ResidualDipolarCouplingEnergy_RohlCreator
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
RotamerBuildingDataAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
reinitialize_for_new_input()
(in
ClassicAbinitio
)
ResidualDipolarCouplingEnergy_RohlCreatorAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
RotamerBuildingDataCAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
reinitialize_for_new_input()
(in
ConstraintFragmentSampler
)
ResidualDipolarCouplingEnergy_RohlCreatorCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
RotamerConstraint
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
reinitialize_for_new_input()
(in
DomainAssembly
)
ResidualDipolarCouplingEnergyAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
RotamerConstraintAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
reinitialize_for_new_input()
(in
DoubleLayerKinematicAbinitio
)
ResidualDipolarCouplingEnergyCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
RotamerConstraintCAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
reinitialize_for_new_input()
(in
FoldConstraints
)
ResidualDipolarCouplingEnergyCreator
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
RotamerCouplings
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
FragmentSampler
)
ResidualDipolarCouplingEnergyCreatorAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
RotamerCouplingsAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
JumpingFoldConstraintsWrapper
)
ResidualDipolarCouplingEnergyCreatorCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
RotamerCouplingsCAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
KinematicAbinitio
)
ResidualDipolarCouplingEnergyRigidSegments
(in
rosetta.protocols.scoring.methods._protocols_scoring_methods_
)
RotamerDNAHBondFilter
(in
rosetta.protocols.dna._protocols_dna_
)
reinitialize_for_new_input()
(in
KinematicTaskControl
)
ResidualDipolarCouplingEnergyRigidSegmentsAP
(in
rosetta.protocols.scoring.methods._protocols_scoring_methods_
)
RotamerDNAHBondFilterAP
(in
rosetta.protocols.dna._protocols_dna_
)
reinitialize_for_new_input()
(in
LoopJumpFoldCst
)
ResidualDipolarCouplingEnergyRigidSegmentsCAP
(in
rosetta.protocols.scoring.methods._protocols_scoring_methods_
)
RotamerDNAHBondFilterCAP
(in
rosetta.protocols.dna._protocols_dna_
)
reinitialize_for_new_input()
(in
MembraneAbinitio
)
ResidualDipolarCouplingEnergyRigidSegmentsCreator
(in
rosetta.protocols.scoring.methods._protocols_scoring_methods_
)
RotamerDots
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
reinitialize_for_new_input()
(in
Protocol
)
ResidualDipolarCouplingEnergyRigidSegmentsCreatorAP
(in
rosetta.protocols.scoring.methods._protocols_scoring_methods_
)
RotamerDotsAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
reinitialize_for_new_input()
(in
ResolutionSwitcher
)
ResidualDipolarCouplingEnergyRigidSegmentsCreatorCAP
(in
rosetta.protocols.scoring.methods._protocols_scoring_methods_
)
RotamerDotsCache
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
reinitialize_for_new_input()
(in
AbscriptLoopCloserCM
)
ResidualDipolarCouplingRigidSegments
(in
rosetta.protocols.scoring._protocols_scoring_
)
RotamerDotsCacheAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
reinitialize_for_new_input()
(in
AbscriptMover
)
ResidualDipolarCouplingRigidSegmentsAP
(in
rosetta.protocols.scoring._protocols_scoring_
)
RotamerDotsCacheCAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
reinitialize_for_new_input()
(in
AbscriptStageMover
)
ResidualDipolarCouplingRigidSegmentsCAP
(in
rosetta.protocols.scoring._protocols_scoring_
)
RotamerDotsCAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
reinitialize_for_new_input()
(in
ConstraintPreparer
)
Residue
(in
rosetta.core.conformation._core_conformation_
)
RotamerDotsRadiusData
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
reinitialize_for_new_input()
(in
FragmentCM
)
RESIDUE
(in
IdentityEvent
)
RotamerDotsRadiusDataAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
reinitialize_for_new_input()
(in
FragmentJumpCM
)
RESIDUE
(in
Tag
)
RotamerDotsRadiusDataCAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
reinitialize_for_new_input()
(in
RigidChunkCM
)
residue()
(in
Conformation
)
RotamerDump
(in
rosetta.protocols
)
reinitialize_for_new_input()
(in
StagePreparer
)
residue()
(in
UltraLightResidue
)
RotamerDumpMover
(in
rosetta.protocols.RotamerDump._protocols_RotamerDump_
)
reinitialize_for_new_input()
(in
StructPerturberCM
)
residue()
(in
Parameters
)
RotamerDumpMoverAP
(in
rosetta.protocols.RotamerDump._protocols_RotamerDump_
)
reinitialize_for_new_input()
(in
InterfaceAnalyzerMover
)
residue()
(in
Pose
)
RotamerDumpMoverCAP
(in
rosetta.protocols.RotamerDump._protocols_RotamerDump_
)
reinitialize_for_new_input()
(in
LoopAnalyzerMover
)
residue()
(in
ConformationXYZ
)
RotamerExplosion
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
reinitialize_for_new_input()
(in
PackStatMover
)
residue()
(in
FourPointsFunc
)
RotamerExplosionAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
reinitialize_for_new_input()
(in
AnchoredDesignMover
)
residue()
(in
ResiduePairXYZ
)
RotamerExplosionCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
reinitialize_for_new_input()
(in
AnchoredPerturbMover
)
residue()
(in
ResidueXYZ
)
RotamerExplosionCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
reinitialize_for_new_input()
(in
AnchoredRefineMover
)
residue()
(in
XYZ_Func
)
RotamerExplosionCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
reinitialize_for_new_input()
(in
AntibodyModelerProtocol
)
residue()
(in
BundleParameters
)
RotamerExplosionCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
reinitialize_for_new_input()
(in
CDRsMinPackMin
)
residue()
(in
HotspotStub
)
RotamerFeatures
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
CloseOneCDRLoop
)
residue()
(in
ResidueBurialFilter
)
RotamerFeaturesAP
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
GraftCDRLoopsProtocol
)
residue_action()
(in
ALLAA
)
RotamerFeaturesCAP
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
GraftOneCDRLoop
)
residue_action()
(in
ALLAAwc
)
RotamerFeaturesCreator
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
GraftedStemOptimizer
)
residue_action()
(in
ALLAAxc
)
RotamerFeaturesCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
H3CterInsert
)
residue_action()
(in
APOLA
)
RotamerFeaturesCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
H3PerturbCCD
)
residue_action()
(in
APOLAR
)
rotameric_chi_mimic_EX_flags
(in
ChiStrategy
)
reinitialize_for_new_input()
(in
H3RefineCCD
)
residue_action()
(in
AUTO
)
rotameric_chi_mimic_EX_flags
(in
rosetta.protocols.match.upstream._protocols_match_upstream_
)
reinitialize_for_new_input()
(in
LHRepulsiveRamp
)
residue_action()
(in
EMPTY
)
rotameric_chi_mimic_EX_flags
(in
rosetta.protocols.match.upstream
)
reinitialize_for_new_input()
(in
ModelCDRH3
)
residue_action()
(in
EX
)
rotameric_chi_partition_sd_range
(in
ChiStrategy
)
reinitialize_for_new_input()
(in
RefineBetaBarrel
)
residue_action()
(in
EX_CUTOFF
)
rotameric_chi_partition_sd_range
(in
rosetta.protocols.match.upstream._protocols_match_upstream_
)
reinitialize_for_new_input()
(in
RefineOneCDRLoop
)
residue_action()
(in
FIX_HIS_TAUTOMER
)
rotameric_chi_partition_sd_range
(in
rosetta.protocols.match.upstream
)
reinitialize_for_new_input()
(in
RefineOneCDRLoopCentroid
)
residue_action()
(in
NATAA
)
rotameric_chi_step_by_value
(in
ChiStrategy
)
reinitialize_for_new_input()
(in
CDRDihedralConstraintMover
)
residue_action()
(in
NATRO
)
rotameric_chi_step_by_value
(in
rosetta.protocols.match.upstream._protocols_match_upstream_
)
reinitialize_for_new_input()
(in
ParatopeEpitopeSiteConstraintMover
)
residue_action()
(in
NC
)
rotameric_chi_step_by_value
(in
rosetta.protocols.match.upstream
)
reinitialize_for_new_input()
(in
ParatopeSiteConstraintMover
)
residue_action()
(in
NOTAA
)
rotameric_chi_step_wi_sd_range
(in
ChiStrategy
)
reinitialize_for_new_input()
(in
AntibodyDesignMover
)
residue_action()
(in
NO_ADDUCTS
)
rotameric_chi_step_wi_sd_range
(in
rosetta.protocols.match.upstream._protocols_match_upstream_
)
reinitialize_for_new_input()
(in
AntibodyDesignProtocol
)
residue_action()
(in
PIKAA
)
rotameric_chi_step_wi_sd_range
(in
rosetta.protocols.match.upstream
)
reinitialize_for_new_input()
(in
MutateFrameworkForCluster
)
residue_action()
(in
PIKNA
)
RotamerizeMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
reinitialize_for_new_input()
(in
AntibodyModeler
)
residue_action()
(in
PIKRNA
)
RotamerizeMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
reinitialize_for_new_input()
(in
CDRH3Modeler
)
residue_action()
(in
POLAR
)
RotamerizeMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
reinitialize_for_new_input()
(in
CloseOneMover
)
residue_action()
(in
RESET
)
RotamerLibrary
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
reinitialize_for_new_input()
(in
GraftMover
)
residue_action()
(in
ResfileCommand
)
RotamerLibraryAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
reinitialize_for_new_input()
(in
GraftOneMover
)
residue_action()
(in
SCAN
)
RotamerLibraryCAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
reinitialize_for_new_input()
(in
LoopRlxMover
)
residue_action()
(in
TARGET
)
RotamerLibraryScratchSpace
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
reinitialize_for_new_input()
(in
BackrubMover
)
residue_action()
(in
USE_INPUT_SC
)
RotamerLibraryScratchSpaceAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
reinitialize_for_new_input()
(in
BackrubProtocol
)
RESIDUE_ALTERNATIVE
(in
rosetta.protocols.stepwise.sampler
)
RotamerLibraryScratchSpaceCAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
reinitialize_for_new_input()
(in
BackrubSidechainMover
)
RESIDUE_ALTERNATIVE
(in
rosetta.protocols.stepwise.sampler._protocols_stepwise_sampler_
)
RotamerLinks
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
CanonicalSamplingMover
)
RESIDUE_ALTERNATIVE
(in
StepWiseSamplerType
)
RotamerLinksAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
FixedTemperatureController
)
RESIDUE_ALTERNATIVE_COMB
(in
rosetta.protocols.stepwise.sampler
)
RotamerLinksCAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
MetricRecorder
)
RESIDUE_ALTERNATIVE_COMB
(in
rosetta.protocols.stepwise.sampler._protocols_stepwise_sampler_
)
RotamerOperation
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
MetropolisHastingsMover
)
RESIDUE_ALTERNATIVE_COMB
(in
StepWiseSamplerType
)
RotamerOperationAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
ParallelTempering
)
residue_alternative_set()
(in
VirtualSugarJustInTimeInstantiator
)
RotamerOperationCAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
ProgressBarObserver
)
residue_alternatives_rotamer()
(in
RigidBodyStepWiseSamplerWithResidueAlternatives
)
RotamerRecovery
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
SidechainMetropolisHastingsMover
)
RESIDUE_APPEND
(in
LengthEvent
)
RotamerRecovery
(in
rosetta.protocols.toolbox.pose_metric_calculators._protocols_toolbox_pose_metric_calculators_
)
reinitialize_for_new_input()
(in
SimulatedTempering
)
RESIDUE_APPEND
(in
Tag
)
RotamerRecoveryAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
TemperatureController
)
RESIDUE_APPLIER
(in
rosetta.protocols.stepwise.screener
)
RotamerRecoveryAP
(in
rosetta.protocols.toolbox.pose_metric_calculators._protocols_toolbox_pose_metric_calculators_
)
reinitialize_for_new_input()
(in
TemperingBase
)
RESIDUE_APPLIER
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
RotamerRecoveryCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
ThermodynamicMover
)
RESIDUE_APPLIER
(in
StepWiseScreenerType
)
RotamerRecoveryCAP
(in
rosetta.protocols.toolbox.pose_metric_calculators._protocols_toolbox_pose_metric_calculators_
)
reinitialize_for_new_input()
(in
ThermodynamicObserver
)
residue_atom_pair_energy()
(in
AnalyticEtableEvaluator
)
RotamerRecoveryFactory
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
TrialCounterObserver
)
residue_atom_pair_energy()
(in
TableLookupEvaluator
)
RotamerRecoveryFactoryAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
AssignToClustersMover
)
residue_atom_pair_energy()
(in
CountPairAll
)
RotamerRecoveryFactoryCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
ClusterBase
)
residue_atom_pair_energy()
(in
CountPairFunction
)
RotamerRecoveryFeatures
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
ClusterPhilStyle
)
residue_atom_pair_energy()
(in
CountPairGeneric
)
RotamerRecoveryFeaturesAP
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
ClusterPhilStyle_Loop
)
residue_atom_pair_energy()
(in
CountPairNone
)
RotamerRecoveryFeaturesCAP
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
ClusterPhilStyle_PoseReporter
)
residue_atom_pair_energy_backbone_backbone()
(in
AnalyticEtableEvaluator
)
RotamerRecoveryFeaturesCreator
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
EnsembleConstraints
)
residue_atom_pair_energy_backbone_backbone()
(in
TableLookupEvaluator
)
RotamerRecoveryFeaturesCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
EnsembleConstraints_Simple
)
residue_atom_pair_energy_backbone_backbone()
(in
CountPairAll
)
RotamerRecoveryFeaturesCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
GatherPosesMover
)
residue_atom_pair_energy_backbone_backbone()
(in
CountPairFunction
)
RotamerRecoveryMover
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
CoarseRNA_LoopCloser
)
residue_atom_pair_energy_backbone_backbone()
(in
CountPairGeneric
)
RotamerRecoveryMoverAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
ExtraThreadingMover
)
residue_atom_pair_energy_backbone_backbone()
(in
CountPairNone
)
RotamerRecoveryMoverCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
LoopRelaxMover
)
residue_atom_pair_energy_sidechain_backbone()
(in
AnalyticEtableEvaluator
)
RotamerRecoveryMoverCreator
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
LoopRelaxThreadingMover
)
residue_atom_pair_energy_sidechain_backbone()
(in
TableLookupEvaluator
)
RotamerRecoveryMoverCreatorAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
MultiThreadingMover
)
residue_atom_pair_energy_sidechain_backbone()
(in
CountPairAll
)
RotamerRecoveryMoverCreatorCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
PartialThreadingMover
)
residue_atom_pair_energy_sidechain_backbone()
(in
CountPairFunction
)
rotamers_for_trials()
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
reinitialize_for_new_input()
(in
RecoverSideChainsMover
)
residue_atom_pair_energy_sidechain_backbone()
(in
CountPairGeneric
)
rotamers_on_same_bbconf()
(in
FlexbbRotamerSets
)
reinitialize_for_new_input()
(in
StealLigandMover
)
residue_atom_pair_energy_sidechain_backbone()
(in
CountPairNone
)
RotamerSet
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
StealSideChainsMover
)
residue_atom_pair_energy_sidechain_sidechain()
(in
AnalyticEtableEvaluator
)
RotamerSet_
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
ThreadingMover
)
residue_atom_pair_energy_sidechain_sidechain()
(in
TableLookupEvaluator
)
RotamerSet_AP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
ContactMap
)
residue_atom_pair_energy_sidechain_sidechain()
(in
CountPairAll
)
RotamerSet_CAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
FitBfactorsMover
)
residue_atom_pair_energy_sidechain_sidechain()
(in
CountPairFunction
)
RotamerSetAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
LoadDensityMapMover
)
residue_atom_pair_energy_sidechain_sidechain()
(in
CountPairGeneric
)
RotamerSetBase
(in
rosetta.core.conformation._core_conformation_
)
reinitialize_for_new_input()
(in
RecomputeDensityMapMover
)
residue_atom_pair_energy_sidechain_sidechain()
(in
CountPairNone
)
RotamerSetBaseAP
(in
rosetta.core.conformation._core_conformation_
)
reinitialize_for_new_input()
(in
SetCrystWeightMover
)
residue_atom_pair_energy_sidechain_whole()
(in
AnalyticEtableEvaluator
)
RotamerSetBaseCAP
(in
rosetta.core.conformation._core_conformation_
)
reinitialize_for_new_input()
(in
SetRefinementOptionsMover
)
residue_atom_pair_energy_sidechain_whole()
(in
TableLookupEvaluator
)
RotamerSetCAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
TagPoseWithRefinementStatsMover
)
residue_atom_pair_energy_sidechain_whole()
(in
CountPairAll
)
RotamerSetFactory
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
UpdateSolventMover
)
residue_atom_pair_energy_sidechain_whole()
(in
CountPairFunction
)
RotamerSetFactoryAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
CreateAngleConstraint
)
residue_atom_pair_energy_sidechain_whole()
(in
CountPairGeneric
)
RotamerSetFactoryCAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
CreateDistanceConstraint
)
residue_atom_pair_energy_sidechain_whole()
(in
CountPairNone
)
RotamerSetOperation
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
CreateTorsionConstraint
)
residue_atoms()
(in
ResidueVicinityInfo
)
RotamerSetOperationAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
DeclareBond
)
residue_atomtree_collection()
(in
AtomTreeCollection
)
RotamerSetOperationCAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
PeptideStubMover
)
residue_atomtree_collection_op()
(in
AtomTreeCollection
)
RotamerSets
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
ddGMover
)
residue_base2_atoms()
(in
ResidueVicinityInfo
)
RotamerSetsAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
GreedyOptMutationMover
)
residue_base_atoms()
(in
ResidueVicinityInfo
)
RotamerSetsBase
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
ParetoOptMutationMover
)
residue_center_of_mass()
(in
rosetta.core.conformation.symmetry._core_conformation_symmetry_
)
RotamerSetsBaseAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
DesignProteinBackboneAroundDNA
)
residue_center_of_mass()
(in
rosetta.core.pose._core_pose_
)
RotamerSetsBaseCAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
DnaInterfaceMinMover
)
residue_center_of_mass()
(in
rosetta.protocols.membrane.geometry._protocols_membrane_geometry_
)
RotamerSetsCAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
DnaInterfaceMultiStateDesign
)
residue_conformations_redundant()
(in
EnzCstTemplateRes
)
RotamerSubset
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
DnaInterfacePacker
)
residue_connect_atom_index()
(in
ResidueType
)
RotamerSubsetAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
SeparateDnaFromNonDna
)
residue_connect_atom_index()
(in
Residue
)
RotamerSubsetCAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
ConformerSwitchMover
)
residue_connection()
(in
ResidueType
)
RotamerSubsetRepacker
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
reinitialize_for_new_input()
(in
DockMCMCycle
)
residue_connection()
(in
Residue
)
RotamerSubsetRepackerAP
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
reinitialize_for_new_input()
(in
DockMCMProtocol
)
residue_connection_conn_id()
(in
Residue
)
RotamerSubsetRepackerCAP
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
reinitialize_for_new_input()
(in
DockMinMover
)
residue_connection_id_for_atom()
(in
ResidueType
)
RotamerSubsets
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
DockSetupMover
)
residue_connection_is_polymeric()
(in
ResidueType
)
RotamerSubsetsAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
DockingEnsemblePrepackProtocol
)
residue_connection_partner()
(in
Residue
)
RotamerSubsetsCAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
reinitialize_for_new_input()
(in
DockingHighRes
)
residue_connections_for_atom()
(in
ResidueType
)
RotamerTrialsMinMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
reinitialize_for_new_input()
(in
DockingHighResLegacy
)
RESIDUE_CONTACT
(in
rosetta.protocols.stepwise.screener
)
RotamerTrialsMinMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
reinitialize_for_new_input()
(in
DockingInitialPerturbation
)
RESIDUE_CONTACT
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
RotamerTrialsMinMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
reinitialize_for_new_input()
(in
DockingLowRes
)
RESIDUE_CONTACT
(in
StepWiseScreenerType
)
RotamerTrialsMinMoverCreator
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
reinitialize_for_new_input()
(in
DockingLowResEnsemble
)
residue_cop()
(in
Conformation
)
RotamerTrialsMinMoverCreatorAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
reinitialize_for_new_input()
(in
DockingPrepackProtocol
)
residue_cop()
(in
Parameters
)
RotamerTrialsMinMoverCreatorCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
reinitialize_for_new_input()
(in
DockingProtocol
)
residue_cop()
(in
BundleParameters
)
RotamerTrialsMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
reinitialize_for_new_input()
(in
DockingSlideIntoContact
)
residue_decomposition_calculator()
(in
DecomposeAndReweightEnergiesCalculator
)
RotamerTrialsMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
reinitialize_for_new_input()
(in
EllipsoidalRandomizationMover
)
RESIDUE_DELETE
(in
LengthEvent
)
RotamerTrialsMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
reinitialize_for_new_input()
(in
FaDockingSlideIntoContact
)
RESIDUE_DELETE
(in
Tag
)
RotamerTrialsMoverCreator
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
reinitialize_for_new_input()
(in
InterfaceSidechainMinMover
)
residue_energy()
(in
DunbrackEnergy
)
RotamerTrialsMoverCreatorAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
reinitialize_for_new_input()
(in
SidechainMinMover
)
residue_energy()
(in
CenRotDunEnergy
)
RotamerTrialsMoverCreatorCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
reinitialize_for_new_input()
(in
TemperedDocking
)
residue_energy()
(in
HPatchEnergy
)
RotamerTrialsRefiner
(in
rosetta.protocols.loop_modeling.refiners._protocols_loop_modeling_refiners_
)
reinitialize_for_new_input()
(in
MPDockingMover
)
residue_energy()
(in
SurfaceEnergy
)
RotamerTrialsRefinerAP
(in
rosetta.protocols.loop_modeling.refiners._protocols_loop_modeling_refiners_
)
reinitialize_for_new_input()
(in
MPDockingSetupMover
)
residue_energy()
(in
DNAChiEnergy
)
RotamerTrialsRefinerCAP
(in
rosetta.protocols.loop_modeling.refiners._protocols_loop_modeling_refiners_
)
reinitialize_for_new_input()
(in
SaneDockingProtocol
)
residue_energy()
(in
ExactOccludedHbondSolEnergy
)
RotamerTrialsRefinerCreator
(in
rosetta.protocols.loop_modeling.refiners._protocols_loop_modeling_refiners_
)
reinitialize_for_new_input()
(in
AddAssemblyConstraints
)
residue_energy()
(in
OccludedHbondSolEnergy_onebody
)
RotamerTrialsRefinerCreatorAP
(in
rosetta.protocols.loop_modeling.refiners._protocols_loop_modeling_refiners_
)
reinitialize_for_new_input()
(in
AssembleLinkerMover
)
residue_energy()
(in
FaMPEnvEnergy
)
RotamerTrialsRefinerCreatorCAP
(in
rosetta.protocols.loop_modeling.refiners._protocols_loop_modeling_refiners_
)
reinitialize_for_new_input()
(in
CombineChainsMover
)
residue_energy()
(in
FaMPEnvSmoothEnergy
)
RotamerTrieBase
(in
rosetta.core.scoring.trie._core_scoring_trie_
)
reinitialize_for_new_input()
(in
PostDockAssemblyScorer
)
residue_energy()
(in
MPCbetaEnergy
)
RotamerTrieBaseAP
(in
rosetta.core.scoring.trie._core_scoring_trie_
)
reinitialize_for_new_input()
(in
BfactorFittingMover
)
residue_energy()
(in
MPEnvEnergy
)
RotamerTrieBaseCAP
(in
rosetta.core.scoring.trie._core_scoring_trie_
)
reinitialize_for_new_input()
(in
DensityMorphingMover
)
residue_energy()
(in
MPNonHelixPenalty
)
Rotate
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
reinitialize_for_new_input()
(in
ReportFSC
)
residue_energy()
(in
MPTerminiPenalty
)
rotate()
(in
rosetta.protocols.toolbox.rigid_body._protocols_toolbox_rigid_body_
)
reinitialize_for_new_input()
(in
ScaleMapIntensities
)
residue_energy()
(in
BurialEnergy
)
rotate_anchor_to_x_axis()
(in
rosetta.core.pose.symmetry._core_pose_symmetry_
)
reinitialize_for_new_input()
(in
SetupForDensityScoringMover
)
residue_energy()
(in
CenRotEnvEnergy
)
rotate_around_atom()
(in
RigidSearchMover
)
reinitialize_for_new_input()
(in
ClientMover
)
residue_energy()
(in
ContextDependentOneBodyEnergy
)
rotate_around_downstream_centroid()
(in
RigidSearchMover
)
reinitialize_for_new_input()
(in
CoMTrackerCM
)
residue_energy()
(in
ContextIndependentOneBodyEnergy
)
Rotate_info
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
reinitialize_for_new_input()
(in
EnvMover
)
residue_energy()
(in
EnvEnergy
)
Rotate_infoAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
reinitialize_for_new_input()
(in
ScriptCM
)
residue_energy()
(in
EnvSmoothEnergy
)
Rotate_infoCAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
reinitialize_for_new_input()
(in
MultipleDomainMover
)
residue_energy()
(in
Fa_MbenvEnergy
)
rotate_into_nucleobase_frame()
(in
rosetta.protocols.toolbox.sample_around._protocols_toolbox_sample_around_
)
reinitialize_for_new_input()
(in
RNA_DeNovoProtocol
)
residue_energy()
(in
FreeDOF_Energy
)
rotate_into_phosphate_frame()
(in
rosetta.protocols.toolbox.sample_around._protocols_toolbox_sample_around_
)
reinitialize_for_new_input()
(in
RNA_FragmentMover
)
residue_energy()
(in
MembraneCbetaEnergy
)
rotate_segment()
(in
BackrubMover
)
reinitialize_for_new_input()
(in
RNA_LoopCloser
)
residue_energy()
(in
MembraneEnvEnergy
)
RotateAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
reinitialize_for_new_input()
(in
RNA_Minimizer
)
residue_energy()
(in
MembraneEnvSmoothEnergy
)
RotateCAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
reinitialize_for_new_input()
(in
RNA_Relaxer
)
residue_energy()
(in
NMerPSSMEnergy
)
RotateCreator
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
reinitialize_for_new_input()
(in
ReportToDB
)
residue_energy()
(in
NMerRefEnergy
)
RotateCreatorAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
reinitialize_for_new_input()
(in
TrajectoryReportToDB
)
residue_energy()
(in
NMerSVMEnergy
)
RotateCreatorCAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
reinitialize_for_new_input()
(in
SetupForFibrilMover
)
residue_energy()
(in
OmegaTetherEnergy
)
RotateJumpAxisMover
(in
rosetta.protocols.rigid._protocols_rigid_
)
reinitialize_for_new_input()
(in
BluePrintBDR
)
residue_energy()
(in
OneBodyEnergy
)
RotateJumpAxisMoverAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
reinitialize_for_new_input()
(in
CircularPermutation
)
residue_energy()
(in
P_AA_Energy
)
RotateJumpAxisMoverCAP
(in
rosetta.protocols.rigid._protocols_rigid_
)
reinitialize_for_new_input()
(in
MatchResiduesMover
)
residue_energy()
(in
P_AA_pp_Energy
)
Rotates
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
reinitialize_for_new_input()
(in
SheetConstraintsRCG
)
residue_energy()
(in
RamachandranEnergy
)
RotatesAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
reinitialize_for_new_input()
(in
SetAACompositionPotential
)
residue_energy()
(in
ReferenceEnergy
)
RotatesCAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
reinitialize_for_new_input()
(in
SetSecStructEnergies
)
residue_energy()
(in
ReferenceEnergyNoncanonical
)
RotatesCreator
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
reinitialize_for_new_input()
(in
FlexPacker
)
residue_energy()
(in
SequenceDependentRefEnergy
)
RotatesCreatorAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
reinitialize_for_new_input()
(in
FlexPepDockingAbInitio
)
residue_energy()
(in
SmoothEnvEnergy
)
RotatesCreatorCAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
reinitialize_for_new_input()
(in
FlexPepDockingLowRes
)
residue_energy()
(in
SymmetricLigandEnergy
)
rotation()
(in
Stub
)
reinitialize_for_new_input()
(in
FlexPepDockingProtocol
)
residue_energy()
(in
UnfoldedStateEnergy
)
rotation()
(in
RigidSearchMover
)
reinitialize_for_new_input()
(in
FloppyTailMover
)
residue_energy()
(in
WaterAdductIntraEnergy
)
rotation_angle()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
FlxbbDesign
)
residue_energy()
(in
YHHPlanarityEnergy
)
rotation_angle()
(in
xyzTransform_T_double_T
)
reinitialize_for_new_input()
(in
FlxbbDesignPack
)
residue_energy()
(in
pHEnergy
)
rotation_angle()
(in
xyzTransform_T_float_T
)
reinitialize_for_new_input()
(in
InterlockAroma
)
residue_energy()
(in
SugarBackboneEnergy
)
rotation_angle_degrees()
(in
xyzTransform_T_double_T
)
reinitialize_for_new_input()
(in
BDR
)
residue_energy()
(in
DFIRE_Energy
)
rotation_angle_degrees()
(in
xyzTransform_T_float_T
)
reinitialize_for_new_input()
(in
VarLengthBuild
)
residue_energy()
(in
NVscore
)
rotation_angle_double()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
RemodelConstraintGenerator
)
residue_energy()
(in
RNA_BulgeEnergy
)
rotation_angle_float()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
NonlocalFrags
)
residue_energy()
(in
RNA_FullAtomVDW_BasePhosphate
)
rotation_angle_Real()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
TorsionFragmentMover
)
residue_energy()
(in
RNA_SugarCloseEnergy
)
rotation_axis()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
GeneralizedKIC
)
residue_energy()
(in
AACompositionEnergy
)
rotation_axis()
(in
xyzTransform_T_double_T
)
reinitialize_for_new_input()
(in
AnchoredGraftMover
)
residue_energy()
(in
InterchainEnvEnergy
)
rotation_axis()
(in
xyzTransform_T_float_T
)
reinitialize_for_new_input()
(in
CCDEndsGraftMover
)
residue_energy()
(in
SpecialRotamerEnergy
)
rotation_axis_angle()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
GraftMoverBase
)
residue_energy_ext()
(in
DunbrackEnergy
)
rotation_axis_angle_double()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
DeleteRegionMover
)
residue_energy_ext()
(in
CenRotDunEnergy
)
rotation_axis_angle_float()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
InsertPoseIntoPoseMover
)
residue_energy_ext()
(in
HPatchEnergy
)
rotation_axis_angle_Real()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
KeepRegionMover
)
residue_energy_ext()
(in
SurfaceEnergy
)
rotation_by_axis()
(in
Jump
)
reinitialize_for_new_input()
(in
ReplaceRegionMover
)
residue_energy_ext()
(in
DNAChiEnergy
)
rotation_by_matrix()
(in
Jump
)
reinitialize_for_new_input()
(in
BackboneGridSampler
)
residue_energy_ext()
(in
ExactOccludedHbondSolEnergy
)
rotation_cosine()
(in
xyzTransform_T_double_T
)
reinitialize_for_new_input()
(in
BundleGridSampler
)
residue_energy_ext()
(in
OccludedHbondSolEnergy_onebody
)
rotation_cosine()
(in
xyzTransform_T_float_T
)
reinitialize_for_new_input()
(in
FitSimpleHelix
)
residue_energy_ext()
(in
FaMPEnvEnergy
)
rotation_matrix()
(in
Quaternion
)
reinitialize_for_new_input()
(in
MakeBundle
)
residue_energy_ext()
(in
FaMPEnvSmoothEnergy
)
rotation_matrix()
(in
HomogeneousTransform_T_double_T
)
reinitialize_for_new_input()
(in
MakeBundleHelix
)
residue_energy_ext()
(in
MPCbetaEnergy
)
rotation_matrix()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
PerturbBundle
)
residue_energy_ext()
(in
MPEnvEnergy
)
rotation_matrix_degrees()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
PerturbBundleHelix
)
residue_energy_ext()
(in
MPNonHelixPenalty
)
rotation_matrix_degrees_double()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
PlaceProbeMover
)
residue_energy_ext()
(in
MPTerminiPenalty
)
rotation_matrix_degrees_float()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
PlaceSurfaceProbe
)
residue_energy_ext()
(in
BurialEnergy
)
rotation_matrix_degrees_Real()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
BackboneTorsionPerturbation
)
residue_energy_ext()
(in
CenRotEnvEnergy
)
rotation_matrix_double()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
BackboneTorsionSampler
)
residue_energy_ext()
(in
ContextDependentOneBodyEnergy
)
rotation_matrix_float()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
CartesianHybridize
)
residue_energy_ext()
(in
ContextIndependentOneBodyEnergy
)
rotation_matrix_radians()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
CartesianSampler
)
residue_energy_ext()
(in
EnvEnergy
)
rotation_matrix_radians_double()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
ChunkTrialMover
)
residue_energy_ext()
(in
EnvSmoothEnergy
)
rotation_matrix_radians_float()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
DomainAssembly
)
residue_energy_ext()
(in
Fa_MbenvEnergy
)
rotation_matrix_radians_Real()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
FoldTreeHybridize
)
residue_energy_ext()
(in
FreeDOF_Energy
)
rotation_matrix_Real()
(in
rosetta.numeric._numeric_
)
reinitialize_for_new_input()
(in
HybridizeProtocol
)
residue_energy_ext()
(in
MembraneCbetaEnergy
)
rotation_sine()
(in
xyzTransform_T_double_T
)
reinitialize_for_new_input()
(in
InsertChunkMover
)
residue_energy_ext()
(in
MembraneEnvEnergy
)
rotation_sine()
(in
xyzTransform_T_float_T
)
reinitialize_for_new_input()
(in
MRMover
)
residue_energy_ext()
(in
MembraneEnvSmoothEnergy
)
RotationMover
(in
rosetta.protocols.membrane._protocols_membrane_
)
reinitialize_for_new_input()
(in
WeightedFragmentSmoothTrialMover
)
residue_energy_ext()
(in
NMerPSSMEnergy
)
RotationMoverAP
(in
rosetta.protocols.membrane._protocols_membrane_
)
reinitialize_for_new_input()
(in
WeightedFragmentTrialMover
)
residue_energy_ext()
(in
NMerRefEnergy
)
RotationMoverCAP
(in
rosetta.protocols.membrane._protocols_membrane_
)
reinitialize_for_new_input()
(in
IdealizeMover
)
residue_energy_ext()
(in
NMerSVMEnergy
)
RotationMoverCreator
(in
rosetta.protocols.membrane._protocols_membrane_
)
reinitialize_for_new_input()
(in
BalancedKicMover
)
residue_energy_ext()
(in
OmegaTetherEnergy
)
RotationMoverCreatorAP
(in
rosetta.protocols.membrane._protocols_membrane_
)
reinitialize_for_new_input()
(in
KicMover
)
residue_energy_ext()
(in
OneBodyEnergy
)
RotationMoverCreatorCAP
(in
rosetta.protocols.membrane._protocols_membrane_
)
reinitialize_for_new_input()
(in
AddHydrogen
)
residue_energy_ext()
(in
P_AA_Energy
)
RotationSearchPattern
(in
rosetta.protocols.hotspot_hashing._protocols_hotspot_hashing_
)
reinitialize_for_new_input()
(in
AddHydrogens
)
residue_energy_ext()
(in
P_AA_pp_Energy
)
RotationSearchPatternAP
(in
rosetta.protocols.hotspot_hashing._protocols_hotspot_hashing_
)
reinitialize_for_new_input()
(in
CompoundTranslate
)
residue_energy_ext()
(in
RamachandranEnergy
)
RotationSearchPatternCAP
(in
rosetta.protocols.hotspot_hashing._protocols_hotspot_hashing_
)
reinitialize_for_new_input()
(in
ComputeLigandRDF
)
residue_energy_ext()
(in
ReferenceEnergy
)
RotData
(in
rosetta.protocols.make_rot_lib._protocols_make_rot_lib_
)
reinitialize_for_new_input()
(in
FinalMinimizer
)
residue_energy_ext()
(in
ReferenceEnergyNoncanonical
)
RotDataAP
(in
rosetta.protocols.make_rot_lib._protocols_make_rot_lib_
)
reinitialize_for_new_input()
(in
GrowLigand
)
residue_energy_ext()
(in
SequenceDependentRefEnergy
)
RotDataCAP
(in
rosetta.protocols.make_rot_lib._protocols_make_rot_lib_
)
reinitialize_for_new_input()
(in
HighResDocker
)
residue_energy_ext()
(in
SmoothEnvEnergy
)
rotid_on_moltenresidue()
(in
FixbbRotamerSets
)
reinitialize_for_new_input()
(in
InterfaceScoreCalculator
)
residue_energy_ext()
(in
SymmetricLigandEnergy
)
rotid_on_moltenresidue()
(in
RotamerSets
)
reinitialize_for_new_input()
(in
LigandDesign
)
residue_energy_ext()
(in
UnfoldedStateEnergy
)
rotid_on_moltenresidue()
(in
RotamerSetsBase
)
reinitialize_for_new_input()
(in
MinimizeBackbone
)
residue_energy_ext()
(in
WaterAdductIntraEnergy
)
rotid_on_moltenresidue()
(in
RotamerSubsets
)
reinitialize_for_new_input()
(in
MinimizeLigand
)
residue_energy_ext()
(in
YHHPlanarityEnergy
)
rotid_on_moltenresidue()
(in
FlexbbRotamerSets
)
reinitialize_for_new_input()
(in
RandomConformerMover
)
residue_energy_ext()
(in
pHEnergy
)
rotno_2_packed_rotno()
(in
SingleResidueDunbrackLibrary
)
reinitialize_for_new_input()
(in
RandomConformers
)
residue_energy_ext()
(in
SugarBackboneEnergy
)
rotno_2_packed_rotno()
(in
SingleResiduePeptoidLibrary
)
reinitialize_for_new_input()
(in
RigidSearchMover
)
residue_energy_ext()
(in
NVscore
)
rotno_2_rotwell()
(in
SingleResidueDunbrackLibrary
)
reinitialize_for_new_input()
(in
Rotate
)
residue_energy_ext()
(in
RNA_BulgeEnergy
)
rotno_2_rotwell()
(in
SingleResiduePeptoidLibrary
)
reinitialize_for_new_input()
(in
Rotates
)
residue_energy_ext()
(in
RNA_FullAtomVDW_BasePhosphate
)
rotprob()
(in
RotamerLibraryScratchSpace
)
reinitialize_for_new_input()
(in
SlideTogether
)
residue_energy_ext()
(in
RNA_SugarCloseEnergy
)
rots_from_pose()
(in
RotamerRecovery
)
reinitialize_for_new_input()
(in
StartFrom
)
residue_energy_ext()
(in
AACompositionEnergy
)
rotset_for_moltenres()
(in
FlexbbRotamerSets
)
reinitialize_for_new_input()
(in
TetherLigand
)
residue_energy_ext()
(in
InterchainEnvEnergy
)
rotset_for_residue()
(in
FlexbbRotamerSets
)
reinitialize_for_new_input()
(in
Transform
)
residue_energy_ext()
(in
SpecialRotamerEnergy
)
RotSub
(in
rosetta.core.pack.annealer._core_pack_annealer_
)
reinitialize_for_new_input()
(in
Translate
)
residue_fast_pair_energy_attached_H()
(in
RNA_FullAtomVDW_BasePhosphate
)
RotSubAP
(in
rosetta.core.pack.annealer._core_pack_annealer_
)
reinitialize_for_new_input()
(in
UnconstrainedTorsionsMover
)
residue_forms_disulfide()
(in
CentroidDisulfideEnergyContainer
)
RotSubCAP
(in
rosetta.core.pack.annealer._core_pack_annealer_
)
reinitialize_for_new_input()
(in
WriteLigandMolFile
)
residue_forms_disulfide()
(in
DisulfideMatchingEnergyContainer
)
rotwell()
(in
RotamerLibraryScratchSpace
)
reinitialize_for_new_input()
(in
LoopBuildMover
)
residue_forms_disulfide()
(in
FullatomDisulfideEnergyContainer
)
rotwell_2_packed_rotno()
(in
SingleResidueDunbrackLibrary
)
reinitialize_for_new_input()
(in
LoopmodelWrapper
)
residue_fraction_buried()
(in
ResidueBurialFilter
)
rotwell_2_packed_rotno()
(in
SingleResiduePeptoidLibrary
)
reinitialize_for_new_input()
(in
LoopBuilder
)
residue_gws_string()
(in
rosetta.core.io.carbohydrates._core_io_carbohydrates_
)
rotwell_2_rotno()
(in
SingleResidueDunbrackLibrary
)
reinitialize_for_new_input()
(in
LoopModeler
)
residue_hbonds()
(in
HBondSet
)
rotwell_2_rotno()
(in
SingleResiduePeptoidLibrary
)
reinitialize_for_new_input()
(in
LoopMover
)
residue_id()
(in
AtomGraphVertexData
)
round()
(in
HierarchicalLevel
)
reinitialize_for_new_input()
(in
LoopProtocol
)
residue_in_chains()
(in
PoissonBoltzmannEnergy
)
round()
(in
StrandBundleFeatures
)
reinitialize_for_new_input()
(in
MinimizationRefiner
)
residue_index()
(in
BackboneGridSamplerHelper
)
round()
(in
rosetta.utility._utility_
)
reinitialize_for_new_input()
(in
RepackingRefiner
)
residue_indices()
(in
OperateOnCertainResidues
)
round_expired()
(in
Scheduler
)
reinitialize_for_new_input()
(in
RotamerTrialsRefiner
)
Residue_info
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
round_to_float()
(in
rosetta.protocols.features.strand_assembly._protocols_features_strand_assembly_
)
reinitialize_for_new_input()
(in
LegacyKicSampler
)
residue_info()
(in
GenBornPoseInfo
)
round_to_Real()
(in
rosetta.protocols.features.strand_assembly._protocols_features_strand_assembly_
)
reinitialize_for_new_input()
(in
AcceptanceCheck
)
residue_info()
(in
GenBornRotamerSetInfo
)
round_to_Real()
(in
ResidueCountFilter
)
reinitialize_for_new_input()
(in
LoopFilter
)
Residue_infoAP
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
round_to_Size()
(in
rosetta.protocols.features.strand_assembly._protocols_features_strand_assembly_
)
reinitialize_for_new_input()
(in
LoopMoverGroup
)
Residue_infoCAP
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
roundtype()
(in
Scheduler
)
reinitialize_for_new_input()
(in
PrepareForCentroid
)
residue_is_floppy()
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
row()
(in
xyzMatrix_Real
)
reinitialize_for_new_input()
(in
PrepareForFullatom
)
residue_is_surface()
(in
SurfaceEnergies
)
row()
(in
xyzMatrix_SSize
)
reinitialize_for_new_input()
(in
FastGapMover
)
residue_iterated_on()
(in
DenseNeighborConstIterator
)
row()
(in
xyzMatrix_Size
)
reinitialize_for_new_input()
(in
LoopHashDiversifier
)
residue_iterated_on()
(in
DenseNeighborIterator
)
row()
(in
xyzMatrix_T_float_T
)
reinitialize_for_new_input()
(in
LoopHashLibrary
)
residue_iterated_on()
(in
OneToAllNeighborConstIterator
)
row()
(in
xyzMatrix_double
)
reinitialize_for_new_input()
(in
LoopHashMoverWrapper
)
residue_iterated_on()
(in
OneToAllNeighborIterator
)
row()
(in
xyzMatrix_float
)
reinitialize_for_new_input()
(in
LoopHashRelaxProtocol
)
residue_iterated_on()
(in
PeptideBondedNeighborConstIterator
)
row_x()
(in
xyzMatrix_Real
)
reinitialize_for_new_input()
(in
Mover_LoopHashRefine
)
residue_iterated_on()
(in
PeptideBondedNeighborIterator
)
row_x()
(in
xyzMatrix_SSize
)
reinitialize_for_new_input()
(in
FoldTreeFromLoops
)
residue_iterated_on()
(in
ResidueNeighborConstIterator
)
row_x()
(in
xyzMatrix_Size
)
reinitialize_for_new_input()
(in
CCDLoopClosureMover
)
residue_iterated_on()
(in
ResidueNeighborIterator
)
row_x()
(in
xyzMatrix_T_float_T
)
reinitialize_for_new_input()
(in
FASelectSlidingWindowLoopClosure
)
residue_iterated_on()
(in
CstResNeighbConstIterator
)
row_x()
(in
xyzMatrix_double
)
reinitialize_for_new_input()
(in
SlidingWindowLoopClosure
)
residue_iterated_on()
(in
CstResNeighbIterator
)
row_x()
(in
xyzMatrix_float
)
reinitialize_for_new_input()
(in
WidthFirstSlidingWindowLoopClosure
)
residue_iterated_on()
(in
CentroidDisulfideNeighborConstIterator
)
row_y()
(in
xyzMatrix_Real
)
reinitialize_for_new_input()
(in
KinematicMover
)
residue_iterated_on()
(in
CentroidDisulfideNeighborIterator
)
row_y()
(in
xyzMatrix_SSize
)
reinitialize_for_new_input()
(in
KinematicWrapper
)
residue_iterated_on()
(in
DisulfResNeighbConstIterator
)
row_y()
(in
xyzMatrix_Size
)
reinitialize_for_new_input()
(in
LoopCM
)
residue_iterated_on()
(in
DisulfResNeighbIterator
)
row_y()
(in
xyzMatrix_T_float_T
)
reinitialize_for_new_input()
(in
LoopRefineInnerCycle
)
residue_iterated_on()
(in
DisulfideMatchingNeighborConstIterator
)
row_y()
(in
xyzMatrix_double
)
reinitialize_for_new_input()
(in
LoopRefineInnerCycleContainer
)
residue_iterated_on()
(in
DisulfideMatchingNeighborIterator
)
row_y()
(in
xyzMatrix_float
)
reinitialize_for_new_input()
(in
RepackTrial
)
RESIDUE_LIST
(in
rosetta.protocols.stepwise.sampler
)
row_z()
(in
xyzMatrix_Real
)
reinitialize_for_new_input()
(in
ShearMinCCDTrial
)
RESIDUE_LIST
(in
rosetta.protocols.stepwise.sampler._protocols_stepwise_sampler_
)
row_z()
(in
xyzMatrix_SSize
)
reinitialize_for_new_input()
(in
SmallMinCCDTrial
)
RESIDUE_LIST
(in
StepWiseSamplerType
)
row_z()
(in
xyzMatrix_Size
)
reinitialize_for_new_input()
(in
MakeRotLibMover
)
residue_list()
(in
SetTorsion
)
row_z()
(in
xyzMatrix_T_float_T
)
reinitialize_for_new_input()
(in
MatcherMover
)
residue_name()
(in
MakeBundleHelix
)
row_z()
(in
xyzMatrix_double
)
reinitialize_for_new_input()
(in
ExtractSubposeMover
)
residue_neighbors()
(in
NonSequentialNeighborsFilter
)
row_z()
(in
xyzMatrix_float
)
reinitialize_for_new_input()
(in
MatDesGreedyOptMutationMover
)
residue_neighbors_updated()
(in
Energies
)
RowDataBase
(in
rosetta.basic.database.insert_statement_generator._basic_database_insert_statement_generator_
)
reinitialize_for_new_input()
(in
SchemePlaceMotifsMover
)
residue_num()
(in
PCS_line_data
)
RowDataBaseAP
(in
rosetta.basic.database.insert_statement_generator._basic_database_insert_statement_generator_
)
reinitialize_for_new_input()
(in
SymDofMover
)
residue_num()
(in
PCS_line_data_Ts1
)
RowDataBaseCAP
(in
rosetta.basic.database.insert_statement_generator._basic_database_insert_statement_generator_
)
reinitialize_for_new_input()
(in
CartesianMD
)
residue_num()
(in
PCS_line_data_Ts2
)
rows()
(in
DP_Matrix
)
reinitialize_for_new_input()
(in
MDBase
)
residue_num()
(in
PCS_line_data_Ts3
)
rows()
(in
xyzMatrix_Real
)
reinitialize_for_new_input()
(in
MedalExchangeMover
)
residue_num()
(in
PCS_line_data_Ts4
)
rows()
(in
xyzMatrix_SSize
)
reinitialize_for_new_input()
(in
MedalMover
)
residue_numbers_into_pose()
(in
SilentStruct
)
rows()
(in
xyzMatrix_Size
)
reinitialize_for_new_input()
(in
AddMPLigandMover
)
residue_op()
(in
Conformation
)
rows()
(in
xyzMatrix_T_float_T
)
reinitialize_for_new_input()
(in
AddMembraneMover
)
residue_packed()
(in
SidechainMover
)
rows()
(in
xyzMatrix_double
)
reinitialize_for_new_input()
(in
FlipMover
)
residue_packed()
(in
SidechainMoverBase
)
rows()
(in
xyzMatrix_float
)
reinitialize_for_new_input()
(in
MembranePositionFromTopologyMover
)
residue_packer_states()
(in
rosetta.protocols.rosetta_scripts._protocols_rosetta_scripts_
)
rpc
(in
rosetta.protocols
)
reinitialize_for_new_input()
(in
RandomPositionRotationMover
)
residue_pair()
(in
StrandPairing
)
RPM_FilterStats
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
reinitialize_for_new_input()
(in
RandomPositionTranslationMover
)
residue_pair_constraint_exists()
(in
ConstraintSet
)
RPM_FilterStatsAP
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
reinitialize_for_new_input()
(in
RotationMover
)
residue_pair_constraint_exists()
(in
IgnoreSubsetConstraintSet
)
RPM_FilterStatsCAP
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
reinitialize_for_new_input()
(in
SetMembraneCenterMover
)
residue_pair_constraint_exists()
(in
MaxSeqSepConstraintSet
)
RPM_Type
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
reinitialize_for_new_input()
(in
SetMembraneNormalMover
)
residue_pair_constraints_begin()
(in
ConstraintSet
)
rpm_type1()
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
reinitialize_for_new_input()
(in
SetMembranePositionMover
)
residue_pair_constraints_end()
(in
ConstraintSet
)
rpm_type2()
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
reinitialize_for_new_input()
(in
TransformIntoMembraneMover
)
residue_pair_constraints_exists()
(in
ConstraintSet
)
RPM_Type_NONE
(in
rosetta.core.scoring.motif
)
reinitialize_for_new_input()
(in
TranslationMover
)
residue_pair_constraints_exists()
(in
IgnoreSubsetConstraintSet
)
RPM_Type_NONE
(in
RPM_Type
)
reinitialize_for_new_input()
(in
TranslationRotationMover
)
residue_pair_constraints_exists()
(in
MaxSeqSepConstraintSet
)
RPM_Type_NONE
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
reinitialize_for_new_input()
(in
SymmetricAddMembraneMover
)
residue_pair_energy()
(in
CarbonHBondEnergy
)
RRComparer
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
VisualizeEmbeddingMover
)
residue_pair_energy()
(in
ConstraintSet
)
RRComparerAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
VisualizeMembraneMover
)
residue_pair_energy()
(in
Constraints
)
RRComparerAutomorphicRMSD
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
ZincHeterodimerMover
)
residue_pair_energy()
(in
ConstraintsEnergy
)
RRComparerAutomorphicRMSDAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
MotifGraftMover
)
residue_pair_energy()
(in
FullatomCustomPairDistanceEnergy
)
RRComparerAutomorphicRMSDCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
MotifDnaPacker
)
residue_pair_energy()
(in
CentroidDisulfideEnergy
)
RRComparerAutomorphicRMSDCreator
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
CompositionMover
)
residue_pair_energy()
(in
DisulfideMatchingEnergy
)
RRComparerAutomorphicRMSDCreatorAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
CycleMover
)
residue_pair_energy()
(in
FullatomDisulfideEnergy
)
RRComparerAutomorphicRMSDCreatorCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
CyclicMover
)
residue_pair_energy()
(in
DNATorsionEnergy
)
RRComparerCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
DsspMover
)
residue_pair_energy()
(in
FA_ElecEnergy
)
RRComparerChiDiff
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
FilterMover
)
residue_pair_energy()
(in
FA_ElecEnergyAroAll
)
RRComparerChiDiffAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
FilterReporterMover
)
residue_pair_energy()
(in
FA_ElecEnergyAroAro
)
RRComparerChiDiffCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
IfMover
)
residue_pair_energy()
(in
FA_GrpElecEnergy
)
RRComparerChiDiffCreator
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
IteratedConvergenceMover
)
residue_pair_energy()
(in
RNA_FA_ElecEnergy
)
RRComparerChiDiffCreatorAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
JumpOutMover
)
residue_pair_energy()
(in
ElecDensAllAtomCenEnergy
)
RRComparerChiDiffCreatorCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
MCShowMover
)
residue_pair_energy()
(in
ElecDensCenEnergy
)
RRComparerCreator
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
MonteCarloUtil
)
residue_pair_energy()
(in
ElecDensEnergy
)
RRComparerCreatorAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
MoveMapMover
)
residue_pair_energy()
(in
FastDensEnergy
)
RRComparerCreatorCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
Mover
)
residue_pair_energy()
(in
PattersonCorrEnergy
)
RRComparerElecDensDiff
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
MoverApplyingMover
)
residue_pair_energy()
(in
ElecDensAtomwiseEnergy
)
RRComparerElecDensDiffAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
MoverContainer
)
residue_pair_energy()
(in
AnalyticEtableEnergy
)
RRComparerElecDensDiffCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
MoverForPoseList
)
residue_pair_energy()
(in
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T
)
RRComparerElecDensDiffCreator
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
NullMover
)
residue_pair_energy()
(in
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T
)
RRComparerElecDensDiffCreatorAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
PDBDumpMover
)
residue_pair_energy()
(in
TableLookupEtableEnergy
)
RRComparerElecDensDiffCreatorCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
ProfilerMover
)
residue_pair_energy()
(in
ContextDependentGeometricSolEnergy
)
RRComparerRotBins
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
PyMolMover
)
residue_pair_energy()
(in
ContextIndependentGeometricSolEnergy
)
RRComparerRotBinsAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
RampingMover
)
residue_pair_energy()
(in
GeometricSolEnergyEvaluator
)
RRComparerRotBinsCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
RandomMover
)
residue_pair_energy()
(in
OccludedHbondSolEnergy
)
RRComparerRotBinsCreator
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
RepeatMover
)
residue_pair_energy()
(in
HackAroEnergy
)
RRComparerRotBinsCreatorAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
SequenceMover
)
residue_pair_energy()
(in
HBondEnergy
)
RRComparerRotBinsCreatorCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
StructureRestrictor
)
residue_pair_energy()
(in
DDPscore
)
RRProtocol
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
TrialMover
)
residue_pair_energy()
(in
FaMPSolvEnergy
)
RRProtocolAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
VectorPoseMover
)
residue_pair_energy()
(in
MPPairEnergy
)
RRProtocolCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
WhileMover
)
residue_pair_energy()
(in
CartesianBondedEnergy
)
RRProtocolCreator
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
StructAvrgMover
)
residue_pair_energy()
(in
CenHBEnergy
)
RRProtocolCreatorAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
NcbbDockDesignProtocol
)
residue_pair_energy()
(in
CenPairEnergy
)
RRProtocolCreatorCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
OopCreatorMover
)
residue_pair_energy()
(in
CenRotPairEnergy
)
RRProtocolMinPack
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
OopDockDesignProtocol
)
residue_pair_energy()
(in
ContextDependentLRTwoBodyEnergy
)
RRProtocolMinPackAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
CartesianNormalModeMover
)
residue_pair_energy()
(in
ContextDependentTwoBodyEnergy
)
RRProtocolMinPackCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
NormalModeMinimizer
)
residue_pair_energy()
(in
ContextIndependentLRTwoBodyEnergy
)
RRProtocolMinPackCreator
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
NormalModeRelaxMover
)
residue_pair_energy()
(in
ContextIndependentTwoBodyEnergy
)
RRProtocolMinPackCreatorAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
TorsionNormalModeMover
)
residue_pair_energy()
(in
CustomAtomPairEnergy
)
RRProtocolMinPackCreatorCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
SetupPoissonBoltzmannPotential
)
residue_pair_energy()
(in
DNA_BaseEnergy
)
RRProtocolMover
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
AddChainBreak
)
residue_pair_energy()
(in
Fa_MbsolvEnergy
)
RRProtocolMoverAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
AddSidechainConstraintsToHotspots
)
residue_pair_energy()
(in
GaussianOverlapEnergy
)
RRProtocolMoverCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
BackrubDDMover
)
residue_pair_energy()
(in
GenBornEnergy
)
RRProtocolMoverCreator
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
BestHotspotCstMover
)
residue_pair_energy()
(in
GoapEnergy
)
RRProtocolMoverCreatorAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
BuildAlaPose
)
residue_pair_energy()
(in
HybridVDW_Energy
)
RRProtocolMoverCreatorCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
DesignMinimizeHbonds
)
residue_pair_energy()
(in
LK_BallEnergy
)
RRProtocolPackRotamers
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
DisulfideMover
)
residue_pair_energy()
(in
LK_PolarNonPolarEnergy
)
RRProtocolPackRotamersAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
DockAndRetrieveSidechains
)
residue_pair_energy()
(in
LK_hack
)
RRProtocolPackRotamersCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
DockWithHotspotMover
)
residue_pair_energy()
(in
LongRangeTwoBodyEnergy
)
RRProtocolPackRotamersCreator
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
FavorNativeResiduePreCycle
)
residue_pair_energy()
(in
MMBondAngleEnergy
)
RRProtocolPackRotamersCreatorAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
FavorNonNativeResiduePreCycle
)
residue_pair_energy()
(in
MMBondLengthEnergy
)
RRProtocolPackRotamersCreatorCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
HotspotDisjointedFoldTreeMover
)
residue_pair_energy()
(in
MMLJEnergyInter
)
RRProtocolReferenceStructure
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
HotspotHasherMover
)
residue_pair_energy()
(in
MMLJEnergyIntra
)
RRProtocolReferenceStructureAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
InterfaceRecapitulationMover
)
residue_pair_energy()
(in
MMTorsionEnergy
)
RRProtocolReferenceStructureCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
LoopFinder
)
residue_pair_energy()
(in
MembraneCenPairEnergy
)
RRProtocolReferenceStructureCreator
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
LoopLengthChange
)
residue_pair_energy()
(in
PairEnergy
)
RRProtocolReferenceStructureCreatorAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
LoopMoverFromCommandLine
)
residue_pair_energy()
(in
PeptideBondEnergy
)
RRProtocolReferenceStructureCreatorCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
LoopOver
)
residue_pair_energy()
(in
PoissonBoltzmannEnergy
)
RRProtocolRelax
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
LoopRemodel
)
residue_pair_energy()
(in
ProClosureEnergy
)
RRProtocolRelaxAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
MapHotspot
)
residue_pair_energy()
(in
Rama2BOffsetEnergy
)
RRProtocolRelaxCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
PatchdockTransform
)
residue_pair_energy()
(in
RamachandranEnergy2B
)
RRProtocolRelaxCreator
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
PeptideStapleDesignMover
)
residue_pair_energy()
(in
ShortRangeTwoBodyEnergy
)
RRProtocolRelaxCreatorAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
PlaceOnLoop
)
residue_pair_energy()
(in
SmoothCenPairEnergy
)
RRProtocolRelaxCreatorCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
PlaceSimultaneouslyMover
)
residue_pair_energy()
(in
SuckerEnergy
)
RRProtocolRotamerTrials
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
PlaceStubMover
)
residue_pair_energy()
(in
TwoBodyEnergy
)
RRProtocolRotamerTrialsAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
PlacementAuctionMover
)
residue_pair_energy()
(in
WaterAdductHBondEnergy
)
RRProtocolRotamerTrialsCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
PlacementMinimizationMover
)
residue_pair_energy()
(in
DFIRE_Energy
)
RRProtocolRotamerTrialsCreator
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
PrepackMover
)
residue_pair_energy()
(in
OrbitalsScore
)
RRProtocolRotamerTrialsCreatorAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
ProteinInterfaceMultiStateDesignMover
)
residue_pair_energy()
(in
RNA_FullAtomStackingEnergy
)
RRProtocolRotamerTrialsCreatorCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
RandomMutation
)
residue_pair_energy()
(in
RNA_JR_SuiteEnergy
)
RRProtocolRTMin
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
RepackMinimize
)
residue_pair_energy()
(in
RNA_LJ_BaseEnergy
)
RRProtocolRTMinAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
SaveAndRetrieveSidechains
)
residue_pair_energy()
(in
RNA_Mg_Energy
)
RRProtocolRTMinCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
SetAtomTree
)
residue_pair_energy()
(in
RNA_PairwiseLowResolutionEnergy
)
RRProtocolRTMinCreator
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
SetTemperatureFactor
)
residue_pair_energy()
(in
RNA_SuiteEnergy
)
RRProtocolRTMinCreatorAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
SetupHotspotConstraintsLoopsMover
)
residue_pair_energy()
(in
RNA_TorsionEnergy
)
RRProtocolRTMinCreatorCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
SetupHotspotConstraintsMover
)
residue_pair_energy()
(in
RNA_TorsionPotential
)
RRReporter
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
ShoveResidueMover
)
residue_pair_energy()
(in
RNA_VDW_Energy
)
RRReporterAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
SpinMover
)
residue_pair_energy()
(in
StackElecEnergy
)
RRReporterCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
SubroutineMover
)
residue_pair_energy()
(in
RNA_DataBackboneEnergy
)
RRReporterCreator
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
TaskAwareCsts
)
residue_pair_energy()
(in
symEnergy
)
RRReporterCreatorAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
TopologyBrokerMover
)
residue_pair_energy()
(in
IgnoreSubsetConstraintSet
)
RRReporterCreatorCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
TryRotamers
)
residue_pair_energy()
(in
MaxSeqSepConstraintSet
)
RRReporterHuman
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
VLB
)
residue_pair_energy()
(in
InterchainPairEnergy
)
RRReporterHumanAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
AutoRBMover
)
residue_pair_energy_aro_aro()
(in
FA_ElecEnergyAroAll
)
RRReporterHumanCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
FragInsertAndAlignMover
)
residue_pair_energy_aro_aro()
(in
FA_ElecEnergyAroAro
)
RRReporterHumanCreator
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
GaussianRBSegmentMover
)
residue_pair_energy_ext()
(in
CarbonHBondEnergy
)
RRReporterHumanCreatorAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
HelicalGaussianMover
)
residue_pair_energy_ext()
(in
ConstraintsEnergy
)
RRReporterHumanCreatorCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
IdealizeHelicesMover
)
residue_pair_energy_ext()
(in
FullatomCustomPairDistanceEnergy
)
RRReporterSimple
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
MakeStarTopologyMover
)
residue_pair_energy_ext()
(in
CentroidDisulfideEnergy
)
RRReporterSimpleAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
OptimizeThreadingMover
)
residue_pair_energy_ext()
(in
DisulfideMatchingEnergy
)
RRReporterSimpleCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
RBSegmentMover
)
residue_pair_energy_ext()
(in
FullatomDisulfideEnergy
)
RRReporterSimpleCreator
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
RBSegmentRelax
)
residue_pair_energy_ext()
(in
DNATorsionEnergy
)
RRReporterSimpleCreatorAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
SequenceShiftMover
)
residue_pair_energy_ext()
(in
FA_ElecEnergy
)
RRReporterSimpleCreatorCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
StrandTwistingMover
)
residue_pair_energy_ext()
(in
FA_ElecEnergyAroAll
)
RRReporterSQLite
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
AtomCoordinateCstMover
)
residue_pair_energy_ext()
(in
FA_ElecEnergyAroAro
)
RRReporterSQLiteAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
CentroidRelax
)
residue_pair_energy_ext()
(in
FA_GrpElecEnergy
)
RRReporterSQLiteCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
ClassicRelax
)
residue_pair_energy_ext()
(in
RNA_FA_ElecEnergy
)
RRReporterSQLiteCreator
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
FastRelax
)
residue_pair_energy_ext()
(in
ElecDensAllAtomCenEnergy
)
RRReporterSQLiteCreatorAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
LocalRelax
)
residue_pair_energy_ext()
(in
ElecDensCenEnergy
)
RRReporterSQLiteCreatorCAP
(in
rosetta.protocols.rotamer_recovery._protocols_rotamer_recovery_
)
reinitialize_for_new_input()
(in
MiniRelax
)
residue_pair_energy_ext()
(in
ElecDensEnergy
)
rsd()
(in
AtomID
)
reinitialize_for_new_input()
(in
RelaxProtocolBase
)
residue_pair_energy_ext()
(in
FastDensEnergy
)
rsd()
(in
DOF_ID
)
reinitialize_for_new_input()
(in
MPFastRelaxMover
)
residue_pair_energy_ext()
(in
PattersonCorrEnergy
)
rsd()
(in
NamedAtomID
)
reinitialize_for_new_input()
(in
MembraneCenterPerturbationMover
)
residue_pair_energy_ext()
(in
ElecDensAtomwiseEnergy
)
rsd()
(in
TorsionID
)
reinitialize_for_new_input()
(in
MembraneNormalPerturbationMover
)
residue_pair_energy_ext()
(in
AnalyticEtableEnergy
)
rsd()
(in
DOF_Node
)
reinitialize_for_new_input()
(in
MovePoseToMembraneCenterMover
)
residue_pair_energy_ext()
(in
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T
)
rsd()
(in
AtomNeighbor
)
reinitialize_for_new_input()
(in
RigidBodyDeterministicSpinMover
)
residue_pair_energy_ext()
(in
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T
)
rsd()
(in
PhosphateMove
)
reinitialize_for_new_input()
(in
RigidBodyDofPerturbMover
)
residue_pair_energy_ext()
(in
TableLookupEtableEnergy
)
rsd1()
(in
JumpID
)
reinitialize_for_new_input()
(in
RigidBodyDofRandomTransMover
)
residue_pair_energy_ext()
(in
ContextDependentGeometricSolEnergy
)
rsd2()
(in
JumpID
)
reinitialize_for_new_input()
(in
RigidBodyDofRandomizeMover
)
residue_pair_energy_ext()
(in
ContextIndependentGeometricSolEnergy
)
rsd_library_already_loaded()
(in
RotamerLibrary
)
reinitialize_for_new_input()
(in
RigidBodyDofSeqPerturbMover
)
residue_pair_energy_ext()
(in
GeometricSolEnergyEvaluator
)
rsd_rsd_energy()
(in
DirectReadoutPotential
)
reinitialize_for_new_input()
(in
RigidBodyDofSeqRandomizeMover
)
residue_pair_energy_ext()
(in
OccludedHbondSolEnergy
)
rsd_sasa()
(in
SelectResiduesByLayer
)
reinitialize_for_new_input()
(in
RigidBodyDofSeqTransMover
)
residue_pair_energy_ext()
(in
HackAroEnergy
)
rsd_set_from_cmd_line()
(in
rosetta.core.chemical._core_chemical_
)
reinitialize_for_new_input()
(in
RigidBodyDofTransMover
)
residue_pair_energy_ext()
(in
HBondEnergy
)
rsigma
(in
ScoreType
)
reinitialize_for_new_input()
(in
RigidBodyMotionMover
)
residue_pair_energy_ext()
(in
DDPscore
)
rsigma
(in
rosetta.core.scoring._core_scoring_
)
reinitialize_for_new_input()
(in
RigidBodyMover
)
residue_pair_energy_ext()
(in
FaMPSolvEnergy
)
rsigma
(in
rosetta.core.scoring
)
reinitialize_for_new_input()
(in
RigidBodyPerturbMover
)
residue_pair_energy_ext()
(in
MPPairEnergy
)
rsigma
(in
rosetta
)
reinitialize_for_new_input()
(in
RigidBodyPerturbNoCenterMover
)
residue_pair_energy_ext()
(in
CartesianBondedEnergy
)
rsigma_dot_initializer()
(in
SecondaryStructurePotential
)
reinitialize_for_new_input()
(in
RigidBodyPerturbRandomJumpMover
)
residue_pair_energy_ext()
(in
CenHBEnergy
)
Rsmn2x2
(in
rosetta.protocols.fldsgn.topology
)
reinitialize_for_new_input()
(in
RigidBodyRandomizeMover
)
residue_pair_energy_ext()
(in
CenPairEnergy
)
Rsmn2x2
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
reinitialize_for_new_input()
(in
RigidBodySpinMover
)
residue_pair_energy_ext()
(in
CenRotPairEnergy
)
Rsmn2x2
(in
SheetFoldType
)
reinitialize_for_new_input()
(in
RigidBodyTransMover
)
residue_pair_energy_ext()
(in
ContextDependentLRTwoBodyEnergy
)
Rsmn3x3
(in
rosetta.protocols.fldsgn.topology
)
reinitialize_for_new_input()
(in
RollMover
)
residue_pair_energy_ext()
(in
ContextDependentTwoBodyEnergy
)
Rsmn3x3
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
reinitialize_for_new_input()
(in
RotateJumpAxisMover
)
residue_pair_energy_ext()
(in
ContextIndependentLRTwoBodyEnergy
)
Rsmn3x3
(in
SheetFoldType
)
reinitialize_for_new_input()
(in
UniformRigidBodyCM
)
residue_pair_energy_ext()
(in
ContextIndependentTwoBodyEnergy
)
Rsmn3x3_Half
(in
rosetta.protocols.fldsgn.topology
)
reinitialize_for_new_input()
(in
UniformRigidBodyMover
)
residue_pair_energy_ext()
(in
CustomAtomPairEnergy
)
Rsmn3x3_Half
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
reinitialize_for_new_input()
(in
UniformSphereTransMover
)
residue_pair_energy_ext()
(in
DNA_BaseEnergy
)
Rsmn3x3_Half
(in
SheetFoldType
)
reinitialize_for_new_input()
(in
WholeBodyRotationMover
)
residue_pair_energy_ext()
(in
Fa_MbsolvEnergy
)
rswitch()
(in
BoundFunc
)
reinitialize_for_new_input()
(in
WholeBodyTranslationMover
)
residue_pair_energy_ext()
(in
GaussianOverlapEnergy
)
rsym_eigenval()
(in
rosetta.numeric.model_quality._numeric_model_quality_
)
reinitialize_for_new_input()
(in
AdditionalOutputWrapper
)
residue_pair_energy_ext()
(in
GenBornEnergy
)
rsym_evector()
(in
rosetta.numeric.model_quality._numeric_model_quality_
)
reinitialize_for_new_input()
(in
MultipleOutputWrapper
)
residue_pair_energy_ext()
(in
GoapEnergy
)
rsym_rotation()
(in
rosetta.numeric.model_quality._numeric_model_quality_
)
reinitialize_for_new_input()
(in
MultiplePoseMover
)
residue_pair_energy_ext()
(in
HybridVDW_Energy
)
RT
(in
rosetta.core.kinematics._core_kinematics_
)
reinitialize_for_new_input()
(in
ParsedProtocol
)
residue_pair_energy_ext()
(in
LK_BallEnergy
)
rt()
(in
Jump
)
reinitialize_for_new_input()
(in
SavePoseMover
)
residue_pair_energy_ext()
(in
LK_PolarNonPolarEnergy
)
rt()
(in
ResPairMotif
)
reinitialize_for_new_input()
(in
RotamerRecoveryMover
)
residue_pair_energy_ext()
(in
LK_hack
)
rt()
(in
ConnectRight
)
reinitialize_for_new_input()
(in
CAcstGenerator
)
residue_pair_energy_ext()
(in
LongRangeTwoBodyEnergy
)
rt6()
(in
Xfrag
)
reinitialize_for_new_input()
(in
CloseFold
)
residue_pair_energy_ext()
(in
MMBondAngleEnergy
)
rt6()
(in
xyzTransform_T_double_T
)
reinitialize_for_new_input()
(in
CoordinateCst
)
residue_pair_energy_ext()
(in
MMBondLengthEnergy
)
rt6()
(in
xyzTransform_T_float_T
)
reinitialize_for_new_input()
(in
DefineMovableLoops
)
residue_pair_energy_ext()
(in
MMLJEnergyInter
)
RT_from_epos()
(in
RT_helper
)
reinitialize_for_new_input()
(in
GrowPeptides
)
residue_pair_energy_ext()
(in
MMLJEnergyIntra
)
RT_helper
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
reinitialize_for_new_input()
(in
SeedFoldTree
)
residue_pair_energy_ext()
(in
MMTorsionEnergy
)
RT_helperAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
reinitialize_for_new_input()
(in
SeedSetupMover
)
residue_pair_energy_ext()
(in
MembraneCenPairEnergy
)
RT_helperCAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
reinitialize_for_new_input()
(in
SegmentHybridizer
)
residue_pair_energy_ext()
(in
PairEnergy
)
rt_min()
(in
DockingHighRes
)
reinitialize_for_new_input()
(in
SwapSegment
)
residue_pair_energy_ext()
(in
PeptideBondEnergy
)
rt_min()
(in
DockingHighResLegacy
)
reinitialize_for_new_input()
(in
EvaluatedTrialMover
)
residue_pair_energy_ext()
(in
PoissonBoltzmannEnergy
)
rt_templates()
(in
MembraneJump
)
reinitialize_for_new_input()
(in
AddCavitiesMover
)
residue_pair_energy_ext()
(in
ProClosureEnergy
)
RTAP
(in
rosetta.core.kinematics._core_kinematics_
)
reinitialize_for_new_input()
(in
AddChainMover
)
residue_pair_energy_ext()
(in
Rama2BOffsetEnergy
)
RTCAP
(in
rosetta.core.kinematics._core_kinematics_
)
reinitialize_for_new_input()
(in
AddConstraintsToCurrentConformationMover
)
residue_pair_energy_ext()
(in
RamachandranEnergy2B
)
RTMin
(in
rosetta.core.pack._core_pack_
)
reinitialize_for_new_input()
(in
AddJobPairData
)
residue_pair_energy_ext()
(in
ShortRangeTwoBodyEnergy
)
rtmin()
(in
RTMin
)
reinitialize_for_new_input()
(in
AlignChainMover
)
residue_pair_energy_ext()
(in
SmoothCenPairEnergy
)
rtmin()
(in
GreedyOptMutationMover
)
reinitialize_for_new_input()
(in
BBConRotMover
)
residue_pair_energy_ext()
(in
SuckerEnergy
)
rtmin()
(in
ParetoOptMutationMover
)
reinitialize_for_new_input()
(in
BBG8T3AMover
)
residue_pair_energy_ext()
(in
TwoBodyEnergy
)
rtmin()
(in
PointMutationCalculator
)
reinitialize_for_new_input()
(in
BBGaussianMover
)
residue_pair_energy_ext()
(in
WaterAdductHBondEnergy
)
rtmin()
(in
MatDesGreedyOptMutationMover
)
reinitialize_for_new_input()
(in
BackboneMover
)
residue_pair_energy_ext()
(in
DFIRE_Energy
)
rtmin()
(in
MatDesPointMutationCalculator
)
reinitialize_for_new_input()
(in
BoltzmannRotamerMover
)
residue_pair_energy_ext()
(in
OrbitalsScore
)
rtmin()
(in
FilterScanFilter
)
reinitialize_for_new_input()
(in
ChainSplitMover
)
residue_pair_energy_ext()
(in
RNA_FullAtomStackingEnergy
)
rtmin()
(in
RelativePoseFilter
)
reinitialize_for_new_input()
(in
ChangeAndResetFoldTreeMover
)
residue_pair_energy_ext()
(in
RNA_JR_SuiteEnergy
)
RTMinAP
(in
rosetta.core.pack._core_pack_
)
reinitialize_for_new_input()
(in
ClearConstraintsMover
)
residue_pair_energy_ext()
(in
RNA_LJ_BaseEnergy
)
RTMinCAP
(in
rosetta.core.pack._core_pack_
)
reinitialize_for_new_input()
(in
CombinePoseMover
)
residue_pair_energy_ext()
(in
RNA_Mg_Energy
)
run()
(in
AtomTreeMinimizer
)
reinitialize_for_new_input()
(in
ConsensusDesignMover
)
residue_pair_energy_ext()
(in
RNA_PairwiseLowResolutionEnergy
)
run()
(in
CartesianMinimizer
)
reinitialize_for_new_input()
(in
ConstrainToIdealMover
)
residue_pair_energy_ext()
(in
RNA_SuiteEnergy
)
run()
(in
GA_Minimizer
)
reinitialize_for_new_input()
(in
ConstraintSetMover
)
residue_pair_energy_ext()
(in
RNA_TorsionEnergy
)
run()
(in
JJH_Minimizer
)
reinitialize_for_new_input()
(in
ContingentAcceptMover
)
residue_pair_energy_ext()
(in
RNA_VDW_Energy
)
run()
(in
Minimizer
)
reinitialize_for_new_input()
(in
CopyDofMover
)
residue_pair_energy_ext()
(in
StackElecEnergy
)
run()
(in
NelderMeadSimplex
)
reinitialize_for_new_input()
(in
CoupledMover
)
residue_pair_energy_ext()
(in
RNA_DataBackboneEnergy
)
run()
(in
ParticleSwarmMinimizer
)
reinitialize_for_new_input()
(in
CutChainMover
)
residue_pair_energy_ext()
(in
symEnergy
)
run()
(in
SymAtomTreeMinimizer
)
reinitialize_for_new_input()
(in
CyclizationMover
)
residue_pair_energy_ext()
(in
InterchainPairEnergy
)
run()
(in
DebuggingAnnealer
)
reinitialize_for_new_input()
(in
DME_FilterMover
)
residue_point_graph_from_conformation()
(in
rosetta.core.conformation._core_conformation_
)
run()
(in
FASTERAnnealer
)
reinitialize_for_new_input()
(in
DeleteChainsMover
)
RESIDUE_PREPEND
(in
LengthEvent
)
run()
(in
FixbbCoupledRotamerSimAnnealer
)
reinitialize_for_new_input()
(in
DesignRepackMover
)
RESIDUE_PREPEND
(in
Tag
)
run()
(in
FixbbLinkingRotamerSimAnnealer
)
reinitialize_for_new_input()
(in
DisulfideInsertionMover
)
residue_properties
(in
rosetta.core.chemical
)
run()
(in
FixbbSimAnnealer
)
reinitialize_for_new_input()
(in
DumpPdb
)
residue_range_gws_string()
(in
rosetta.core.io.carbohydrates._core_io_carbohydrates_
)
run()
(in
MultiCoolAnnealer
)
reinitialize_for_new_input()
(in
EnergyCutRotamerTrialsMinMover
)
residue_range_is_protein()
(in
BetaTurnDetection
)
run()
(in
SimAnnealerBase
)
reinitialize_for_new_input()
(in
EnergyCutRotamerTrialsMover
)
residue_sc_rmsd_no_super()
(in
rosetta.core.scoring._core_scoring_
)
run()
(in
AbrelaxApplication
)
reinitialize_for_new_input()
(in
ExtendedPoseMover
)
residue_sc_rmsd_no_super()
(in
rosetta.protocols.hotspot_hashing._protocols_hotspot_hashing_
)
run()
(in
FlexbbSimAnnealer
)
reinitialize_for_new_input()
(in
FavorSequenceProfile
)
residue_score()
(in
ElectronDensityAtomwise
)
run()
(in
DomainAssembly
)
reinitialize_for_new_input()
(in
FavorSymmetricSequence
)
residue_selector
(in
rosetta.core.pack.task
)
run()
(in
MpiFileBuffer
)
reinitialize_for_new_input()
(in
FindConsensusSequence
)
residue_selector_single_from_line()
(in
rosetta.core.chemical._core_chemical_
)
run()
(in
WorkUnit_LoopHash
)
reinitialize_for_new_input()
(in
ForceDisulfidesMover
)
residue_subset()
(in
rosetta.protocols.toolbox.pose_metric_calculators._protocols_toolbox_pose_metric_calculators_
)
run()
(in
LigandMotifSearch
)
reinitialize_for_new_input()
(in
GenericMonteCarloMover
)
residue_task()
(in
PackerTask
)
run()
(in
MotifSearch
)
reinitialize_for_new_input()
(in
GreenPacker
)
residue_task()
(in
PackerTask_
)
run()
(in
WorkUnit_CombinePose
)
reinitialize_for_new_input()
(in
LoadPDBMover
)
residue_to_constrain()
(in
AddConstraintsToCurrentConformationMover
)
run()
(in
WorkUnit_FragInsert
)
reinitialize_for_new_input()
(in
LoadUnboundRotMover
)
residue_total_energies()
(in
Energies
)
run()
(in
WorkUnit_KicCloser
)
reinitialize_for_new_input()
(in
MSDMover
)
residue_total_energy()
(in
Energies
)
run()
(in
WorkUnit_LoopHash
)
reinitialize_for_new_input()
(in
MakePolyXMover
)
residue_type()
(in
Conformation
)
run()
(in
WorkUnit_MD
)
reinitialize_for_new_input()
(in
MembraneTopology
)
residue_type()
(in
Pose
)
run()
(in
WorkUnit_NormalMode
)
reinitialize_for_new_input()
(in
MinMover
)
residue_type()
(in
LKB_ResidueInfo
)
run()
(in
WorkUnit_PartialAbinitio
)
reinitialize_for_new_input()
(in
MinPackMover
)
residue_type_all_patches_name()
(in
rosetta.core.chemical._core_chemical_
)
run()
(in
WorkUnit_RamaPerturber
)
reinitialize_for_new_input()
(in
MissingDensityToJumpMover
)
residue_type_base_name()
(in
rosetta.core.chemical._core_chemical_
)
run()
(in
WorkUnit_Relax
)
reinitialize_for_new_input()
(in
ModifyVariantTypeMover
)
residue_type_param_set()
(in
MMBondAngleEnergy
)
run()
(in
WorkUnit_Sampler
)
reinitialize_for_new_input()
(in
MonteCarloRecover
)
residue_type_set()
(in
ChemicalManager
)
run()
(in
WorkUnit_bbGauss
)
reinitialize_for_new_input()
(in
MonteCarloReset
)
residue_type_set()
(in
ResidueType
)
run()
(in
WorkUnit_BatchRelax
)
reinitialize_for_new_input()
(in
MonteCarloTest
)
residue_type_set()
(in
Residue
)
run()
(in
WorkUnit_BatchRelax_and_PostRescore
)
reinitialize_for_new_input()
(in
MutateResidue
)
residue_type_set()
(in
ImportPoseOptions
)
run()
(in
RRProtocol
)
reinitialize_for_new_input()
(in
O2M_MutateMover
)
residue_type_set()
(in
BuildInstruction
)
run()
(in
RRProtocolMinPack
)
reinitialize_for_new_input()
(in
PDBReloadMover
)
residue_type_set()
(in
ExtendedPoseMover
)
run()
(in
RRProtocolMover
)
reinitialize_for_new_input()
(in
PSSM2BfactorMover
)
residue_type_set_tag()
(in
ResidueLoaderOptions
)
run()
(in
RRProtocolPackRotamers
)
reinitialize_for_new_input()
(in
PackRotamersMover
)
residue_types()
(in
ResidueTypeSet
)
run()
(in
RRProtocolRTMin
)
reinitialize_for_new_input()
(in
PackRotamersMoverLazy
)
residue_types_from_saccharide_sequence()
(in
rosetta.core.pose._core_pose_
)
run()
(in
RRProtocolReferenceStructure
)
reinitialize_for_new_input()
(in
PeptideStapleMover
)
residue_types_from_sequence()
(in
rosetta.core.pose._core_pose_
)
run()
(in
RRProtocolRelax
)
reinitialize_for_new_input()
(in
PeriodicBoxMover
)
residue_xyz_change_list_begin()
(in
AtomTree
)
run()
(in
RRProtocolRotamerTrials
)
reinitialize_for_new_input()
(in
ProlineFixMover
)
residue_xyz_change_list_end()
(in
AtomTree
)
run()
(in
RotamerRecovery
)
reinitialize_for_new_input()
(in
RandomOmegaFlipMover
)
residue_z_position()
(in
MembraneInfo
)
run()
(in
JSON_RPC
)
reinitialize_for_new_input()
(in
RandomTorsionMover
)
ResidueAlternativeSet
(in
rosetta.protocols.stepwise.sampler.copy_dofs._protocols_stepwise_sampler_copy_dofs_
)
run()
(in
StepWiseSampleAndScreen
)
reinitialize_for_new_input()
(in
RepackSidechainsMover
)
ResidueAlternativeSetAP
(in
rosetta.protocols.stepwise.sampler.copy_dofs._protocols_stepwise_sampler_copy_dofs_
)
run()
(in
DatabaseEntryWorkUnit
)
reinitialize_for_new_input()
(in
RepeatPropagationMover
)
ResidueAlternativeSetCAP
(in
rosetta.protocols.stepwise.sampler.copy_dofs._protocols_stepwise_sampler_copy_dofs_
)
run()
(in
WorkUnitBase
)
reinitialize_for_new_input()
(in
ReportEffectivePKA
)
ResidueAlternativeStepWiseSampler
(in
rosetta.protocols.stepwise.sampler.copy_dofs._protocols_stepwise_sampler_copy_dofs_
)
run()
(in
WorkUnit_MoverWrapper
)
reinitialize_for_new_input()
(in
RepulsiveOnlyMover
)
ResidueAlternativeStepWiseSamplerAP
(in
rosetta.protocols.stepwise.sampler.copy_dofs._protocols_stepwise_sampler_copy_dofs_
)
run()
(in
WorkUnit_SilentStructStore
)
reinitialize_for_new_input()
(in
ResetBaselineMover
)
ResidueAlternativeStepWiseSamplerCAP
(in
rosetta.protocols.stepwise.sampler.copy_dofs._protocols_stepwise_sampler_copy_dofs_
)
run()
(in
WorkUnit_Wait
)
reinitialize_for_new_input()
(in
ResidueTypeConstraintMover
)
ResidueAlternativeStepWiseSamplerComb
(in
rosetta.protocols.stepwise.sampler.copy_dofs._protocols_stepwise_sampler_copy_dofs_
)
run()
(in
WorkUnit
)
reinitialize_for_new_input()
(in
ReturnSidechainMover
)
ResidueAlternativeStepWiseSamplerCombAP
(in
rosetta.protocols.stepwise.sampler.copy_dofs._protocols_stepwise_sampler_copy_dofs_
)
run()
(in
WorkUnit_ElScripts
)
reinitialize_for_new_input()
(in
RingConformationMover
)
ResidueAlternativeStepWiseSamplerCombCAP
(in
rosetta.protocols.stepwise.sampler.copy_dofs._protocols_stepwise_sampler_copy_dofs_
)
run()
(in
WorkUnit_Wait
)
reinitialize_for_new_input()
(in
RotamerTrialsMinMover
)
ResidueAP
(in
rosetta.core.conformation._core_conformation_
)
run_A_ANN_Prediction()
(in
Sparta
)
reinitialize_for_new_input()
(in
RotamerTrialsMover
)
ResidueAtomTreeCollectionMomento
(in
rosetta.core.pack.scmin._core_pack_scmin_'
)
run_boinc_debug()
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
reinitialize_for_new_input()
(in
RotamerizeMover
)
ResidueAtomTreeCollectionMomentoAP
(in
rosetta.core.pack.scmin._core_pack_scmin_'
)
run_decomp_svd()
(in
SVD_Solver
)
reinitialize_for_new_input()
(in
SaneMinMover
)
ResidueAtomTreeCollectionMomentoCAP
(in
rosetta.core.pack.scmin._core_pack_scmin_'
)
run_mc()
(in
SymShakeStructureMover
)
reinitialize_for_new_input()
(in
ScoreMover
)
ResidueBurialFeatures
(in
rosetta.protocols.features._protocols_features_
)
run_rattle1()
(in
Rattle
)
reinitialize_for_new_input()
(in
SequenceProfileMover
)
ResidueBurialFeaturesAP
(in
rosetta.protocols.features._protocols_features_
)
run_rattle2()
(in
Rattle
)
reinitialize_for_new_input()
(in
SetReturningPackRotamersMover
)
ResidueBurialFeaturesCAP
(in
rosetta.protocols.features._protocols_features_
)
run_score_svd_on_matrix()
(in
SVD_Solver
)
reinitialize_for_new_input()
(in
SetTorsion
)
ResidueBurialFeaturesCreator
(in
rosetta.protocols.features._protocols_features_
)
run_score_svd_without_solving()
(in
SVD_Solver
)
reinitialize_for_new_input()
(in
ShakeStructureMover
)
ResidueBurialFeaturesCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
run_solve_svd()
(in
SVD_Solver
)
reinitialize_for_new_input()
(in
ShearMover
)
ResidueBurialFeaturesCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
Run_WriteToDB_sandwich()
(in
rosetta.protocols.features.strand_assembly._protocols_features_strand_assembly_
)
reinitialize_for_new_input()
(in
ShortBackrubMover
)
ResidueBurialFilter
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
RunAll
(in
ExecutionMode
)
reinitialize_for_new_input()
(in
SmallMover
)
ResidueBurialFilterAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
RunAll
(in
PlaceProbeMover
)
reinitialize_for_new_input()
(in
SuperimposeMover
)
ResidueBurialFilterCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
runSpartaANN()
(in
ANN
)
reinitialize_for_new_input()
(in
SwitchChainOrderMover
)
ResidueBurialFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
runtime()
(in
JSON_RPC
)
reinitialize_for_new_input()
(in
SwitchResidueTypeSetMover
)
ResidueBurialFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
RuntimeFeatures
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
TailsScoreMover
)
ResidueBurialFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
RuntimeFeaturesAP
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
TaskAwareMinMover
)
ResidueCAP
(in
rosetta.core.conformation._core_conformation_
)
RuntimeFeaturesCAP
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
TorsionDOFMover
)
ResidueCartBondedParameters
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
RuntimeFeaturesCreator
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
TorsionSetMover
)
ResidueCartBondedParametersAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
RuntimeFeaturesCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
Tumble
)
ResidueCartBondedParametersCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
RuntimeFeaturesCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
reinitialize_for_new_input()
(in
UniformRotationMover
)
ResidueConformationFeatures
(in
rosetta.protocols.features._protocols_features_
)
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