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A
A
(in
rosetta.protocols.comparative_modeling.features
)
AHO_Scheme
(in
rosetta.protocols.antibody
)
apply()
(in
TruncatedScoreEvaluator
)
A
(in
rosetta.protocols.comparative_modeling.features._protocols_comparative_modeling_features_
)
AHO_Scheme
(in
rosetta.protocols.antibody._protocols_antibody_
)
apply()
(in
AddCavitiesMover
)
A
(in
TorsionBin
)
AHO_Scheme
(in
AntibodyNumberingSchemeEnum
)
apply()
(in
AddChainMover
)
A
(in
rosetta.protocols.features
)
ala_pose_loop()
(in
PlaceOnLoop
)
apply()
(in
AddConstraintsToCurrentConformationMover
)
A
(in
rosetta.protocols.features._protocols_features_
)
AlaScan
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
apply()
(in
AddJobPairData
)
A
(in
RamachandranHash
)
AlaScanAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
apply()
(in
AlignChainMover
)
A()
(in
CrystInfo
)
AlaScanCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
apply()
(in
BBConRotMover
)
a()
(in
OneGaussianScattering
)
AlaScanFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
apply()
(in
BBG8T3AMover
)
a()
(in
OneGaussianScattering
)
AlaScanFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
apply()
(in
BBGaussianMover
)
a_to_i()
(in
NormalMode
)
AlaScanFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
apply()
(in
BackboneMover
)
AA
(in
rosetta.core.chemical._core_chemical_
)
ALDONIC_ACID
(in
rosetta
)
apply()
(in
BoltzmannRotamerMover
)
aa()
(in
ResidueType
)
ALDONIC_ACID
(in
rosetta.core.chemical
)
apply()
(in
ChainSplitMover
)
aa()
(in
Conformation
)
ALDONIC_ACID
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
ChangeAndResetFoldTreeMover
)
aa()
(in
Residue
)
ALDONIC_ACID
(in
ResidueProperty
)
apply()
(in
ClassicFragmentMover
)
aa()
(in
VallResidue
)
ALDONIC_ACID_VARIANT
(in
rosetta
)
apply()
(in
ClearConstraintsMover
)
aa()
(in
SingleResidueDunbrackLibrary
)
ALDONIC_ACID_VARIANT
(in
rosetta.core.chemical
)
apply()
(in
CombinePoseMover
)
aa()
(in
SingleResiduePeptoidLibrary
)
ALDONIC_ACID_VARIANT
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
ConsensusDesignMover
)
aa()
(in
SingleResidueCenrotLibrary
)
ALDONIC_ACID_VARIANT
(in
VariantType
)
apply()
(in
ConstrainToIdealMover
)
aa()
(in
WaterAnchorInfo
)
ALDOSE
(in
rosetta
)
apply()
(in
ConstraintSetMover
)
aa()
(in
Pose
)
ALDOSE
(in
rosetta.core.chemical
)
apply()
(in
ContingentAcceptMover
)
aa()
(in
Xfres
)
ALDOSE
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
CopyDofMover
)
aa()
(in
RNA_CS_residue_parameters
)
ALDOSE
(in
ResidueProperty
)
apply()
(in
CoupledMover
)
aa()
(in
AnnotatedSequence
)
algorithm()
(in
BuildSet
)
apply()
(in
CutChainMover
)
aa()
(in
GrowLeft
)
algorithm_inputs()
(in
MatchConstraintFileInfo
)
apply()
(in
CyclizationMover
)
aa()
(in
GrowRight
)
align
(in
rosetta.protocols.stepwise.modeler
)
apply()
(in
DME_FilterMover
)
aa()
(in
SegmentRebuild
)
align()
(in
Frame
)
apply()
(in
DeleteChainsMover
)
aa()
(in
VallResidue
)
align()
(in
JumpingFrame
)
apply()
(in
DesignRepackMover
)
aa()
(in
PNatRotOptEPositionData
)
align()
(in
NonContinuousFrame
)
apply()
(in
DisulfideInsertionMover
)
aa()
(in
MinimalRotamer
)
align()
(in
Aligner
)
apply()
(in
DumpPdb
)
aa1()
(in
ResPairMotif
)
align()
(in
MCAligner
)
apply()
(in
EnergyCutRotamerTrialsMinMover
)
aa2()
(in
ResPairMotif
)
align()
(in
NWAligner
)
apply()
(in
EnergyCutRotamerTrialsMover
)
aa2idx()
(in
rosetta.core.scoring.saxs._core_scoring_saxs_
)
align()
(in
SWAligner
)
apply()
(in
ExtendedPoseMover
)
aa_ala
(in
rosetta
)
align()
(in
xyzTransform_T_double_T
)
apply()
(in
FavorSequenceProfile
)
aa_ala
(in
AA
)
align()
(in
xyzTransform_T_float_T
)
apply()
(in
FavorSymmetricSequence
)
aa_ala
(in
rosetta.core.chemical._core_chemical_
)
align()
(in
SetupForFibrilMover
)
apply()
(in
FindConsensusSequence
)
aa_ala
(in
rosetta.core.chemical
)
align_and_output_to_silent_file()
(in
RNA_DeNovoProtocol
)
apply()
(in
ForceDisulfidesMover
)
aa_arg
(in
rosetta
)
align_angle()
(in
HelixPairing
)
apply()
(in
FragmentMover
)
aa_arg
(in
AA
)
align_by_domain()
(in
HybridizeProtocol
)
apply()
(in
GenericMonteCarloMover
)
aa_arg
(in
rosetta.core.chemical._core_chemical_
)
align_c()
(in
Rose
)
apply()
(in
GreenPacker
)
aa_arg
(in
rosetta.core.chemical
)
align_fast()
(in
xyzTransform_T_double_T
)
apply()
(in
LoadPDBMover
)
aa_asn
(in
rosetta
)
align_fast()
(in
xyzTransform_T_float_T
)
apply()
(in
LoadUnboundRotMover
)
aa_asn
(in
AA
)
align_mainchain_atoms()
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
apply()
(in
MSDMover
)
aa_asn
(in
rosetta.core.chemical._core_chemical_
)
align_mainchain_atoms_of_residue_range()
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
apply()
(in
MakePolyXMover
)
aa_asn
(in
rosetta.core.chemical
)
align_motif_pose()
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
apply()
(in
MembraneTopology
)
aa_asp
(in
rosetta
)
align_motif_pose_break()
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
apply()
(in
MinMover
)
aa_asp
(in
AA
)
align_motif_pose_by_one_frame()
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
apply()
(in
MinPackMover
)
aa_asp
(in
rosetta.core.chemical._core_chemical_
)
align_motif_pose_super()
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
apply()
(in
MissingDensityToJumpMover
)
aa_asp
(in
rosetta.core.chemical
)
align_n()
(in
Rose
)
apply()
(in
ModifyVariantTypeMover
)
aa_b3a
(in
rosetta
)
align_naive()
(in
rosetta.core.sequence._core_sequence_
)
apply()
(in
MonteCarloRecover
)
aa_b3a
(in
AA
)
align_pose()
(in
StepWiseProteinPoseSetup
)
apply()
(in
MonteCarloReset
)
aa_b3a
(in
rosetta.core.chemical._core_chemical_
)
align_pose_and_add_rmsd_constraints()
(in
rosetta.protocols.stepwise.modeler.align._protocols_stepwise_modeler_align_
)
apply()
(in
MonteCarloTest
)
aa_b3a
(in
rosetta.core.chemical
)
align_poses()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
apply()
(in
MutateResidue
)
aa_b3c
(in
rosetta
)
align_poses_naive()
(in
rosetta.core.sequence._core_sequence_
)
apply()
(in
O2M_MutateMover
)
aa_b3c
(in
AA
)
ALIGN_RMSD
(in
rosetta.protocols.stepwise.screener
)
apply()
(in
PDBReloadMover
)
aa_b3c
(in
rosetta.core.chemical._core_chemical_
)
ALIGN_RMSD
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
apply()
(in
PSSM2BfactorMover
)
aa_b3c
(in
rosetta.core.chemical
)
ALIGN_RMSD
(in
StepWiseScreenerType
)
apply()
(in
PackRotamersMover
)
aa_b3cisACHC
(in
rosetta
)
Align_RmsdEvaluator
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
apply()
(in
PackRotamersMoverLazy
)
aa_b3cisACHC
(in
AA
)
Align_RmsdEvaluatorAP
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
apply()
(in
PeptideStapleMover
)
aa_b3cisACHC
(in
rosetta.core.chemical._core_chemical_
)
Align_RmsdEvaluatorCAP
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
apply()
(in
PeriodicBoxMover
)
aa_b3cisACHC
(in
rosetta.core.chemical
)
Align_RotamerEvaluator
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
apply()
(in
ProlineFixMover
)
aa_b3cisACPC
(in
rosetta
)
Align_RotamerEvaluatorAP
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
apply()
(in
RandomOmegaFlipMover
)
aa_b3cisACPC
(in
AA
)
Align_RotamerEvaluatorCAP
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
apply()
(in
RandomTorsionMover
)
aa_b3cisACPC
(in
rosetta.core.chemical._core_chemical_
)
align_templates_by_domain()
(in
HybridizeProtocol
)
apply()
(in
RepackSidechainsMover
)
aa_b3cisACPC
(in
rosetta.core.chemical
)
align_to_native()
(in
rosetta.protocols.antibody._protocols_antibody_
)
apply()
(in
RepeatPropagationMover
)
aa_b3cisACPrC
(in
rosetta
)
align_to_native()
(in
Antibody
)
apply()
(in
ReportEffectivePKA
)
aa_b3cisACPrC
(in
AA
)
align_to_residue()
(in
UltraLightResidue
)
apply()
(in
RepulsiveOnlyMover
)
aa_b3cisACPrC
(in
rosetta.core.chemical._core_chemical_
)
align_virtual_atoms_in_carbohydrate_residue()
(in
rosetta.core.pose.carbohydrates._core_pose_carbohydrates_
)
apply()
(in
ResetBaselineMover
)
aa_b3cisACPrC
(in
rosetta.core.chemical
)
alignaxis()
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
apply()
(in
ResidueTypeConstraintMover
)
aa_b3d
(in
rosetta
)
alignaxis_xform()
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
apply()
(in
ReturnSidechainMover
)
aa_b3d
(in
AA
)
AlignChainMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
RingConformationMover
)
aa_b3d
(in
rosetta.core.chemical._core_chemical_
)
AlignChainMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
RotamerTrialsMinMover
)
aa_b3d
(in
rosetta.core.chemical
)
AlignChainMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
RotamerTrialsMover
)
aa_b3e
(in
rosetta
)
AlignChainMoverCreator
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
RotamerizeMover
)
aa_b3e
(in
AA
)
AlignChainMoverCreatorAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
SaneMinMover
)
aa_b3e
(in
rosetta.core.chemical._core_chemical_
)
AlignChainMoverCreatorCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
ScoreMover
)
aa_b3e
(in
rosetta.core.chemical
)
AlignedThreadOperation
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
apply()
(in
SequenceProfileMover
)
aa_b3f
(in
rosetta
)
AlignedThreadOperationAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
apply()
(in
SetReturningPackRotamersMover
)
aa_b3f
(in
AA
)
AlignedThreadOperationCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
apply()
(in
SetTorsion
)
aa_b3f
(in
rosetta.core.chemical._core_chemical_
)
AlignedThreadOperationCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
apply()
(in
ShakeStructureMover
)
aa_b3f
(in
rosetta.core.chemical
)
AlignedThreadOperationCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
apply()
(in
ShearMover
)
aa_b3g
(in
rosetta
)
AlignedThreadOperationCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
apply()
(in
ShortBackrubMover
)
aa_b3g
(in
AA
)
Aligner
(in
rosetta.core.sequence._core_sequence_
)
apply()
(in
SmallMover
)
aa_b3g
(in
rosetta.core.chemical._core_chemical_
)
AlignerAP
(in
rosetta.core.sequence._core_sequence_
)
apply()
(in
SuperimposeMover
)
aa_b3g
(in
rosetta.core.chemical
)
AlignerCAP
(in
rosetta.core.sequence._core_sequence_
)
apply()
(in
SwitchChainOrderMover
)
aa_b3h
(in
rosetta
)
AlignerFactory
(in
rosetta.core.sequence._core_sequence_
)
apply()
(in
SwitchResidueTypeSetMover
)
aa_b3h
(in
AA
)
AlignerFactoryAP
(in
rosetta.core.sequence._core_sequence_
)
apply()
(in
TailsScoreMover
)
aa_b3h
(in
rosetta.core.chemical._core_chemical_
)
AlignerFactoryCAP
(in
rosetta.core.sequence._core_sequence_
)
apply()
(in
TaskAwareMinMover
)
aa_b3h
(in
rosetta.core.chemical
)
AlignEvaluator
(in
rosetta.protocols.evaluation._protocols_evaluation_
)
apply()
(in
TorsionDOFMover
)
aa_b3i
(in
rosetta
)
AlignEvaluatorAP
(in
rosetta.protocols.evaluation._protocols_evaluation_
)
apply()
(in
TorsionSetMover
)
aa_b3i
(in
AA
)
AlignEvaluatorCAP
(in
rosetta.protocols.evaluation._protocols_evaluation_
)
apply()
(in
Tumble
)
aa_b3i
(in
rosetta.core.chemical._core_chemical_
)
alignment
(in
rosetta.numeric
)
apply()
(in
UniformRotationMover
)
aa_b3i
(in
rosetta.core.chemical
)
alignment()
(in
ExtraThreadingMover
)
apply()
(in
UniformTranslationMover
)
aa_b3k
(in
rosetta
)
alignment()
(in
ThreadingJob
)
apply()
(in
VirtualRootMover
)
aa_b3k
(in
AA
)
alignment()
(in
ThreadingMover
)
apply()
(in
ddG
)
aa_b3k
(in
rosetta.core.chemical._core_chemical_
)
alignment2AtomMap()
(in
TMalign
)
apply()
(in
AsymFoldandDockMoveRbJumpMover
)
aa_b3k
(in
rosetta.core.chemical
)
alignment2strings()
(in
TMalign
)
apply()
(in
AsymFoldandDockRbTrialMover
)
aa_b3l
(in
rosetta
)
alignment_file()
(in
AlignedThreadOperation
)
apply()
(in
InitializeByBins
)
aa_b3l
(in
AA
)
alignment_from_pose()
(in
rosetta.core.sequence._core_sequence_
)
apply()
(in
PerturbByBins
)
aa_b3l
(in
rosetta.core.chemical._core_chemical_
)
alignment_id()
(in
SequenceAlignment
)
apply()
(in
ChiralMover
)
aa_b3l
(in
rosetta.core.chemical
)
alignment_id()
(in
ThreadingJob
)
apply()
(in
HbsPatcher
)
aa_b3m
(in
rosetta
)
alignment_into_pose()
(in
rosetta.core.sequence._core_sequence_
)
apply()
(in
OopDPuckMinusMover
)
aa_b3m
(in
AA
)
alignment_probabilities()
(in
rosetta.protocols.medal._protocols_medal_
)
apply()
(in
OopDPuckPlusMover
)
aa_b3m
(in
rosetta.core.chemical._core_chemical_
)
AlignmentCluster
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
apply()
(in
OopMover
)
aa_b3m
(in
rosetta.core.chemical
)
AlignmentClusterAP
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
apply()
(in
OopPatcher
)
aa_b3n
(in
rosetta
)
AlignmentClusterCAP
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
apply()
(in
OopPuckMinusMover
)
aa_b3n
(in
AA
)
AlignmentClustering
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
apply()
(in
OopPuckPlusMover
)
aa_b3n
(in
rosetta.core.chemical._core_chemical_
)
AlignmentClusteringAP
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
apply()
(in
OopRandomPuckMover
)
aa_b3n
(in
rosetta.core.chemical
)
AlignmentClusteringCAP
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
apply()
(in
OopRandomSmallMover
)
aa_b3p
(in
rosetta
)
alignments()
(in
AlignmentSet
)
apply()
(in
RationalMonteCarlo
)
aa_b3p
(in
AA
)
alignments()
(in
InnerMultiThreadingJob
)
apply()
(in
JumpRotamerSidechainMover
)
aa_b3p
(in
rosetta.core.chemical._core_chemical_
)
alignments_from_cmd_line()
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
apply()
(in
PerturbChiSidechainMover
)
aa_b3p
(in
rosetta.core.chemical
)
AlignmentSet
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
apply()
(in
PerturbRotamerSidechainMover
)
aa_b3q
(in
rosetta
)
AlignmentSetAP
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
apply()
(in
SetChiMover
)
aa_b3q
(in
AA
)
AlignmentSetCAP
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
apply()
(in
SidechainMCMover
)
aa_b3q
(in
rosetta.core.chemical._core_chemical_
)
AlignMove
(in
rosetta.core.sequence._core_sequence_
)
apply()
(in
SidechainMover
)
aa_b3q
(in
rosetta.core.chemical
)
AlignOption
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
apply()
(in
SidechainMoverBase
)
aa_b3r
(in
rosetta
)
AlignPoseToInvrotTreeMover
(in
rosetta.protocols.toolbox.match_enzdes_util._protocols_toolbox_match_enzdes_util_
)
apply()
(in
DetectSymmetry
)
aa_b3r
(in
AA
)
AlignPoseToInvrotTreeMoverAP
(in
rosetta.protocols.toolbox.match_enzdes_util._protocols_toolbox_match_enzdes_util_
)
apply()
(in
ExtractAsymmetricPoseMover
)
aa_b3r
(in
rosetta.core.chemical._core_chemical_
)
AlignPoseToInvrotTreeMoverCAP
(in
rosetta.protocols.toolbox.match_enzdes_util._protocols_toolbox_match_enzdes_util_
)
apply()
(in
ExtractAsymmetricUnitMover
)
aa_b3r
(in
rosetta.core.chemical
)
AlignRMSD_Screener
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
apply()
(in
FaSymDockingSlideTogether
)
aa_b3s
(in
rosetta
)
AlignRMSD_ScreenerAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
apply()
(in
SetupForSymmetryMover
)
aa_b3s
(in
AA
)
AlignRMSD_ScreenerCAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
apply()
(in
SetupNCSMover
)
aa_b3s
(in
rosetta.core.chemical._core_chemical_
)
AlignRmsdTargetEvaluatorCreator
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
apply()
(in
SymDockingInitialPerturbation
)
aa_b3s
(in
rosetta.core.chemical
)
AlignRmsdTargetEvaluatorCreatorAP
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
apply()
(in
SymDockingSlideIntoContact
)
aa_b3t
(in
rosetta
)
AlignRmsdTargetEvaluatorCreatorCAP
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
apply()
(in
SymEnergyCutRotamerTrialsMover
)
aa_b3t
(in
AA
)
all_add_energy()
(in
SilentStructStore
)
apply()
(in
SymMinMover
)
aa_b3t
(in
rosetta.core.chemical._core_chemical_
)
all_aligned()
(in
SequenceMapping
)
apply()
(in
SymPackRotamersMover
)
aa_b3t
(in
rosetta.core.chemical
)
all_atom_rmsd()
(in
rosetta.core.scoring._core_scoring_
)
apply()
(in
SymRotamerTrialsMover
)
aa_b3v
(in
rosetta
)
all_atom_rmsd_nosuper()
(in
rosetta.core.scoring._core_scoring_
)
apply()
(in
SymShakeStructureMover
)
aa_b3v
(in
AA
)
all_bb_atoms()
(in
ResidueType
)
apply()
(in
SymmetricRMSMover
)
aa_b3v
(in
rosetta.core.chemical._core_chemical_
)
all_bb_atoms()
(in
Residue
)
apply()
(in
SymmetrySlider
)
aa_b3v
(in
rosetta.core.chemical
)
all_broker_files()
(in
Batch
)
apply()
(in
TaskAwareSymMinMover
)
aa_b3w
(in
rosetta
)
all_cdr_fold_tree()
(in
Antibody
)
apply()
(in
ChemicalShiftEvaluator
)
aa_b3w
(in
AA
)
all_cdr_VL_VH_fold_tree()
(in
AntibodyModeler
)
apply()
(in
StepWiseProteinMinimizer
)
aa_b3w
(in
rosetta.core.chemical._core_chemical_
)
all_chunks
(in
AlignOption
)
apply()
(in
StepWiseProteinPoseSetup
)
aa_b3w
(in
rosetta.core.chemical
)
all_chunks
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
apply()
(in
StepWiseRNA_PoseSetup
)
aa_b3y
(in
rosetta
)
all_chunks
(in
rosetta.protocols.hybridization
)
apply()
(in
StepWiseWorkingParametersSetup
)
aa_b3y
(in
AA
)
all_energies()
(in
DecoySetEvaluation
)
apply()
(in
StepWiseConnectionSampler
)
aa_b3y
(in
rosetta.core.chemical._core_chemical_
)
all_energies_begin()
(in
ScoreFunction
)
apply()
(in
StepWiseMinimizer
)
aa_b3y
(in
rosetta.core.chemical
)
all_energies_end()
(in
ScoreFunction
)
apply()
(in
StepWiseModeler
)
aa_cmp
(in
rosetta
)
all_methods()
(in
ScoreFunction
)
apply()
(in
StepWiseClusterer
)
aa_cmp
(in
ScoreType
)
all_pairs_shortest_paths()
(in
Graph
)
apply()
(in
StepWisePoseAligner
)
aa_cmp
(in
rosetta.core.scoring._core_scoring_
)
all_ref_poses()
(in
AtomTreeDiff
)
apply()
(in
SideChainCopier
)
aa_cmp
(in
rosetta.core.scoring
)
all_ref_poses()
(in
AtomTreeDiffJobInputter
)
apply()
(in
StepWisePacker
)
aa_cys
(in
rosetta
)
all_residues_begin()
(in
ResidueTypeSet
)
apply()
(in
PolarHydrogenPacker
)
aa_cys
(in
AA
)
all_residues_end()
(in
ResidueTypeSet
)
apply()
(in
PrecomputedLibraryMover
)
aa_cys
(in
rosetta.core.chemical._core_chemical_
)
all_sc_atoms()
(in
ResidueType
)
apply()
(in
StepWiseProteinBackboneSampler
)
aa_cys
(in
rosetta.core.chemical
)
all_scatom_rmsd_nosuper()
(in
rosetta.core.scoring._core_scoring_
)
apply()
(in
StepWiseProteinCCD_Closer
)
aa_dal
(in
rosetta
)
all_sort_silent_scores()
(in
SilentStructStore
)
apply()
(in
StepWiseProteinCCD_MultiPoseCloser
)
aa_dal
(in
AA
)
ALL_STAGES
(in
rosetta
)
apply()
(in
StepWiseProteinKIC_LoopBridger
)
aa_dal
(in
rosetta.core.chemical._core_chemical_
)
ALL_STAGES
(in
rosetta.protocols.abinitio
)
apply()
(in
BulgeApplyMover
)
aa_dal
(in
rosetta.core.chemical
)
ALL_STAGES
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
apply()
(in
BulgeUnApplyMover
)
aa_dan
(in
rosetta
)
ALL_STAGES
(in
ClassicAbinitio
)
apply()
(in
RNA_ChainClosureChecker
)
aa_dan
(in
AA
)
ALL_STAGES
(in
StageID
)
apply()
(in
RNA_HelixAssembler
)
aa_dan
(in
rosetta.core.chemical._core_chemical_
)
ALL_STAGES
(in
MembraneAbinitio
)
apply()
(in
O2PrimePacker
)
aa_dan
(in
rosetta.core.chemical
)
ALL_STAGES
(in
StageID
)
apply()
(in
MultiPhosphateSampler
)
aa_dar
(in
rosetta
)
ALL_STAGES
(in
StageID
)
apply()
(in
PhosphateMover
)
aa_dar
(in
AA
)
all_stats
(in
rosetta
)
apply()
(in
SugarInstantiateMover
)
aa_dar
(in
rosetta.core.chemical._core_chemical_
)
all_stats
(in
StatsType
)
apply()
(in
SugarVirtualizeMover
)
aa_dar
(in
rosetta.core.chemical
)
all_stats
(in
rosetta.protocols.moves._protocols_moves_
)
apply()
(in
VirtualSugarJustInTimeInstantiator
)
aa_das
(in
rosetta
)
all_stats
(in
rosetta.protocols.moves
)
apply()
(in
VirtualSugarSampler
)
aa_das
(in
AA
)
all_target_res()
(in
InvrotTarget
)
apply()
(in
VirtualSugarSamplerFromStringList
)
aa_das
(in
rosetta.core.chemical._core_chemical_
)
all_target_residues()
(in
InvrotTarget
)
apply()
(in
StepWiseMonteCarlo
)
aa_das
(in
rosetta.core.chemical
)
all_target_residues()
(in
InvrotTreeNode
)
apply()
(in
AddMover
)
aa_dcs
(in
rosetta
)
all_target_residues()
(in
InvrotTreeNodeBase
)
apply()
(in
AddOrDeleteMover
)
aa_dcs
(in
AA
)
all_tracers()
(in
TracerManager
)
apply()
(in
DeleteMover
)
aa_dcs
(in
rosetta.core.chemical._core_chemical_
)
all_turn_residues_are_on_the_same_chain()
(in
BetaTurnDetection
)
apply()
(in
FromScratchMover
)
aa_dcs
(in
rosetta.core.chemical
)
ALLAA
(in
rosetta.core.pack.task._core_pack_task_
)
apply()
(in
ResampleMover
)
aa_dgn
(in
rosetta
)
ALLAAAP
(in
rosetta.core.pack.task._core_pack_task_
)
apply()
(in
StepWiseMasterMover
)
aa_dgn
(in
AA
)
ALLAACAP
(in
rosetta.core.pack.task._core_pack_task_
)
apply()
(in
RNA_AddDeleteMonteCarlo
)
aa_dgn
(in
rosetta.core.chemical._core_chemical_
)
ALLAAwc
(in
rosetta.core.pack.task._core_pack_task_
)
apply()
(in
RNA_O2PrimeMover
)
aa_dgn
(in
rosetta.core.chemical
)
ALLAAwcAP
(in
rosetta.core.pack.task._core_pack_task_
)
apply()
(in
RNA_TorsionMover
)
aa_dgu
(in
rosetta
)
ALLAAwcCAP
(in
rosetta.core.pack.task._core_pack_task_
)
apply()
(in
JumpStepWiseSampler
)
aa_dgu
(in
AA
)
ALLAAxc
(in
rosetta.core.pack.task._core_pack_task_
)
apply()
(in
MC_Comb
)
aa_dgu
(in
rosetta.core.chemical._core_chemical_
)
ALLAAxcAP
(in
rosetta.core.pack.task._core_pack_task_
)
apply()
(in
MC_OneTorsion
)
aa_dgu
(in
rosetta.core.chemical
)
ALLAAxcCAP
(in
rosetta.core.pack.task._core_pack_task_
)
apply()
(in
NoOpStepWiseSampler
)
aa_dhi
(in
rosetta
)
alllevel()
(in
ABEGOManager
)
apply()
(in
StepWiseSamplerAny
)
aa_dhi
(in
AA
)
allocate_matrix()
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
apply()
(in
StepWiseSamplerBase
)
aa_dhi
(in
rosetta.core.chemical._core_chemical_
)
allow_aa()
(in
ResidueLevelTask
)
apply()
(in
StepWiseSamplerComb
)
aa_dhi
(in
rosetta.core.chemical
)
allow_aa()
(in
ResidueLevelTask_
)
apply()
(in
StepWiseSamplerOneTorsion
)
aa_dil
(in
rosetta
)
allow_all_aas()
(in
ProteinInterfaceDesignOperation
)
apply()
(in
StepWiseSamplerOneValue
)
aa_dil
(in
AA
)
allow_base_pair_only_centroid_screen()
(in
StepWiseRNA_ModelerOptions
)
apply()
(in
StepWiseSamplerOneValueComb
)
aa_dil
(in
rosetta.core.chemical._core_chemical_
)
allow_base_pair_only_screen()
(in
RNA_BaseCentroidChecker
)
apply()
(in
StepWiseSamplerSized
)
aa_dil
(in
rosetta.core.chemical
)
allow_bondangles()
(in
MakeBundleHelix
)
apply()
(in
StepWiseSamplerSizedAny
)
aa_dle
(in
rosetta
)
allow_bondangles()
(in
BundleParameters
)
apply()
(in
StepWiseSamplerSizedComb
)
aa_dle
(in
AA
)
allow_bondlengths()
(in
MakeBundleHelix
)
apply()
(in
CopyDofStepWiseSampler
)
aa_dle
(in
rosetta.core.chemical._core_chemical_
)
allow_bondlengths()
(in
BundleParameters
)
apply()
(in
ResidueAlternativeStepWiseSampler
)
aa_dle
(in
rosetta.core.chemical
)
allow_bulge_at_chainbreak()
(in
StepWiseRNA_ModelerOptions
)
apply()
(in
ResidueAlternativeStepWiseSamplerComb
)
aa_dly
(in
rosetta
)
allow_claim()
(in
FoldandDockClaimer
)
apply()
(in
ResidueListStepWiseSampler
)
aa_dly
(in
AA
)
allow_claim()
(in
MembraneTopologyClaimer
)
apply()
(in
InputStreamStepWiseSampler
)
aa_dly
(in
rosetta.core.chemical._core_chemical_
)
allow_claim()
(in
TopologyClaimer
)
apply()
(in
ProteinBetaAntiParallelStepWiseSampler
)
aa_dly
(in
rosetta.core.chemical
)
allow_delete()
(in
StepWiseMoveSelector
)
apply()
(in
ProteinFragmentStepWiseSampler
)
aa_dme
(in
rosetta
)
allow_design()
(in
DesignAroundOperation
)
apply()
(in
ProteinMainChainStepWiseSampler
)
aa_dme
(in
AA
)
allow_design()
(in
SelectResiduesWithinChainOperation
)
apply()
(in
RigidBodyStepWiseSampler
)
aa_dme
(in
rosetta.core.chemical._core_chemical_
)
allow_design_around()
(in
DatabaseThread
)
apply()
(in
RigidBodyStepWiseSamplerWithResidueAlternatives
)
aa_dme
(in
rosetta.core.chemical
)
allow_design_around()
(in
ThreadSequenceOperation
)
apply()
(in
RigidBodyStepWiseSamplerWithResidueList
)
aa_dph
(in
rosetta
)
allow_dihedrals()
(in
MakeBundleHelix
)
apply()
(in
RNA_ChiStepWiseSampler
)
aa_dph
(in
AA
)
allow_dihedrals()
(in
BundleParameters
)
apply()
(in
RNA_KIC_Sampler
)
aa_dph
(in
rosetta.core.chemical._core_chemical_
)
allow_dof()
(in
SymDof
)
apply()
(in
RNA_KinematicCloser
)
aa_dph
(in
rosetta.core.chemical
)
allow_hbond()
(in
HBondSet
)
apply()
(in
RNA_MC_MultiSuite
)
aa_dpr
(in
rosetta
)
allow_insert()
(in
CoarseRNA_LoopCloser
)
apply()
(in
RNA_MC_Sugar
)
aa_dpr
(in
AA
)
allow_insert()
(in
RNA_ChunkLibrary
)
apply()
(in
RNA_MC_Suite
)
aa_dpr
(in
rosetta.core.chemical._core_chemical_
)
allow_insert()
(in
RNA_StructureParameters
)
apply()
(in
RNA_NucleosideStepWiseSampler
)
aa_dpr
(in
rosetta.core.chemical
)
allow_internal_hinge()
(in
StepWiseMoveSelector
)
apply()
(in
RNA_SugarStepWiseSampler
)
aa_dse
(in
rosetta
)
allow_internal_hinge_moves()
(in
StepWiseMonteCarloOptions
)
apply()
(in
RNA_SuiteStepWiseSampler
)
aa_dse
(in
AA
)
allow_internal_local()
(in
StepWiseMoveSelector
)
apply()
(in
StepWiseCSA_JobDistributor
)
aa_dse
(in
rosetta.core.chemical._core_chemical_
)
allow_internal_local_moves()
(in
StepWiseMonteCarloOptions
)
apply()
(in
StepWiseJobDistributor
)
aa_dse
(in
rosetta.core.chemical
)
allow_noncanonical_aa()
(in
ResidueLevelTask
)
apply()
(in
StepWiseMonteCarloJobDistributor
)
aa_dth
(in
rosetta
)
allow_noncanonical_aa()
(in
ResidueLevelTask_
)
apply()
(in
CentroidRelaxMover
)
aa_dth
(in
AA
)
allow_phosphate_virtualization()
(in
RNA_ResidueLevelTask
)
apply()
(in
FullatomRelaxMover
)
aa_dth
(in
rosetta.core.chemical._core_chemical_
)
allow_pure_movers()
(in
Environment
)
apply()
(in
SurfaceDockingProtocol
)
aa_dth
(in
rosetta.core.chemical
)
allow_reading_cancelled_decoys()
(in
Batch
)
apply()
(in
SurfaceOrientMover
)
aa_dtr
(in
rosetta
)
allow_rebuild_bulge_mode()
(in
StepWiseRNA_ModelerOptions
)
apply()
(in
SymDockBaseProtocol
)
aa_dtr
(in
AA
)
allow_repacking()
(in
SelectResiduesWithinChainOperation
)
apply()
(in
SymDockProtocol
)
aa_dtr
(in
rosetta.core.chemical._core_chemical_
)
allow_scoring()
(in
MembraneTopology
)
apply()
(in
SymDockingHiRes
)
aa_dtr
(in
rosetta.core.chemical
)
allow_split_off()
(in
StepWiseMonteCarloOptions
)
apply()
(in
SymDockingLowRes
)
aa_dty
(in
rosetta
)
allow_syn_pyrimidine()
(in
StepWiseRNA_ModelerOptions
)
apply()
(in
SymFoldandDockMoveRbJumpMover
)
aa_dty
(in
AA
)
allow_tmh_scoring()
(in
MembraneTopology
)
apply()
(in
SymFoldandDockRbTrialMover
)
aa_dty
(in
rosetta.core.chemical._core_chemical_
)
allow_virtual_o2prime_hydrogens()
(in
StepWiseRNA_ModelerOptions
)
apply()
(in
SymFoldandDockSlideTrialMover
)
aa_dty
(in
rosetta.core.chemical
)
allow_virtual_o2prime_hydrogens()
(in
StepWisePacker
)
apply()
(in
SymInterfaceSidechainMinMover
)
aa_dva
(in
rosetta
)
allow_virtual_o2prime_hydrogens()
(in
StepWiseMonteCarloOptions
)
apply()
(in
SymRestrictTaskForDocking
)
aa_dva
(in
AA
)
allow_virtual_side_chains()
(in
StepWiseProteinModelerOptions
)
apply()
(in
SymSidechainMinMover
)
aa_dva
(in
rosetta.core.chemical._core_chemical_
)
allow_virtual_side_chains()
(in
StepWisePacker
)
apply()
(in
MPSymDockMover
)
aa_dva
(in
rosetta.core.chemical
)
allow_virtual_side_chains()
(in
StepWiseMonteCarloOptions
)
apply()
(in
AlignPoseToInvrotTreeMover
)
aa_from_name()
(in
rosetta.core.chemical._core_chemical_
)
allowed_current_slide()
(in
SymmetrySlider
)
apply()
(in
AlignedThreadOperation
)
aa_from_oneletter_code()
(in
rosetta.core.chemical._core_chemical_
)
allowed_res_name3_at_position()
(in
EnzConstraintIO
)
apply()
(in
ConservativeDesignOperation
)
aa_gln
(in
rosetta
)
allowed_res_name3_at_position()
(in
EnzConstraintParameters
)
apply()
(in
CrystalContactsOperation
)
aa_gln
(in
AA
)
allowed_res_name3s()
(in
MatchConstraintFileInfo
)
apply()
(in
DatabaseThread
)
aa_gln
(in
rosetta.core.chemical._core_chemical_
)
allowed_res_types()
(in
EnzCstTemplateRes
)
apply()
(in
DesignAroundOperation
)
aa_gln
(in
rosetta.core.chemical
)
allowed_res_types_pointers()
(in
EnzCstTemplateRes
)
apply()
(in
DockingNoRepack1
)
aa_glu
(in
rosetta
)
allowed_residue_types()
(in
ResidueLevelTask
)
apply()
(in
DockingNoRepack2
)
aa_glu
(in
AA
)
allowed_residue_types()
(in
ResidueLevelTask_
)
apply()
(in
DsspDesignOperation
)
aa_glu
(in
rosetta.core.chemical._core_chemical_
)
allowed_residue_types_begin()
(in
ResidueLevelTask
)
apply()
(in
ImportUnboundRotamersOperation
)
aa_glu
(in
rosetta.core.chemical
)
allowed_residue_types_begin()
(in
ResidueLevelTask_
)
apply()
(in
InteractingRotamerExplosion
)
aa_gly
(in
rosetta
)
allowed_residue_types_end()
(in
ResidueLevelTask
)
apply()
(in
JointSequenceOperation
)
aa_gly
(in
AA
)
allowed_residue_types_end()
(in
ResidueLevelTask_
)
apply()
(in
LimitAromaChi2Operation
)
aa_gly
(in
rosetta.core.chemical._core_chemical_
)
allowed_restypes()
(in
MatchConstraintFileInfo
)
apply()
(in
LinkResidues
)
aa_gly
(in
rosetta.core.chemical
)
allowed_seqpos()
(in
MatchConstraintFileInfo
)
apply()
(in
ModifyAnnealer
)
aa_h2o
(in
rosetta
)
allowed_types()
(in
DnaInterfacePacker
)
apply()
(in
MutationSetDesignOperation
)
aa_h2o
(in
AA
)
allowed_types()
(in
BuildPosition
)
apply()
(in
PreventChainFromRepackingOperation
)
aa_h2o
(in
rosetta.core.chemical._core_chemical_
)
AllowedSeqposForGeomCst
(in
rosetta.protocols.toolbox.match_enzdes_util._protocols_toolbox_match_enzdes_util_
)
apply()
(in
PreventResiduesFromRepackingOperation
)
aa_h2o
(in
rosetta.core.chemical
)
AllowedSeqposForGeomCstAP
(in
rosetta.protocols.toolbox.match_enzdes_util._protocols_toolbox_match_enzdes_util_
)
apply()
(in
ProteinInterfaceDesignOperation
)
aa_his
(in
rosetta
)
AllowedSeqposForGeomCstCAP
(in
rosetta.protocols.toolbox.match_enzdes_util._protocols_toolbox_match_enzdes_util_
)
apply()
(in
ReadResfileFromDB
)
aa_his
(in
AA
)
AllowInsert
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
apply()
(in
ResidueProbDesignOperation
)
aa_his
(in
rosetta.core.chemical._core_chemical_
)
AllowInsertAP
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
apply()
(in
RestrictByCalculatorsOperation
)
aa_his
(in
rosetta.core.chemical
)
AllowInsertCAP
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
apply()
(in
RestrictChainToRepackingOperation
)
aa_ile
(in
rosetta
)
AllowPdbIdFilter
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
apply()
(in
RestrictConservedLowDdgOperation
)
aa_ile
(in
AA
)
AllowPdbIdFilterAP
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
apply()
(in
RestrictIdentitiesAtAlignedPositionsOperation
)
aa_ile
(in
rosetta.core.chemical._core_chemical_
)
AllowPdbIdFilterCAP
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
apply()
(in
RestrictIdentitiesOperation
)
aa_ile
(in
rosetta.core.chemical
)
AllResFilter
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
apply()
(in
RestrictInterGroupVectorOperation
)
aa_leu
(in
rosetta
)
AllResFilterAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
apply()
(in
RestrictNativeResiduesOperation
)
aa_leu
(in
AA
)
AllResFilterCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
apply()
(in
RestrictNonSurfaceToRepackingOperation
)
aa_leu
(in
rosetta.core.chemical._core_chemical_
)
AllResFilterCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
apply()
(in
RestrictOperationsBase
)
aa_leu
(in
rosetta.core.chemical
)
AllResFilterCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
apply()
(in
RestrictResiduesToRepackingOperation
)
aa_lys
(in
rosetta
)
AllResFilterCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
apply()
(in
RestrictToAlignedSegmentsOperation
)
aa_lys
(in
AA
)
AllResiduesChanged
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
apply()
(in
RestrictToCDRH3Loop
)
aa_lys
(in
rosetta.core.chemical._core_chemical_
)
AllResiduesChanged
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
apply()
(in
RestrictToInterface
)
aa_lys
(in
rosetta.core.chemical
)
AllResiduesChangedAP
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
apply()
(in
RestrictToInterfaceOperation
)
aa_map()
(in
ResidueTypeSet
)
AllResiduesChangedAP
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
apply()
(in
RestrictToInterfaceVectorOperation
)
aa_met
(in
rosetta
)
AllResiduesChangedCAP
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
apply()
(in
RestrictToLoops
)
aa_met
(in
AA
)
AllResiduesChangedCAP
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
apply()
(in
RestrictToLoopsAndNeighbors
)
aa_met
(in
rosetta.core.chemical._core_chemical_
)
allsc()
(in
SaveAndRetrieveSidechains
)
apply()
(in
RestrictToMoveMapChiOperation
)
aa_met
(in
rosetta.core.chemical
)
ALPHA
(in
rosetta.core.chemical.rna
)
apply()
(in
RestrictToNeighborhoodOperation
)
aa_penalty()
(in
IdentityEval
)
ALPHA
(in
rosetta.core.chemical.rna._core_chemical_rna_
)
apply()
(in
RestrictToTerminiOperation
)
aa_phe
(in
rosetta
)
ALPHA
(in
RNA_Torsion
)
apply()
(in
RetrieveStoredTaskOperation
)
aa_phe
(in
AA
)
alpha()
(in
CrystInfo
)
apply()
(in
SelectByDeltaScoreOperation
)
aa_phe
(in
rosetta.core.chemical._core_chemical_
)
alpha()
(in
Pose
)
apply()
(in
SelectByDensityFitOperation
)
aa_phe
(in
rosetta.core.chemical
)
alpha()
(in
CSA
)
apply()
(in
SelectBySASAOperation
)
aa_pro
(in
rosetta
)
ALPHA()
(in
rosetta.numeric.crick_equations._numeric_crick_equations_
)
apply()
(in
SelectResiduesWithinChainOperation
)
aa_pro
(in
AA
)
alpha()
(in
DNABase
)
apply()
(in
SeqprofConsensusOperation
)
aa_pro
(in
rosetta.core.chemical._core_chemical_
)
alpha()
(in
EulerAngles
)
apply()
(in
SetIGTypeOperation
)
aa_pro
(in
rosetta.core.chemical
)
ALPHA_AA
(in
rosetta
)
apply()
(in
StoreCombinedStoredTasksMover
)
aa_ser
(in
rosetta
)
ALPHA_AA
(in
rosetta.core.chemical
)
apply()
(in
StoreCompoundTaskMover
)
aa_ser
(in
AA
)
ALPHA_AA
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
StoreTaskMover
)
aa_ser
(in
rosetta.core.chemical._core_chemical_
)
ALPHA_AA
(in
ResidueProperty
)
apply()
(in
ThreadSequenceOperation
)
aa_ser
(in
rosetta.core.chemical
)
alpha_aform()
(in
RNA_FittedTorsionInfo
)
apply()
(in
UnfoldedStateEnergyCalculatorMover
)
aa_str()
(in
IdentityEval
)
alpha_components()
(in
DNATorsionPotential
)
apply()
(in
VIP_Mover
)
aa_submatrix_energies_retrievable()
(in
DensePDInteractionGraph
)
alpha_deriv_func()
(in
rosetta.core.scoring.fiber_diffraction._core_scoring_fiber_diffraction_
)
apply_adducts_to_residue()
(in
rosetta.core.chemical._core_chemical_
)
aa_submatrix_energies_retrievable()
(in
DoubleLazyInteractionGraph
)
alpha_func()
(in
rosetta.core.scoring.fiber_diffraction._core_scoring_fiber_diffraction_
)
apply_Aform_torsions()
(in
rosetta.core.pose.rna._core_pose_rna_
)
aa_submatrix_energies_retrievable()
(in
FixedBBInteractionGraph
)
ALPHA_LINKS
(in
rosetta.core.scoring.carbohydrates
)
apply_after_jump_change()
(in
CoarseRNA_LoopCloser
)
aa_submatrix_energies_retrievable()
(in
LazyInteractionGraph
)
ALPHA_LINKS
(in
rosetta.core.scoring.carbohydrates._core_scoring_carbohydrates_
)
apply_and_return_jump()
(in
MultipleDomainMover
)
aa_submatrix_energies_retrievable()
(in
PDInteractionGraph
)
ALPHA_LINKS
(in
LinkageType
)
apply_and_to_subset()
(in
AndResidueSelector
)
aa_thr
(in
rosetta
)
ALPHA_SUGAR
(in
rosetta
)
apply_at_all_positions()
(in
FragmentMover
)
aa_thr
(in
AA
)
ALPHA_SUGAR
(in
rosetta.core.chemical
)
apply_at_domain()
(in
MultipleDomainMover
)
aa_thr
(in
rosetta.core.chemical._core_chemical_
)
ALPHA_SUGAR
(in
rosetta.core.chemical._core_chemical_
)
APPLY_BB_MOVE
(in
rosetta.basic
)
aa_thr
(in
rosetta.core.chemical
)
ALPHA_SUGAR
(in
ResidueProperty
)
APPLY_BB_MOVE
(in
rosetta.basic._basic_
)
aa_trp
(in
rosetta
)
alphabet()
(in
ChemicalShiftSequence
)
APPLY_BB_MOVE
(in
ProfTag
)
aa_trp
(in
AA
)
alphabet()
(in
SequenceProfile
)
apply_best_scoring_fragdata()
(in
rosetta.core.fragment._core_fragment_
)
aa_trp
(in
rosetta.core.chemical._core_chemical_
)
ALREADY_SYMMETRIZED
(in
rosetta
)
apply_body()
(in
DockingInitialPerturbation
)
aa_trp
(in
rosetta.core.chemical
)
ALREADY_SYMMETRIZED
(in
rosetta.core.pack.task
)
apply_check()
(in
Motif
)
aa_trustworthiness()
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
ALREADY_SYMMETRIZED
(in
rosetta.core.pack.task._core_pack_task_
)
apply_const()
(in
InterfaceAnalyzerMover
)
aa_tyr
(in
rosetta
)
ALREADY_SYMMETRIZED
(in
PackerTaskSymmetryStatus
)
apply_current_pose_segment()
(in
InputStreamWithResidueInfo
)
aa_tyr
(in
AA
)
alt_bb()
(in
FlexbbNode
)
apply_disulfides()
(in
RelaxProtocolBase
)
aa_tyr
(in
rosetta.core.chemical._core_chemical_
)
alt_energy()
(in
FlexbbEdge
)
apply_dof_conformer()
(in
ResiduePairJump
)
aa_tyr
(in
rosetta.core.chemical
)
alt_loc()
(in
PDBInfo
)
apply_dofs()
(in
rosetta.core.pose.copydofs._core_pose_copydofs_
)
aa_unk
(in
rosetta
)
alt_sc_centroid()
(in
SimpleNode
)
apply_fragment()
(in
ClassicFragmentMover
)
aa_unk
(in
AA
)
alt_sc_radius()
(in
SimpleNode
)
apply_fragment()
(in
LoggedFragmentMover
)
aa_unk
(in
rosetta.core.chemical._core_chemical_
)
alt_state_energy()
(in
SymmMinimalistEdge
)
apply_frame()
(in
SegmentHybridizer
)
aa_unk
(in
rosetta.core.chemical
)
alter_espGrid()
(in
PocketGrid
)
apply_frames()
(in
VallLookbackFragMover
)
aa_unp
(in
rosetta
)
alter_espGrid_with_bound_ligand()
(in
PocketGrid
)
apply_full_to_sub_mapping()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
aa_unp
(in
AA
)
alter_rotamer_set()
(in
AddResiduesRotamerSetOperation
)
apply_full_to_sub_mapping()
(in
StepWiseBasicWorkingParameters
)
aa_unp
(in
rosetta.core.chemical._core_chemical_
)
alter_rotamer_set()
(in
RotamerSetOperation
)
apply_holes()
(in
VIP_Mover
)
aa_unp
(in
rosetta.core.chemical
)
alter_rotamer_set()
(in
UnboundRotamersOperation
)
apply_ideal_c2endo_sugar_coords()
(in
rosetta.core.pose.rna._core_pose_rna_
)
aa_val
(in
rosetta
)
alter_rotamer_set()
(in
SearchPatternRotSetOp
)
apply_if_reasonable()
(in
ClosureSolution
)
aa_val
(in
AA
)
alter_rotamer_set()
(in
AddGood2BPairEnergyRotamers
)
apply_legacy()
(in
StepWiseMasterMover
)
aa_val
(in
rosetta.core.chemical._core_chemical_
)
alter_rotamer_set()
(in
RigidBodyMoveBaseRSO
)
apply_LH_A_foldtree()
(in
AntibodyDesignModeler
)
aa_val
(in
rosetta.core.chemical
)
alter_rotamer_set()
(in
RigidBodyMoveRSO
)
apply_linked_constraints()
(in
MSDMover
)
aa_vrt
(in
rosetta
)
alter_rotamer_set()
(in
SpecialRotamerRSO
)
APPLY_MOVE
(in
rosetta.basic
)
aa_vrt
(in
AA
)
alter_rotamer_set()
(in
LimitAromaChi2_RotamerSetOperation
)
APPLY_MOVE
(in
rosetta.basic._basic_
)
aa_vrt
(in
rosetta.core.chemical._core_chemical_
)
alternate_state()
(in
FlexbbNode
)
APPLY_MOVE
(in
ProfTag
)
aa_vrt
(in
rosetta.core.chemical
)
alternate_state_info()
(in
FlexbbNode
)
apply_mover()
(in
AlignRMSD_Screener
)
AACompositionEnergy
(in
rosetta.protocols.fldsgn.potentials._protocols_fldsgn_potentials_
)
alternate_state_is_being_considered()
(in
FlexbbNode
)
apply_mover()
(in
AnchorSugarScreener
)
AACompositionEnergyAP
(in
rosetta.protocols.fldsgn.potentials._protocols_fldsgn_potentials_
)
alternate_state_one_body_energy()
(in
FlexbbNode
)
apply_mover()
(in
BaseBinMapUpdater
)
AACompositionEnergyCAP
(in
rosetta.protocols.fldsgn.potentials._protocols_fldsgn_potentials_
)
alternate_state_total_energy()
(in
FlexbbNode
)
apply_mover()
(in
BaseCentroidScreener
)
AACompositionEnergyCreator
(in
rosetta.protocols.fldsgn.potentials._protocols_fldsgn_potentials_
)
alternate_state_two_body_energies()
(in
FlexbbNode
)
apply_mover()
(in
BulgeApplier
)
AACompositionEnergyCreatorAP
(in
rosetta.protocols.fldsgn.potentials._protocols_fldsgn_potentials_
)
alternative_decoys_out()
(in
Batch
)
apply_mover()
(in
CentroidDistanceScreener
)
AACompositionEnergyCreatorCAP
(in
rosetta.protocols.fldsgn.potentials._protocols_fldsgn_potentials_
)
ALTERNATIVE_PROTONATION
(in
rosetta
)
apply_mover()
(in
FastForwardToNextResidueAlternative
)
aas_defined_begin()
(in
ResidueTypeSet
)
ALTERNATIVE_PROTONATION
(in
rosetta.core.chemical
)
apply_mover()
(in
FastForwardToNextRigidBody
)
aas_defined_end()
(in
ResidueTypeSet
)
ALTERNATIVE_PROTONATION
(in
rosetta.core.chemical._core_chemical_
)
apply_mover()
(in
IntegrationTestBreaker
)
aas_to_keep()
(in
RestrictAbsentCanonicalAASRLT
)
ALTERNATIVE_PROTONATION
(in
VariantType
)
apply_mover()
(in
O2PrimeScreener
)
aatype_for_node_state()
(in
DensePDInteractionGraph
)
AlternativePairings
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
apply_mover()
(in
PackScreener
)
aatype_for_node_state()
(in
DoubleLazyInteractionGraph
)
AlternativePairingsAP
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
apply_mover()
(in
PartitionContactScreener
)
aatype_for_node_state()
(in
FixedBBInteractionGraph
)
AlternativePairingsCAP
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
apply_mover()
(in
PhosphateScreener
)
aatype_for_node_state()
(in
LazyInteractionGraph
)
AlterSpecDisruptionDriver
(in
rosetta.protocols.pmut_scan._protocols_pmut_scan_
)
apply_mover()
(in
PoseSelectionScreener
)
aatype_for_node_state()
(in
PDInteractionGraph
)
AlterSpecDisruptionDriverAP
(in
rosetta.protocols.pmut_scan._protocols_pmut_scan_
)
apply_mover()
(in
ProteinCCD_ClosureScreener
)
aatype_for_state()
(in
DoubleLazyNode
)
AlterSpecDisruptionDriverCAP
(in
rosetta.protocols.pmut_scan._protocols_pmut_scan_
)
apply_mover()
(in
RNA_ChainClosableGeometryResidueBasedScreener
)
aatype_for_state()
(in
LazyNode
)
AmberPeriodicFunc
(in
rosetta.core.scoring.func._core_scoring_func_
)
apply_mover()
(in
RNA_ChainClosableGeometryScreener
)
aatype_for_state()
(in
PDNode
)
AmberPeriodicFuncAP
(in
rosetta.core.scoring.func._core_scoring_func_
)
apply_mover()
(in
RNA_ChainClosableGeometryStubBasedScreener
)
ab_dock_chains()
(in
AntibodyDesignModeler
)
AmberPeriodicFuncCAP
(in
rosetta.core.scoring.func._core_scoring_func_
)
apply_mover()
(in
RNA_ChainClosureScreener
)
ab_fold_tree()
(in
SetAtomTree
)
AmbigCSScore
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
apply_mover()
(in
ResidueContactScreener
)
Ab_TemplateInfo
(in
rosetta.protocols.antibody._protocols_antibody_
)
AmbigCSScoreAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
apply_mover()
(in
SampleApplier
)
Ab_TemplateInfoAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
AmbigCSScoreCAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
apply_mover()
(in
Scorer
)
Ab_TemplateInfoCAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
ambiguous_hnq()
(in
AtomCoordinateCstMover
)
apply_mover()
(in
StepWiseResiduePairScreener
)
abase2()
(in
ResidueType
)
AmbiguousConstraint
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply_mover()
(in
StepWiseScreener
)
abase2()
(in
Residue
)
AmbiguousConstraintAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply_mover()
(in
StubApplier
)
abego
(in
rosetta
)
AmbiguousConstraintCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply_mover()
(in
StubDistanceScreener
)
abego
(in
ScoreType
)
AmbiguousConstraintCreator
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply_mover()
(in
SugarInstantiator
)
abego
(in
rosetta.core.scoring._core_scoring_
)
AmbiguousConstraintCreatorAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply_mover()
(in
TagDefinition
)
abego
(in
rosetta.core.scoring
)
AmbiguousConstraintCreatorCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply_mover()
(in
VDW_BinScreener
)
ABEGO
(in
rosetta.core.sequence._core_sequence_
)
AmbiguousMultiConstraint
(in
rosetta.protocols.constraints_additional._protocols_constraints_additional_
)
apply_non_main_chain_sugar_coords()
(in
rosetta.core.pose.rna._core_pose_rna_
)
abego()
(in
BluePrint
)
AmbiguousMultiConstraintAP
(in
rosetta.protocols.constraints_additional._protocols_constraints_additional_
)
apply_nucleoside_torsion_Aform()
(in
RNA_TorsionMover
)
abego_char()
(in
ABEGO_SS_Map
)
AmbiguousMultiConstraintCAP
(in
rosetta.protocols.constraints_additional._protocols_constraints_additional_
)
apply_or_to_subset()
(in
OrResidueSelector
)
abego_index()
(in
rosetta.protocols.frag_picker.quota._protocols_frag_picker_quota_
)
AmbiguousNMRConstraint
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply_parsed_protocol()
(in
MSDJobDistributor
)
ABEGO_SS_Config
(in
rosetta.protocols.frag_picker.quota._protocols_frag_picker_quota_
)
AmbiguousNMRConstraintAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply_patch_from_file()
(in
ScoreFunction
)
ABEGO_SS_ConfigAP
(in
rosetta.protocols.frag_picker.quota._protocols_frag_picker_quota_
)
AmbiguousNMRConstraintCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply_patches()
(in
ResidueTypeSet
)
ABEGO_SS_ConfigCAP
(in
rosetta.protocols.frag_picker.quota._protocols_frag_picker_quota_
)
AmbiguousNMRConstraintCreator
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply_probability()
(in
ParsedProtocol
)
ABEGO_SS_Map
(in
rosetta.protocols.frag_picker.quota._protocols_frag_picker_quota_
)
AmbiguousNMRConstraintCreatorAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply_protonated_H1_adenosine_variant_type()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
ABEGO_SS_MapAP
(in
rosetta.protocols.frag_picker.quota._protocols_frag_picker_quota_
)
AmbiguousNMRConstraintCreatorCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply_pucker()
(in
RNA_IdealCoord
)
ABEGO_SS_MapCAP
(in
rosetta.protocols.frag_picker.quota._protocols_frag_picker_quota_
)
AmbiguousNMRDistanceConstraint
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply_pucker()
(in
rosetta.core.pose.rna._core_pose_rna_
)
ABEGO_SS_Pool
(in
rosetta.protocols.frag_picker.quota._protocols_frag_picker_quota_
)
AmbiguousNMRDistanceConstraintAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply_random()
(in
LoopHashLibrary
)
ABEGO_SS_PoolAP
(in
rosetta.protocols.frag_picker.quota._protocols_frag_picker_quota_
)
AmbiguousNMRDistanceConstraintCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply_random_fragment()
(in
FullAtomRNA_Fragments
)
ABEGO_SS_PoolCAP
(in
rosetta.protocols.frag_picker.quota._protocols_frag_picker_quota_
)
AmbiguousNMRDistanceConstraintCreator
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply_random_fragment()
(in
RNA_Fragments
)
ABEGO_SS_Score
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
AmbiguousNMRDistanceConstraintCreatorAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply_random_nucleoside_torsion()
(in
RNA_TorsionMover
)
ABEGO_SS_ScoreAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
AmbiguousNMRDistanceConstraintCreatorCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply_random_suite_torsion()
(in
RNA_TorsionMover
)
ABEGO_SS_ScoreCAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
AMINO_SUGAR
(in
rosetta
)
apply_rigid_body_only()
(in
RigidBodyStepWiseSamplerWithResidueAlternatives
)
abego_str()
(in
ABEGOEval
)
AMINO_SUGAR
(in
rosetta.core.chemical
)
apply_rotamer()
(in
rosetta.protocols.stepwise.legacy.modeler.rna._protocols_stepwise_legacy_modeler_rna_'
)
ABEGOAP
(in
rosetta.core.sequence._core_sequence_
)
AMINO_SUGAR
(in
rosetta.core.chemical._core_chemical_
)
apply_rotate()
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
ABEGOCAP
(in
rosetta.core.sequence._core_sequence_
)
AMINO_SUGAR
(in
ResidueProperty
)
APPLY_SC_MOVE
(in
rosetta.basic
)
ABEGOEval
(in
rosetta.core.fragment.picking_old.vall.eval._core_fragment_picking_old_vall_eval_
)
AminoAcidNeighborSparseMatrix_T_float_T
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
APPLY_SC_MOVE
(in
rosetta.basic._basic_
)
ABEGOEvalAP
(in
rosetta.core.fragment.picking_old.vall.eval._core_fragment_picking_old_vall_eval_
)
AminoAcidNeighborSparseMatrix_T_float_TAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
APPLY_SC_MOVE
(in
ProfTag
)
ABEGOEvalCAP
(in
rosetta.core.fragment.picking_old.vall.eval._core_fragment_picking_old_vall_eval_
)
AminoAcidNeighborSparseMatrix_T_float_TCAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
apply_sequence_mapping()
(in
FoldTree
)
ABEGOManager
(in
rosetta.core.sequence._core_sequence_
)
amplitude()
(in
DNABase
)
apply_sequence_mapping()
(in
rosetta.protocols.loops._protocols_loops_
)
ABEGOManagerAP
(in
rosetta.core.sequence._core_sequence_
)
ana_deriv()
(in
DOF_DataPoint
)
apply_ss()
(in
AnnotatedFragData
)
ABEGOManagerCAP
(in
rosetta.core.sequence._core_sequence_
)
ana_deriv()
(in
DerivCheckDataPoint
)
apply_ss()
(in
BBTorsionAndAnglesSRFD
)
ABINITIO
(in
rosetta.basic
)
analysis
(in
rosetta.protocols
)
apply_ss()
(in
BBTorsionSRFD
)
ABINITIO
(in
rosetta.basic._basic_
)
analytic_etable_derivatives()
(in
Etable
)
apply_ss()
(in
DownJumpSRFD
)
ABINITIO
(in
ProfTag
)
analytic_etable_evaluation()
(in
Etable
)
apply_ss()
(in
FragData
)
abinitio
(in
rosetta.protocols
)
analytic_etable_evaluation()
(in
EnergyMethodOptions
)
apply_ss()
(in
FragID
)
AbinitioBaseFilter
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
analytic_lk_derivatives()
(in
Etable
)
apply_ss()
(in
Frame
)
AbinitioBaseFilterAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
analytic_lk_energy()
(in
Etable
)
apply_ss()
(in
IndependentBBTorsionSRFD
)
AbinitioBaseFilterCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
analytic_params_for_pair()
(in
Etable
)
apply_ss()
(in
SecstructSRFD
)
AbinitioMoverWeight
(in
rosetta.protocols.topology_broker.weights._protocols_topology_broker_weights_
)
AnalyticEtableEnergy
(in
rosetta.core.scoring.etable._core_scoring_etable_
)
apply_ss()
(in
SingleResidueFragData
)
AbinitioMoverWeightAP
(in
rosetta.protocols.topology_broker.weights._protocols_topology_broker_weights_
)
AnalyticEtableEnergyAP
(in
rosetta.core.scoring.etable._core_scoring_etable_
)
apply_ss()
(in
UpJumpSRFD
)
AbinitioMoverWeightCAP
(in
rosetta.protocols.topology_broker.weights._protocols_topology_broker_weights_
)
AnalyticEtableEnergyCAP
(in
rosetta.core.scoring.etable._core_scoring_etable_
)
apply_sub_to_full_mapping()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
abort_min()
(in
AtomTreeMultifunc
)
AnalyticEtableEvaluator
(in
rosetta.core.scoring.etable._core_scoring_etable_
)
apply_suite_torsion_Aform()
(in
RNA_TorsionMover
)
abort_min()
(in
CartesianMultifunc
)
AnalyticEtableEvaluatorAP
(in
rosetta.core.scoring.etable._core_scoring_etable_
)
apply_superposition_transform()
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
abort_min()
(in
Multifunc
)
AnalyticEtableEvaluatorCAP
(in
rosetta.core.scoring.etable._core_scoring_etable_
)
apply_superposition_transform_to_jump()
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
abort_min()
(in
SingleResidueMultifunc
)
analyze_base_bin_map()
(in
rosetta.protocols.stepwise.modeler.rna.rigid_body._protocols_stepwise_modeler_rna_rigid_body_
)
apply_to_failure()
(in
RosettaScriptWrapper
)
abort_min()
(in
SymAtomTreeMultifunc
)
Anchor
(in
rosetta.protocols.anchored_design._protocols_anchored_design_
)
apply_to_pose()
(in
BackboneSegment
)
abort_min()
(in
BfactorMultifunc
)
anchor_atom()
(in
WaterAnchorInfo
)
apply_to_rotpack()
(in
PackRotamersMoverLazy
)
abort_min()
(in
FitSimpleHelixMultiFunc
)
anchor_end()
(in
AnchorMoversData
)
apply_transform_Rx_plus_v()
(in
Residue
)
abort_min()
(in
NormalModeMultifunc
)
anchor_noise_constraints_setup()
(in
AnchorMoversData
)
apply_transform_Rx_plus_v()
(in
Pose
)
abort_min()
(in
OptEMultifunc
)
anchor_residue()
(in
WaterAnchorInfo
)
apply_transformation()
(in
SymmetricConformation
)
abort_min()
(in
WrapperOptEMultifunc
)
anchor_resnum()
(in
TaskAwareCsts
)
apply_transformation()
(in
rosetta.protocols.forge.methods._protocols_forge_methods_
)
abort_min()
(in
FingerprintMultifunc
)
anchor_specified()
(in
SeedFoldTree
)
apply_transformation()
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
abort_min()
(in
PocketExemplarMultifunc
)
anchor_start()
(in
AnchorMoversData
)
apply_transformation()
(in
RepeatParameterFilter
)
abort_min()
(in
TensorsOptimizer
)
ANCHOR_SUGAR
(in
rosetta.protocols.stepwise.screener
)
apply_transformation_norecompute()
(in
SymmetricConformation
)
abort_min()
(in
TensorsOptimizer
)
ANCHOR_SUGAR
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
apply_virtual_rna_residue_variant_type()
(in
rosetta.core.pose.rna._core_pose_rna_
)
abort_min()
(in
TensorsOptimizerFix
)
ANCHOR_SUGAR
(in
StepWiseScreenerType
)
applyANNTransformation()
(in
ANN
)
abort_min()
(in
TensorsOptimizerSvd
)
anchor_sugar_modeling()
(in
VirtualSugarJustInTimeInstantiator
)
applyRotation()
(in
RBSegmentMover
)
abort_min()
(in
TensorsOptimizer_Ts1
)
anchor_sugar_solution_number()
(in
AnchorSugarScreener
)
applySpin()
(in
RBSegmentMover
)
abort_min()
(in
TensorsOptimizer_Ts2
)
AnchorAP
(in
rosetta.protocols.anchored_design._protocols_anchored_design_
)
applyTransformation()
(in
RBSegmentMover
)
abort_min()
(in
TensorsOptimizer_Ts3
)
AnchorCAP
(in
rosetta.protocols.anchored_design._protocols_anchored_design_
)
applyTranslation()
(in
RBSegmentMover
)
abort_min()
(in
TensorsOptimizer_Ts4
)
anchored_design
(in
rosetta.protocols
)
applyVecAverage()
(in
ANN
)
above
(in
AlignMove
)
anchored_loop()
(in
AnchorMoversData
)
applyVecNormalization()
(in
ANN
)
above
(in
rosetta.core.sequence._core_sequence_
)
AnchoredDesignMover
(in
rosetta.protocols.anchored_design._protocols_anchored_design_
)
approved()
(in
DofClaim
)
above
(in
rosetta.core.sequence
)
AnchoredDesignMoverAP
(in
rosetta.protocols.anchored_design._protocols_anchored_design_
)
approx_lever_distance()
(in
xyzTransform_T_double_T
)
AbrelaxApplication
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
AnchoredDesignMoverCAP
(in
rosetta.protocols.anchored_design._protocols_anchored_design_
)
approx_lever_distance()
(in
xyzTransform_T_float_T
)
AbrelaxApplicationAP
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
AnchoredGraftMover
(in
rosetta.protocols.grafting._protocols_grafting_
)
approximate_vdw_radius()
(in
AtomVDW
)
AbrelaxApplicationCAP
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
AnchoredGraftMoverAP
(in
rosetta.protocols.grafting._protocols_grafting_
)
ARBITRARY_FLOAT_DATA
(in
CacheableDataType
)
AbrelaxMover
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
AnchoredGraftMoverCAP
(in
rosetta.protocols.grafting._protocols_grafting_
)
ARBITRARY_FLOAT_DATA
(in
Enum
)
AbrelaxMoverAP
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
AnchoredGraftMoverCreator
(in
rosetta.protocols.grafting._protocols_grafting_
)
ARBITRARY_STRING_DATA
(in
CacheableDataType
)
AbrelaxMoverCAP
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
AnchoredGraftMoverCreatorAP
(in
rosetta.protocols.grafting._protocols_grafting_
)
ARBITRARY_STRING_DATA
(in
Enum
)
ABS
(in
rosetta.protocols.simple_filters
)
AnchoredGraftMoverCreatorCAP
(in
rosetta.protocols.grafting._protocols_grafting_
)
archive
(in
rosetta.protocols.jd2
)
ABS
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
AnchoredPerturbMover
(in
rosetta.protocols.anchored_design._protocols_anchored_design_
)
ARCHIVE_BLOCK_FILE
(in
rosetta.basic
)
ABS
(in
Operation
)
AnchoredPerturbMoverAP
(in
rosetta.protocols.anchored_design._protocols_anchored_design_
)
ARCHIVE_BLOCK_FILE
(in
rosetta.basic._basic_
)
abs_deriv_dev()
(in
SimpleDerivCheckResult
)
AnchoredPerturbMoverCAP
(in
rosetta.protocols.anchored_design._protocols_anchored_design_
)
ARCHIVE_BLOCK_FILE
(in
ProfTag
)
abscript
(in
rosetta.protocols.abinitio
)
AnchoredRefineMover
(in
rosetta.protocols.anchored_design._protocols_anchored_design_
)
ARCHIVE_CRITICAL_JOBSCOMPLETE
(in
rosetta.basic
)
AbscriptLoopCloserCM
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
AnchoredRefineMoverAP
(in
rosetta.protocols.anchored_design._protocols_anchored_design_
)
ARCHIVE_CRITICAL_JOBSCOMPLETE
(in
rosetta.basic._basic_
)
AbscriptLoopCloserCMAP
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
AnchoredRefineMoverCAP
(in
rosetta.protocols.anchored_design._protocols_anchored_design_
)
ARCHIVE_CRITICAL_JOBSCOMPLETE
(in
ProfTag
)
AbscriptLoopCloserCMCAP
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
AnchorMoversData
(in
rosetta.protocols.anchored_design._protocols_anchored_design_
)
ARCHIVE_EVAL_DECOYS
(in
rosetta.basic
)
AbscriptLoopCloserCMCreator
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
AnchorMoversDataAP
(in
rosetta.protocols.anchored_design._protocols_anchored_design_
)
ARCHIVE_EVAL_DECOYS
(in
rosetta.basic._basic_
)
AbscriptLoopCloserCMCreatorAP
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
AnchorMoversDataCAP
(in
rosetta.protocols.anchored_design._protocols_anchored_design_
)
ARCHIVE_EVAL_DECOYS
(in
ProfTag
)
AbscriptLoopCloserCMCreatorCAP
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
anchors()
(in
BoltzmannFilter
)
ARCHIVE_EVALUATORS
(in
rosetta.basic
)
AbscriptMover
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
AnchorSugarScreener
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
ARCHIVE_EVALUATORS
(in
rosetta.basic._basic_
)
AbscriptMoverAP
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
AnchorSugarScreenerAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
ARCHIVE_EVALUATORS
(in
ProfTag
)
AbscriptMoverCAP
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
AnchorSugarScreenerCAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
ARCHIVE_FILL_POSE
(in
rosetta.basic
)
AbscriptMoverCreator
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
AND
(in
rosetta.protocols.filters
)
ARCHIVE_FILL_POSE
(in
rosetta.basic._basic_
)
AbscriptMoverCreatorAP
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
AND
(in
rosetta.protocols.filters._protocols_filters_
)
ARCHIVE_FILL_POSE
(in
ProfTag
)
AbscriptMoverCreatorCAP
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
AND
(in
boolean_operations
)
ARCHIVE_GEN_BATCH
(in
rosetta.basic
)
AbscriptStageMover
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
AND
(in
rosetta.protocols.toolbox.task_operations
)
ARCHIVE_GEN_BATCH
(in
rosetta.basic._basic_
)
AbscriptStageMoverAP
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
AND
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
ARCHIVE_GEN_BATCH
(in
ProfTag
)
AbscriptStageMoverCAP
(in
rosetta.protocols.abinitio.abscript._protocols_abinitio_abscript_
)
AND
(in
boolean_operations
)
ARCHIVE_JOBSCOMPLETE
(in
rosetta.basic
)
absolute()
(in
FileName
)
and_allow_insert()
(in
AllowInsert
)
ARCHIVE_JOBSCOMPLETE
(in
rosetta.basic._basic_
)
absolute()
(in
PathName
)
and_extrachi_cutoff()
(in
ResidueLevelTask
)
ARCHIVE_JOBSCOMPLETE
(in
ProfTag
)
absolute_vec()
(in
rosetta.protocols.features.strand_assembly._protocols_features_strand_assembly_
)
and_extrachi_cutoff()
(in
ResidueLevelTask_
)
ARCHIVE_READ_DECOYS
(in
rosetta.basic
)
AbsoluteValueExpression
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
and_max_rotbump_energy()
(in
PackerTask
)
ARCHIVE_READ_DECOYS
(in
rosetta.basic._basic_
)
AbsoluteValueExpressionAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
and_max_rotbump_energy()
(in
PackerTask_
)
ARCHIVE_READ_DECOYS
(in
ProfTag
)
AbsoluteValueExpressionCAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
and_with()
(in
Bool3DGrid
)
ARCHIVE_SCORE_POSE
(in
rosetta.basic
)
AbstractArchiveBase
(in
rosetta.protocols.jd2.archive._protocols_jd2_archive_
)
and_with()
(in
BumpGrid
)
ARCHIVE_SCORE_POSE
(in
rosetta.basic._basic_
)
AbstractArchiveBaseAP
(in
rosetta.protocols.jd2.archive._protocols_jd2_archive_
)
AndExpression
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
ARCHIVE_SCORE_POSE
(in
ProfTag
)
AbstractArchiveBaseCAP
(in
rosetta.protocols.jd2.archive._protocols_jd2_archive_
)
AndExpressionAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
ARCHIVE_SYNC_BATCHES
(in
rosetta.basic
)
AbstractRotamerTrie
(in
rosetta.core.conformation._core_conformation_
)
AndExpressionCAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
ARCHIVE_SYNC_BATCHES
(in
rosetta.basic._basic_
)
AbstractRotamerTrieAP
(in
rosetta.core.conformation._core_conformation_
)
ANDNOT
(in
rosetta.protocols.filters
)
ARCHIVE_SYNC_BATCHES
(in
ProfTag
)
AbstractRotamerTrieCAP
(in
rosetta.core.conformation._core_conformation_
)
ANDNOT
(in
rosetta.protocols.filters._protocols_filters_
)
ArchiveBase
(in
rosetta.protocols.jd2.archive._protocols_jd2_archive_
)
acc_atm()
(in
HBond
)
ANDNOT
(in
boolean_operations
)
ArchiveBaseAP
(in
rosetta.protocols.jd2.archive._protocols_jd2_archive_
)
acc_atm_is_backbone()
(in
HBond
)
ANDNOT
(in
rosetta.protocols.toolbox.task_operations
)
ArchiveBaseCAP
(in
rosetta.protocols.jd2.archive._protocols_jd2_archive_
)
acc_atm_is_protein_backbone()
(in
HBond
)
ANDNOT
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
ArchiveManager
(in
rosetta.protocols.jd2.archive._protocols_jd2_archive_
)
acc_bbg_in_bb_bb_hbond()
(in
HBondSet
)
ANDNOT
(in
boolean_operations
)
ArchiveManagerAP
(in
rosetta.protocols.jd2.archive._protocols_jd2_archive_
)
acc_chem_type_from_name()
(in
HBondTypeManager
)
AndResidueSelector
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
ArchiveManagerCAP
(in
rosetta.protocols.jd2.archive._protocols_jd2_archive_
)
acc_dist_cutoff()
(in
WaterFeatures
)
AndResidueSelectorAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
are_colliding()
(in
DownstreamAlgorithm
)
acc_res()
(in
HBond
)
AndResidueSelectorCAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
are_seqs_different()
(in
rosetta.protocols.vip._protocols_vip_
)
acc_res_is_dna()
(in
HBond
)
AndResidueSelectorCreator
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
are_they_neighbors()
(in
ScoreFunction
)
acc_res_is_protein()
(in
HBond
)
AndResidueSelectorCreatorAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
AreaAccumulator
(in
rosetta.core.scoring.packstat._core_scoring_packstat_
)
acc_strength()
(in
HBondDatabase
)
AndResidueSelectorCreatorCAP
(in
rosetta.core.pack.task.residue_selector._core_pack_task_residue_selector_
)
AreaAccumulatorAP
(in
rosetta.core.scoring.packstat._core_scoring_packstat_
)
acc_type()
(in
HBEvalTuple
)
ang_U1D2()
(in
MatchConstraintFileInfo
)
AreaAccumulatorCAP
(in
rosetta.core.scoring.packstat._core_scoring_packstat_
)
accept
(in
StubStatus
)
ang_U1D2_samples()
(in
ExternalGeomSampler
)
argrot_dna_dis2()
(in
rosetta.protocols.dna._protocols_dna_
)
accept
(in
rosetta.protocols.hotspot_hashing._protocols_hotspot_hashing_
)
ang_U2D1()
(in
MatchConstraintFileInfo
)
ArithmeticASTExpression
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
accept
(in
rosetta.protocols.hotspot_hashing
)
ang_U2D1_samples()
(in
ExternalGeomSampler
)
ArithmeticASTExpressionAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
accept()
(in
GenericMonteCarloMover
)
angle
(in
Quaternion_Real
)
ArithmeticASTExpressionCAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
accept_counter()
(in
GenericMonteCarloMover
)
angle
(in
Quaternion_double
)
ArithmeticASTFactor
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
accept_declined_claim()
(in
DensityScoringClaimer
)
angle
(in
Quaternion_float
)
ArithmeticASTFactorAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
accept_declined_claim()
(in
FoldandDockClaimer
)
angle()
(in
CentroidRotamerSampleData
)
ArithmeticASTFactorCAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
accept_declined_claim()
(in
MembraneTopologyClaimer
)
angle()
(in
BackboneDB
)
ArithmeticASTFunction
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
accept_declined_claim()
(in
TopologyClaimer
)
angle()
(in
GetRBDOFValues
)
ArithmeticASTFunctionAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
accept_new_conformation()
(in
RamaCheckBase
)
angle()
(in
SetTorsion
)
ArithmeticASTFunctionCAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
accept_reject
(in
rosetta
)
angle()
(in
SetChiMover
)
ArithmeticASTNode
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
accept_reject
(in
StatsType
)
angle_constraint
(in
rosetta
)
ArithmeticASTNodeAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
accept_reject
(in
rosetta.protocols.moves._protocols_moves_
)
angle_constraint
(in
ScoreType
)
ArithmeticASTNodeCAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
accept_reject
(in
rosetta.protocols.moves
)
angle_constraint
(in
rosetta.core.scoring._core_scoring_
)
ArithmeticASTRestExpression
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
acceptance_rate()
(in
MoverStatistics
)
angle_constraint
(in
rosetta.core.scoring
)
ArithmeticASTRestExpressionAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
acceptance_rate()
(in
TrialMover
)
angle_constraint_energy()
(in
ConstraintEdge
)
ArithmeticASTRestExpressionCAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
AcceptanceCheck
(in
rosetta.protocols.loop_modeling.utilities._protocols_loop_modeling_utilities_
)
angle_degrees()
(in
rosetta.numeric._numeric_
)
ArithmeticASTRestTerm
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
AcceptanceCheckAP
(in
rosetta.protocols.loop_modeling.utilities._protocols_loop_modeling_utilities_
)
angle_degrees_double()
(in
rosetta.numeric._numeric_
)
ArithmeticASTRestTermAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
AcceptanceCheckCAP
(in
rosetta.protocols.loop_modeling.utilities._protocols_loop_modeling_utilities_
)
angle_diff()
(in
MakeRotLibMover
)
ArithmeticASTRestTermCAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
accepted()
(in
MoverStatistics
)
angle_disp()
(in
BackrubSegment
)
ArithmeticASTTerm
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
accepted()
(in
TrialCounter
)
angle_distance()
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
ArithmeticASTTermAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
acceptor_atoms()
(in
ResidueType
)
angle_in_range()
(in
rosetta.basic._basic_
)
ArithmeticASTTermCAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
AcceptorAtomFilter
(in
rosetta.core.chemical._core_chemical_
)
angle_magnitude()
(in
RigidBodyDeterministicSpinMover
)
ArithmeticASTValue
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
AcceptorAtomFilterAP
(in
rosetta.core.chemical._core_chemical_
)
angle_max()
(in
BackboneMover
)
ArithmeticASTValueAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
AcceptorAtomFilterCAP
(in
rosetta.core.chemical._core_chemical_
)
angle_parameters()
(in
ResidueCartBondedParameters
)
ArithmeticASTValueCAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
accepts()
(in
ABEGO_SS_Pool
)
angle_radians()
(in
rosetta.numeric._numeric_
)
ArithmeticScanner
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
accepts_since_last_batch()
(in
ArchiveBase
)
angle_radians_double()
(in
rosetta.numeric._numeric_
)
ArithmeticScannerAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
accpt_pos()
(in
ResidueType
)
angle_tolerance()
(in
NumericTraits_T_double_T
)
ArithmeticScannerCAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
accpt_pos()
(in
Residue
)
angle_tolerance()
(in
NumericTraits_T_float_T
)
Armijo()
(in
ArmijoLineMinimization
)
accpt_pos_sc()
(in
ResidueType
)
angle_tolerance()
(in
NumericTraits_T_long_double_T
)
ArmijoLineMinimization
(in
rosetta.core.optimization._core_optimization_
)
accpt_pos_sc()
(in
Residue
)
angleA
(in
rosetta.protocols.jumping._protocols_jumping_
)
ArmijoLineMinimizationAP
(in
rosetta.core.optimization._core_optimization_
)
accumulate()
(in
EMapVector
)
angleA
(in
cstType
)
ArmijoLineMinimizationCAP
(in
rosetta.core.optimization._core_optimization_
)
accumulate_area()
(in
Accumulator
)
angleA
(in
rosetta.protocols.jumping
)
AROMATIC
(in
rosetta
)
accumulate_area()
(in
AreaAccumulator
)
angleB
(in
rosetta.protocols.jumping._protocols_jumping_
)
AROMATIC
(in
rosetta.core.chemical
)
accumulate_area()
(in
MultiProbePerSphereAccumulator
)
angleB
(in
cstType
)
AROMATIC
(in
rosetta.core.chemical._core_chemical_
)
accumulate_area()
(in
MultiProbePoseAccumulator
)
angleB
(in
rosetta.protocols.jumping
)
AROMATIC
(in
ResidueProperty
)
accumulate_area()
(in
PerSphereAccumulator
)
AngleConstraint
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
aromatic_atoms()
(in
ResidueType
)
accumulate_dxdy()
(in
Accumulator
)
AngleConstraintAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
AromaticAtomFilter
(in
rosetta.core.chemical._core_chemical_
)
accumulate_dxdy()
(in
AreaAccumulator
)
AngleConstraintCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
AromaticAtomFilterAP
(in
rosetta.core.chemical._core_chemical_
)
accumulate_dxdy()
(in
MultiProbePerSphereAccumulator
)
AngleConstraintCreator
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
AromaticAtomFilterCAP
(in
rosetta.core.chemical._core_chemical_
)
accumulate_dxdy()
(in
MultiProbePoseAccumulator
)
AngleConstraintCreatorAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
AromaticBond
(in
rosetta
)
accumulate_dxdy()
(in
PerSphereAccumulator
)
AngleConstraintCreatorCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
AromaticBond
(in
rosetta.core.chemical
)
accumulate_energy()
(in
DenseNeighborConstIterator
)
AngleToVector
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
AromaticBond
(in
rosetta.core.chemical._core_chemical_
)
accumulate_energy()
(in
DenseNeighborIterator
)
AngleToVectorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
AromaticBond
(in
BondName
)
accumulate_energy()
(in
OneToAllNeighborConstIterator
)
AngleToVectorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
aromaticity()
(in
Bond
)
accumulate_energy()
(in
OneToAllNeighborIterator
)
AngleToVectorFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
Aroop
(in
rosetta.protocols.antibody
)
accumulate_energy()
(in
PeptideBondedNeighborConstIterator
)
AngleToVectorFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
Aroop
(in
rosetta.protocols.antibody._protocols_antibody_
)
accumulate_energy()
(in
PeptideBondedNeighborIterator
)
AngleToVectorFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
Aroop
(in
CDRDefinitionEnum
)
accumulate_energy()
(in
ResidueNeighborConstIterator
)
angular_distance_between()
(in
EulerAngles_Real
)
Array2D
(in
rosetta.core.scoring.packstat._core_scoring_packstat_
)
accumulate_energy()
(in
ResidueNeighborIterator
)
angular_distance_between()
(in
EulerAngles_double
)
Array2DAP
(in
rosetta.core.scoring.packstat._core_scoring_packstat_
)
accumulate_energy()
(in
CstResNeighbConstIterator
)
angular_distance_between()
(in
EulerAngles_float
)
Array2DCAP
(in
rosetta.core.scoring.packstat._core_scoring_packstat_
)
accumulate_energy()
(in
CstResNeighbIterator
)
AngularMomentumQuantumNumber
(in
ElectronConfiguration
)
array_pool()
(in
EnergyGraph
)
accumulate_energy()
(in
CentroidDisulfideEnergyContainer
)
AngularMomentumQuantumNumber_strings()
(in
ElectronConfiguration
)
array_to_farray()
(in
DataBuffer
)
accumulate_energy()
(in
CentroidDisulfideNeighborConstIterator
)
animate()
(in
ResidueKinWriter
)
as_set()
(in
rosetta.protocols.medal._protocols_medal_
)
accumulate_energy()
(in
CentroidDisulfideNeighborIterator
)
animate()
(in
ResidueKinemageWriter
)
asp_corrections()
(in
rosetta.protocols.make_rot_lib._protocols_make_rot_lib_
)
accumulate_energy()
(in
DisulfResNeighbConstIterator
)
animate()
(in
WriteUpstreamHitKinemage
)
asR()
(in
urs_Quat
)
accumulate_energy()
(in
DisulfResNeighbIterator
)
ANN
(in
rosetta.protocols.sparta._protocols_sparta_
)
assemble_remark_line()
(in
rosetta.protocols.toolbox.match_enzdes_util._protocols_toolbox_match_enzdes_util_
)
accumulate_energy()
(in
DisulfideMatchingEnergyContainer
)
ANNAP
(in
rosetta.protocols.sparta._protocols_sparta_
)
assemble_remark_lines()
(in
PDBWriter
)
accumulate_energy()
(in
DisulfideMatchingNeighborConstIterator
)
ANNCAP
(in
rosetta.protocols.sparta._protocols_sparta_
)
AssembleLinkerMover
(in
rosetta.protocols.domain_assembly._protocols_domain_assembly_
)
accumulate_energy()
(in
DisulfideMatchingNeighborIterator
)
annealer
(in
rosetta.core.pack
)
AssembleLinkerMoverAP
(in
rosetta.protocols.domain_assembly._protocols_domain_assembly_
)
accumulate_energy()
(in
FullatomDisulfideEnergyContainer
)
annealer
(in
rosetta.protocols.flexpack
)
AssembleLinkerMoverCAP
(in
rosetta.protocols.domain_assembly._protocols_domain_assembly_
)
accumulate_single_atom_contributions()
(in
LK_BallEnergy
)
annealer_file()
(in
DebuggingAnnealer
)
assert_phosphate_nomenclature_matches_mini()
(in
rosetta.protocols.farna._protocols_farna_
)
Accumulator
(in
rosetta.core.scoring.packstat._core_scoring_packstat_
)
AnnealerFactory
(in
rosetta.core.pack.annealer._core_pack_annealer_
)
assign()
(in
BasicDataCache
)
AccumulatorAP
(in
rosetta.core.scoring.packstat._core_scoring_packstat_
)
AnnealerFactoryAP
(in
rosetta.core.pack.annealer._core_pack_annealer_
)
assign()
(in
DataCache_T_basic_datacache_CacheableData_T
)
AccumulatorCAP
(in
rosetta.core.scoring.packstat._core_scoring_packstat_
)
AnnealerFactoryCAP
(in
rosetta.core.pack.annealer._core_pack_annealer_
)
assign()
(in
SVD_Solver
)
ACETYL_SUGAR
(in
rosetta
)
annotate()
(in
EnvClaim
)
assign()
(in
Atom
)
ACETYL_SUGAR
(in
rosetta.core.chemical
)
annotated_atom_graph_from_conformation()
(in
rosetta.core.conformation._core_conformation_
)
assign()
(in
ResConnID
)
ACETYL_SUGAR
(in
rosetta.core.chemical._core_chemical_
)
annotated_sequence()
(in
Pose
)
assign()
(in
RingConformerSet
)
ACETYL_SUGAR
(in
ResidueProperty
)
annotated_sequence()
(in
SequenceClaim
)
assign()
(in
Conformation
)
ACETYLAMINO_SUGAR
(in
rosetta
)
annotated_to_oneletter_sequence()
(in
rosetta.core.pose._core_pose_
)
assign()
(in
PseudoBond
)
ACETYLAMINO_SUGAR
(in
rosetta.core.chemical
)
AnnotatedFragData
(in
rosetta.core.fragment._core_fragment_
)
assign()
(in
UpperEdgeGraph_T_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_T
)
ACETYLAMINO_SUGAR
(in
rosetta.core.chemical._core_chemical_
)
AnnotatedFragDataAP
(in
rosetta.core.fragment._core_fragment_
)
assign()
(in
LipidAccInfo
)
ACETYLAMINO_SUGAR
(in
ResidueProperty
)
AnnotatedFragDataCAP
(in
rosetta.core.fragment._core_fragment_
)
assign()
(in
MembraneInfo
)
ACETYLATED_NTERMINUS
(in
rosetta
)
AnnotatedSequence
(in
rosetta.core.sequence._core_sequence_
)
assign()
(in
Span
)
ACETYLATED_NTERMINUS
(in
rosetta.core.chemical
)
AnnotatedSequenceAP
(in
rosetta.core.sequence._core_sequence_
)
assign()
(in
SpanningTopology
)
ACETYLATED_NTERMINUS
(in
rosetta.core.chemical._core_chemical_
)
AnnotatedSequenceCAP
(in
rosetta.core.sequence._core_sequence_
)
assign()
(in
ConnectionEvent
)
ACETYLATED_NTERMINUS
(in
ResidueProperty
)
annotations()
(in
RDAT
)
assign()
(in
GeneralEvent
)
ACETYLATED_NTERMINUS_VARIANT
(in
rosetta
)
annotations()
(in
Environment
)
assign()
(in
IdentityEvent
)
ACETYLATED_NTERMINUS_VARIANT
(in
rosetta.core.chemical
)
annotations()
(in
ProtectedConformation
)
assign()
(in
LengthEvent
)
ACETYLATED_NTERMINUS_VARIANT
(in
rosetta.core.chemical._core_chemical_
)
anomer()
(in
CarbohydrateInfo
)
assign()
(in
XYZEvent
)
ACETYLATED_NTERMINUS_VARIANT
(in
VariantType
)
anomeric_carbon()
(in
CarbohydrateInfo
)
assign()
(in
SymDof
)
ACETYLATION
(in
rosetta
)
anomeric_carbon_index()
(in
CarbohydrateInfo
)
assign()
(in
SymSlideInfo
)
ACETYLATION
(in
rosetta.core.chemical
)
anomeric_carbon_name()
(in
CarbohydrateInfo
)
assign()
(in
SymmetricConformation
)
ACETYLATION
(in
rosetta.core.chemical._core_chemical_
)
ANTI
(in
rosetta.core.chemical.rna
)
assign()
(in
VirtualCoordinate
)
ACETYLATION
(in
VariantType
)
ANTI
(in
rosetta.core.chemical.rna._core_chemical_rna_
)
assign()
(in
BBTorsionSRFD
)
acid_base_coefficient()
(in
IonizableResidue
)
ANTI
(in
ChiState
)
assign()
(in
ConstFrameIterator
)
acknowledge_last_substititon_not_committed()
(in
LinearMemNode
)
antibody
(in
rosetta.protocols
)
assign()
(in
FragID
)
acknowledge_last_substititon_not_committed()
(in
SymmLinearMemNode
)
Antibody
(in
rosetta.protocols.antibody_legacy._protocols_antibody_legacy_
)
assign()
(in
FragID_Iterator
)
acknowledge_last_substititon_not_committed()
(in
SymmMinimalistNode
)
antibody_legacy
(in
rosetta.protocols
)
assign()
(in
FrameIterator
)
acknowledge_neighbors_partial_state_assignment()
(in
FASTERNode
)
antibody_modeling_insert_ter()
(in
CDRH3Modeler
)
assign()
(in
IndependentBBTorsionSRFD
)
acknowledge_neighbors_partial_state_substitution()
(in
DoubleLazyNode
)
antibody_region_enum_to_string()
(in
AntibodyEnumManager
)
assign()
(in
VallResidue
)
acknowledge_neighbors_partial_state_substitution()
(in
LazyNode
)
antibody_region_string_to_enum()
(in
AntibodyEnumManager
)
assign()
(in
ABEGOEval
)
acknowledge_neighbors_partial_state_substitution()
(in
LinearMemNode
)
AntibodyAP
(in
rosetta.protocols.antibody_legacy._protocols_antibody_legacy_
)
assign()
(in
EnergyEval
)
acknowledge_neighbors_partial_state_substitution()
(in
SymmLinearMemNode
)
AntibodyCAP
(in
rosetta.protocols.antibody_legacy._protocols_antibody_legacy_
)
assign()
(in
IdentityEval
)
acknowledge_neighbors_partial_state_substitution()
(in
SymmMinimalistNode
)
AntibodyDesignModeler
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
assign()
(in
VallFragmentEval
)
acknowledge_neighbors_perturbed_state()
(in
FASTERNode
)
AntibodyDesignModelerAP
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
assign()
(in
LengthGen
)
acknowledge_neighbors_state_substitution()
(in
DensePDNode
)
AntibodyDesignModelerCAP
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
assign()
(in
SecStructGen
)
acknowledge_neighbors_state_substitution()
(in
DoubleDensePDNode
)
AntibodyDesignMover
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
assign()
(in
VallFragmentGen
)
acknowledge_neighbors_state_substitution()
(in
DoubleLazyNode
)
AntibodyDesignMoverAP
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
assign()
(in
VallFragmentScore
)
acknowledge_neighbors_state_substitution()
(in
FASTERNode
)
AntibodyDesignMoverCAP
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
assign()
(in
EdgeListConstIterator
)
acknowledge_neighbors_state_substitution()
(in
LazyNode
)
AntibodyDesignMoverCreator
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
assign()
(in
EdgeListIterator
)
acknowledge_neighbors_state_substitution()
(in
LinearMemNode
)
AntibodyDesignMoverCreatorAP
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
assign()
(in
Graph
)
acknowledge_neighbors_state_substitution()
(in
PDNode
)
AntibodyDesignMoverCreatorCAP
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
assign()
(in
SequenceMapping
)
acknowledge_neighbors_state_substitution()
(in
SymmLinearMemNode
)
AntibodyDesignProtocol
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
assign()
(in
PDBSilentStruct
)
acknowledge_neighbors_state_substitution()
(in
SymmMinimalistNode
)
AntibodyDesignProtocolAP
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
assign()
(in
BinarySilentStruct
)
acknowledge_neighbors_substitution()
(in
MinimalistFlexbbNode
)
AntibodyDesignProtocolCAP
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
assign()
(in
RNA_SilentStruct
)
acknowledge_partial_state_assignment()
(in
FASTEREdge
)
AntibodyDesignProtocolCreator
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
assign()
(in
RigidBodySilentStruct
)
acknowledge_partial_state_assignment()
(in
FlexbbEdge
)
AntibodyDesignProtocolCreatorAP
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
assign()
(in
ScoreFileSilentStruct
)
acknowledge_partial_state_change()
(in
DoubleLazyEdge
)
AntibodyDesignProtocolCreatorCAP
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
assign()
(in
ScoreJumpFileSilentStruct
)
acknowledge_partial_state_change()
(in
LazyEdge
)
AntibodyDesignProtocolEnum
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
assign()
(in
SilentStruct
)
acknowledge_partial_state_change()
(in
LinearMemEdge
)
AntibodyEnumManager
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
AtomTree
)
acknowledge_partial_state_change()
(in
SymmLinearMemEdge
)
AntibodyEnumManagerAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
FoldTree
)
acknowledge_partial_state_change()
(in
SymmMinimalistEdge
)
AntibodyEnumManagerCAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
Jump
)
acknowledge_participation_in_perturbation()
(in
FASTEREdge
)
AntibodyFeatures
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
RT
)
acknowledge_perturbed_state()
(in
FASTEREdge
)
AntibodyFeaturesAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
ResidueCoordinateChangeList
)
acknowledge_state_change()
(in
DensePDEdge
)
AntibodyFeaturesCAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
DotSphere
)
acknowledge_state_change()
(in
DoubleDensePDEdge
)
AntibodyFeaturesCreator
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
InvRotamerDots
)
acknowledge_state_change()
(in
DoubleLazyEdge
)
AntibodyFeaturesCreatorAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
RotamerDots
)
acknowledge_state_change()
(in
FASTEREdge
)
AntibodyFeaturesCreatorCAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
RotamerDotsCache
)
acknowledge_state_change()
(in
LazyEdge
)
AntibodyInfo
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
ResidueAtomTreeCollectionMomento
)
acknowledge_state_change()
(in
LinearMemEdge
)
AntibodyInfoAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
TaskFactory
)
acknowledge_state_change()
(in
PDEdge
)
AntibodyInfoCAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
OperateOnCertainResidues
)
acknowledge_state_change()
(in
SymmLinearMemEdge
)
AntibodyModeler
(in
rosetta.protocols.antibody_legacy._protocols_antibody_legacy_
)
assign()
(in
OperateOnResidueSubset
)
acknowledge_state_change()
(in
SymmMinimalistEdge
)
AntibodyModelerAP
(in
rosetta.protocols.antibody_legacy._protocols_antibody_legacy_
)
assign()
(in
SetRotamerCouplings
)
acknowledge_state_zeroed()
(in
DensePDEdge
)
AntibodyModelerCAP
(in
rosetta.protocols.antibody_legacy._protocols_antibody_legacy_
)
assign()
(in
SetRotamerLinks
)
acknowledge_state_zeroed()
(in
DoubleDensePDEdge
)
AntibodyModelerProtocol
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
PDBInfo
)
acknowledge_state_zeroed()
(in
DoubleLazyEdge
)
AntibodyModelerProtocolAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
PDBPoseMap
)
acknowledge_state_zeroed()
(in
FASTEREdge
)
AntibodyModelerProtocolCAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
Pose
)
acknowledge_state_zeroed()
(in
LazyEdge
)
AntibodyNumbering
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
CacheableObserver
)
acknowledge_state_zeroed()
(in
LinearMemEdge
)
AntibodyNumberingAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
LengthEventCollector
)
acknowledge_state_zeroed()
(in
PDEdge
)
AntibodyNumberingCAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
ObserverCache
)
acknowledge_state_zeroed()
(in
SymmLinearMemEdge
)
AntibodyNumberingParser
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
SpecialSegmentsObserver
)
acknowledge_state_zeroed()
(in
SymmMinimalistEdge
)
AntibodyNumberingParserAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
PoseMetricContainer
)
acknowledge_state_zeroed()
(in
MinimalistFlexbbEdge
)
AntibodyNumberingParserCAP
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
RNA_SuiteName
)
acknowledge_substitution()
(in
DensePDEdge
)
AntibodyNumberingSchemeEnum
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
ConformationEvent
)
acknowledge_substitution()
(in
DoubleDensePDEdge
)
AntibodyNumberingSchemeEnum_start
(in
rosetta.protocols.antibody
)
assign()
(in
DestructionEvent
)
acknowledge_substitution()
(in
DoubleLazyEdge
)
AntibodyNumberingSchemeEnum_start
(in
AntibodyNumberingSchemeEnum
)
assign()
(in
EnergyEvent
)
acknowledge_substitution()
(in
FASTEREdge
)
AntibodyNumberingSchemeEnum_start
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
GeneralEvent
)
acknowledge_substitution()
(in
LazyEdge
)
AntibodyNumberingSchemeEnum_total
(in
rosetta.protocols.antibody
)
assign()
(in
ChemicalShiftAnisotropy
)
acknowledge_substitution()
(in
LinearMemEdge
)
AntibodyNumberingSchemeEnum_total
(in
AntibodyNumberingSchemeEnum
)
assign()
(in
ContextGraph
)
acknowledge_substitution()
(in
PDEdge
)
AntibodyNumberingSchemeEnum_total
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
DenseNeighborConstIterator
)
acknowledge_substitution()
(in
SymmLinearMemEdge
)
AntibodyRegionEnum
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
DenseNeighborIterator
)
acknowledge_substitution()
(in
SymmMinimalistEdge
)
AntibodyRegionEnum_start
(in
rosetta.protocols.antibody
)
assign()
(in
DipolarCoupling
)
acknowledge_substitution()
(in
MinimalistFlexbbEdge
)
AntibodyRegionEnum_start
(in
AntibodyRegionEnum
)
assign()
(in
DockingScoreFunction
)
actcoord()
(in
Residue
)
AntibodyRegionEnum_start
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
EMapVector
)
actcoord_atoms()
(in
ResidueType
)
AntibodyRegionEnum_total
(in
rosetta.protocols.antibody
)
assign()
(in
Energies
)
actcoord_atoms()
(in
Residue
)
AntibodyRegionEnum_total
(in
AntibodyRegionEnum
)
assign()
(in
EnergyGraph
)
activate_daemon_mode()
(in
DaemonSet
)
AntibodyRegionEnum_total
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
Hairpin
)
active_1benmeths_begin()
(in
MinimizationNode
)
AntibodySeqDesignTFCreator
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
assign()
(in
Hairpins
)
active_1benmeths_end()
(in
MinimizationNode
)
AntibodySeqDesignTFCreatorAP
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
assign()
(in
Helices
)
active_1benmeths_ext_begin()
(in
MinimizationNode
)
AntibodySeqDesignTFCreatorCAP
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
assign()
(in
MinScoreScoreFunction
)
active_1benmeths_ext_end()
(in
MinimizationNode
)
antigen_present()
(in
AntibodyInfo
)
assign()
(in
MinimizationGraph
)
active_1benmeths_std_begin()
(in
MinimizationNode
)
antigen_region
(in
AntibodyRegionEnum
)
assign()
(in
OneToAllNeighborConstIterator
)
active_1benmeths_std_end()
(in
MinimizationNode
)
antigen_region
(in
rosetta.protocols.antibody._protocols_antibody_
)
assign()
(in
OneToAllNeighborIterator
)
active_2b_score_types()
(in
EnergyGraph
)
antigen_region
(in
rosetta.protocols.antibody
)
assign()
(in
PeptideBondedNeighborConstIterator
)
active_2benmeths_begin()
(in
MinimizationEdge
)
antiparallel()
(in
StrandPairing
)
assign()
(in
PeptideBondedNeighborIterator
)
active_2benmeths_end()
(in
MinimizationEdge
)
antiparallel()
(in
AlternativePairings
)
assign()
(in
ResPairMinimizationData
)
active_2benmeths_ext_begin()
(in
MinimizationEdge
)
ANY
(in
rosetta.protocols.stepwise.sampler
)
assign()
(in
ResSingleMinimizationData
)
active_2benmeths_ext_end()
(in
MinimizationEdge
)
ANY
(in
rosetta.protocols.stepwise.sampler._protocols_stepwise_sampler_
)
assign()
(in
ResidualDipolarCoupling
)
active_2benmeths_std_begin()
(in
MinimizationEdge
)
ANY
(in
StepWiseSamplerType
)
assign()
(in
ResidueNeighborConstIterator
)
active_2benmeths_std_end()
(in
MinimizationEdge
)
any_active_enmeths()
(in
MinimizationEdge
)
assign()
(in
ResidueNeighborIterator
)
active_angle()
(in
MC_OneTorsion
)
ANY_BASE_EDGE
(in
rosetta.core.chemical.rna
)
assign()
(in
ScoreFunction
)
active_constraint()
(in
AmbiguousConstraint
)
ANY_BASE_EDGE
(in
rosetta.core.chemical.rna._core_chemical_rna_
)
assign()
(in
SecondaryStructureWeights
)
active_constraints()
(in
KofNConstraint
)
ANY_BASE_EDGE
(in
BaseEdge
)
assign()
(in
Strands
)
active_dofs()
(in
DofPassport
)
ANY_CHI
(in
rosetta.core.chemical.rna
)
assign()
(in
TenANeighborGraph
)
active_intrares2benmeths_begin()
(in
MinimizationNode
)
ANY_CHI
(in
rosetta.core.chemical.rna._core_chemical_rna_
)
assign()
(in
TwelveANeighborGraph
)
active_intrares2benmeths_end()
(in
MinimizationNode
)
ANY_CHI
(in
ChiState
)
assign()
(in
ConstraintGraph
)
active_intrares2benmeths_ext_begin()
(in
MinimizationNode
)
any_lr_residue_pair_energy()
(in
ScoreFunction
)
assign()
(in
Constraints
)
active_intrares2benmeths_ext_end()
(in
MinimizationNode
)
any_neighbors_for_residue()
(in
DenseEnergyContainer
)
assign()
(in
CstResNeighbConstIterator
)
active_intrares2benmeths_std_begin()
(in
MinimizationNode
)
any_neighbors_for_residue()
(in
LREnergyContainer
)
assign()
(in
CstResNeighbIterator
)
active_intrares2benmeths_std_end()
(in
MinimizationNode
)
any_neighbors_for_residue()
(in
OneToAllEnergyContainer
)
assign()
(in
CentroidDisulfideNeighborConstIterator
)
active_jumps()
(in
DofPassport
)
any_neighbors_for_residue()
(in
PeptideBondedEnergyContainer
)
assign()
(in
CentroidDisulfideNeighborIterator
)
active_pose_constraints()
(in
EnzdesCstParamCache
)
any_neighbors_for_residue()
(in
CstEnergyContainer
)
assign()
(in
DisulfResNeighbConstIterator
)
active_score_types()
(in
EnergyGraph
)
any_neighbors_for_residue()
(in
CentroidDisulfideEnergyContainer
)
assign()
(in
DisulfResNeighbIterator
)
active_variables()
(in
AbsoluteValueExpression
)
any_neighbors_for_residue()
(in
DisulfideMatchingEnergyContainer
)
assign()
(in
DisulfideMatchingNeighborConstIterator
)
active_variables()
(in
AddExpression
)
any_neighbors_for_residue()
(in
FullatomDisulfideEnergyContainer
)
assign()
(in
DisulfideMatchingNeighborIterator
)
active_variables()
(in
AndExpression
)
ANY_PUCKER
(in
rosetta.core.chemical.rna
)
assign()
(in
EtableOptions
)
active_variables()
(in
BinaryExpression
)
ANY_PUCKER
(in
rosetta.core.chemical.rna._core_chemical_rna_
)
assign()
(in
HBEvalTuple
)
active_variables()
(in
DivideExpression
)
ANY_PUCKER
(in
PuckerState
)
assign()
(in
HBondOptions
)
active_variables()
(in
EqualsExpression
)
ANY_TORSION
(in
rosetta.core.chemical.rna
)
assign()
(in
Loop
)
active_variables()
(in
Expression
)
ANY_TORSION
(in
rosetta.core.chemical.rna._core_chemical_rna_
)
assign()
(in
EnergyMethodOptions
)
active_variables()
(in
GTE_Expression
)
ANY_TORSION
(in
RNA_Torsion
)
assign()
(in
LinearChainbreakEnergy
)
active_variables()
(in
GT_Expression
)
any_upper_neighbors_for_residue()
(in
DenseEnergyContainer
)
assign()
(in
RNA_DataInfo
)
active_variables()
(in
ITEExpression
)
any_upper_neighbors_for_residue()
(in
LREnergyContainer
)
assign()
(in
SurfaceEnergies
)
active_variables()
(in
LTE_Expression
)
any_upper_neighbors_for_residue()
(in
OneToAllEnergyContainer
)
assign()
(in
SymmetricEnergies
)
active_variables()
(in
LT_Expression
)
any_upper_neighbors_for_residue()
(in
PeptideBondedEnergyContainer
)
assign()
(in
SymmetricScoreFunction
)
active_variables()
(in
LiteralExpression
)
any_upper_neighbors_for_residue()
(in
CstEnergyContainer
)
assign()
(in
AnnotatedSequence
)
active_variables()
(in
MaxExpression
)
any_upper_neighbors_for_residue()
(in
CentroidDisulfideEnergyContainer
)
assign()
(in
Cell
)
active_variables()
(in
MetaMaxExpression
)
any_upper_neighbors_for_residue()
(in
DisulfideMatchingEnergyContainer
)
assign()
(in
ChemicalShiftSequence
)
active_variables()
(in
MetaMinExpression
)
any_upper_neighbors_for_residue()
(in
FullatomDisulfideEnergyContainer
)
assign()
(in
CompositeSequence
)
active_variables()
(in
MinExpression
)
any_vertex_state_unassigned()
(in
InteractionGraphBase
)
assign()
(in
DerivedSequenceMapping
)
active_variables()
(in
MultiplyExpression
)
AnyResFilter
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
Line
)
active_variables()
(in
NotExpression
)
AnyResFilterAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
Sequence
)
active_variables()
(in
OrExpression
)
AnyResFilterCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
SequenceAlignment
)
active_variables()
(in
SquarerootExpression
)
AnyResFilterCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
SequenceCoupling
)
active_variables()
(in
SubtractExpression
)
AnyResFilterCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
SequenceProfile
)
active_variables()
(in
UnaryExpression
)
AnyResFilterCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
HomogeneousTransform_T_double_T
)
active_variables()
(in
VariableExpression
)
APBSConfig
(in
rosetta.core.scoring._core_scoring_
)
assign()
(in
MultiDimensionalHistogram
)
active_variables()
(in
ExpExpression
)
APBSConfigAP
(in
rosetta.core.scoring._core_scoring_
)
assign()
(in
xyzMatrix_T_float_T
)
active_variables()
(in
InSetExpression
)
APBSConfigCAP
(in
rosetta.core.scoring._core_scoring_
)
assign()
(in
xyzTriple_Real
)
active_variables()
(in
IterativeVectorExpression
)
APBSResult
(in
rosetta.core.scoring._core_scoring_
)
assign()
(in
xyzTriple_SSize
)
active_variables()
(in
LnExpression
)
APBSResultAP
(in
rosetta.core.scoring._core_scoring_
)
assign()
(in
xyzTriple_Size
)
active_variables()
(in
PowExpression
)
APBSResultCAP
(in
rosetta.core.scoring._core_scoring_
)
assign()
(in
xyzTriple_double
)
active_variables()
(in
SurrogateVariableExpression
)
APBSWrapper
(in
rosetta.core.scoring._core_scoring_
)
assign()
(in
xyzTriple_float
)
active_variables()
(in
VMax
)
APBSWrapperAP
(in
rosetta.core.scoring._core_scoring_
)
assign()
(in
xyzVector_Real
)
active_variables()
(in
VMaxBy
)
APBSWrapperCAP
(in
rosetta.core.scoring._core_scoring_
)
assign()
(in
xyzVector_SSize
)
active_variables()
(in
VMin
)
APCluster
(in
rosetta.protocols.cluster._protocols_cluster_
)
assign()
(in
xyzVector_Size
)
active_variables()
(in
VMinBy
)
APClusterAP
(in
rosetta.protocols.cluster._protocols_cluster_
)
assign()
(in
xyzVector_double
)
active_variables()
(in
VariableVectorExpression
)
APClusterCAP
(in
rosetta.protocols.cluster._protocols_cluster_
)
assign()
(in
xyzVector_float
)
active_variables()
(in
VectorExpression
)
APOLA
(in
rosetta.core.pack.task._core_pack_task_
)
assign()
(in
HyperRectangle
)
active_variables_vector()
(in
IterativeVectorExpression
)
APOLAAP
(in
rosetta.core.pack.task._core_pack_task_
)
assign()
(in
KDPoint
)
active_variables_vector()
(in
VariableVectorExpression
)
APOLACAP
(in
rosetta.core.pack.task._core_pack_task_
)
assign()
(in
WeightedSampler
)
active_variables_vector()
(in
VectorExpression
)
APOLAR
(in
rosetta.core.pack.task._core_pack_task_
)
assign()
(in
PeptideDeriverFilter
)
ActiveSiteGrid
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
apolar_hydrogens()
(in
ResidueType
)
assign()
(in
Anchor
)
ActiveSiteGridAP
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
APOLARAP
(in
rosetta.core.pack.task._core_pack_task_
)
assign()
(in
AnchorMoversData
)
ActiveSiteGridCAP
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
APOLARCAP
(in
rosetta.core.pack.task._core_pack_task_
)
assign()
(in
AnchoredDesignMover
)
actual_bb()
(in
Bool3DGrid
)
APolarHydrogenFilter
(in
rosetta.core.chemical._core_chemical_
)
assign()
(in
GraftOneCDRLoop
)
actual_cycles()
(in
CCDLoopClosureMover
)
APolarHydrogenFilterAP
(in
rosetta.core.chemical._core_chemical_
)
assign()
(in
GraftedStemOptimizer
)
actual_residue_connection()
(in
Residue
)
APolarHydrogenFilterCAP
(in
rosetta.core.chemical._core_chemical_
)
assign()
(in
PDBLandmark
)
actual_twobody_memory_use()
(in
DoubleLazyEdge
)
append
(in
StubMode
)
assign()
(in
AsyncMPITemperingBase
)
actually_moving_res()
(in
StepWiseBasicWorkingParameters
)
append
(in
rosetta.protocols.cyclic_peptide._protocols_cyclic_peptide_
)
assign()
(in
HamiltonianExchange
)
actually_moving_res()
(in
StepWiseWorkingParameters
)
append
(in
rosetta.protocols.cyclic_peptide
)
assign()
(in
MetricRecorder
)
adaptation_period()
(in
GenericMonteCarloMover
)
append()
(in
vector1_AtomID
)
assign()
(in
ParallelTempering
)
adaptive_movers()
(in
GenericMonteCarloMover
)
append()
(in
vector1_Pose
)
assign()
(in
LoopRelaxMover
)
AdaptiveScoreHistogram
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
append()
(in
vector1_PoseOP
)
assign()
(in
DnaInterfaceMinMover
)
AdaptiveScoreHistogramAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
append()
(in
vector1_ScoreType
)
assign()
(in
DockSetupMover
)
AdaptiveScoreHistogramCAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
append()
(in
vector1_core_conformation_Atom
)
assign()
(in
DockingProtocol
)
ADD
(in
rosetta.protocols.stepwise.monte_carlo.mover
)
append()
(in
vector1_pair_Real_Real
)
assign()
(in
EllipsoidalRandomizationMover
)
ADD
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
append()
(in
vector1_pair_Real_string
)
assign()
(in
TemperedDocking
)
ADD
(in
MoveType
)
append()
(in
vector1_pair_SSize_SSize
)
assign()
(in
ProtectedConformation
)
add()
(in
DataMap
)
append()
(in
vector1_pair_SSize_string
)
assign()
(in
TorsionSet
)
Add()
(in
QuatSet
)
append()
(in
vector1_pair_Size_Real
)
assign()
(in
OtherContextScoreFunction
)
add()
(in
FragSet
)
append()
(in
vector1_pair_Size_Size
)
assign()
(in
FloppyTailMover
)
add()
(in
AminoAcidNeighborSparseMatrix_T_float_T
)
append()
(in
vector1_pair_Size_SymDof
)
assign()
(in
Bridge
)
add()
(in
Pool_RMSD
)
append()
(in
vector1_pair_Size_string
)
assign()
(in
BuildInstruction
)
add()
(in
BuildManager
)
append()
(in
vector1_pair_char_pair_Size_Size
)
assign()
(in
BuildManager
)
add()
(in
BoundedCollector_T_protocols_frag_picker_CompareTotalScore_T
)
append()
(in
vector1_pair_int_int
)
assign()
(in
ConnectRight
)
add()
(in
CandidatesCollector
)
append()
(in
vector1_pair_int_string
)
assign()
(in
GrowLeft
)
add()
(in
GrabAllCollector
)
append()
(in
vector1_pair_string_Real
)
assign()
(in
GrowRight
)
add()
(in
ABEGO_SS_Pool
)
append()
(in
vector1_pair_string_SSize
)
assign()
(in
Interval
)
add()
(in
QuotaCollector
)
append()
(in
vector1_pair_string_Size
)
assign()
(in
RelativeConnectRight
)
add()
(in
QuotaPool
)
append()
(in
vector1_pair_string_int
)
assign()
(in
SegmentRebuild
)
add()
(in
SecondaryStructurePool
)
append()
(in
vector1_pair_string_string
)
assign()
(in
SegmentSwap
)
add()
(in
PerturberSet
)
append()
(in
vector1_xyzVector_Real
)
assign()
(in
VallResidue
)
add()
(in
CCluster
)
append()
(in
vector1_xyzVector_SSize
)
assign()
(in
Entity
)
add()
(in
CClusterSet
)
append()
(in
vector1_xyzVector_Size
)
assign()
(in
EntityElement
)
add()
(in
PCluster
)
append()
(in
vector1_xyzVector_bool
)
assign()
(in
HotspotStub
)
add()
(in
PClusterSet
)
append()
(in
vector1_xyzVector_char
)
assign()
(in
LoopHashMap
)
add()
(in
SilentStructStore
)
append()
(in
vector1_xyzVector_float
)
assign()
(in
GuardedLoopsFromFile
)
add()
(in
WorkUnitQueue
)
append()
(in
vector1_xyzVector_int
)
assign()
(in
Loops
)
add()
(in
WorkUnitQueue_Swapped
)
append()
(in
vector1_xyzVector_uint
)
assign()
(in
CCDLoopClosureMover
)
add()
(in
set_Real
)
append()
(in
vector1_FragData
)
assign()
(in
RamaCheck1B
)
add()
(in
set_SSize
)
append()
(in
vector1_FragDataOP
)
assign()
(in
RamaCheck2B
)
add()
(in
set_Size
)
append()
(in
vector1_Frame
)
assign()
(in
RamaCheckBase
)
add()
(in
set_char
)
append()
(in
vector1_FrameOP
)
assign()
(in
LoopMover
)
add()
(in
set_double
)
append()
(in
LKB_ResiduesInfo
)
assign()
(in
LoopRefineInnerCycle
)
add()
(in
set_float
)
append()
(in
vector1_numeric_geometry_hashing_Ball
)
assign()
(in
LoopRefineInnerCycleContainer
)
add()
(in
set_int
)
append()
(in
TokenSet
)
assign()
(in
RepackTrial
)
add()
(in
set_string
)
append()
(in
vector1_basicjob
)
assign()
(in
ShearMinCCDTrial
)
add()
(in
set_uint
)
append()
(in
LoadPDBMover
)
assign()
(in
SmallMinCCDTrial
)
add_acceptance_check()
(in
LoopProtocol
)
append()
(in
std_vector_Real
)
assign()
(in
BumpGrid
)
add_actcoord_atom()
(in
ResidueType
)
append()
(in
std_vector_SSize
)
assign()
(in
MatcherTask
)
add_additional_low_resolution_step()
(in
DockingProtocol
)
append()
(in
std_vector_Size
)
assign()
(in
ActiveSiteGrid
)
add_additional_task_operaration()
(in
DockTaskFactory
)
append()
(in
std_vector_char
)
assign()
(in
DownstreamAlgorithm
)
add_additional_task_operaration()
(in
DockingHighRes
)
append()
(in
std_vector_double
)
assign()
(in
MatchScoreWriter
)
add_additional_task_operaration()
(in
DockingProtocol
)
append()
(in
std_vector_float
)
assign()
(in
BuildSet
)
add_adduct()
(in
ResidueType
)
append()
(in
std_vector_int
)
assign()
(in
FlipMover
)
add_all_evaluators()
(in
EvaluatorFactory
)
append()
(in
std_vector_string
)
assign()
(in
RandomPositionRotationMover
)
add_aln()
(in
AlignmentCluster
)
append()
(in
std_vector_uint
)
assign()
(in
RandomPositionTranslationMover
)
add_angle_parameter()
(in
ResidueCartBondedParameters
)
append()
(in
vec1_vec1_Real
)
assign()
(in
SetMembraneCenterMover
)
add_another_virtual_res()
(in
rosetta.protocols.toolbox.sample_around._protocols_toolbox_sample_around_
)
append()
(in
vec1_vec1_SSize
)
assign()
(in
SetMembraneNormalMover
)
add_apply_mover()
(in
EnvMover
)
append()
(in
vec1_vec1_Size
)
assign()
(in
SetMembranePositionMover
)
add_as_other_struct_if_relevant()
(in
SilentFileData
)
append()
(in
vec1_vec1_bool
)
assign()
(in
Embedding
)
add_at_ind()
(in
AtomGeometrySecMatchRPE
)
append()
(in
vec1_vec1_char
)
assign()
(in
EmbeddingDef
)
add_atmname_using()
(in
GoapRsdType
)
append()
(in
vec1_vec1_double
)
assign()
(in
VisualizeEmbeddingMover
)
add_atom()
(in
ResidueType
)
append()
(in
vec1_vec1_float
)
assign()
(in
VisualizeMembraneMover
)
add_atom()
(in
MolFileIOMolecule
)
append()
(in
vec1_vec1_int
)
assign()
(in
LigandMotifSearch
)
add_atom()
(in
MinimizerMapBase
)
append()
(in
vec1_vec1_string
)
assign()
(in
MotifSearch
)
add_atom()
(in
rosetta.core.kinematics._core_kinematics_
)
append()
(in
vec1_vec1_uint
)
assign()
(in
FilterReporterMover
)
add_atom()
(in
CartesianMinimizerMap
)
append()
(in
vector1_Real
)
assign()
(in
Mover
)
add_atom()
(in
DOF_Node
)
append()
(in
vector1_SSize
)
assign()
(in
EntityCorrespondence
)
add_atom()
(in
MinimizerMap
)
append()
(in
vector1_Size
)
assign()
(in
CClusterSet
)
add_atom()
(in
SymMinimizerMap
)
append()
(in
vector1_bool
)
assign()
(in
PClusterSet
)
add_atom()
(in
SmallMol
)
append()
(in
vector1_char
)
assign()
(in
PocketGrid
)
add_atom_alias()
(in
ResidueType
)
append()
(in
vector1_double
)
assign()
(in
VLB
)
add_atom_set()
(in
GeneralizedKICperturber
)
append()
(in
vector1_float
)
assign()
(in
JSON_RPC
)
add_atom_type_set_parameters_from_command_line()
(in
rosetta.core.chemical._core_chemical_
)
append()
(in
vector1_int
)
assign()
(in
GridSearchIterator
)
add_atomgeom_evaluator()
(in
GeometrySecMatchRPE
)
append()
(in
vector1_string
)
assign()
(in
PCS_Energy
)
add_atomset_to_perturber_atomset_list()
(in
GeneralizedKIC
)
append()
(in
vector1_uint
)
assign()
(in
PCS_data
)
add_backrub_mover()
(in
MetropolisHastingsMover
)
append_atom()
(in
Atom
)
assign()
(in
PCS_data_input
)
add_batch()
(in
JobDistributor
)
append_atom()
(in
Atom_
)
assign()
(in
PCS_data_per_lanthanides
)
add_bb_clone()
(in
SymmetryInfo
)
append_automorphic_rmsd()
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
assign()
(in
PCS_file_data
)
add_bb_csts_to_loop()
(in
PlaceOnLoop
)
append_char()
(in
Sequence
)
assign()
(in
PCS_line_data
)
add_bbdep_angle_parameter()
(in
ResidueCartBondedParameters
)
append_choices()
(in
Mutate1Randomizer
)
assign()
(in
PCS_tensor
)
add_bbdep_length_parameter()
(in
ResidueCartBondedParameters
)
append_choices()
(in
PositionSpecificRandomizer
)
assign()
(in
GridSearchIterator
)
add_behavior()
(in
PackerTask
)
append_combine_history()
(in
CombinePoseMover
)
assign()
(in
GridSearchIteratorCA
)
add_behavior()
(in
PackerTask_
)
append_downstream_atom_to_active_site_required_list()
(in
MatcherTask
)
assign()
(in
PcsDataCenter
)
add_behavior()
(in
ResidueLevelTask
)
append_fold_tree_to_file()
(in
rosetta.protocols.backrub._protocols_backrub_
)
assign()
(in
PcsDataCenterManager
)
add_behavior()
(in
ResidueLevelTask_
)
append_fragment()
(in
SingleResidueTorsionFragmentLibrary
)
assign()
(in
PcsDataLanthanide
)
add_big_fragments()
(in
HybridizeProtocol
)
append_gap()
(in
Sequence
)
assign()
(in
PcsEnergy
)
add_black_listed_file()
(in
Inline_File_Provider
)
append_hairpin()
(in
Hairpins
)
assign()
(in
PcsEnergyParameter
)
add_blacklist()
(in
WorkUnitBase
)
append_hbond()
(in
HBondSet
)
assign()
(in
PcsGridSearchParameter
)
add_bond()
(in
ResidueType
)
append_interface_deltas()
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
assign()
(in
PcsInputCenter
)
add_bond()
(in
MolFileIOMolecule
)
append_ligand_docking_scores()
(in
LigandDockProtocol
)
assign()
(in
PcsInputFile
)
add_boundary_function()
(in
SplineGenerator
)
append_ligand_grid_scores()
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
assign()
(in
PcsInputLine
)
add_build_set()
(in
ProteinUpstreamBuilder
)
append_ligand_RMSD()
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
assign()
(in
PcsTensor
)
add_CDR_to_MoveMap()
(in
AntibodyInfo
)
append_ligand_travel()
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
assign()
(in
GridSearchIterator_Ts1
)
add_chain_ending()
(in
BinarySilentStruct
)
append_multi_residue_ligand_RMSD()
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
assign()
(in
PCS_Energy_Ts1
)
add_chainbreak_variants()
(in
KinematicControl
)
append_peptide()
(in
FoldTreeSketch
)
assign()
(in
PCS_data_Ts1
)
add_chainbreaks()
(in
JumpSample
)
append_polymer_residue_after_seqpos()
(in
Conformation
)
assign()
(in
PCS_data_input_Ts1
)
add_chainbreaks_according_to_jumps()
(in
rosetta.protocols.toolbox.pose_manipulation._protocols_toolbox_pose_manipulation_
)
append_polymer_residue_after_seqpos()
(in
Pose
)
assign()
(in
PCS_data_per_lanthanides_Ts1
)
add_chainbreaks_as_distance_constraint()
(in
JumpSample
)
append_polymer_residue_after_seqpos()
(in
ProtectedConformation
)
assign()
(in
PCS_file_data_Ts1
)
add_chi()
(in
ResidueType
)
append_pose_by_jump()
(in
Pose
)
assign()
(in
PCS_line_data_Ts1
)
add_chi_clone()
(in
SymmetryInfo
)
append_pose_to_pose()
(in
rosetta.core.pose._core_pose_
)
assign()
(in
PCS_tensor_Ts1
)
add_chi_rotamer()
(in
ResidueType
)
append_radius_of_gyration()
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
assign()
(in
GridSearchIterator_Ts2
)
add_chi_rotamer_to_last_chi()
(in
ResidueType
)
append_res()
(in
PDBInfo
)
assign()
(in
PCS_Energy_Ts2
)
add_choice()
(in
DiscreteRandomizer
)
append_residue()
(in
FoldTreeSketch
)
assign()
(in
PCS_data_Ts2
)
add_chunk_filter()
(in
FragmentPicker
)
append_residue()
(in
VallSection
)
assign()
(in
PCS_data_input_Ts2
)
add_chunk_set()
(in
RNA_ChunkLibrary
)
append_residue()
(in
FileData
)
assign()
(in
PCS_data_per_lanthanides_Ts2
)
add_circle()
(in
Slice
)
append_residue()
(in
FoldTree
)
assign()
(in
PCS_file_data_Ts2
)
add_cluster_comments_to_pose()
(in
rosetta.protocols.antibody.clusters._protocols_antibody_clusters_
)
append_residue()
(in
AllowInsert
)
assign()
(in
PCS_line_data_Ts2
)
add_column()
(in
InsertGenerator
)
append_residue_by_bond()
(in
Conformation
)
assign()
(in
PCS_tensor_Ts2
)
add_column()
(in
PrimaryKey
)
append_residue_by_bond()
(in
Pose
)
assign()
(in
GridSearchIterator_Ts3
)
add_column()
(in
Schema
)
append_residue_by_chemical_bond()
(in
FoldTree
)
assign()
(in
PCS_Energy_Ts3
)
add_comment()
(in
SilentStruct
)
append_residue_by_jump()
(in
Conformation
)
assign()
(in
PCS_data_Ts3
)
add_comment()
(in
rosetta.core.pose._core_pose_
)
append_residue_by_jump()
(in
SymmetricConformation
)
assign()
(in
PCS_data_input_Ts3
)
add_components_to_pose_if_necessary()
(in
SymDofMover
)
append_residue_by_jump()
(in
Pose
)
assign()
(in
PCS_data_per_lanthanides_Ts3
)
add_compositeSegmentMover()
(in
RBSegmentRelax
)
append_residue_by_jump()
(in
ProtectedConformation
)
assign()
(in
PCS_file_data_Ts3
)
add_condition()
(in
IfThenFilter
)
append_rotamer_operation()
(in
PackerTask
)
assign()
(in
PCS_line_data_Ts3
)
add_constant()
(in
CalculatorFilter
)
append_rotamer_operation()
(in
PackerTask_
)
assign()
(in
PCS_tensor_Ts3
)
add_constraint()
(in
Schema
)
append_rotamer_operation()
(in
ResidueLevelTask
)
assign()
(in
GridSearchIterator_Ts4
)
add_constraint()
(in
Pose
)
append_rotamer_operation()
(in
ResidueLevelTask_
)
assign()
(in
PCS_Energy_Ts4
)
add_constraint()
(in
ConstraintSet
)
append_rotamerset_operation()
(in
PackerTask
)
assign()
(in
PCS_data_Ts4
)
add_constraint()
(in
Constraints
)
append_rotamerset_operation()
(in
PackerTask_
)
assign()
(in
PCS_data_input_Ts4
)
add_constraints()
(in
Pose
)
append_rotamerset_operation()
(in
ResidueLevelTask
)
assign()
(in
PCS_data_per_lanthanides_Ts4
)
add_constraints()
(in
ConstraintSet
)
append_rotamerset_operation()
(in
ResidueLevelTask_
)
assign()
(in
PCS_file_data_Ts4
)
add_constraints()
(in
AbrelaxApplication
)
append_seq()
(in
SequenceAnnotation
)
assign()
(in
PCS_line_data_Ts4
)
add_constraints()
(in
AddZincSiteConstraints
)
append_subpose_to_pose()
(in
rosetta.core.pose._core_pose_
)
assign()
(in
PCS_tensor_Ts4
)
add_constraints()
(in
ConstraintSetMover
)
append_to_tag()
(in
TagDefinition
)
assign()
(in
ConstrainToIdealMover
)
add_constraints()
(in
DensityScoringClaimer
)
append_upstream_resiue_as_defining_active_site()
(in
MatcherTask
)
assign()
(in
DOFHistogramRecorder
)
add_constraints()
(in
FoldandDockClaimer
)
AppendInterchangeabilityGroup_String
(in
rosetta.core.chemical._core_chemical_
)
assign()
(in
RingConformationMover
)
add_constraints()
(in
MembraneTopologyClaimer
)
AppendInterchangeabilityGroup_StringAP
(in
rosetta.core.chemical._core_chemical_
)
assign()
(in
UniformRotationMover
)
add_constraints()
(in
TopologyClaimer
)
AppendInterchangeabilityGroup_StringCAP
(in
rosetta.core.chemical._core_chemical_
)
assign()
(in
UniformTranslationMover
)
add_constraints_from_cmdline()
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
AppendMainchainAtom
(in
rosetta.core.chemical._core_chemical_
)
assign()
(in
StepWiseModeler
)
add_constraints_from_cmdline_to_pose()
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
AppendMainchainAtomAP
(in
rosetta.core.chemical._core_chemical_
)
assign()
(in
MainChainTorsionSet
)
add_constraints_from_cmdline_to_scorefxn()
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
AppendMainchainAtomCAP
(in
rosetta.core.chemical._core_chemical_
)
assign()
(in
SugarModeling
)
add_constraints_from_file()
(in
rosetta.protocols.dna._protocols_dna_
)
AppendResidueRotamerSet
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
AllowInsert
)
add_constraints_to_pose()
(in
EnzConstraintIO
)
AppendResidueRotamerSetAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
DummyClass
)
add_constraints_to_pose_for_block_without_clearing_and_header_processing()
(in
EnzConstraintIO
)
AppendResidueRotamerSetCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
GreedyKCenter
)
add_coordinate_constraints()
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
AppendResidueRotamerSetCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
KCluster
)
add_coordinate_constraints()
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
AppendResidueRotamerSetCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
KMedoid
)
add_coordinate_constraints_to_pose()
(in
rosetta.protocols.loops._protocols_loops_
)
AppendResidueRotamerSetCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
SF_Replica
)
add_coordinate_constraints_to_pose()
(in
rosetta.protocols.relax._protocols_relax_
)
AppendRotamer
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
ExternalGeomSampler
)
add_coordinate_from_string()
(in
VirtualCoordinate
)
AppendRotamerAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
MetricValueGetter
)
add_coordinatecst_for_hotspot_packing()
(in
PlaceSimultaneouslyMover
)
AppendRotamerCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
ConservativeDesignOperation
)
add_coords()
(in
StartFrom
)
AppendRotamerCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
RestrictToLoops
)
add_coords_hash()
(in
StartFrom
)
AppendRotamerCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
RestrictToLoopsAndNeighbors
)
add_covalent_linkage()
(in
rosetta.core.util._core_util_
)
AppendRotamerCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
RestrictToNeighborhoodOperation
)
add_covalent_linkages_to_metal()
(in
rosetta.core.util._core_util_
)
AppendRotamerSet
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
subset_mapping
)
add_creator()
(in
ResFilterFactory
)
AppendRotamerSetAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
vector0_T_float_std_allocator_T_float_T__T
)
add_creator()
(in
ResLvlTaskOperationFactory
)
AppendRotamerSetCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
vector0_T_int_std_allocator_T_int_T__T
)
add_creator()
(in
TaskOperationFactory
)
AppendRotamerSetCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
vector0_T_std_list_T_boost_shared_ptr_T_utility_SimulateMPIMessage_T__std_allocator_T_boost_shared_ptr_T_utility_SimulateMPIMessage_T__T__T_std_allocator_T_std_list_T_boost_shared_ptr_T_utility_SimulateMPIMessage_T__std_allocator_T_boost_shared_ptr_T_utility_SimulateMPIMessage_T__T__T__T__T
)
add_cut_bond()
(in
ResidueType
)
AppendRotamerSetCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
vector0_T_utility_vector0_T_std_list_T_boost_shared_ptr_T_utility_SimulateMPIMessage_T__std_allocator_T_boost_shared_ptr_T_utility_SimulateMPIMessage_T__T__T__std_allocator_T_std_list_T_boost_shared_ptr_T_utility_SimulateMPIMessage_T__std_allocator_T_boost_shared_ptr_T_utility_SimulateMPIMessage_T__T__T__T__T_std_allocator_T_utility_vector0_T_std_list_T_boost_shared_ptr_T_utility_SimulateMPIMessage_T__std_allocator_T_boost_shared_ptr_T_utility_SimulateMPIMessage_T__T__T__std_allocator_T_std_list_T_boost_shared_ptr_T_utility_SimulateMPIMessage_T__std_allocator_T_boost_shared_ptr_T_utility_SimulateMPIMessage_T__T__T__T__T__T__T
)
add_cutpoint_closed()
(in
rosetta.protocols.stepwise.setup._protocols_stepwise_setup_
)
AppendRotamerSetCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
assign()
(in
vector1_T_utility_history_queue_struct_std_allocator_T_utility_history_queue_struct_T__T
)
add_cutpoint_variants()
(in
rosetta.protocols.forge.methods._protocols_forge_methods_
)
applicable()
(in
Pool_Evaluator
)
assign()
(in
FileName
)
add_cutpoint_variants()
(in
rosetta.protocols.loops._protocols_loops_
)
applicable()
(in
Align_RmsdEvaluator
)
assign()
(in
PathName
)
add_cutpoint_variants_for_ccd()
(in
rosetta.protocols.grafting._protocols_grafting_
)
applicable()
(in
Align_RotamerEvaluator
)
assign()
(in
Link
)
add_daemon
(in
DaemonSetMessage
)
applicable()
(in
CombinedConstraintEvaluator
)
assign()
(in
Tag
)
add_daemon
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
applicable()
(in
ConstraintEvaluator
)
assign_abase_derivs()
(in
rosetta.core.scoring.hbonds._core_scoring_hbonds_
)
add_daemon
(in
rosetta.protocols.pack_daemon
)
applicable()
(in
AlignEvaluator
)
assign_best_rotamer()
(in
CentroidRotamerSampleData
)
add_datum()
(in
RNA_DataInfo
)
applicable()
(in
MetaPoseEvaluator
)
assign_BMEC()
(in
FASTERInteractionGraph
)
add_decoy()
(in
PNatStructureOptEData
)
applicable()
(in
PoseEvaluator
)
assign_conformer_group_to_residue()
(in
LigandConformerBuilder
)
add_delete_frequency()
(in
StepWiseMoveSelector
)
applicable()
(in
SingleValuePoseEvaluator_T_double_T
)
assign_esp_for_atom_grid_points()
(in
ElectrostaticpotentialGrid
)
add_delete_frequency()
(in
StepWiseMonteCarloOptions
)
applicable()
(in
SingleValuePoseEvaluator_T_long_int_T
)
assign_esp_for_protein_grid_points()
(in
ElectrostaticpotentialGrid
)
add_delta_omega1_value()
(in
BundleParameters
)
applicable()
(in
SingleValuePoseEvaluator_T_long_unsigned_int_T
)
assign_esp_for_surface_grid_points()
(in
ElectrostaticpotentialGrid
)
add_delta_z1_value()
(in
BundleParameters
)
applicable()
(in
TimeEvaluator
)
assign_esp_for_surface_grid_points_by_nn()
(in
ElectrostaticpotentialGrid
)
add_dens_scores_from_cmdline_to_scorefxn()
(in
rosetta.core.scoring.electron_density._core_scoring_electron_density_
)
applicable()
(in
BatchEvaluator
)
assign_gasteiger_atom_types()
(in
rosetta.core.chemical.gasteiger._core_chemical_gasteiger_
)
add_dependency_to()
(in
BuildInstruction
)
applicable()
(in
BatchNrEvaluator
)
assign_group_for_match()
(in
MatchGrouper
)
add_deriv_data()
(in
NumericalDerivCheckResult
)
applicable()
(in
CamShiftEvaluator
)
assign_group_for_match()
(in
SameChiBinComboGrouper
)
add_design_task()
(in
FlxbbDesign
)
applicable()
(in
ChiWellRmsdEvaluator
)
assign_group_for_match()
(in
SameRotamerComboGrouper
)
add_diagonal()
(in
xyzMatrix_Real
)
applicable()
(in
ContactMapEvaluator
)
assign_group_for_match()
(in
SameSequenceAndDSPositionGrouper
)
add_diagonal()
(in
xyzMatrix_SSize
)
applicable()
(in
ExternalEvaluator
)
assign_group_for_match()
(in
SameSequenceGrouper
)
add_diagonal()
(in
xyzMatrix_Size
)
applicable()
(in
JScoreEvaluator
)
assign_haro_derivs_one_way()
(in
OrbitalsScore
)
add_diagonal()
(in
xyzMatrix_T_float_T
)
applicable()
(in
JumpEvaluator
)
assign_hpol_derivs_one_way()
(in
OrbitalsScore
)
add_diagonal()
(in
xyzMatrix_double
)
applicable()
(in
JumpNrEvaluator
)
assign_internal_coordinates()
(in
ResidueType
)
add_diagonal()
(in
xyzMatrix_float
)
applicable()
(in
LoopRmsdEvaluator
)
assign_last_rotamers_to_pose()
(in
PackDaemon
)
add_distance()
(in
Contact
)
applicable()
(in
PalesEvaluator
)
assign_neighbor_atom()
(in
ResidueType
)
add_DoF()
(in
BundleGridSamplerHelper
)
applicable()
(in
PredictedBurialEvaluator
)
assign_only_pi_orbitals_to_atom()
(in
AssignOrbitals
)
add_dof_access()
(in
DofPassport
)
applicable()
(in
RDC_Evaluator
)
assign_orb_H_derivs()
(in
OrbitalsScore
)
add_dof_constraint()
(in
ConstraintSet
)
applicable()
(in
RmsdEvaluator
)
assign_orb_orb_derivs()
(in
OrbitalsScore
)
add_dof_from_string()
(in
SymDof
)
applicable()
(in
ScoreEvaluator
)
assign_orbitals()
(in
AssignOrbitals
)
add_edge()
(in
UpperEdgeGraph_T_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_T
)
applicable()
(in
SelectGdtEvaluator
)
assign_pucker()
(in
rosetta.core.pose.rna._core_pose_rna_
)
add_edge()
(in
Graph
)
applicable()
(in
SelectMaxsubEvaluator
)
assign_random_chi()
(in
DunbrackRotamerSampleData
)
add_edge()
(in
Node
)
applicable()
(in
SelectRDC_Evaluator
)
assign_random_rotamer()
(in
CentroidRotamerSampleData
)
add_edge()
(in
FoldTree
)
applicable()
(in
SelectRmsdEvaluator
)
assign_random_rotamer_with_bias()
(in
SingleLigandRotamerLibrary
)
add_edge()
(in
InteractionGraphBase
)
applicable()
(in
StructuralSimilarityEvaluator
)
assign_random_rotamer_with_bias()
(in
SingleResidueRotamerLibrary
)
add_edge()
(in
NodeBase
)
applicable()
(in
SymmetricRmsdEvaluator
)
assign_random_rotamer_with_bias()
(in
SingleResidueCenrotLibrary
)
add_edge()
(in
PDInteractionGraph
)
applicable()
(in
TruncatedScoreEvaluator
)
assign_sp2_orbitals_to_one_bonded_atom()
(in
AssignOrbitals
)
add_encoded_termini()
(in
NMerSVMEnergy
)
applicable()
(in
ChemicalShiftEvaluator
)
assign_sp2_sp_orbitals_to_one_bonded_atom()
(in
AssignOrbitals
)
add_energy()
(in
SilentStruct
)
applies_to()
(in
Patch
)
assign_ss_dssp()
(in
rosetta.protocols.jumping._protocols_jumping_
)
add_energy_edge()
(in
EnergyGraph
)
applies_to()
(in
PatchCase
)
assign_state()
(in
DensePDNode
)
add_entity()
(in
GeneticAlgorithm
)
apply()
(in
PyMOLMover
)
assign_state()
(in
DoubleDensePDNode
)
add_entity()
(in
GeneticAlgorithmBase
)
apply()
(in
AddAtom
)
assign_state()
(in
DoubleLazyNode
)
add_entry()
(in
PairingStatistics
)
apply()
(in
AddAtomAlias
)
assign_state()
(in
FASTERNode
)
add_evaluated_structure()
(in
HedgeArchive
)
apply()
(in
AddBond
)
assign_state()
(in
LazyNode
)
add_evaluated_structure()
(in
IterativeAbrelax
)
apply()
(in
AddBondType
)
assign_state()
(in
LinearMemNode
)
add_evaluated_structure()
(in
IterativeBase
)
apply()
(in
AddChi
)
assign_state()
(in
PDNode
)
add_evaluated_structure()
(in
IterativeCentroid
)
apply()
(in
AddChiRotamer
)
assign_state()
(in
SymmLinearMemNode
)
add_evaluated_structure()
(in
IterativeFullatom
)
apply()
(in
AddConnect
)
assign_state()
(in
SymmMinimalistNode
)
add_evaluated_structure()
(in
EvaluatedArchive
)
apply()
(in
AddProperty
)
assign_state()
(in
MinimalistFlexbbNode
)
add_evaluated_structure()
(in
NormalizedEvaluatedArchive
)
apply()
(in
AddProtonChi
)
assign_type_data()
(in
KClusterElement
)
add_evaluated_structure()
(in
VarianceStatisticsArchive
)
apply()
(in
AppendInterchangeabilityGroup_String
)
assign_zero_state()
(in
DensePDNode
)
add_evaluation()
(in
AbrelaxApplication
)
apply()
(in
AppendMainchainAtom
)
assign_zero_state()
(in
DoubleDensePDNode
)
add_evaluation()
(in
Protocol
)
apply()
(in
DeleteAtom
)
assign_zero_state()
(in
DoubleLazyNode
)
add_evaluation()
(in
MetaPoseEvaluator
)
apply()
(in
DeleteMetalbindingAtom
)
assign_zero_state()
(in
FASTERNode
)
add_evaluation()
(in
JobOutputter
)
apply()
(in
DeleteProperty
)
assign_zero_state()
(in
LazyNode
)
add_evaluation()
(in
EvaluatedArchive
)
apply()
(in
DeleteTerminalChi
)
assign_zero_state()
(in
LinearMemNode
)
add_evaluator()
(in
SecondaryMatcherToDownstreamResidue
)
apply()
(in
NCAARotLibPath
)
assign_zero_state()
(in
NodeBase
)
add_evaluator_for_target_restype()
(in
SecondaryMatcherToUpstreamResidue
)
apply()
(in
Patch
)
assign_zero_state()
(in
OnTheFlyNode
)
add_evaluators()
(in
AlignRmsdTargetEvaluatorCreator
)
apply()
(in
PatchCase
)
assign_zero_state()
(in
PDNode
)
add_evaluators()
(in
CombinedConstraintEvaluatorCreator
)
apply()
(in
PatchOperation
)
assign_zero_state()
(in
SymmLinearMemNode
)
add_evaluators()
(in
ConstraintEvaluatorCreator
)
apply()
(in
PrependMainchainAtom
)
assign_zero_state()
(in
SymmMinimalistNode
)
add_evaluators()
(in
EvaluatorCreator
)
apply()
(in
RedefineChi
)
assign_zero_state()
(in
SymmOnTheFlyNode
)
add_evaluators()
(in
EvaluatorFactory
)
apply()
(in
SetAtomType
)
assign_zero_state()
(in
FlexbbNode
)
add_evaluators()
(in
CamShiftEvaluatorCreator
)
apply()
(in
SetAtomicCharge
)
assign_zero_state()
(in
MinimalistFlexbbNode
)
add_evaluators()
(in
ChiWellRmsdEvaluatorCreator
)
apply()
(in
SetBackboneHeavyatom
)
assign_zero_state()
(in
OTFFlexbbNode
)
add_evaluators()
(in
ContactMapEvaluatorCreator
)
apply()
(in
SetFormalCharge
)
AssignOrbitals
(in
rosetta.core.chemical.orbitals._core_chemical_orbitals_
)
add_evaluators()
(in
ExtraScoreEvaluatorCreator
)
apply()
(in
SetICoor
)
AssignOrbitalsAP
(in
rosetta.core.chemical.orbitals._core_chemical_orbitals_
)
add_evaluators()
(in
JScoreEvaluatorCreator
)
apply()
(in
SetIO_String
)
AssignOrbitalsCAP
(in
rosetta.core.chemical.orbitals._core_chemical_orbitals_
)
add_evaluators()
(in
JumpNrEvaluatorCreator
)
apply()
(in
SetInterchangeabilityGroup_String
)
AssignToClustersMover
(in
rosetta.protocols.cluster._protocols_cluster_
)
add_evaluators()
(in
NativeEvaluatorCreator
)
apply()
(in
SetMMAtomType
)
AssignToClustersMoverAP
(in
rosetta.protocols.cluster._protocols_cluster_
)
add_evaluators()
(in
PalesEvaluatorCreator
)
apply()
(in
SetNbrAtom
)
AssignToClustersMoverCAP
(in
rosetta.protocols.cluster._protocols_cluster_
)
add_evaluators()
(in
PoolEvaluatorCreator
)
apply()
(in
SetNbrRadius
)
ast_string()
(in
ASTPrinter
)
add_evaluators()
(in
PredictedBurialFnEvaluatorCreator
)
apply()
(in
SetOrientAtom
)
ASTPrinter
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
add_evaluators()
(in
RdcEvaluatorCreator
)
apply()
(in
SetPolymerConnectAtom
)
ASTPrinterAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
add_evaluators()
(in
RdcSelectEvaluatorCreator
)
apply()
(in
AnnotatedFragData
)
ASTPrinterCAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
add_evaluators()
(in
RdcTargetEvaluatorCreator
)
apply()
(in
BBTorsionAndAnglesSRFD
)
ASTVisitor
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
add_evaluators()
(in
RmsdEvaluatorCreator
)
apply()
(in
BBTorsionSRFD
)
ASTVisitorAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
add_evaluators()
(in
RmsdTargetEvaluatorCreator
)
apply()
(in
DownJumpSRFD
)
ASTVisitorCAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
add_evaluators()
(in
StructureSimilarityEvaluatorCreator
)
apply()
(in
FragData
)
asym_fold_and_dock
(in
rosetta.protocols.simple_moves
)
add_evaluators()
(in
ChemicalShiftEvaluatorCreator
)
apply()
(in
FragID
)
AsymFoldandDockMoveRbJumpMover
(in
rosetta.protocols.simple_moves.asym_fold_and_dock._protocols_simple_moves_asym_fold_and_dock_
)
add_excluded_chains()
(in
Translate
)
apply()
(in
Frame
)
AsymFoldandDockMoveRbJumpMoverAP
(in
rosetta.protocols.simple_moves.asym_fold_and_dock._protocols_simple_moves_asym_fold_and_dock_
)
add_extent_eval()
(in
Librarian_T_core_fragment_picking_old_vall_scores_VallFragmentScore_core_fragment_picking_old_vall_eval_VallFragmentEval_core_fragment_picking_old_vall_gen_VallFragmentGen_core_fragment_picking_old_vall_VallLibrary_T
)
apply()
(in
IndependentBBTorsionSRFD
)
AsymFoldandDockMoveRbJumpMoverCAP
(in
rosetta.protocols.simple_moves.asym_fold_and_dock._protocols_simple_moves_asym_fold_and_dock_
)
add_extent_gen()
(in
Librarian_T_core_fragment_picking_old_vall_scores_VallFragmentScore_core_fragment_picking_old_vall_eval_VallFragmentEval_core_fragment_picking_old_vall_gen_VallFragmentGen_core_fragment_picking_old_vall_VallLibrary_T
)
apply()
(in
SecstructSRFD
)
AsymFoldandDockRbTrialMover
(in
rosetta.protocols.simple_moves.asym_fold_and_dock._protocols_simple_moves_asym_fold_and_dock_
)
add_external_geom_sampler()
(in
ClassicMatchAlgorithm
)
apply()
(in
SingleResidueFragData
)
AsymFoldandDockRbTrialMoverAP
(in
rosetta.protocols.simple_moves.asym_fold_and_dock._protocols_simple_moves_asym_fold_and_dock_
)
add_external_geometry_samples_for_constraint()
(in
Matcher
)
apply()
(in
UpJumpSRFD
)
AsymFoldandDockRbTrialMoverCAP
(in
rosetta.protocols.simple_moves.asym_fold_and_dock._protocols_simple_moves_asym_fold_and_dock_
)
add_external_loop_rotamer()
(in
MC_Comb
)
apply()
(in
AddBehaviorRLT
)
asymmetric_dof()
(in
SymMinimizerMap
)
add_external_loop_rotamer()
(in
StepWiseSamplerAny
)
apply()
(in
AppendResidueRotamerSet
)
asymmetrize_scorefunction()
(in
rosetta.core.scoring.symmetry._core_scoring_symmetry_
)
add_external_loop_rotamer()
(in
StepWiseSamplerComb
)
apply()
(in
AppendRotamer
)
AsyncMPITemperingBase
(in
rosetta.protocols.canonical_sampling._protocols_canonical_sampling_
)
add_external_loop_rotamer()
(in
StepWiseSamplerOneValueComb
)
apply()
(in
AppendRotamerSet
)
AsyncMPITemperingBaseAP
(in
rosetta.protocols.canonical_sampling._protocols_canonical_sampling_
)
add_external_loop_rotamer()
(in
StepWiseSamplerSizedAny
)
apply()
(in
DisallowIfNonnative
)
AsyncMPITemperingBaseCAP
(in
rosetta.protocols.canonical_sampling._protocols_canonical_sampling_
)
add_external_loop_rotamer()
(in
StepWiseSamplerSizedComb
)
apply()
(in
DisallowIfNonnativeRLT
)
at()
(in
Sequence
)
add_external_loop_rotamer()
(in
ResidueAlternativeStepWiseSamplerComb
)
apply()
(in
ExtraChiCutoff
)
at()
(in
VallChunk
)
add_external_loop_rotamer()
(in
RigidBodyStepWiseSampler
)
apply()
(in
ExtraRotamers
)
at()
(in
VallProvider
)
add_external_loop_rotamer()
(in
RigidBodyStepWiseSamplerWithResidueAlternatives
)
apply()
(in
ExtraRotamersGeneric
)
at()
(in
AdaptiveScoreHistogram
)
add_external_loop_rotamer()
(in
RigidBodyStepWiseSamplerWithResidueList
)
apply()
(in
IncludeCurrent
)
at()
(in
FragmentScoreMap
)
add_external_loop_rotamer()
(in
RNA_MC_MultiSuite
)
apply()
(in
InitializeExtraRotsFromCommandline
)
at_end()
(in
VoxelSetIterator
)
add_external_loop_rotamer()
(in
RNA_MC_Suite
)
apply()
(in
InitializeFromCommandline
)
at_end()
(in
LexicographicalIterator
)
add_external_loop_rotamer()
(in
RNA_NucleosideStepWiseSampler
)
apply()
(in
NoRepackDisulfides
)
at_inds()
(in
AtomGeometrySecMatchRPE
)
add_external_loop_rotamer()
(in
RNA_SuiteStepWiseSampler
)
apply()
(in
OperateOnCertainResidues
)
atm1()
(in
AngleToVector
)
add_extra_data()
(in
BackboneDB
)
apply()
(in
OperateOnResidueSubset
)
atm2()
(in
AngleToVector
)
add_extra_method()
(in
ScoreFunction
)
apply()
(in
OptCysHG
)
atmid()
(in
GoapRsdType
)
add_extra_options()
(in
rosetta
)
apply()
(in
OptH
)
atmname_using()
(in
GoapRsdType
)
add_fa_constraints_from_cmdline()
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply()
(in
PreserveCBeta
)
Atom
(in
rosetta.core.chemical._core_chemical_
)
add_fa_constraints_from_cmdline_to_pose()
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply()
(in
PreventRepacking
)
Atom
(in
rosetta.core.conformation._core_conformation_
)
add_fa_constraints_from_cmdline_to_scorefxn()
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
apply()
(in
PreventRepackingRLT
)
Atom
(in
rosetta.core.kinematics.tree._core_kinematics_tree_
)
add_fade_chain_break_constraint_across_gap()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
apply()
(in
ReadResfile
)
Atom
(in
rosetta.core.scoring.sc._core_scoring_sc_
)
add_features_reporter()
(in
ReportToDB
)
apply()
(in
ReadResfileAndObeyLengthEvents
)
atom()
(in
ResidueType
)
add_file_contents()
(in
DynamicAggregateFunction
)
apply()
(in
ReplicateTask
)
atom()
(in
Residue
)
add_file_provider_hook()
(in
Inline_File_Provider
)
apply()
(in
ResLvlTaskOperation
)
atom()
(in
EXCN_AtomNotFound
)
add_filename()
(in
StemFinder
)
apply()
(in
RestrictAbsentCanonicalAAS
)
atom()
(in
NamedAtomID
)
add_filter()
(in
GreedyOptMutationMover
)
apply()
(in
RestrictAbsentCanonicalAASRLT
)
atom()
(in
NamedStubID
)
add_filter()
(in
ParetoOptMutationMover
)
apply()
(in
RestrictResidueToRepacking
)
atom()
(in
StubID
)
add_filter()
(in
CalculatorFilter
)
apply()
(in
RestrictToRepacking
)
atom()
(in
AtomTree
)
add_filter()
(in
FilterCollection
)
apply()
(in
RestrictToRepackingRLT
)
atom()
(in
DunbrackConstraint
)
add_filter()
(in
GeneralizedKIC
)
apply()
(in
RestrictYSDesign
)
atom()
(in
RotamerConstraint
)
add_filter()
(in
LoopProtocol
)
apply()
(in
RotamerExplosion
)
atom()
(in
AmbiguousConstraint
)
add_filter()
(in
LoopMoverGroup
)
apply()
(in
SetRotamerCouplings
)
atom()
(in
AmbiguousNMRConstraint
)
add_filter()
(in
KinematicMover
)
apply()
(in
SetRotamerLinks
)
atom()
(in
AmbiguousNMRDistanceConstraint
)
add_filter()
(in
MatcherTask
)
apply()
(in
TaskOperation
)
atom()
(in
AngleConstraint
)
add_filter()
(in
MatchProcessor
)
apply()
(in
AndResidueSelector
)
atom()
(in
AtomPairConstraint
)
add_filter()
(in
MatDesGreedyOptMutationMover
)
apply()
(in
ChainSelector
)
atom()
(in
BackboneStubConstraint
)
add_filter()
(in
FilterMover
)
apply()
(in
ClashBasedRepackShellSelector
)
atom()
(in
BackboneStubLinearConstraint
)
add_filter()
(in
Operator
)
apply()
(in
InterGroupInterfaceByVectorSelector
)
atom()
(in
BigBinConstraint
)
add_filter()
(in
GenericMonteCarloMover
)
apply()
(in
JumpDownstreamSelector
)
atom()
(in
ConstantConstraint
)
add_filter_param()
(in
GeneralizedKICfilter
)
apply()
(in
JumpUpstreamSelector
)
atom()
(in
Constraint
)
add_filter_parameter()
(in
GeneralizedKIC
)
apply()
(in
NeighborhoodResidueSelector
)
atom()
(in
CoordinateConstraint
)
add_foreign_key()
(in
Schema
)
apply()
(in
NotResidueSelector
)
atom()
(in
DihedralConstraint
)
add_frag_type()
(in
FragFactory
)
apply()
(in
NumNeighborsSelector
)
atom()
(in
DihedralPairConstraint
)
add_fragment()
(in
Frame
)
apply()
(in
OrResidueSelector
)
atom()
(in
DistancePairConstraint
)
add_fragment_csts()
(in
HybridizeProtocol
)
apply()
(in
ResidueIndexSelector
)
atom()
(in
FabConstraint
)
add_fragment_eval()
(in
VallLibrarian
)
apply()
(in
ResidueNameSelector
)
atom()
(in
KofNConstraint
)
add_fragment_gen()
(in
VallLibrarian
)
apply()
(in
ResidueSelector
)
atom()
(in
LocalCoordinateConstraint
)
add_fragments()
(in
LoopMover
)
apply()
(in
SecondaryStructureSelector
)
atom()
(in
MultiConstraint
)
add_fragset()
(in
FragSetCollection
)
apply()
(in
TrueResidueSelector
)
atom()
(in
NamedAngleConstraint
)
add_frame_type()
(in
FragFactory
)
apply()
(in
CopyDofs
)
atom()
(in
NamedAtomPairConstraint
)
add_from_file()
(in
MotifLibrary
)
apply()
(in
RNA_IdealCoord
)
atom()
(in
NonResidueTypeConstraint
)
add_func()
(in
SumFunc
)
apply()
(in
TMscore
)
atom()
(in
ResidueTypeConstraint
)
add_function()
(in
ArithmeticScanner
)
apply()
(in
TMscoreStore
)
atom()
(in
ResidueTypeLinkingConstraint
)
add_function_name()
(in
RDFBase
)
apply()
(in
Quaternion_Real
)
atom()
(in
SequenceProfileConstraint
)
add_gaussian()
(in
SmoothScoreTermCoeffs
)
apply()
(in
Quaternion_double
)
atom()
(in
SiteConstraint
)
add_genericRBMover()
(in
RBSegmentRelax
)
apply()
(in
Quaternion_float
)
atom()
(in
SiteConstraintResidues
)
add_group()
(in
SetupNCSMover
)
apply()
(in
RotamerDumpMover
)
atom()
(in
SimplePDB
)
add_group()
(in
LinkResidues
)
apply()
(in
AbrelaxMover
)
atom()
(in
AmbiguousMultiConstraint
)
add_groupD()
(in
SetupNCSMover
)
apply()
(in
ClassicAbinitio
)
atom()
(in
BindingSiteConstraint
)
add_groupE()
(in
SetupNCSMover
)
apply()
(in
ConstraintFragmentSampler
)
atom()
(in
COMCoordinateConstraint
)
add_harmonic_chain_break_constraint()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
apply()
(in
DomainAssembly
)
atom()
(in
SequenceCoupling1BDConstraint
)
add_harmonic_dihedral_cst_general()
(in
rosetta.protocols.antibody.constraints._protocols_antibody_constraints_
)
apply()
(in
DoubleLayerKinematicAbinitio
)
atom()
(in
SequenceCouplingConstraint
)
add_hbs_constraint()
(in
rosetta.core.pose.ncbb._core_pose_ncbb_
)
apply()
(in
FoldConstraints
)
atom()
(in
PocketConstraint
)
add_hbs_constraint()
(in
rosetta.protocols.simple_moves.hbs._protocols_simple_moves_hbs_
)
apply()
(in
FragmentSampler
)
atom1()
(in
MolFileIOBond
)
add_helix()
(in
BundleGridSampler
)
apply()
(in
JumpingFoldConstraintsWrapper
)
atom1()
(in
CSA
)
add_helix()
(in
MakeBundle
)
apply()
(in
KinematicAbinitio
)
atom1()
(in
DC
)
add_helix()
(in
PerturbBundle
)
apply()
(in
KinematicTaskControl
)
atom1()
(in
RDC
)
add_helixMover()
(in
RBSegmentRelax
)
apply()
(in
LoopJumpFoldCst
)
atom1()
(in
Obsolet_NamedAtomPairConstraint
)
add_hits()
(in
HitNeighborFinder
)
apply()
(in
MembraneAbinitio
)
atom1()
(in
WaterBuilder
)
add_hits()
(in
MatchCounter
)
apply()
(in
Protocol
)
atom1_atom2_atom3_angle()
(in
DownstreamBuilder
)
add_hotspot_constraints_to_pose()
(in
HotspotStubSet
)
apply()
(in
ResolutionSwitcher
)
atom1_atom2_atom3_angle()
(in
LigandConformerBuilder
)
add_hotspot_constraints_to_wholepose()
(in
HotspotStubSet
)
apply()
(in
AbscriptLoopCloserCM
)
atom1_atom2_atom3_angle()
(in
RigidLigandBuilder
)
add_hsstriplets()
(in
HSSTripletFilter
)
apply()
(in
AbscriptMover
)
atom1_atom2_atom3_angle()
(in
LigandConformer
)
add_hsstriplets()
(in
HSSTripletSet
)
apply()
(in
AbscriptStageMover
)
atom1_atom2_distance()
(in
DownstreamBuilder
)
add_improper_torsion_parameter()
(in
ResidueCartBondedParameters
)
apply()
(in
ConstraintPreparer
)
atom1_atom2_distance()
(in
LigandConformerBuilder
)
add_index()
(in
Schema
)
apply()
(in
FragmentCM
)
atom1_atom2_distance()
(in
RigidLigandBuilder
)
add_individual_constraint()
(in
AmbiguousConstraint
)
apply()
(in
FragmentJumpCM
)
atom1_atom2_distance()
(in
LigandConformer
)
add_individual_constraint()
(in
AmbiguousNMRConstraint
)
apply()
(in
RigidChunkCM
)
atom1_belongs_in_active_site()
(in
DownstreamBuilder
)
add_individual_constraint()
(in
FabConstraint
)
apply()
(in
StagePreparer
)
atom1_belongs_in_active_site()
(in
LigandConformerBuilder
)
add_individual_constraint()
(in
KofNConstraint
)
apply()
(in
StructPerturberCM
)
atom1_belongs_in_active_site()
(in
RigidLigandBuilder
)
add_individual_constraint()
(in
MultiConstraint
)
apply()
(in
InterfaceAnalyzerMover
)
atom1_radius()
(in
DownstreamBuilder
)
add_individual_constraint()
(in
SiteConstraint
)
apply()
(in
LoopAnalyzerMover
)
atom1_radius()
(in
LigandConformerBuilder
)
add_individual_constraint()
(in
SiteConstraintResidues
)
apply()
(in
PackStatMover
)
atom1_radius()
(in
RigidLigandBuilder
)
add_individual_constraint()
(in
AmbiguousMultiConstraint
)
apply()
(in
PeptideDeriverFilter
)
atom2()
(in
MolFileIOBond
)
add_info()
(in
PDBOutput
)
apply()
(in
AnchoredDesignMover
)
atom2()
(in
CSA
)
add_inner_cycle_step()
(in
LoopRefineInnerCycleContainer
)
apply()
(in
AnchoredPerturbMover
)
atom2()
(in
DC
)
add_input_file()
(in
Inline_File_Provider
)
apply()
(in
AnchoredRefineMover
)
atom2()
(in
RDC
)
add_inputter()
(in
InputterStream
)
apply()
(in
AntibodyModelerProtocol
)
atom2()
(in
Obsolet_NamedAtomPairConstraint
)
add_inputvalue()
(in
GeneralizedKICperturber
)
apply()
(in
CDRsMinPackMin
)
atom2()
(in
WaterBuilder
)
add_instruction()
(in
BluePrintBDR
)
apply()
(in
CloseOneCDRLoop
)
atom2_atom3_distance()
(in
DownstreamBuilder
)
add_instruction()
(in
BDR
)
apply()
(in
GraftCDRLoopsProtocol
)
atom2_atom3_distance()
(in
LigandConformerBuilder
)
add_interaction()
(in
AtomPairFuncList
)
apply()
(in
GraftOneCDRLoop
)
atom2_atom3_distance()
(in
RigidLigandBuilder
)
add_internal_loop_rotamer()
(in
StepWiseSamplerOneValueComb
)
apply()
(in
GraftedStemOptimizer
)
atom2_atom3_distance()
(in
LigandConformer
)
add_internal_loop_rotamer()
(in
StepWiseSamplerSizedComb
)
apply()
(in
H3CterInsert
)
atom2_belongs_in_active_site()
(in
DownstreamBuilder
)
add_internal_loop_rotamer()
(in
ResidueAlternativeStepWiseSamplerComb
)
apply()
(in
H3PerturbCCD
)
atom2_belongs_in_active_site()
(in
LigandConformerBuilder
)
add_internal_loop_rotamer()
(in
RigidBodyStepWiseSampler
)
apply()
(in
H3RefineCCD
)
atom2_belongs_in_active_site()
(in
RigidLigandBuilder
)
add_ionized_restype()
(in
IonizableResidue
)
apply()
(in
LHRepulsiveRamp
)
atom2_radius()
(in
DownstreamBuilder
)
add_job_data_to_ss()
(in
rosetta.protocols.jd2._protocols_jd2_
)
apply()
(in
ModelCDRH3
)
atom2_radius()
(in
LigandConformerBuilder
)
add_job_options()
(in
LazyResourceManager
)
apply()
(in
RefineBetaBarrel
)
atom2_radius()
(in
RigidLigandBuilder
)
add_jump()
(in
BinarySilentStruct
)
apply()
(in
RefineOneCDRLoop
)
atom3()
(in
CSA
)
add_jump()
(in
RNA_SilentStruct
)
apply()
(in
RefineOneCDRLoopCentroid
)
atom3()
(in
WaterBuilder
)
add_jump()
(in
RigidBodySilentStruct
)
apply()
(in
CDRDihedralConstraintMover
)
atom3_belongs_in_active_site()
(in
DownstreamBuilder
)
add_jump()
(in
ScoreJumpFileSilentStruct
)
apply()
(in
ParatopeEpitopeSiteConstraintMover
)
atom3_belongs_in_active_site()
(in
LigandConformerBuilder
)
add_jump()
(in
DockingProtocol
)
apply()
(in
ParatopeSiteConstraintMover
)
atom3_belongs_in_active_site()
(in
RigidLigandBuilder
)
add_jump()
(in
RigidBodyInfo
)
apply()
(in
AntibodyDesignMover
)
atom3_radius()
(in
DownstreamBuilder
)
add_jump()
(in
TemperedDocking
)
apply()
(in
AntibodyDesignProtocol
)
atom3_radius()
(in
LigandConformerBuilder
)
add_jump()
(in
JumpSelector
)
apply()
(in
MutateFrameworkForCluster
)
atom3_radius()
(in
RigidLigandBuilder
)
add_jump()
(in
JumpSetup
)
apply()
(in
AddCDRProfileSetsOperation
)
Atom_
(in
rosetta.core.kinematics.tree._core_kinematics_tree_
)
add_jump()
(in
ResiduePairJumpSetup
)
apply()
(in
AddCDRProfilesOperation
)
Atom_AP
(in
rosetta.core.kinematics.tree._core_kinematics_tree_
)
add_jump()
(in
RigidBodyPerturbNoCenterMover
)
apply()
(in
DisableAntibodyRegionOperation
)
atom_base()
(in
ResidueType
)
add_jump()
(in
InterfaceInfo
)
apply()
(in
DisableCDRsOperation
)
atom_base()
(in
Residue
)
add_jump()
(in
InterfaceSasaFilter
)
apply()
(in
RestrictToCDRsAndNeighbors
)
atom_begin()
(in
Residue
)
add_jump()
(in
RestrictToInterface
)
apply()
(in
AntibodyModeler
)
atom_being_shadowed()
(in
ResidueType
)
add_jump_clone()
(in
SymmetryInfo
)
apply()
(in
CDRH3Modeler
)
Atom_Bin
(in
rosetta.protocols.stepwise.modeler.rna.checker._protocols_stepwise_modeler_rna_checker_
)
add_jump_label()
(in
SequenceAnnotation
)
apply()
(in
CloseOneMover
)
Atom_BinAP
(in
rosetta.protocols.stepwise.modeler.rna.checker._protocols_stepwise_modeler_rna_checker_
)
add_kic_mover()
(in
MetropolisHastingsMover
)
apply()
(in
GraftMover
)
Atom_BinCAP
(in
rosetta.protocols.stepwise.modeler.rna.checker._protocols_stepwise_modeler_rna_checker_
)
add_known_value()
(in
SplineGenerator
)
apply()
(in
GraftOneMover
)
Atom_CAP
(in
rosetta.core.kinematics.tree._core_kinematics_tree_
)
add_leap()
(in
LoopHashMap
)
apply()
(in
LoopRlxMover
)
atom_charge()
(in
Adduct
)
add_legacyleap()
(in
LoopHashMap
)
apply()
(in
BackrubMover
)
atom_controlled_by_any_chi()
(in
UpstreamResTypeGeometry
)
add_length_parameter()
(in
ResidueCartBondedParameters
)
apply()
(in
BackrubProtocol
)
atom_data()
(in
RNA_CS_residue_parameters
)
add_ligand_conditionally()
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
apply()
(in
BackrubSidechainMover
)
atom_derivatives()
(in
CartesianMinimizerMap
)
add_ligand_from_file()
(in
MotifLibrary
)
apply()
(in
AsyncMPITemperingBase
)
atom_derivatives()
(in
MinimizerMap
)
add_line()
(in
ResidueSelector
)
apply()
(in
CanonicalSamplingMover
)
atom_derivatives()
(in
SymMinimizerMap
)
add_line()
(in
ABEGO
)
apply()
(in
FixedTemperatureController
)
atom_distance()
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
add_line()
(in
RMSVallData
)
apply()
(in
HamiltonianExchange
)
atom_distance()
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
add_line()
(in
VallData
)
apply()
(in
MetricRecorder
)
atom_dont_do_update()
(in
AtomTree
)
add_list_filenames()
(in
PDBPoseInputStream
)
apply()
(in
MetropolisHastingsMover
)
atom_end()
(in
Residue
)
add_loop()
(in
Loops
)
apply()
(in
ParallelTempering
)
atom_forms_residue_connection()
(in
ResidueType
)
add_loop_flank_residues_bb_to_movemap()
(in
rosetta.protocols.loops._protocols_loops_
)
apply()
(in
ProgressBarObserver
)
atom_geom_rpes()
(in
GeometrySecMatchRPE
)
add_loop_residue()
(in
GeneralizedKIC
)
apply()
(in
SidechainMetropolisHastingsMover
)
atom_gets_derivatives()
(in
DisulfideAtomIndices
)
add_loop_size()
(in
LoopHashDiversifier
)
apply()
(in
SimulatedTempering
)
atom_gradient()
(in
ElectronDensityAtomwise
)
add_loop_size()
(in
LoopHashMoverWrapper
)
apply()
(in
TemperatureController
)
atom_graph_from_conformation()
(in
rosetta.core.conformation._core_conformation_
)
add_loops_from_bool_vector()
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
apply()
(in
TemperingBase
)
atom_has_nonchi_coordinate()
(in
UpstreamResTypeGeometry
)
add_lower_connect_angle_params()
(in
ResidueCartBondedParameters
)
apply()
(in
ThermodynamicMover
)
atom_has_orbital()
(in
AtomType
)
add_lower_terminus_type_to_conformation_residue()
(in
rosetta.core.conformation._core_conformation_
)
apply()
(in
ThermodynamicObserver
)
atom_hbonds()
(in
HBondSet
)
add_lower_terminus_type_to_pose_residue()
(in
rosetta.core.pose._core_pose_
)
apply()
(in
TrajectoryRecorder
)
atom_id()
(in
ICoorAtomID
)
add_lr_gaussian()
(in
CenHBPotential
)
apply()
(in
TrialCounterObserver
)
atom_id()
(in
DOF_ID
)
add_mainchain_segments()
(in
BackrubMover
)
apply()
(in
Pool_Evaluator
)
atom_id()
(in
Atom
)
add_mainchain_segments_from_options()
(in
BackrubMover
)
apply()
(in
AssignToClustersMover
)
atom_id()
(in
Atom_
)
add_match()
(in
BestMatchesCollection
)
apply()
(in
ClusterBase
)
atom_id()
(in
DOF_Node
)
add_match()
(in
MatchScoreWriter
)
apply()
(in
ClusterPhilStyle
)
atom_id_to_named_atom_id()
(in
rosetta.core.conformation._core_conformation_
)
add_match_dspos1()
(in
BestMatchesCollection
)
apply()
(in
ClusterPhilStyle_Loop
)
atom_id_to_named_atom_id()
(in
rosetta.core.pose._core_pose_
)
add_memb_etable()
(in
ScoringManager
)
apply()
(in
ClusterPhilStyle_PoseReporter
)
atom_index()
(in
ResidueType
)
add_member()
(in
Cluster
)
apply()
(in
EnsembleConstraints
)
atom_index()
(in
MolFileIOMolecule
)
add_member_front()
(in
Cluster
)
apply()
(in
EnsembleConstraints_Simple
)
atom_index()
(in
Residue
)
add_metalbinding_atom()
(in
ResidueType
)
apply()
(in
GatherPosesMover
)
atom_inds_for_restype()
(in
EnzCstTemplateRes
)
add_motif()
(in
MotifHash
)
apply()
(in
CoarseRNA_LoopCloser
)
atom_inds_for_restype_begin()
(in
EnzCstTemplateRes
)
add_motif()
(in
SymmetricMotifFilter
)
apply()
(in
Align_RmsdEvaluator
)
atom_inds_for_restype_end()
(in
EnzCstTemplateRes
)
add_motif_bb_constraints()
(in
rosetta.protocols.motifs._protocols_motifs_
)
apply()
(in
Align_RotamerEvaluator
)
atom_is_acceptor()
(in
HBond
)
add_motif_sc_constraints()
(in
rosetta.protocols.motifs._protocols_motifs_
)
apply()
(in
ExtraThreadingMover
)
atom_is_backbone()
(in
ResidueType
)
add_motif_set_name()
(in
MotifHashManager
)
apply()
(in
LoopRelaxMover
)
atom_is_backbone()
(in
Residue
)
add_movable_jump()
(in
InterfaceTaskOperation
)
apply()
(in
LoopRelaxThreadingMover
)
atom_is_backbone_norefold()
(in
Conformation
)
add_movemap_from_loopres()
(in
rosetta.protocols.mpi_refinement._protocols_mpi_refinement_
)
apply()
(in
MultiThreadingMover
)
atom_is_chitip()
(in
UpstreamResTypeGeometry
)
add_movemaps_to_datamap()
(in
rosetta.protocols.rosetta_scripts._protocols_rosetta_scripts_
)
apply()
(in
PartialThreadingMover
)
atom_is_donorH()
(in
HBond
)
add_mover()
(in
CanonicalSamplingMover
)
apply()
(in
RecoverSideChainsMover
)
atom_is_heavy()
(in
GeometricSolEnergyEvaluator
)
add_mover()
(in
MetropolisHastingsMover
)
apply()
(in
StealLigandMover
)
atom_is_hydrogen()
(in
ResidueType
)
add_mover()
(in
SidechainMetropolisHastingsMover
)
apply()
(in
StealSideChainsMover
)
atom_is_hydrogen()
(in
Residue
)
add_mover()
(in
LoopProtocol
)
apply()
(in
ThreadingMover
)
atom_is_independent()
(in
SymmetryInfo
)
add_mover()
(in
LoopMoverGroup
)
apply()
(in
CombinedConstraintEvaluator
)
atom_is_on_path_from_root()
(in
Atom
)
add_mover()
(in
CompositionMover
)
apply()
(in
ConstraintEvaluator
)
atom_is_phosphate()
(in
RNA_ResidueType
)
add_mover()
(in
MoverContainer
)
apply()
(in
ContactMap
)
atom_is_polar_hydrogen()
(in
ResidueType
)
add_mover()
(in
AlignRMSD_Screener
)
apply()
(in
FitBfactorsMover
)
atom_is_polar_hydrogen()
(in
Residue
)
add_mover()
(in
AnchorSugarScreener
)
apply()
(in
LoadDensityMapMover
)
atom_is_virtual()
(in
RNA_ResidueType
)
add_mover()
(in
BaseBinMapUpdater
)
apply()
(in
RecomputeDensityMapMover
)
atom_iterators()
(in
ResidueType
)
add_mover()
(in
BaseCentroidScreener
)
apply()
(in
SetCrystWeightMover
)
atom_map_valid_size()
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
add_mover()
(in
BulgeApplier
)
apply()
(in
SetRefinementOptionsMover
)
atom_name()
(in
Adduct
)
add_mover()
(in
CentroidDistanceScreener
)
apply()
(in
TagPoseWithRefinementStatsMover
)
atom_name()
(in
ResidueType
)
add_mover()
(in
FastForwardToNextResidueAlternative
)
apply()
(in
UpdateSolventMover
)
atom_name()
(in
AtomGraphVertexData
)
add_mover()
(in
FastForwardToNextRigidBody
)
apply()
(in
CreateAngleConstraint
)
atom_name()
(in
Residue
)
add_mover()
(in
IntegrationTestBreaker
)
apply()
(in
CreateDistanceConstraint
)
atom_name()
(in
MiniPose
)
add_mover()
(in
O2PrimeScreener
)
apply()
(in
CreateTorsionConstraint
)
atom_name()
(in
UnrecognizedAtomRecord
)
add_mover()
(in
PackScreener
)
apply()
(in
DeclareBond
)
atom_name()
(in
PoseBalls
)
add_mover()
(in
PartitionContactScreener
)
apply()
(in
PeptideStubMover
)
atom_name()
(in
PCS_line_data
)
add_mover()
(in
PhosphateScreener
)
apply()
(in
ddGMover
)
atom_name()
(in
PCS_line_data_Ts1
)
add_mover()
(in
PoseSelectionScreener
)
apply()
(in
ExposedHydrophobicsFilter
)
atom_name()
(in
PCS_line_data_Ts2
)
add_mover()
(in
ProteinCCD_ClosureScreener
)
apply()
(in
GreedyOptMutationMover
)
atom_name()
(in
PCS_line_data_Ts3
)
add_mover()
(in
RNA_ChainClosableGeometryResidueBasedScreener
)
apply()
(in
ParetoOptMutationMover
)
atom_name()
(in
PCS_line_data_Ts4
)
add_mover()
(in
RNA_ChainClosableGeometryScreener
)
apply()
(in
DesignProteinBackboneAroundDNA
)
atom_name1()
(in
RNA_PairingTemplate
)
add_mover()
(in
RNA_ChainClosableGeometryStubBasedScreener
)
apply()
(in
DnaInterfaceMinMover
)
atom_name2()
(in
RNA_PairingTemplate
)
add_mover()
(in
RNA_ChainClosureScreener
)
apply()
(in
DnaInterfaceMultiStateDesign
)
atom_names_list()
(in
MiniPose
)
add_mover()
(in
ResidueContactScreener
)
apply()
(in
DnaInterfacePacker
)
atom_neighbors()
(in
NeighborList
)
add_mover()
(in
SampleApplier
)
apply()
(in
RestrictDesignToProteinDNAInterface
)
atom_neighbors()
(in
ResidueNblistData
)
add_mover()
(in
Scorer
)
apply()
(in
SeparateDnaFromNonDna
)
atom_neighbors()
(in
ResiduePairNeighborList
)
add_mover()
(in
StepWiseResiduePairScreener
)
apply()
(in
WatsonCrickRotamerCouplings
)
atom_next_to_connect_atom()
(in
rosetta.core.pose.carbohydrates._core_pose_carbohydrates_
)
add_mover()
(in
StepWiseScreener
)
apply()
(in
ConformerSwitchMover
)
atom_num()
(in
PoseBalls
)
add_mover()
(in
StubApplier
)
apply()
(in
DockMCMCycle
)
atom_num()
(in
PoseBallsLite
)
add_mover()
(in
StubDistanceScreener
)
apply()
(in
DockMCMProtocol
)
atom_numbers_for_mg_calculation()
(in
RNA_ScoringInfo
)
add_mover()
(in
SugarInstantiator
)
apply()
(in
DockMinMover
)
atom_numbers_for_vdw_calculation()
(in
RNA_ScoringInfo
)
add_mover()
(in
TagDefinition
)
apply()
(in
DockSetupMover
)
atom_overlap_is_exposed()
(in
InvRotamerDots
)
add_mover()
(in
VDW_BinScreener
)
apply()
(in
DockingEnsemblePrepackProtocol
)
atom_pair_constraint
(in
rosetta
)
add_mover()
(in
FoldandDockClaimer
)
apply()
(in
DockingHighRes
)
atom_pair_constraint
(in
ScoreType
)
add_mover()
(in
MembraneTopologyClaimer
)
apply()
(in
DockingHighResFilter
)
atom_pair_constraint
(in
rosetta.core.scoring._core_scoring_
)
add_mover()
(in
TopologyClaimer
)
apply()
(in
DockingHighResLegacy
)
atom_pair_constraint
(in
rosetta.core.scoring
)
add_mover_group()
(in
LoopMoverGroup
)
apply()
(in
DockingInitialPerturbation
)
atom_pair_constraint_energy()
(in
ConstraintEdge
)
add_msg()
(in
EXCN_InvalidFoldTree
)
apply()
(in
DockingLowRes
)
atom_pair_constraint_weight()
(in
IdealizeMover
)
add_msg()
(in
EXCN_Msg_Exception
)
apply()
(in
DockingLowResEnsemble
)
atom_pair_distance
(in
rosetta.protocols.generalized_kinematic_closure.filter._protocols_generalized_kinematic_closure_filter_
)
add_mutant()
(in
DDGMutationOptEData
)
apply()
(in
DockingLowResFilter
)
atom_pair_distance
(in
filter_type
)
add_mutant_complex()
(in
DDGBindOptEData
)
apply()
(in
DockingPrepackProtocol
)
atom_pair_distance
(in
rosetta.protocols.generalized_kinematic_closure.filter
)
add_mutant_unbounds()
(in
DDGBindOptEData
)
apply()
(in
DockingProtocol
)
atom_pair_energy()
(in
AnalyticEtableEnergy
)
add_mutation()
(in
DDGBindOptEData
)
apply()
(in
DockingSlideIntoContact
)
atom_pair_energy()
(in
AnalyticEtableEvaluator
)
add_mutation()
(in
Mutant
)
apply()
(in
EllipsoidalRandomizationMover
)
atom_pair_energy()
(in
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T
)
add_mutation_set()
(in
MutationSetDesignOperation
)
apply()
(in
FaDockingSlideIntoContact
)
atom_pair_energy()
(in
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T
)
add_native()
(in
PNatStructureOptEData
)
apply()
(in
InterfaceSidechainMinMover
)
atom_pair_energy()
(in
TableLookupEtableEnergy
)
add_native_fasta()
(in
JointSequenceOperation
)
apply()
(in
SidechainMinMover
)
atom_pair_energy()
(in
TableLookupEvaluator
)
add_native_pdb()
(in
JointSequenceOperation
)
apply()
(in
TemperedDocking
)
atom_pair_energy_v()
(in
AnalyticEtableEvaluator
)
add_native_pose()
(in
JointSequenceOperation
)
apply()
(in
MPDockingMover
)
atom_pair_energy_v()
(in
EtableEvaluator
)
add_negative_filter()
(in
BoltzmannFilter
)
apply()
(in
MPDockingSetupMover
)
atom_pair_energy_v()
(in
TableLookupEvaluator
)
add_neighbors_mass()
(in
TenANeighborNode
)
apply()
(in
SaneDockingProtocol
)
atom_pair_lk_energy_and_deriv_v()
(in
AnalyticEtableEvaluator
)
add_neutral_restype()
(in
IonizableResidue
)
apply()
(in
AddAssemblyConstraints
)
atom_pair_lk_energy_and_deriv_v()
(in
EtableEvaluator
)
ADD_NEW
(in
rosetta.protocols.enzdes._protocols_enzdes_'
)
apply()
(in
AssembleLinkerMover
)
atom_pair_lk_energy_and_deriv_v()
(in
TableLookupEvaluator
)
ADD_NEW
(in
CstAction
)
apply()
(in
CombineChainsMover
)
atom_pair_lk_energy_and_deriv_v_efficient()
(in
AnalyticEtableEvaluator
)
add_new()
(in
HierarchicalLevel
)
apply()
(in
PostDockAssemblyScorer
)
atom_pair_lk_energy_and_deriv_v_efficient()
(in
EtableEvaluator
)
add_new_chain()
(in
AddChainMover
)
apply()
(in
BfactorFittingMover
)
atom_pair_lk_energy_and_deriv_v_efficient()
(in
TableLookupEvaluator
)
add_new_cluster()
(in
KClusterElement
)
apply()
(in
DensityMorphingMover
)
atom_radius()
(in
BuildSet
)
add_new_data()
(in
KClusterElement
)
apply()
(in
ReportFSC
)
atom_radius_squared()
(in
AtomGraphVertexData
)
add_non_protein_cst()
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
apply()
(in
ScaleMapIntensities
)
atom_set()
(in
Etable
)
add_npd_property_calculator_for_state()
(in
DaemonSet
)
apply()
(in
SetupForDensityScoringMover
)
atom_specific_rms()
(in
rosetta.protocols.motifs._protocols_motifs_
)
add_npdpro_calculator_creator()
(in
DaemonSet
)
apply()
(in
ClientMover
)
atom_square_deviation()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
add_nu()
(in
ResidueType
)
apply()
(in
CoMTrackerCM
)
atom_tree()
(in
Conformation
)
add_null_template()
(in
HybridizeProtocol
)
apply()
(in
EnvMover
)
atom_tree()
(in
Pose
)
add_numeric_property()
(in
ResidueProperties
)
apply()
(in
ScriptCM
)
atom_tree_dfunc()
(in
rosetta.core.optimization._core_optimization_
)
add_numeric_property()
(in
ResidueType
)
apply()
(in
EnvLabelSelector
)
atom_tree_dfunc()
(in
rosetta.core.optimization.symmetry._core_optimization_symmetry_
)
add_objective_function_info()
(in
MultiObjective
)
apply()
(in
AlignEvaluator
)
atom_tree_diffs
(in
rosetta.core.import_pose
)
add_observer()
(in
PosePyObserver
)
apply()
(in
MetaPoseEvaluator
)
atom_tree_get_atompairE_deriv()
(in
rosetta.core.optimization._core_optimization_
)
add_observer()
(in
MetropolisHastingsMover
)
apply()
(in
PoseEvaluator
)
atom_tree_get_atompairE_deriv()
(in
rosetta.core.optimization.symmetry._core_optimization_symmetry_
)
add_onebody_enmeth()
(in
MinimizationNode
)
apply()
(in
SingleValuePoseEvaluator_T_double_T
)
ATOM_TREE_UPDATE_INTERNAL_COORDS
(in
rosetta.basic
)
add_oop_constraint()
(in
rosetta.core.pose.ncbb._core_pose_ncbb_
)
apply()
(in
SingleValuePoseEvaluator_T_long_int_T
)
ATOM_TREE_UPDATE_INTERNAL_COORDS
(in
rosetta.basic._basic_
)
add_operation()
(in
PatchCase
)
apply()
(in
SingleValuePoseEvaluator_T_long_unsigned_int_T
)
ATOM_TREE_UPDATE_INTERNAL_COORDS
(in
ProfTag
)
add_option()
(in
JobOptions
)
apply()
(in
TimeEvaluator
)
ATOM_TREE_UPDATE_XYZ_COORDS
(in
rosetta.basic
)
add_orbital()
(in
ResidueType
)
apply()
(in
MultipleDomainMover
)
ATOM_TREE_UPDATE_XYZ_COORDS
(in
rosetta.basic._basic_
)
add_orbital_bond()
(in
ResidueType
)
apply()
(in
RNA_DeNovoProtocol
)
ATOM_TREE_UPDATE_XYZ_COORDS
(in
ProfTag
)
add_orbitals_to_restype()
(in
AssignOrbitals
)
apply()
(in
RNA_FragmentMover
)
atom_type()
(in
ResidueType
)
add_other_pose()
(in
FullModelInfo
)
apply()
(in
RNA_LoopCloser
)
atom_type()
(in
GasteigerAtomTypeSet
)
add_other_struct()
(in
SilentStruct
)
apply()
(in
RNA_Minimizer
)
atom_type()
(in
Residue
)
add_output_observer()
(in
Job
)
apply()
(in
RNA_Relaxer
)
atom_type()
(in
ElecAtom
)
add_overlap_loop()
(in
Loops
)
apply()
(in
ProteinSilentReport
)
atom_type()
(in
EtableAtom
)
add_pack_daemon()
(in
DaemonSet
)
apply()
(in
Report
)
atom_type()
(in
PoseBalls
)
add_packer_screeners()
(in
StepWiseMasterPacker
)
apply()
(in
ReportToDB
)
atom_type_index()
(in
Atom
)
add_pair()
(in
StrandPairing
)
apply()
(in
TrajectoryReportToDB
)
atom_type_index()
(in
AtomTypeSet
)
add_pairing()
(in
AlternativePairings
)
apply()
(in
SetupForFibrilMover
)
atom_type_index()
(in
MMAtomTypeSet
)
add_pairing()
(in
PairingStatEntry
)
apply()
(in
CalculatorFilter
)
atom_type_index()
(in
GasteigerAtomTypeSet
)
add_pairing()
(in
StrandConstraints
)
apply()
(in
CombinedFilter
)
atom_type_index()
(in
Residue
)
add_parameters()
(in
ParametersSet
)
apply()
(in
CompoundFilter
)
atom_type_name()
(in
Adduct
)
add_parameters()
(in
BundleParametersSet
)
apply()
(in
ContingentFilter
)
atom_type_name()
(in
AtomType
)
add_parameters_from_file()
(in
AtomTypeSet
)
apply()
(in
FalseFilter
)
atom_type_name()
(in
OrbitalType
)
add_parameters_set()
(in
Conformation
)
apply()
(in
Filter
)
atom_type_set()
(in
ChemicalManager
)
add_parameters_set()
(in
SymmetricConformation
)
apply()
(in
FilterCollection
)
atom_type_set()
(in
ResidueType
)
add_parameters_set()
(in
ProtectedConformation
)
apply()
(in
IfThenFilter
)
atom_type_set()
(in
ResidueTypeSet
)
add_parent_entity()
(in
GeneticAlgorithm
)
apply()
(in
MoveBeforeFilter
)
atom_type_set()
(in
Residue
)
add_parent_entity()
(in
GeneticAlgorithmBase
)
apply()
(in
ReplicateFilter
)
atom_type_set_name()
(in
AtomVDW
)
add_parent_remark()
(in
SilentStruct
)
apply()
(in
StochasticFilter
)
atom_type_set_ptr()
(in
ResidueType
)
add_parents_from_current_generation()
(in
GeneticAlgorithm
)
apply()
(in
TimeFilter
)
atom_type_set_tag()
(in
ResidueLoaderOptions
)
add_parents_from_current_generation()
(in
GeneticAlgorithmBase
)
apply()
(in
TrueFilter
)
atom_vdw_atom_type_set_name()
(in
EnergyMethodOptions
)
add_pdb()
(in
JointSequenceOperation
)
apply()
(in
BluePrintBDR
)
atom_vertex()
(in
ResidueType
)
add_pdb_id()
(in
PdbIdChunkFilter
)
apply()
(in
CircularPermutation
)
atom_weights()
(in
LKB_ResidueInfo
)
add_pdb_ids()
(in
PdbIdChunkFilter
)
apply()
(in
MatchResiduesMover
)
atom_z_position()
(in
MembraneInfo
)
add_perturber()
(in
GeneralizedKIC
)
apply()
(in
SheetConstraintsRCG
)
AtomAngleSecMatchRPE
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
add_perturber()
(in
BalancedKicMover
)
apply()
(in
CoreDunbrackFilter
)
AtomAngleSecMatchRPEAP
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
add_perturber()
(in
KicMover
)
apply()
(in
FragQualFilter
)
AtomAngleSecMatchRPECAP
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
add_pool()
(in
QuotaCollector
)
apply()
(in
HSSTripletFilter
)
AtomAP
(in
rosetta.core.chemical._core_chemical_
)
add_pose()
(in
UnboundRotamersOperation
)
apply()
(in
HelixKinkFilter
)
AtomAP
(in
rosetta.core.conformation._core_conformation_
)
add_pose()
(in
xyzStripeHashPose
)
apply()
(in
HelixPairingFilter
)
AtomAP
(in
rosetta.core.kinematics.tree._core_kinematics_tree_
)
add_pose()
(in
BackboneDB
)
apply()
(in
InterlockingAromaFilter
)
AtomAP
(in
rosetta.core.scoring.sc._core_scoring_sc_
)
add_pose()
(in
JointSequenceOperation
)
apply()
(in
NcontactsFilter
)
AtomAtomPairFeatures
(in
rosetta.protocols.features._protocols_features_
)
add_pose_input_stream()
(in
MetaPoseInputStream
)
apply()
(in
ParallelBetaPairingPreferenceFilter
)
AtomAtomPairFeaturesAP
(in
rosetta.protocols.features._protocols_features_
)
add_poseinfo_to_ss()
(in
rosetta.protocols.mpi_refinement._protocols_mpi_refinement_
)
apply()
(in
SecondaryStructureCountFilter
)
AtomAtomPairFeaturesCAP
(in
rosetta.protocols.features._protocols_features_
)
add_position()
(in
EnvLabelSelector
)
apply()
(in
SecondaryStructureFilter
)
AtomAtomPairFeaturesCreator
(in
rosetta.protocols.features._protocols_features_
)
add_position_data()
(in
OptEData
)
apply()
(in
SecondaryStructureHasResidueFilter
)
AtomAtomPairFeaturesCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
add_position_in_pose()
(in
EnzCstTemplateResCache
)
apply()
(in
SheetTopologyFilter
)
AtomAtomPairFeaturesCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
add_positive_filter()
(in
BoltzmannFilter
)
apply()
(in
SetAACompositionPotential
)
AtomBasedConstraintsScore
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
ADD_PREGENERATED
(in
rosetta.protocols.enzdes._protocols_enzdes_'
)
apply()
(in
SetSecStructEnergies
)
AtomBasedConstraintsScoreAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
ADD_PREGENERATED
(in
CstAction
)
apply()
(in
FlexPacker
)
AtomBasedConstraintsScoreCAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
add_pregenerated_constraints_to_pose()
(in
EnzConstraintIO
)
apply()
(in
FlexPepDockingAbInitio
)
AtomCAP
(in
rosetta.core.chemical._core_chemical_
)
add_preparer()
(in
AbscriptStageMover
)
apply()
(in
FlexPepDockingLowRes
)
AtomCAP
(in
rosetta.core.conformation._core_conformation_
)
add_ProCorrection_values()
(in
SymmOnTheFlyEdge
)
apply()
(in
FlexPepDockingProtocol
)
AtomCAP
(in
rosetta.core.kinematics.tree._core_kinematics_tree_
)
add_ProCorrection_values_for_edge()
(in
SymmOnTheFlyInteractionGraph
)
apply()
(in
FloppyTailMover
)
AtomCAP
(in
rosetta.core.scoring.sc._core_scoring_sc_
)
add_property()
(in
AtomType
)
apply()
(in
CombinedTaskOperation
)
AtomCoordinateCstMover
(in
rosetta.protocols.relax._protocols_relax_
)
add_property()
(in
ResidueType
)
apply()
(in
FilterStructs
)
AtomCoordinateCstMoverAP
(in
rosetta.protocols.relax._protocols_relax_
)
add_property_i()
(in
BinTransitionData
)
apply()
(in
FilterStructs_Packstat
)
AtomCoordinateCstMoverCAP
(in
rosetta.protocols.relax._protocols_relax_
)
add_property_iplus1()
(in
BinTransitionData
)
apply()
(in
FilterStructs_TotalCharge
)
AtomCoordinateCstMoverCreator
(in
rosetta.protocols.relax._protocols_relax_
)
add_protein()
(in
BackboneDB
)
apply()
(in
FlxbbDesign
)
AtomCoordinateCstMoverCreatorAP
(in
rosetta.protocols.relax._protocols_relax_
)
add_pssm_features()
(in
NMerSVMEnergy
)
apply()
(in
FlxbbDesignPack
)
AtomCoordinateCstMoverCreatorCAP
(in
rosetta.protocols.relax._protocols_relax_
)
add_query_ss()
(in
FragmentPicker
)
apply()
(in
InterlockAroma
)
AtomCountFilter
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
add_r1_value()
(in
BundleParameters
)
apply()
(in
LayerDesignOperation
)
AtomCountFilterAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
add_range()
(in
CompoundInterpolator
)
apply()
(in
BDR
)
AtomCountFilterCAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
add_rcg()
(in
VarLengthBuild
)
apply()
(in
VarLengthBuild
)
AtomCountFilterCreator
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
add_reactivity()
(in
RNA_DataInfo
)
apply()
(in
RemodelConstraintGenerator
)
AtomCountFilterCreatorAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
add_refiner()
(in
LoopProtocol
)
apply()
(in
RemodelRotamerLinks
)
AtomCountFilterCreatorCAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
add_registered_mover()
(in
EnvMover
)
apply()
(in
NonlocalFrags
)
AtomDihedralSecMatchRPE
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
add_relevant_restypes_to_subset()
(in
rosetta.protocols.toolbox.match_enzdes_util._protocols_toolbox_match_enzdes_util_
)
apply()
(in
TorsionFragmentMover
)
AtomDihedralSecMatchRPEAP
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
add_remodel_constraints_to_pose()
(in
RemodelConstraintGenerator
)
apply()
(in
GeneralizedKIC
)
AtomDihedralSecMatchRPECAP
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
add_required_connection_for_residue()
(in
PackerNeighborGraphFilter
)
apply()
(in
GeneralizedKICfilter
)
AtomDistanceSecMatchRPE
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
add_required_connections_between_regions()
(in
PackerNeighborGraphFilter
)
apply()
(in
GeneralizedKICperturber
)
AtomDistanceSecMatchRPEAP
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
add_rerelaxed()
(in
Scheduler
)
apply()
(in
GeneralizedKICselector
)
AtomDistanceSecMatchRPECAP
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
add_res()
(in
SelectResiduesWithinChainOperation
)
apply()
(in
AnchoredGraftMover
)
AtomGeometrySecMatchRPE
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
add_res_identity_i()
(in
BinTransitionData
)
apply()
(in
CCDEndsGraftMover
)
AtomGeometrySecMatchRPEAP
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
add_res_identity_iplus1()
(in
BinTransitionData
)
apply()
(in
GraftMoverBase
)
AtomGeometrySecMatchRPECAP
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
add_resid_to_entity_list()
(in
EntityCorrespondence
)
apply()
(in
DeleteRegionMover
)
AtomGraphEdgeData
(in
rosetta.core.conformation._core_conformation_
)
add_residue()
(in
Parameters
)
apply()
(in
InsertPoseIntoPoseMover
)
AtomGraphEdgeDataAP
(in
rosetta.core.conformation._core_conformation_
)
add_residue()
(in
FragData
)
apply()
(in
KeepRegionMover
)
AtomGraphEdgeDataCAP
(in
rosetta.core.conformation._core_conformation_
)
add_residue()
(in
RotamerConstraint
)
apply()
(in
ReplaceRegionMover
)
AtomGraphVertexData
(in
rosetta.core.conformation._core_conformation_
)
add_residue()
(in
PeptideStubMover
)
apply()
(in
BackboneGridSampler
)
AtomGraphVertexDataAP
(in
rosetta.core.conformation._core_conformation_
)
add_residue()
(in
GeneralizedKICperturber
)
apply()
(in
BundleGridSampler
)
AtomGraphVertexDataCAP
(in
rosetta.core.conformation._core_conformation_
)
add_residue()
(in
BundleParameters
)
apply()
(in
FitSimpleHelix
)
atomic_charge()
(in
Residue
)
add_residue()
(in
AddSidechainConstraintsToHotspots
)
apply()
(in
MakeBundle
)
atomic_interaction_cutoff()
(in
CarbonHBondEnergy
)
add_residue()
(in
HotspotDisjointedFoldTreeMover
)
apply()
(in
MakeBundleHelix
)
atomic_interaction_cutoff()
(in
XtalMLEnergy
)
add_residue_alternative_rotamer()
(in
ResidueAlternativeStepWiseSamplerComb
)
apply()
(in
PerturbBundle
)
atomic_interaction_cutoff()
(in
FullatomCustomPairDistanceEnergy
)
add_residue_alternative_set()
(in
StepWiseConnectionSampler
)
apply()
(in
PerturbBundleHelix
)
atomic_interaction_cutoff()
(in
DNATorsionEnergy
)
add_residue_connection()
(in
ResidueType
)
apply()
(in
HelixNCapperMover
)
atomic_interaction_cutoff()
(in
FA_ElecEnergy
)
add_residue_dis()
(in
TMscoreStore
)
apply()
(in
AddSearchPatternRotSetOp
)
atomic_interaction_cutoff()
(in
FA_ElecEnergyAroAll
)
add_residue_library()
(in
RotamerLibrary
)
apply()
(in
PlaceProbeMover
)
atomic_interaction_cutoff()
(in
FA_ElecEnergyAroAro
)
add_residue_pair()
(in
ResiduePairJump
)
apply()
(in
BackboneTorsionPerturbation
)
atomic_interaction_cutoff()
(in
FA_GrpElecEnergy
)
add_residue_pair_jump()
(in
ResiduePairJumpSetup
)
apply()
(in
BackboneTorsionSampler
)
atomic_interaction_cutoff()
(in
RNA_FA_ElecEnergy
)
add_residue_selector()
(in
AndResidueSelector
)
apply()
(in
CartesianHybridize
)
atomic_interaction_cutoff()
(in
AnalyticEtableEnergy
)
add_residue_selector()
(in
OrResidueSelector
)
apply()
(in
CartesianSampler
)
atomic_interaction_cutoff()
(in
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T
)
add_residue_single()
(in
ResiduePairJump
)
apply()
(in
ChunkTrialMover
)
atomic_interaction_cutoff()
(in
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T
)
add_residue_to_perturber_residue_list()
(in
GeneralizedKIC
)
apply()
(in
DomainAssembly
)
atomic_interaction_cutoff()
(in
TableLookupEtableEnergy
)
add_residue_type()
(in
ResidueTypeSet
)
apply()
(in
FoldTreeHybridize
)
atomic_interaction_cutoff()
(in
FiberDiffractionEnergy
)
add_residue_type_by_name()
(in
ResidueCountFilter
)
apply()
(in
HybridizeProtocol
)
atomic_interaction_cutoff()
(in
FiberDiffractionEnergyDens
)
add_reslabel()
(in
PDBInfo
)
apply()
(in
InsertChunkMover
)
atomic_interaction_cutoff()
(in
ContextDependentGeometricSolEnergy
)
add_resource_configuration()
(in
LazyResourceManager
)
apply()
(in
MRMover
)
atomic_interaction_cutoff()
(in
ContextIndependentGeometricSolEnergy
)
add_resource_locator()
(in
LazyResourceManager
)
apply()
(in
TMalign
)
atomic_interaction_cutoff()
(in
DatabaseOccSolEne
)
add_resource_options()
(in
LazyResourceManager
)
apply()
(in
WeightedFragmentSmoothTrialMover
)
atomic_interaction_cutoff()
(in
ExactOccludedHbondSolEnergy
)
add_resource_tag_by_job_tag()
(in
LazyResourceManager
)
apply()
(in
WeightedFragmentTrialMover
)
atomic_interaction_cutoff()
(in
GeometricSolEnergyEvaluator
)
add_reverse_motifs()
(in
ResPairMotifs
)
apply()
(in
IdealizeMover
)
atomic_interaction_cutoff()
(in
OccludedHbondSolEnergy
)
add_reweighter()
(in
IGEdgeReweightContainer
)
apply()
(in
FragmentLookupFilter
)
atomic_interaction_cutoff()
(in
OccludedHbondSolEnergy_onebody
)
add_rms()
(in
RmsData
)
apply()
(in
RosettaScriptWrapper
)
atomic_interaction_cutoff()
(in
HackAroEnergy
)
add_rotamer()
(in
RotamerSet
)
apply()
(in
FragmentReader
)
atomic_interaction_cutoff()
(in
HBondEnergy
)
add_rotamer()
(in
RotamerSet_
)
apply()
(in
BalancedKicMover
)
atomic_interaction_cutoff()
(in
DDPscore
)
add_rotamer()
(in
RotamerSubset
)
apply()
(in
ClosureSolution
)
atomic_interaction_cutoff()
(in
LoopCloseEnergy
)
add_rotamer()
(in
SymmetricRotamerSet_
)
apply()
(in
KicMover
)
atomic_interaction_cutoff()
(in
FaMPEnvSmoothEnergy
)
add_rotamer()
(in
FlexbbRotamerSet
)
apply()
(in
AddHydrogen
)
atomic_interaction_cutoff()
(in
FaMPSolvEnergy
)
add_rotamer_line_data()
(in
PNatAAOptEPositionData
)
apply()
(in
AddHydrogens
)
atomic_interaction_cutoff()
(in
MPLipoEnergy
)
add_rotamer_line_data()
(in
PNatRotOptEPositionData
)
apply()
(in
AtomCountFilter
)
atomic_interaction_cutoff()
(in
MPPairEnergy
)
add_row()
(in
InsertGenerator
)
apply()
(in
ChainExistsFilter
)
atomic_interaction_cutoff()
(in
MPTMProjPenalty
)
add_rt()
(in
RigidBodySilentStruct
)
apply()
(in
CompleteConnectionsFilter
)
atomic_interaction_cutoff()
(in
CartesianBondedEnergy
)
add_score()
(in
XformScore
)
apply()
(in
CompoundTranslate
)
atomic_interaction_cutoff()
(in
CenHBEnergy
)
add_score()
(in
MoverStatistics
)
apply()
(in
ComputeLigandRDF
)
atomic_interaction_cutoff()
(in
CenPairEnergy
)
add_score()
(in
JointScore
)
apply()
(in
FinalMinimizer
)
atomic_interaction_cutoff()
(in
CenRotPairEnergy
)
add_score_line_string()
(in
rosetta.core.pose._core_pose_
)
apply()
(in
GrowLigand
)
atomic_interaction_cutoff()
(in
ChainbreakEnergy
)
add_score_type()
(in
ScoreCutoffFilter
)
apply()
(in
HBondAcceptorFilter
)
atomic_interaction_cutoff()
(in
ChemicalShiftAnisotropyEnergy
)
add_score_weights()
(in
CoordinateConstraintKC
)
apply()
(in
HBondDonorFilter
)
atomic_interaction_cutoff()
(in
ContactOrderEnergy
)
add_score_weights()
(in
KinematicControl
)
apply()
(in
HeavyAtomFilter
)
atomic_interaction_cutoff()
(in
ContextDependentTwoBodyEnergy
)
add_scored_pair()
(in
PairScoringScheme
)
apply()
(in
HighResDocker
)
atomic_interaction_cutoff()
(in
ContextIndependentTwoBodyEnergy
)
add_scoring_method()
(in
FragmentPicker
)
apply()
(in
InterfaceScoreCalculator
)
atomic_interaction_cutoff()
(in
CustomAtomPairEnergy
)
add_scoring_method()
(in
FragmentScoreManager
)
apply()
(in
LigandBaseProtocol
)
atomic_interaction_cutoff()
(in
D2H_SA_Energy
)
add_scoring_scheme()
(in
CompositeScoringScheme
)
apply()
(in
LigandDesign
)
atomic_interaction_cutoff()
(in
DNA_BaseEnergy
)
add_secondary_downstream_match_geometry_for_constraint()
(in
Matcher
)
apply()
(in
LigandDockProtocol
)
atomic_interaction_cutoff()
(in
DipolarCouplingEnergy
)
add_secondary_upstream_match_geometry_for_constraint()
(in
Matcher
)
apply()
(in
MinimizeBackbone
)
atomic_interaction_cutoff()
(in
DirectReadoutEnergy
)
add_section()
(in
VallLibrary
)
apply()
(in
MinimizeLigand
)
atomic_interaction_cutoff()
(in
DistanceChainbreakEnergy
)
add_segment()
(in
SpecialSegmentsObserver
)
apply()
(in
MolarMassFilter
)
atomic_interaction_cutoff()
(in
EnvSmoothEnergy
)
add_segment()
(in
BackrubMover
)
apply()
(in
MolecularMassFilter
)
atomic_interaction_cutoff()
(in
Fa_MbsolvEnergy
)
add_selector()
(in
CompositeFragmentSelector
)
apply()
(in
RandomConformerMover
)
atomic_interaction_cutoff()
(in
GaussianOverlapEnergy
)
add_seq_label()
(in
SequenceAnnotation
)
apply()
(in
RandomConformers
)
atomic_interaction_cutoff()
(in
GoapEnergy
)
add_sequence()
(in
CompositeSequence
)
apply()
(in
RigidSearchMover
)
atomic_interaction_cutoff()
(in
HybridVDW_Energy
)
add_sequence()
(in
SequenceAlignment
)
apply()
(in
Rotate
)
atomic_interaction_cutoff()
(in
IntermolEnergy
)
add_setup_mover()
(in
VarLengthBuild
)
apply()
(in
Rotates
)
atomic_interaction_cutoff()
(in
LK_BallEnergy
)
add_shear_mover()
(in
MetropolisHastingsMover
)
apply()
(in
SlideTogether
)
atomic_interaction_cutoff()
(in
LK_PolarNonPolarEnergy
)
add_sidechain_mc_mover()
(in
MetropolisHastingsMover
)
apply()
(in
StartFrom
)
atomic_interaction_cutoff()
(in
LK_hack
)
add_sidechain_mover()
(in
MetropolisHastingsMover
)
apply()
(in
TetherLigand
)
atomic_interaction_cutoff()
(in
LinearChainbreakEnergy
)
add_sigmoid()
(in
SmoothScoreTermCoeffs
)
apply()
(in
Transform
)
atomic_interaction_cutoff()
(in
MMBondAngleEnergy
)
add_similarity()
(in
DataPoint
)
apply()
(in
Translate
)
atomic_interaction_cutoff()
(in
MMBondLengthEnergy
)
add_single_cutpoint_variant()
(in
rosetta.protocols.loops._protocols_loops_
)
apply()
(in
UnconstrainedTorsionsMover
)
atomic_interaction_cutoff()
(in
MMLJEnergyInter
)
add_small_fragments()
(in
HybridizeProtocol
)
apply()
(in
WriteLigandMolFile
)
atomic_interaction_cutoff()
(in
MMLJEnergyIntra
)
add_small_mover()
(in
MetropolisHastingsMover
)
apply()
(in
LoopBuildMover
)
atomic_interaction_cutoff()
(in
MMTorsionEnergy
)
add_spaces_left_align()
(in
rosetta.utility._utility_
)
apply()
(in
LoopmodelWrapper
)
atomic_interaction_cutoff()
(in
MembraneCenPairEnergy
)
add_spaces_right_align()
(in
rosetta.utility._utility_
)
apply()
(in
LoopBuilder
)
atomic_interaction_cutoff()
(in
MembraneEnvPenalties
)
add_span()
(in
SpanningTopology
)
apply()
(in
LoopModeler
)
atomic_interaction_cutoff()
(in
MembraneEnvSmoothEnergy
)
add_spanning_region()
(in
MembraneAbinitio
)
apply()
(in
LoopMover
)
atomic_interaction_cutoff()
(in
MembraneLipo
)
add_sr_gaussian()
(in
CenHBPotential
)
apply()
(in
LoopProtocol
)
atomic_interaction_cutoff()
(in
MissingEnergy
)
add_standard_functions()
(in
ArithmeticScanner
)
apply()
(in
MinimizationRefiner
)
atomic_interaction_cutoff()
(in
OtherPoseEnergy
)
add_start_from()
(in
LigandDockProtocol
)
apply()
(in
RepackingRefiner
)
atomic_interaction_cutoff()
(in
PackStatEnergy
)
add_str_str_data()
(in
MolFileIOMolecule
)
apply()
(in
RotamerTrialsRefiner
)
atomic_interaction_cutoff()
(in
PairEnergy
)
add_strand_pairs_cst()
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
apply()
(in
LegacyKicSampler
)
atomic_interaction_cutoff()
(in
PeptideBondEnergy
)
add_strandMover()
(in
RBSegmentRelax
)
apply()
(in
AcceptanceCheck
)
atomic_interaction_cutoff()
(in
ProClosureEnergy
)
add_string()
(in
Job
)
apply()
(in
LoopFilter
)
atomic_interaction_cutoff()
(in
ProQ_Energy
)
add_string_property()
(in
ResidueProperties
)
apply()
(in
LoopMoverGroup
)
atomic_interaction_cutoff()
(in
RG_Energy_Fast
)
add_string_property()
(in
ResidueType
)
apply()
(in
PrepareForCentroid
)
atomic_interaction_cutoff()
(in
RG_LocalEnergy
)
add_string_real_pair()
(in
Job
)
apply()
(in
PrepareForFullatom
)
atomic_interaction_cutoff()
(in
RMS_Energy
)
add_string_string_pair()
(in
Job
)
apply()
(in
FastGapMover
)
atomic_interaction_cutoff()
(in
Rama2BOffsetEnergy
)
add_string_value()
(in
SilentStruct
)
apply()
(in
LoopHashDiversifier
)
atomic_interaction_cutoff()
(in
RamachandranEnergy2B
)
add_strings()
(in
Job
)
apply()
(in
LoopHashLibrary
)
atomic_interaction_cutoff()
(in
ResidualDipolarCouplingEnergy
)
add_structure()
(in
SilentFileData
)
apply()
(in
LoopHashMoverWrapper
)
atomic_interaction_cutoff()
(in
ResidualDipolarCouplingEnergy_Rohl
)
add_structure()
(in
HedgeArchive
)
apply()
(in
LoopHashRelaxProtocol
)
atomic_interaction_cutoff()
(in
SA_Energy
)
add_structure()
(in
IterativeAbrelax
)
apply()
(in
Mover_LoopHashRefine
)
atomic_interaction_cutoff()
(in
SecondaryStructureEnergy
)
add_structure()
(in
IterativeBase
)
apply()
(in
FoldTreeFromLoops
)
atomic_interaction_cutoff()
(in
ShortRangeTwoBodyEnergy
)
add_structure()
(in
IterativeCentroid
)
apply()
(in
CCDLoopClosureMover
)
atomic_interaction_cutoff()
(in
SmoothCenPairEnergy
)
add_structure()
(in
IterativeFullatom
)
apply()
(in
FASelectSlidingWindowLoopClosure
)
atomic_interaction_cutoff()
(in
SuckerEnergy
)
add_structure()
(in
ClusterBase
)
apply()
(in
LoopClosure
)
atomic_interaction_cutoff()
(in
WaterAdductHBondEnergy
)
add_structure()
(in
ArchiveBase
)
apply()
(in
ShortLoopClosure
)
atomic_interaction_cutoff()
(in
WholeStructureEnergy
)
add_structure()
(in
EvaluatedArchive
)
apply()
(in
SlidingWindowLoopClosure
)
atomic_interaction_cutoff()
(in
OrbitalsScore
)
add_structure()
(in
NormalizedEvaluatedArchive
)
apply()
(in
WidthFirstSlidingWindowLoopClosure
)
atomic_interaction_cutoff()
(in
HolesEnergy
)
add_structure()
(in
VarianceStatisticsArchive
)
apply()
(in
KinematicMover
)
atomic_interaction_cutoff()
(in
HolesEnergyRes
)
add_structure_replace_tag_if_necessary()
(in
SilentFileData
)
apply()
(in
KinematicWrapper
)
atomic_interaction_cutoff()
(in
SurfEnergy
)
add_stub_()
(in
HotspotStubSet
)
apply()
(in
IndependentLoopMover
)
atomic_interaction_cutoff()
(in
SurfVolEnergy
)
add_stub_set()
(in
HotspotStubSet
)
apply()
(in
LoopCM
)
atomic_interaction_cutoff()
(in
RG_Energy_RNA
)
ADD_SUBMOTIF
(in
rosetta.protocols.stepwise.monte_carlo.mover
)
apply()
(in
LoopMover
)
atomic_interaction_cutoff()
(in
RNA_FullAtomStackingEnergy
)
ADD_SUBMOTIF
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
apply()
(in
LoopMover_Refine_Backrub
)
atomic_interaction_cutoff()
(in
RNA_JR_SuiteEnergy
)
ADD_SUBMOTIF
(in
MoveType
)
apply()
(in
LoopMover_Refine_CCD
)
atomic_interaction_cutoff()
(in
RNA_LJ_BaseEnergy
)
add_submover()
(in
AbscriptStageMover
)
apply()
(in
LoopMover_Refine_KIC
)
atomic_interaction_cutoff()
(in
RNA_Mg_Energy
)
add_suckers()
(in
AddCavitiesMover
)
apply()
(in
LoopRefineInnerCycle
)
atomic_interaction_cutoff()
(in
RNA_PairwiseLowResolutionEnergy
)
add_sugar_ring_closure_constraints()
(in
DNATorsionPotential
)
apply()
(in
LoopRefineInnerCycleContainer
)
atomic_interaction_cutoff()
(in
RNA_SuiteEnergy
)
add_sugar_ring_closure_constraints()
(in
RNA_SugarCloseEnergy
)
apply()
(in
RepackTrial
)
atomic_interaction_cutoff()
(in
RNA_TorsionEnergy
)
add_sym_dof_name()
(in
InterfaceSasaFilter
)
apply()
(in
ShearMinCCDTrial
)
atomic_interaction_cutoff()
(in
RNA_VDW_Energy
)
add_tail_residue()
(in
GeneralizedKIC
)
apply()
(in
SmallMinCCDTrial
)
atomic_interaction_cutoff()
(in
StackElecEnergy
)
add_target_constraints()
(in
Templates
)
apply()
(in
LoopsDatabaseDefiner
)
atomic_interaction_cutoff()
(in
RNA_ChemicalShiftEnergy
)
add_target_restype()
(in
SecondaryMatcherToUpstreamResidue
)
apply()
(in
LoopsDefiner
)
atomic_interaction_cutoff()
(in
RNA_ChemicalMappingEnergy
)
add_task_operation()
(in
DesignTask
)
apply()
(in
LoopsExplicitDefiner
)
atomic_interaction_cutoff()
(in
RNA_DataBackboneEnergy
)
add_task_operations()
(in
DesignTask
)
apply()
(in
LoopsFileDefiner
)
atomic_interaction_cutoff()
(in
FastSAXSEnergy
)
add_template()
(in
HybridizeProtocol
)
apply()
(in
MakeRotLibMover
)
atomic_interaction_cutoff()
(in
SAXSEnergy
)
add_threshold_distance_allFrag()
(in
FragmentStore
)
apply()
(in
MatcherMover
)
atomic_interaction_cutoff()
(in
NatbiasSecondaryStructureEnergy
)
add_to_allowed_aas()
(in
ConservativeDesignOperation
)
apply()
(in
BuildingBlockInterfaceOperation
)
atomic_interaction_cutoff()
(in
EnsembleEnergy
)
add_to_allowed_aas()
(in
MutationSetDesignOperation
)
apply()
(in
ClashCheckFilter
)
atomic_interaction_cutoff()
(in
InterchainPairEnergy
)
add_to_energy_map()
(in
EnergyEdge
)
apply()
(in
ExtractSubposeMover
)
atomic_interaction_cutoff()
(in
ResidualDipolarCouplingEnergyRigidSegments
)
add_to_individual_sol_energies()
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
apply()
(in
GetRBDOFValues
)
atomic_interaction_cutoff()
(in
PCS_Energy
)
add_to_library()
(in
MotifLibrary
)
apply()
(in
InterfacePackingFilter
)
atomic_interaction_cutoff()
(in
PcsEnergy
)
add_to_nodes_one_body_energy()
(in
InteractionGraphBase
)
apply()
(in
MatDesGreedyOptMutationMover
)
atomic_interaction_cutoff()
(in
PCS_Energy_Ts1
)
add_to_one_body_energies()
(in
DensePDNode
)
apply()
(in
OligomericAverageDegreeFilter
)
atomic_interaction_cutoff()
(in
PCS_Energy_Ts2
)
add_to_one_body_energies()
(in
DoubleDensePDNode
)
apply()
(in
SchemePlaceMotifsMover
)
atomic_interaction_cutoff()
(in
PCS_Energy_Ts3
)
add_to_one_body_energies()
(in
DoubleLazyNode
)
apply()
(in
SymDofMover
)
atomic_interaction_cutoff()
(in
PCS_Energy_Ts4
)
add_to_one_body_energies()
(in
FASTERNode
)
apply()
(in
SymUnsatHbondFilter
)
atomic_interaction_cutoff()
(in
PDDFEnergy
)
add_to_one_body_energies()
(in
InteractionGraphBase
)
apply()
(in
CartesianMD
)
atomic_radius()
(in
GenBornResidueInfo
)
add_to_one_body_energies()
(in
LazyNode
)
apply()
(in
MDBase
)
AtomicContactCountFilter
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
add_to_one_body_energies()
(in
LinearMemNode
)
apply()
(in
MedalExchangeMover
)
AtomicContactCountFilterAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
add_to_one_body_energies()
(in
NodeBase
)
apply()
(in
MedalMover
)
AtomicContactCountFilterCAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
add_to_one_body_energies()
(in
OnTheFlyNode
)
apply()
(in
AddMPLigandMover
)
AtomicContactCountFilterCreator
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
add_to_one_body_energies()
(in
PDNode
)
apply()
(in
AddMembraneMover
)
AtomicContactCountFilterCreatorAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
add_to_one_body_energies()
(in
SymmLinearMemNode
)
apply()
(in
FlipMover
)
AtomicContactCountFilterCreatorCAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
add_to_one_body_energies()
(in
SymmMinimalistNode
)
apply()
(in
MembranePositionFromTopologyMover
)
AtomicContactFilter
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
add_to_one_body_energies()
(in
SymmOnTheFlyNode
)
apply()
(in
RandomPositionRotationMover
)
AtomicContactFilterAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
add_to_one_body_energies()
(in
FlexbbNode
)
apply()
(in
RandomPositionTranslationMover
)
AtomicContactFilterCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
add_to_one_body_energies()
(in
MinimalistFlexbbNode
)
apply()
(in
RotationMover
)
AtomicContactFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
add_to_one_body_energies()
(in
OTFFlexbbNode
)
apply()
(in
SetMembraneCenterMover
)
AtomicContactFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
add_to_one_body_energy()
(in
DensePDNode
)
apply()
(in
SetMembraneNormalMover
)
AtomicContactFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
add_to_one_body_energy()
(in
DoubleDensePDNode
)
apply()
(in
SetMembranePositionMover
)
AtomicDistanceFilter
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
add_to_one_body_energy()
(in
DoubleLazyNode
)
apply()
(in
TransformIntoMembraneMover
)
AtomicDistanceFilterAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
add_to_one_body_energy()
(in
FASTERNode
)
apply()
(in
TranslationMover
)
AtomicDistanceFilterCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
add_to_one_body_energy()
(in
LazyNode
)
apply()
(in
TranslationRotationMover
)
AtomicDistanceFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
add_to_one_body_energy()
(in
LinearMemNode
)
apply()
(in
SymmetricAddMembraneMover
)
AtomicDistanceFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
add_to_one_body_energy()
(in
NodeBase
)
apply()
(in
VisualizeEmbeddingMover
)
AtomicDistanceFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
add_to_one_body_energy()
(in
OnTheFlyNode
)
apply()
(in
VisualizeMembraneMover
)
AtomICoor
(in
rosetta.core.chemical._core_chemical_
)
add_to_one_body_energy()
(in
PDNode
)
apply()
(in
ZincHeterodimerMover
)
AtomICoorAP
(in
rosetta.core.chemical._core_chemical_
)
add_to_one_body_energy()
(in
SymmLinearMemNode
)
apply()
(in
MotifGraftMover
)
AtomICoorCAP
(in
rosetta.core.chemical._core_chemical_
)
add_to_one_body_energy()
(in
SymmMinimalistNode
)
apply()
(in
MotifDnaPacker
)
AtomicOrbitalTypes
(in
GasteigerAtomTypeData
)
add_to_one_body_energy()
(in
SymmOnTheFlyNode
)
apply()
(in
CompositionMover
)
AtomicOrbitalTypes_strings()
(in
GasteigerAtomTypeData
)
add_to_one_body_energy()
(in
FlexbbNode
)
apply()
(in
CycleMover
)
AtomID
(in
rosetta.core.id._core_id_
)
add_to_one_body_energy()
(in
MinimalistFlexbbNode
)
apply()
(in
CyclicMover
)
AtomID_Map_AtomID
(in
rosetta.core.id._core_id_
)
add_to_one_body_energy()
(in
OTFFlexbbNode
)
apply()
(in
DsspMover
)
AtomID_Map_AtomIDAP
(in
rosetta.core.id._core_id_
)
add_to_one_body_energy_for_node_state()
(in
OnTheFlyInteractionGraph
)
apply()
(in
FilterMover
)
AtomID_Map_AtomIDCAP
(in
rosetta.core.id._core_id_
)
add_to_one_body_energy_for_node_state()
(in
SymmOnTheFlyInteractionGraph
)
apply()
(in
FilterReporterMover
)
AtomID_Map_bool
(in
rosetta.core.id._core_id_
)
add_to_pose_list()
(in
rosetta.protocols.stepwise.modeler._protocols_stepwise_modeler_
)
apply()
(in
IfMover
)
AtomID_Map_boolAP
(in
rosetta.core.id._core_id_
)
add_to_top_level()
(in
HierarchicalLevel
)
apply()
(in
IteratedConvergenceMover
)
AtomID_Map_boolCAP
(in
rosetta.core.id._core_id_
)
add_to_two_body_energies()
(in
DensePDEdge
)
apply()
(in
JumpOutMover
)
AtomID_Map_Real
(in
rosetta.core.id._core_id_
)
add_to_two_body_energies()
(in
DoubleDensePDEdge
)
apply()
(in
MCShowMover
)
AtomID_Map_RealAP
(in
rosetta.core.id._core_id_
)
add_to_two_body_energies()
(in
FASTEREdge
)
apply()
(in
MonteCarloUtil
)
AtomID_Map_RealCAP
(in
rosetta.core.id._core_id_
)
add_to_two_body_energies()
(in
PDEdge
)
apply()
(in
MoveMapMover
)
AtomID_Map_T_bool_T
(in
rosetta.core.id._core_id_
)
add_to_two_body_energies()
(in
PrecomputedPairEnergiesEdge
)
apply()
(in
Mover
)
AtomID_Map_T_bool_TAP
(in
rosetta.core.id._core_id_
)
add_to_two_body_energies_for_edge()
(in
PrecomputedPairEnergiesInteractionGraph
)
apply()
(in
MoverApplyingMover
)
AtomID_Map_T_bool_TCAP
(in
rosetta.core.id._core_id_
)
add_to_two_body_energy()
(in
DensePDEdge
)
apply()
(in
MoverContainer
)
AtomID_Map_T_core_id_AtomID_T
(in
rosetta.core.id._core_id_
)
add_to_two_body_energy()
(in
DoubleDensePDEdge
)
apply()
(in
MoverForPoseList
)
AtomID_Map_T_core_id_AtomID_TAP
(in
rosetta.core.id._core_id_
)
add_to_two_body_energy()
(in
FASTEREdge
)
apply()
(in
NullMover
)
AtomID_Map_T_core_id_AtomID_TCAP
(in
rosetta.core.id._core_id_
)
add_to_two_body_energy()
(in
PDEdge
)
apply()
(in
PDBDumpMover
)
AtomID_Map_T_double_T
(in
rosetta.core.id._core_id_
)
add_to_two_body_energy()
(in
PrecomputedPairEnergiesEdge
)
apply()
(in
ProfilerMover
)
AtomID_Map_T_double_TAP
(in
rosetta.core.id._core_id_
)
add_topology()
(in
PairingStatistics
)
apply()
(in
PyMolMover
)
AtomID_Map_T_double_TCAP
(in
rosetta.core.id._core_id_
)
add_torerelax()
(in
Scheduler
)
apply()
(in
RampingMover
)
AtomID_Map_T_numeric_xyzVector_T_double_T__T
(in
rosetta.core.id._core_id_
)
add_torsion()
(in
MinimizerMapBase
)
apply()
(in
RandomMover
)
AtomID_Map_T_numeric_xyzVector_T_double_T__TAP
(in
rosetta.core.id._core_id_
)
add_torsion()
(in
CartesianMinimizerMap
)
apply()
(in
RepeatMover
)
AtomID_Map_T_numeric_xyzVector_T_double_T__TCAP
(in
rosetta.core.id._core_id_
)
add_torsion()
(in
MinimizerMap
)
apply()
(in
SequenceMover
)
AtomIDAP
(in
rosetta.core.id._core_id_
)
add_torsion()
(in
SymMinimizerMap
)
apply()
(in
StructureRestrictor
)
AtomIDCAP
(in
rosetta.core.id._core_id_
)
add_torsion()
(in
MetricRecorder
)
apply()
(in
TrialMover
)
AtomIDHashFunction
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
add_torsion()
(in
FragmentLibrary
)
apply()
(in
VectorPoseMover
)
AtomIDHashFunctionAP
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
add_torsion_parameter()
(in
ResidueCartBondedParameters
)
apply()
(in
WhileMover
)
AtomIDHashFunctionCAP
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
add_torsion_to_fix()
(in
BackboneGridSampler
)
apply()
(in
Clusterer
)
atomids()
(in
PoseBalls
)
add_torsion_to_sample()
(in
BackboneGridSampler
)
apply()
(in
Serial_Refine
)
AtomInformation
(in
rosetta.core.io.pdb._core_io_pdb_
)
add_trigger()
(in
GenericMonteCarloMover
)
apply()
(in
StructAvrgMover
)
AtomInformationAP
(in
rosetta.core.io.pdb._core_io_pdb_
)
add_trigger()
(in
RationalMonteCarlo
)
apply()
(in
NcbbDockDesignProtocol
)
AtomInformationCAP
(in
rosetta.core.io.pdb._core_io_pdb_
)
add_twobody_enmeth()
(in
MinimizationEdge
)
apply()
(in
OopCreatorMover
)
AtomInResidueAtomInResiduePairFeatures
(in
rosetta.protocols.features._protocols_features_
)
add_twobody_enmeth()
(in
MinimizationNode
)
apply()
(in
OopDockDesignProtocol
)
AtomInResidueAtomInResiduePairFeaturesAP
(in
rosetta.protocols.features._protocols_features_
)
add_type()
(in
FuncFactory
)
apply()
(in
CartesianNormalModeMover
)
AtomInResidueAtomInResiduePairFeaturesCAP
(in
rosetta.protocols.features._protocols_features_
)
add_type()
(in
ScoringSchemeFactory
)
apply()
(in
NormalModeMinimizer
)
AtomInResidueAtomInResiduePairFeaturesCreator
(in
rosetta.protocols.features._protocols_features_
)
add_type()
(in
ResidueFeatureFactory
)
apply()
(in
NormalModeRelaxMover
)
AtomInResidueAtomInResiduePairFeaturesCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
add_type()
(in
DockDesignFilterFactory
)
apply()
(in
TorsionNormalModeMover
)
AtomInResidueAtomInResiduePairFeaturesCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
add_unfolded_energy_data()
(in
UnfoldedStateEnergyCalculatorJobDistributor
)
apply()
(in
SetupPoissonBoltzmannPotential
)
atomitem
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
add_unfolded_energy_data()
(in
UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
)
apply()
(in
Revert
)
atomname()
(in
ContactPartner
)
add_unrecognized_atom()
(in
PDBInfo
)
apply()
(in
AtomicContactCountFilter
)
AtomNeighbor
(in
rosetta.core.scoring._core_scoring_
)
add_upper_connect_angle_params()
(in
ResidueCartBondedParameters
)
apply()
(in
AverageDegreeFilter
)
AtomNeighborAP
(in
rosetta.core.scoring._core_scoring_
)
add_upper_terminus_type_to_conformation_residue()
(in
rosetta.core.conformation._core_conformation_
)
apply()
(in
BindingStrainFilter
)
AtomNeighborCAP
(in
rosetta.core.scoring._core_scoring_
)
add_upper_terminus_type_to_pose_residue()
(in
rosetta.core.pose._core_pose_
)
apply()
(in
BoltzmannFilter
)
atomno()
(in
ICoorAtomID
)
add_upstream_restype_for_constraint()
(in
Matcher
)
apply()
(in
ClashWithTargetFilter
)
atomno()
(in
ResidueConnection
)
add_user_provided_mover()
(in
VarLengthBuild
)
apply()
(in
DesignableResiduesFilter
)
atomno()
(in
AtomID
)
add_vall_cheating_fragments()
(in
rosetta.protocols.frags._protocols_frags_
)
apply()
(in
DisulfideFilter
)
atomno()
(in
DOF_ID
)
add_vall_fragments()
(in
rosetta.protocols.frags._protocols_frags_
)
apply()
(in
FNatFilter
)
atomno()
(in
DOF_Node
)
add_value_to_perturber_value_list()
(in
GeneralizedKIC
)
apply()
(in
FilterScanFilter
)
atomno()
(in
AtomNeighbor
)
add_values_from_center()
(in
rosetta.core.chemical.rna._core_chemical_rna_
)
apply()
(in
HbondsToAtomFilter
)
atomno()
(in
Ball
)
add_values_to_job()
(in
BiasEnergy
)
apply()
(in
HbondsToResidueFilter
)
atomno1()
(in
SmallAtNb
)
add_values_to_job()
(in
JobOutputterObserver
)
apply()
(in
IRmsdFilter
)
atomno2()
(in
SmallAtNb
)
add_values_to_job()
(in
ParsedProtocol
)
apply()
(in
InterfaceHolesFilter
)
AtomPairConstraint
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
add_variable()
(in
ArithmeticScanner
)
apply()
(in
LRmsdFilter
)
AtomPairConstraintAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
add_variable()
(in
SimpleExpressionCreator
)
apply()
(in
RelativeSegmentFilter
)
AtomPairConstraintCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
add_variant_type()
(in
ResidueType
)
apply()
(in
RmsdFilter
)
AtomPairConstraintCreator
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
add_variant_type_to_conformation_residue()
(in
rosetta.core.conformation._core_conformation_
)
apply()
(in
RmsdSimpleFilter
)
AtomPairConstraintCreatorAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
add_variant_type_to_pose_residue()
(in
rosetta.core.pose._core_pose_
)
apply()
(in
SSamountFilter
)
AtomPairConstraintCreatorCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
add_variant_type_to_residue()
(in
rosetta.core.pose._core_pose_
)
apply()
(in
SequenceRecoveryFilter
)
AtomPairConstraintsData
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
add_virt_res_as_root()
(in
StepWiseWorkingParameters
)
apply()
(in
SpecificResiduesNearInterfaceFilter
)
AtomPairConstraintsDataAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
add_virtual_O2Prime_hydrogen()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
apply()
(in
StubScoreFilter
)
AtomPairConstraintsDataCAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
add_virtual_res()
(in
rosetta.protocols.toolbox.sample_around._protocols_toolbox_sample_around_
)
apply()
(in
StubScoreLoopsFilter
)
AtomPairConstraintsScore
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
add_virtual_residue_to_cterm()
(in
rosetta.protocols.relax._protocols_relax_
)
apply()
(in
Torsion
)
AtomPairConstraintsScoreAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
add_virtual_sugar_res()
(in
rosetta.protocols.stepwise.setup._protocols_stepwise_setup_
)
apply()
(in
AddChainBreak
)
AtomPairConstraintsScoreCAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
add_weight()
(in
WeightedSampler
)
apply()
(in
AddSidechainConstraintsToHotspots
)
AtomPairData
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
add_weights_from_file()
(in
ScoreFunction
)
apply()
(in
BackrubDDMover
)
AtomPairDataAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
add_whole_pose_context_enmeth()
(in
MinimizationGraph
)
apply()
(in
BestHotspotCstMover
)
AtomPairDataCAP
(in
rosetta.protocols.ligand_docking.rdf._protocols_ligand_docking_rdf_
)
add_wholeStructureMover()
(in
RBSegmentRelax
)
apply()
(in
BuildAlaPose
)
AtomPairEnergy
(in
rosetta.core.scoring.etable._core_scoring_etable_
)
add_wt()
(in
DDGMutationOptEData
)
apply()
(in
DesignMinimizeHbonds
)
AtomPairEnergyAP
(in
rosetta.core.scoring.etable._core_scoring_etable_
)
add_wt_complex()
(in
DDGBindOptEData
)
apply()
(in
DisulfideMover
)
AtomPairEnergyCAP
(in
rosetta.core.scoring.etable._core_scoring_etable_
)
add_wt_unbounds()
(in
DDGBindOptEData
)
apply()
(in
DockAndRetrieveSidechains
)
AtomPairFuncList
(in
rosetta.core.scoring.custom_pair_distance._core_scoring_custom_pair_distance_
)
AddAllPositionsMPM
(in
rosetta.protocols.match._protocols_match_
)
apply()
(in
DockWithHotspotMover
)
AtomPairFuncListAP
(in
rosetta.core.scoring.custom_pair_distance._core_scoring_custom_pair_distance_
)
AddAllPositionsMPMAP
(in
rosetta.protocols.match._protocols_match_
)
apply()
(in
FavorNativeResiduePreCycle
)
AtomPairFuncListCAP
(in
rosetta.core.scoring.custom_pair_distance._core_scoring_custom_pair_distance_
)
AddAllPositionsMPMCAP
(in
rosetta.protocols.match._protocols_match_
)
apply()
(in
FavorNonNativeResiduePreCycle
)
AtomRadiusMap
(in
rosetta.core.scoring.packstat._core_scoring_packstat_
)
AddAromaticAtomType()
(in
PossibleAtomTypesForAtom
)
apply()
(in
HotspotDisjointedFoldTreeMover
)
AtomRadiusMapAP
(in
rosetta.core.scoring.packstat._core_scoring_packstat_
)
AddAssemblyConstraints
(in
rosetta.protocols.domain_assembly._protocols_domain_assembly_
)
apply()
(in
HotspotHasherMover
)
AtomRadiusMapCAP
(in
rosetta.core.scoring.packstat._core_scoring_packstat_
)
AddAssemblyConstraintsAP
(in
rosetta.protocols.domain_assembly._protocols_domain_assembly_
)
apply()
(in
InterfaceRecapitulationMover
)
atoms()
(in
Residue
)
AddAssemblyConstraintsCAP
(in
rosetta.protocols.domain_assembly._protocols_domain_assembly_
)
apply()
(in
LoopFinder
)
atoms()
(in
DOF_Node
)
AddAtom
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
LoopLengthChange
)
atoms()
(in
SimplePDB
)
AddAtom()
(in
MolecularSurfaceCalculator
)
apply()
(in
LoopMoverFromCommandLine
)
atoms()
(in
JumpClaim
)
AddAtomAlias
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
LoopOver
)
atoms_and_func_struct
(in
rosetta.core.scoring.custom_pair_distance._core_scoring_custom_pair_distance_
)
AddAtomAliasAP
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
LoopRemodel
)
atoms_and_func_structAP
(in
rosetta.core.scoring.custom_pair_distance._core_scoring_custom_pair_distance_
)
AddAtomAliasCAP
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
MapHotspot
)
atoms_and_func_structCAP
(in
rosetta.core.scoring.custom_pair_distance._core_scoring_custom_pair_distance_
)
AddAtomAP
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
PatchdockTransform
)
atoms_are_bonded()
(in
ResidueType
)
AddAtomCAP
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
PeptideStapleDesignMover
)
atoms_begin()
(in
Atom
)
AddAtomType()
(in
PossibleAtomTypesForAtom
)
apply()
(in
PlaceOnLoop
)
atoms_begin()
(in
Atom_
)
AddBehaviorRLT
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
apply()
(in
PlaceSimultaneouslyMover
)
atoms_end()
(in
Atom
)
AddBehaviorRLTAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
apply()
(in
PlaceStubMover
)
atoms_end()
(in
Atom_
)
AddBehaviorRLTCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
apply()
(in
PlacementAuctionMover
)
atoms_interact()
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
AddBehaviorRLTCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
apply()
(in
PlacementMinimizationMover
)
atoms_last_controlled_by_chi()
(in
ResidueType
)
AddBehaviorRLTCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
apply()
(in
PrepackMover
)
atoms_with_orb_index()
(in
ResidueType
)
AddBehaviorRLTCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
apply()
(in
ProteinInterfaceMultiStateDesignMover
)
atoms_with_orb_index()
(in
Residue
)
AddBond
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
RandomMutation
)
atoms_within_one_bond_of_a_residue_connection()
(in
ResidueType
)
AddBondAP
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
RepackMinimize
)
atoms_within_two_bonds_of_a_residue_connection()
(in
ResidueType
)
AddBondCAP
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
SaveAndRetrieveSidechains
)
AtomTree
(in
rosetta.core.kinematics._core_kinematics_
)
AddBondType
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
SetAtomTree
)
AtomTreeAP
(in
rosetta.core.kinematics._core_kinematics_
)
AddBondTypeAP
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
SetTemperatureFactor
)
AtomTreeCAP
(in
rosetta.core.kinematics._core_kinematics_
)
AddBondTypeCAP
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
SetupHotspotConstraintsLoopsMover
)
AtomTreeCollection
(in
rosetta.core.pack.scmin._core_pack_scmin_'
)
AddCavitiesMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
SetupHotspotConstraintsMover
)
AtomTreeCollectionAP
(in
rosetta.core.pack.scmin._core_pack_scmin_'
)
AddCavitiesMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
ShoveResidueMover
)
AtomTreeCollectionCAP
(in
rosetta.core.pack.scmin._core_pack_scmin_'
)
AddCavitiesMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
SpinMover
)
AtomTreeDiff
(in
rosetta.core.import_pose.atom_tree_diffs._core_import_pose_atom_tree_diffs_
)
AddCDRProfileSetsOperation
(in
rosetta.protocols.antibody.task_operations._protocols_antibody_task_operations_
)
apply()
(in
SubroutineMover
)
AtomTreeDiffAP
(in
rosetta.core.import_pose.atom_tree_diffs._core_import_pose_atom_tree_diffs_
)
AddCDRProfileSetsOperationAP
(in
rosetta.protocols.antibody.task_operations._protocols_antibody_task_operations_
)
apply()
(in
TaskAwareCsts
)
AtomTreeDiffCAP
(in
rosetta.core.import_pose.atom_tree_diffs._core_import_pose_atom_tree_diffs_
)
AddCDRProfileSetsOperationCAP
(in
rosetta.protocols.antibody.task_operations._protocols_antibody_task_operations_
)
apply()
(in
TopologyBrokerMover
)
AtomTreeDiffJobDistributor
(in
rosetta.protocols.jobdist._protocols_jobdist_
)
AddCDRProfilesOperation
(in
rosetta.protocols.antibody.task_operations._protocols_antibody_task_operations_
)
apply()
(in
TryRotamers
)
AtomTreeDiffJobDistributorAP
(in
rosetta.protocols.jobdist._protocols_jobdist_
)
AddCDRProfilesOperationAP
(in
rosetta.protocols.antibody.task_operations._protocols_antibody_task_operations_
)
apply()
(in
VLB
)
AtomTreeDiffJobDistributorCAP
(in
rosetta.protocols.jobdist._protocols_jobdist_
)
AddCDRProfilesOperationCAP
(in
rosetta.protocols.antibody.task_operations._protocols_antibody_task_operations_
)
apply()
(in
AutoRBMover
)
AtomTreeDiffJobInputter
(in
rosetta.protocols.jd2._protocols_jd2_
)
AddChainBreak
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
apply()
(in
FragInsertAndAlignMover
)
AtomTreeDiffJobInputterAP
(in
rosetta.protocols.jd2._protocols_jd2_
)
AddChainBreakAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
apply()
(in
GaussianRBSegmentMover
)
AtomTreeDiffJobInputterCAP
(in
rosetta.protocols.jd2._protocols_jd2_
)
AddChainBreakCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
apply()
(in
HelicalGaussianMover
)
AtomTreeDiffJobInputterCreator
(in
rosetta.protocols.jd2._protocols_jd2_
)
AddChainBreakCreator
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
apply()
(in
IdealizeHelicesMover
)
AtomTreeDiffJobInputterCreatorAP
(in
rosetta.protocols.jd2._protocols_jd2_
)
AddChainBreakCreatorAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
apply()
(in
MakeStarTopologyMover
)
AtomTreeDiffJobInputterCreatorCAP
(in
rosetta.protocols.jd2._protocols_jd2_
)
AddChainBreakCreatorCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
apply()
(in
OptimizeThreadingMover
)
AtomTreeDiffJobOutputter
(in
rosetta.protocols.jd2._protocols_jd2_
)
AddChainMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
RBSegmentMover
)
AtomTreeDiffJobOutputterAP
(in
rosetta.protocols.jd2._protocols_jd2_
)
AddChainMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
RBSegmentRelax
)
AtomTreeDiffJobOutputterCAP
(in
rosetta.protocols.jd2._protocols_jd2_
)
AddChainMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
SequenceShiftMover
)
AtomTreeDiffJobOutputterCreator
(in
rosetta.protocols.jd2._protocols_jd2_
)
AddChainMoverCreator
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
StrandTwistingMover
)
AtomTreeDiffJobOutputterCreatorAP
(in
rosetta.protocols.jd2._protocols_jd2_
)
AddChainMoverCreatorAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
AtomCoordinateCstMover
)
AtomTreeDiffJobOutputterCreatorCAP
(in
rosetta.protocols.jd2._protocols_jd2_
)
AddChainMoverCreatorCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
CentroidRelax
)
AtomTreeMinimizer
(in
rosetta.core.optimization._core_optimization_
)
AddChi
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
ClassicRelax
)
AtomTreeMinimizerAP
(in
rosetta.core.optimization._core_optimization_
)
AddChiAP
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
FastRelax
)
AtomTreeMinimizerCAP
(in
rosetta.core.optimization._core_optimization_
)
AddChiCAP
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
LocalRelax
)
AtomTreeMultifunc
(in
rosetta.core.optimization._core_optimization_
)
AddChiRotamer
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
MiniRelax
)
AtomTreeMultifuncAP
(in
rosetta.core.optimization._core_optimization_
)
AddChiRotamerAP
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
RelaxProtocolBase
)
AtomTreeMultifuncCAP
(in
rosetta.core.optimization._core_optimization_
)
AddChiRotamerCAP
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
MPFastRelaxMover
)
AtomType
(in
rosetta.core.chemical._core_chemical_
)
AddConnect
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
MembraneCenterPerturbationMover
)
AtomTypeAP
(in
rosetta.core.chemical._core_chemical_
)
AddConnectAP
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
MembraneNormalPerturbationMover
)
AtomTypeCAP
(in
rosetta.core.chemical._core_chemical_
)
AddConnectCAP
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
MovePoseToMembraneCenterMover
)
AtomTypeDatabaseIO
(in
rosetta.core.chemical._core_chemical_
)
AddConstraintsToCurrentConformationMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
RigidBodyDeterministicSpinMover
)
AtomTypeDatabaseIOAP
(in
rosetta.core.chemical._core_chemical_
)
AddConstraintsToCurrentConformationMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
RigidBodyDofPerturbMover
)
AtomTypeDatabaseIOCAP
(in
rosetta.core.chemical._core_chemical_
)
AddConstraintsToCurrentConformationMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
RigidBodyDofRandomTransMover
)
AtomTypeSet
(in
rosetta.core.chemical._core_chemical_
)
AddConstraintsToCurrentConformationMoverCreator
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
RigidBodyDofRandomizeMover
)
AtomTypeSetAP
(in
rosetta.core.chemical._core_chemical_
)
AddConstraintsToCurrentConformationMoverCreatorAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
RigidBodyDofSeqPerturbMover
)
AtomTypeSetCAP
(in
rosetta.core.chemical._core_chemical_
)
AddConstraintsToCurrentConformationMoverCreatorCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
RigidBodyDofSeqRandomizeMover
)
AtomTypesFeatures
(in
rosetta.protocols.features._protocols_features_
)
addcount()
(in
ResPairMotif
)
apply()
(in
RigidBodyDofSeqTransMover
)
AtomTypesFeaturesAP
(in
rosetta.protocols.features._protocols_features_
)
ADDED_STRUCTURE_AS_INTENDED
(in
rosetta.protocols.optimize_weights
)
apply()
(in
RigidBodyDofTransMover
)
AtomTypesFeaturesCAP
(in
rosetta.protocols.features._protocols_features_
)
ADDED_STRUCTURE_AS_INTENDED
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
apply()
(in
RigidBodyMotionMover
)
AtomTypesFeaturesCreator
(in
rosetta.protocols.features._protocols_features_
)
ADDED_STRUCTURE_AS_INTENDED
(in
AddStatus
)
apply()
(in
RigidBodyMover
)
AtomTypesFeaturesCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
ADDED_STRUCTURE_OPPOSITE_AS_INTENDED
(in
rosetta.protocols.optimize_weights
)
apply()
(in
RigidBodyPerturbMover
)
AtomTypesFeaturesCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
ADDED_STRUCTURE_OPPOSITE_AS_INTENDED
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
apply()
(in
RigidBodyPerturbNoCenterMover
)
AtomVDW
(in
rosetta.core.scoring._core_scoring_
)
ADDED_STRUCTURE_OPPOSITE_AS_INTENDED
(in
AddStatus
)
apply()
(in
RigidBodyPerturbRandomJumpMover
)
AtomVDWAP
(in
rosetta.core.scoring._core_scoring_
)
addEntry()
(in
GDB
)
apply()
(in
RigidBodyRandomizeMover
)
AtomVDWCAP
(in
rosetta.core.scoring._core_scoring_
)
AddExpression
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
apply()
(in
RigidBodySpinMover
)
AtomWithDOFChange
(in
rosetta.core.kinematics._core_kinematics_
)
AddExpressionAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
apply()
(in
RigidBodyTransMover
)
AtomWithDOFChangeAP
(in
rosetta.core.kinematics._core_kinematics_
)
AddExpressionCAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
apply()
(in
RollMover
)
AtomWithDOFChangeCAP
(in
rosetta.core.kinematics._core_kinematics_
)
AddGood2BPairEnergyRotamers
(in
rosetta.protocols.toolbox.rotamer_set_operations._protocols_toolbox_rotamer_set_operations_
)
apply()
(in
RotateJumpAxisMover
)
ATR_REP
(in
rosetta.protocols.stepwise.screener
)
AddGood2BPairEnergyRotamersAP
(in
rosetta.protocols.toolbox.rotamer_set_operations._protocols_toolbox_rotamer_set_operations_
)
apply()
(in
UniformRigidBodyCM
)
ATR_REP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
AddGood2BPairEnergyRotamersCAP
(in
rosetta.protocols.toolbox.rotamer_set_operations._protocols_toolbox_rotamer_set_operations_
)
apply()
(in
UniformRigidBodyMover
)
ATR_REP
(in
StepWiseScreenerType
)
AddHydrogen
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
apply()
(in
UniformSphereTransMover
)
atr_rep_screen()
(in
StepWiseBasicOptions
)
AddHydrogenAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
apply()
(in
WholeBodyRotationMover
)
atr_weight()
(in
EtableEvaluator
)
AddHydrogenCAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
apply()
(in
WholeBodyTranslationMover
)
ats_n_func_list()
(in
AtomPairFuncList
)
AddHydrogens
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
apply()
(in
AdditionalOutputWrapper
)
attach()
(in
ObserverCache
)
AddHydrogensAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
apply()
(in
MultipleOutputWrapper
)
attach()
(in
PyMolObserver
)
AddHydrogensCAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
apply()
(in
MultiplePoseMover
)
attach_secondary_structure_pools()
(in
QuotaCollector
)
AddHydrogensCreator
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
apply()
(in
ParsedProtocol
)
attach_to()
(in
PDBInfo
)
AddHydrogensCreatorAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
apply()
(in
SavePoseMover
)
attach_to()
(in
CacheableObserver
)
AddHydrogensCreatorCAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
apply()
(in
RotamerRecoveryMover
)
attach_to()
(in
PoseMetricContainer
)
AdditionalOutputWrapper
(in
rosetta.protocols.rosetta_scripts._protocols_rosetta_scripts_
)
apply()
(in
CAcstGenerator
)
attach_to()
(in
BuildInstruction
)
AdditionalOutputWrapperAP
(in
rosetta.protocols.rosetta_scripts._protocols_rosetta_scripts_
)
apply()
(in
CloseFold
)
attach_to_conformation()
(in
ConstraintSet
)
AdditionalOutputWrapperCAP
(in
rosetta.protocols.rosetta_scripts._protocols_rosetta_scripts_
)
apply()
(in
CoordinateCst
)
attached_H_begin()
(in
ResidueType
)
AdditionalOutputWrapperCreator
(in
rosetta.protocols.rosetta_scripts._protocols_rosetta_scripts_
)
apply()
(in
DefineMovableLoops
)
attached_H_begin()
(in
Residue
)
AdditionalOutputWrapperCreatorAP
(in
rosetta.protocols.rosetta_scripts._protocols_rosetta_scripts_
)
apply()
(in
GrowPeptides
)
attached_H_end()
(in
ResidueType
)
AdditionalOutputWrapperCreatorCAP
(in
rosetta.protocols.rosetta_scripts._protocols_rosetta_scripts_
)
apply()
(in
SeedFoldTree
)
attached_H_end()
(in
Residue
)
AdditiveAtomicPolarizability
(in
GasteigerAtomTypeData
)
apply()
(in
SeedSetupMover
)
attached_res()
(in
Attachment
)
AdditiveAtomicPolarizability
(in
Properties
)
apply()
(in
SegmentHybridizer
)
attached_res()
(in
StepWiseMove
)
AddJobPairData
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
SwapSegment
)
attaches_to_residue_type()
(in
WaterAnchorInfo
)
AddJobPairDataAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
AbinitioBaseFilter
)
Attachment
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
AddJobPairDataCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
AlaScan
)
attachment_type()
(in
Attachment
)
AddJobPairDataCreator
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
AngleToVector
)
attachment_type()
(in
StepWiseMove
)
AddJobPairDataCreatorAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
AtomicContactFilter
)
attachment_type_from_string()
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
AddJobPairDataCreatorCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
apply()
(in
AtomicDistanceFilter
)
AttachmentAP
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
AddMembraneMover
(in
rosetta.protocols.membrane._protocols_membrane_
)
apply()
(in
AveragePathLengthFilter
)
AttachmentCAP
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
AddMembraneMoverAP
(in
rosetta.protocols.membrane._protocols_membrane_
)
apply()
(in
BatchEvaluator
)
attachments()
(in
StepWiseMove
)
AddMembraneMoverCAP
(in
rosetta.protocols.membrane._protocols_membrane_
)
apply()
(in
BatchNrEvaluator
)
AttachmentType
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
AddMembraneMoverCreator
(in
rosetta.protocols.membrane._protocols_membrane_
)
apply()
(in
BuriedUnsatHbondFilter
)
ATTEN_2
(in
rosetta.core.scoring.sc
)
AddMembraneMoverCreatorAP
(in
rosetta.protocols.membrane._protocols_membrane_
)
apply()
(in
COFilter
)
ATTEN_2
(in
rosetta.core.scoring.sc._core_scoring_sc_
)
AddMembraneMoverCreatorCAP
(in
rosetta.protocols.membrane._protocols_membrane_
)
apply()
(in
CamShiftEvaluator
)
ATTEN_2
(in
__ATTEN_ENUM__
)
AddMover
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
apply()
(in
ChiWellRmsdEvaluator
)
ATTEN_6
(in
rosetta.core.scoring.sc
)
AddMoverAP
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
apply()
(in
ConservedPosMutationFilter
)
ATTEN_6
(in
rosetta.core.scoring.sc._core_scoring_sc_
)
AddMoverCAP
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
apply()
(in
ConstraintScoreCutoffFilter
)
ATTEN_6
(in
__ATTEN_ENUM__
)
AddMPLigandMover
(in
rosetta.protocols.membrane._protocols_membrane_
)
apply()
(in
ContactMapEvaluator
)
ATTEN_BLOCKER
(in
rosetta.core.scoring.sc
)
AddMPLigandMoverAP
(in
rosetta.protocols.membrane._protocols_membrane_
)
apply()
(in
DdGScan
)
ATTEN_BLOCKER
(in
rosetta.core.scoring.sc._core_scoring_sc_
)
AddMPLigandMoverCAP
(in
rosetta.protocols.membrane._protocols_membrane_
)
apply()
(in
DdgFilter
)
ATTEN_BLOCKER
(in
__ATTEN_ENUM__
)
AddMPLigandMoverCreator
(in
rosetta.protocols.membrane._protocols_membrane_
)
apply()
(in
DeltaFilter
)
ATTEN_BURIED_FLAGGED
(in
rosetta.core.scoring.sc
)
AddMPLigandMoverCreatorAP
(in
rosetta.protocols.membrane._protocols_membrane_
)
apply()
(in
DisulfideEntropyFilter
)
ATTEN_BURIED_FLAGGED
(in
rosetta.core.scoring.sc._core_scoring_sc_
)
AddMPLigandMoverCreatorCAP
(in
rosetta.protocols.membrane._protocols_membrane_
)
apply()
(in
DomainInterfaceFilter
)
ATTEN_BURIED_FLAGGED
(in
__ATTEN_ENUM__
)
AddOrDeleteMover
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
apply()
(in
EnergyPerResidueFilter
)
attractive
(in
AtomPairEnergy
)
AddOrDeleteMoverAP
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
apply()
(in
EvaluatedTrialMover
)
auction_results()
(in
PlacementAuctionMover
)
AddOrDeleteMoverCAP
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
apply()
(in
ExpiryFilter
)
AUTO
(in
rosetta.core.pack.task._core_pack_task_
)
AddProperty
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
ExternalEvaluator
)
auto_choose_cutpoint()
(in
Loop
)
AddPropertyAP
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
FileExistFilter
)
auto_choose_cutpoints()
(in
Loops
)
AddPropertyCAP
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
FileRemoveFilter
)
auto_clash()
(in
ResPairMotifQuery
)
AddProtonChi
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
GeometryFilter
)
auto_cut()
(in
Environment
)
AddProtonChiAP
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
HolesFilter
)
auto_increment()
(in
Column
)
AddProtonChiCAP
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
InterRepeatContactFilter
)
auto_increment_base()
(in
Column
)
AddPyMolObserver()
(in
rosetta.protocols.moves._protocols_moves_
)
apply()
(in
InterfaceBindingEnergyDensityFilter
)
auto_setup_all_metal_bonds()
(in
rosetta.core.util._core_util_
)
AddPyMolObserver_to_conformation()
(in
rosetta.protocols.moves._protocols_moves_
)
apply()
(in
InterfaceSasaFilter
)
auto_setup_all_metal_constraints()
(in
rosetta.core.util._core_util_
)
AddPyMolObserver_to_energies()
(in
rosetta.protocols.moves._protocols_moves_
)
apply()
(in
IntraRepeatContactFilter
)
auto_setup_metal_bonds()
(in
rosetta.core.util._core_util_
)
addRemark()
(in
GDB
)
apply()
(in
JScoreEvaluator
)
auto_trim_floppy_termini()
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
AddResidue()
(in
MolecularSurfaceCalculator
)
apply()
(in
JumpEvaluator
)
AUTOAP
(in
rosetta.core.pack.task._core_pack_task_
)
AddResiduesRotamerSetOperation
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
apply()
(in
JumpNrEvaluator
)
AUTOCAP
(in
rosetta.core.pack.task._core_pack_task_
)
AddResiduesRotamerSetOperationAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
apply()
(in
LeastNativeLike9merFilter
)
AutoCutData
(in
rosetta.protocols.environment._protocols_environment_
)
AddResiduesRotamerSetOperationCAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
apply()
(in
LoopRmsdEvaluator
)
AutoCutDataAP
(in
rosetta.protocols.environment._protocols_environment_
)
address()
(in
HierarchicalLevel
)
apply()
(in
MotifScoreFilter
)
AutoCutDataCAP
(in
rosetta.protocols.environment._protocols_environment_
)
address_exists_in_cache()
(in
HierarchicalLevel
)
apply()
(in
MultipleSigmoids
)
AutoCutDataCreator
(in
rosetta.protocols.environment._protocols_environment_
)
address_to_buf()
(in
DataBuffer
)
apply()
(in
MutationsFilter
)
AutoCutDataCreatorAP
(in
rosetta.protocols.environment._protocols_environment_
)
addScoresForLoopParts()
(in
rosetta.protocols.loops._protocols_loops_
)
apply()
(in
NMerPSSMEnergyFilter
)
AutoCutDataCreatorCAP
(in
rosetta.protocols.environment._protocols_environment_
)
AddSearchPatternRotSetOp
(in
rosetta.protocols.hotspot_hashing._protocols_hotspot_hashing_
)
apply()
(in
NMerSVMEnergyFilter
)
autodetermine_chi_bonds()
(in
ResidueType
)
AddSearchPatternRotSetOpAP
(in
rosetta.protocols.hotspot_hashing._protocols_hotspot_hashing_
)
apply()
(in
NeighborTypeFilter
)
autoexpanding_pocket_eval()
(in
PocketGrid
)
AddSearchPatternRotSetOpCAP
(in
rosetta.protocols.hotspot_hashing._protocols_hotspot_hashing_
)
apply()
(in
NetChargeFilter
)
autofill()
(in
HotspotStubSet
)
AddSidechainConstraintsToHotspots
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
apply()
(in
NonSequentialNeighborsFilter
)
autogenerate_constseq_frags()
(in
AnchorMoversData
)
AddSidechainConstraintsToHotspotsAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
apply()
(in
Operator
)
autogenerate_design_frags()
(in
AnchorMoversData
)
AddSidechainConstraintsToHotspotsCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
apply()
(in
PDDFScoreFilter
)
autogenerate_frags()
(in
AnchorMoversData
)
AddSidechainConstraintsToHotspotsCreator
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
apply()
(in
PackStatFilter
)
AUTOMATIC
(in
rosetta
)
AddSidechainConstraintsToHotspotsCreatorAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
apply()
(in
PackerNeighborGraphFilter
)
AUTOMATIC
(in
rosetta.core.conformation
)
AddSidechainConstraintsToHotspotsCreatorCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
apply()
(in
PalesEvaluator
)
AUTOMATIC
(in
rosetta.core.conformation._core_conformation_
)
AddStatus
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
apply()
(in
PoseComment
)
AUTOMATIC
(in
Strategy
)
addTag()
(in
Tag
)
apply()
(in
PoseInfoFilter
)
automatic_distance_cutoff()
(in
AddChainBreak
)
ADDUCT
(in
rosetta
)
apply()
(in
PredictedBurialEvaluator
)
automode()
(in
FragmentBiasAssigner
)
ADDUCT
(in
rosetta.core.chemical
)
apply()
(in
RDC_Evaluator
)
automorphic_rmsd()
(in
rosetta.core.scoring._core_scoring_
)
ADDUCT
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
RGFilter
)
AutomorphismIterator
(in
rosetta.core.chemical._core_chemical_
)
Adduct
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
RangeFilter
)
AutomorphismIteratorAP
(in
rosetta.core.chemical._core_chemical_
)
ADDUCT
(in
ResidueProperty
)
apply()
(in
RelativePoseFilter
)
AutomorphismIteratorCAP
(in
rosetta.core.chemical._core_chemical_
)
adduct_name()
(in
Adduct
)
apply()
(in
RepeatParameterFilter
)
AutoRBMover
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
ADDUCT_VARIANT
(in
rosetta
)
apply()
(in
ReportFilter
)
AutoRBMoverAP
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
ADDUCT_VARIANT
(in
rosetta.core.chemical
)
apply()
(in
ResidueBurialFilter
)
AutoRBMoverCAP
(in
rosetta.protocols.rbsegment_relax._protocols_rbsegment_relax_
)
ADDUCT_VARIANT
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
ResidueCountFilter
)
available_resource_loaders()
(in
ResourceLoaderFactory
)
ADDUCT_VARIANT
(in
VariantType
)
apply()
(in
ResidueDistanceFilter
)
average_antiparallel_embeddings()
(in
rosetta.protocols.membrane.geometry._protocols_membrane_geometry_
)
AdductAP
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
ResidueIEFilter
)
average_change_in_rama_score_over_range()
(in
RamaCheckBase
)
AdductCAP
(in
rosetta.core.chemical._core_chemical_
)
apply()
(in
ResidueSetChainEnergyFilter
)
average_embeddings()
(in
rosetta.protocols.membrane.geometry._protocols_membrane_geometry_
)
adducts()
(in
PackerTask
)
apply()
(in
ResiduesInInterfaceFilter
)
average_residue_hASA()
(in
SurfacePotential
)
adducts()
(in
PackerTask_
)
apply()
(in
RmsdEvaluator
)
average_shortest_path_length()
(in
ResidueNetwork
)
adducts()
(in
ResidueLevelTask
)
apply()
(in
RotamerBoltzmannWeight
)
AverageDegreeFilter
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
adducts()
(in
ResidueLevelTask_
)
apply()
(in
SAXSScoreFilter
)
AverageDegreeFilterAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
addVAR()
(in
GDB
)
apply()
(in
SSMotifFinder
)
AverageDegreeFilterCAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
addVirtualResAsRoot()
(in
rosetta.core.pose._core_pose_
)
apply()
(in
SavePoseConstraintToFileFilter
)
AverageDegreeFilterCreator
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
addVirtualResAsRootMembrane()
(in
MembraneTopologyClaimer
)
apply()
(in
SaveResfileToDiskFilter
)
AverageDegreeFilterCreatorAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
AddZincSiteConstraints
(in
rosetta.protocols.metal_interface._protocols_metal_interface_
)
apply()
(in
ScoreCutoffFilter
)
AverageDegreeFilterCreatorCAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
AddZincSiteConstraintsAP
(in
rosetta.protocols.metal_interface._protocols_metal_interface_
)
apply()
(in
ScoreEvaluator
)
AverageLinkClusterer
(in
rosetta.numeric._numeric_
)
AddZincSiteConstraintsCAP
(in
rosetta.protocols.metal_interface._protocols_metal_interface_
)
apply()
(in
ScoreTypeFilter
)
AverageLinkClustererAP
(in
rosetta.numeric._numeric_
)
AdjacentRemainingNodes()
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
apply()
(in
SelectGdtEvaluator
)
AverageLinkClustererCAP
(in
rosetta.numeric._numeric_
)
adjust_mm_to_length()
(in
rosetta.protocols.seeded_abinitio._protocols_seeded_abinitio_
)
apply()
(in
SelectMaxsubEvaluator
)
AveragePathLengthFilter
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
adjust_relax_movemap()
(in
FoldandDockClaimer
)
apply()
(in
SelectRDC_Evaluator
)
AveragePathLengthFilterAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
adjust_relax_movemap()
(in
MembraneTopologyClaimer
)
apply()
(in
SelectRmsdEvaluator
)
AveragePathLengthFilterCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
adjust_relax_movemap()
(in
TopologyClaimer
)
apply()
(in
ShapeComplementarityFilter
)
AveragePathLengthFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
advance_euler_angles()
(in
rosetta.protocols.match._protocols_match_
)
apply()
(in
SheetFilter
)
AveragePathLengthFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
advance_to_next_pose_segment()
(in
InputStreamWithResidueInfo
)
apply()
(in
SidechainRmsdFilter
)
AveragePathLengthFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
AgglomerativeHierarchicalClusterer
(in
rosetta.numeric._numeric_
)
apply()
(in
Sigmoid
)
avg_cluster_cen_dist()
(in
rosetta.protocols.make_rot_lib._protocols_make_rot_lib_
)
AgglomerativeHierarchicalClustererAP
(in
rosetta.numeric._numeric_
)
apply()
(in
StemFinder
)
avoid_sc_hbonds()
(in
HBCPData
)
AgglomerativeHierarchicalClustererCAP
(in
rosetta.numeric._numeric_
)
apply()
(in
StructuralSimilarityEvaluator
)
ax_init()
(in
MinimizerOptions
)
aggregate_add()
(in
XformScore
)
apply()
(in
SymmetricMotifFilter
)
axis()
(in
Quaternion_Real
)
aggregate_function()
(in
MultistateFitnessFunction
)
apply()
(in
SymmetricRmsdEvaluator
)
axis()
(in
Quaternion_double
)
aggregate_max()
(in
XformScore
)
apply()
(in
TaskAwareSASAFilter
)
axis()
(in
Quaternion_float
)
AHdist_long_fade_lookup()
(in
HBondDatabase
)
apply()
(in
TaskAwareScoreTypeFilter
)
axis()
(in
GetRBDOFValues
)
AHdist_poly_lookup()
(in
HBondDatabase
)
apply()
(in
TerminusDistanceFilter
)
AHdist_short_fade_lookup()
(in
HBondDatabase
)
apply()
(in
TotalSasaFilter
)
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