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D
D
(in
rosetta
)
defines_score_for_residue_pair()
(in
ContextDependentGeometricSolEnergy
)
disulfide_matching_energy
(in
rosetta.core.scoring.methods
)
D
(in
rosetta.core.id
)
defines_score_for_residue_pair()
(in
ContextIndependentGeometricSolEnergy
)
DisulfideAtomIndices
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
D
(in
rosetta.core.id._core_id_
)
defines_score_for_residue_pair()
(in
GeometricSolEnergyEvaluator
)
DisulfideAtomIndicesAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
D
(in
DOF_Type
)
defines_score_for_residue_pair()
(in
OccludedHbondSolEnergy
)
DisulfideAtomIndicesCAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
d()
(in
Adduct
)
defines_score_for_residue_pair()
(in
HackAroEnergy
)
DisulfideCyclizationViability
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
d()
(in
AtomICoor
)
defines_score_for_residue_pair()
(in
HBondEnergy
)
DisulfideDerivativeAtom
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
d2h_sa
(in
ScoreType
)
defines_score_for_residue_pair()
(in
DDPscore
)
DisulfideDistance
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
d2h_sa
(in
rosetta.core.scoring._core_scoring_
)
defines_score_for_residue_pair()
(in
FaMPSolvEnergy
)
DisulfideDistanceAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
d2h_sa
(in
rosetta.core.scoring
)
defines_score_for_residue_pair()
(in
MPPairEnergy
)
DisulfideDistanceCAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
d2h_sa
(in
rosetta
)
defines_score_for_residue_pair()
(in
CartesianBondedEnergy
)
DisulfideEntropyFilter
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
D2H_SA_Energy
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
defines_score_for_residue_pair()
(in
CenHBEnergy
)
DisulfideEntropyFilterAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
D2H_SA_EnergyAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
defines_score_for_residue_pair()
(in
CenPairEnergy
)
DisulfideEntropyFilterCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
D2H_SA_EnergyCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
defines_score_for_residue_pair()
(in
CenRotPairEnergy
)
DisulfideEntropyFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
D2H_SA_EnergyCreator
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
defines_score_for_residue_pair()
(in
ContextDependentLRTwoBodyEnergy
)
DisulfideEntropyFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
D2H_SA_EnergyCreatorAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
defines_score_for_residue_pair()
(in
ContextDependentTwoBodyEnergy
)
DisulfideEntropyFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
D2H_SA_EnergyCreatorCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
defines_score_for_residue_pair()
(in
ContextIndependentLRTwoBodyEnergy
)
DisulfideFile
(in
rosetta.core.io.raw_data._core_io_raw_data_
)
d2s()
(in
subset_mapping
)
defines_score_for_residue_pair()
(in
ContextIndependentTwoBodyEnergy
)
DisulfideFileAP
(in
rosetta.core.io.raw_data._core_io_raw_data_
)
D_AA
(in
rosetta
)
defines_score_for_residue_pair()
(in
CustomAtomPairEnergy
)
DisulfideFileCAP
(in
rosetta.core.io.raw_data._core_io_raw_data_
)
D_AA
(in
rosetta.core.chemical
)
defines_score_for_residue_pair()
(in
DNA_BaseEnergy
)
DisulfideFilter
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
D_AA
(in
rosetta.core.chemical._core_chemical_
)
defines_score_for_residue_pair()
(in
Fa_MbsolvEnergy
)
DisulfideFilterAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
D_AA
(in
ResidueProperty
)
defines_score_for_residue_pair()
(in
GaussianOverlapEnergy
)
DisulfideFilterCAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
d_array_scale()
(in
rosetta.core.scoring.fiber_diffraction._core_scoring_fiber_diffraction_
)
defines_score_for_residue_pair()
(in
GenBornEnergy
)
DisulfideFilterCreator
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
D_CHIRALITY
(in
rosetta.protocols.simple_moves.chiral
)
defines_score_for_residue_pair()
(in
GoapEnergy
)
DisulfideFilterCreatorAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
D_CHIRALITY
(in
Chirality
)
defines_score_for_residue_pair()
(in
HybridVDW_Energy
)
DisulfideFilterCreatorCAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
D_CHIRALITY
(in
rosetta.protocols.simple_moves.chiral._protocols_simple_moves_chiral_
)
defines_score_for_residue_pair()
(in
LK_BallEnergy
)
DisulfideIdentity
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
d_phi()
(in
PhiPsiTalosIO
)
defines_score_for_residue_pair()
(in
LK_PolarNonPolarEnergy
)
DisulfideIdentityAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
d_psi()
(in
PhiPsiTalosIO
)
defines_score_for_residue_pair()
(in
LK_hack
)
DisulfideIdentityCAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
D_SUGAR
(in
rosetta
)
defines_score_for_residue_pair()
(in
LongRangeTwoBodyEnergy
)
DisulfideInsertionMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
D_SUGAR
(in
rosetta.core.chemical
)
defines_score_for_residue_pair()
(in
MMBondAngleEnergy
)
DisulfideInsertionMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
D_SUGAR
(in
rosetta.core.chemical._core_chemical_
)
defines_score_for_residue_pair()
(in
MMBondLengthEnergy
)
DisulfideInsertionMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
D_SUGAR
(in
ResidueProperty
)
defines_score_for_residue_pair()
(in
MMLJEnergyInter
)
DisulfideInsertionMoverCreator
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
dab_sasa
(in
ScoreType
)
defines_score_for_residue_pair()
(in
MMLJEnergyIntra
)
DisulfideInsertionMoverCreatorAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
dab_sasa
(in
rosetta.core.scoring._core_scoring_
)
defines_score_for_residue_pair()
(in
MMTorsionEnergy
)
DisulfideInsertionMoverCreatorCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
dab_sasa
(in
rosetta.core.scoring
)
defines_score_for_residue_pair()
(in
MembraneCenPairEnergy
)
DisulfideMatchingDatabase
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
dab_sasa
(in
rosetta
)
defines_score_for_residue_pair()
(in
PairEnergy
)
DisulfideMatchingDatabaseAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
DAB_SASA_POSE_INFO
(in
CacheableDataType
)
defines_score_for_residue_pair()
(in
PeptideBondEnergy
)
DisulfideMatchingDatabaseCAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
DAB_SASA_POSE_INFO
(in
Enum
)
defines_score_for_residue_pair()
(in
PoissonBoltzmannEnergy
)
DisulfideMatchingEnergy
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
dab_sev
(in
ScoreType
)
defines_score_for_residue_pair()
(in
ProClosureEnergy
)
DisulfideMatchingEnergyAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
dab_sev
(in
rosetta.core.scoring._core_scoring_
)
defines_score_for_residue_pair()
(in
Rama2BOffsetEnergy
)
DisulfideMatchingEnergyCAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
dab_sev
(in
rosetta.core.scoring
)
defines_score_for_residue_pair()
(in
RamachandranEnergy2B
)
DisulfideMatchingEnergyComponents
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
dab_sev
(in
rosetta
)
defines_score_for_residue_pair()
(in
ShortRangeTwoBodyEnergy
)
DisulfideMatchingEnergyComponentsAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
DAB_SEV_POSE_INFO
(in
CacheableDataType
)
defines_score_for_residue_pair()
(in
SmoothCenPairEnergy
)
DisulfideMatchingEnergyComponentsCAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
DAB_SEV_POSE_INFO
(in
Enum
)
defines_score_for_residue_pair()
(in
SuckerEnergy
)
DisulfideMatchingEnergyContainer
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
daemon_set()
(in
MultistateFitnessFunction
)
defines_score_for_residue_pair()
(in
TwoBodyEnergy
)
DisulfideMatchingEnergyContainerAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
daemons()
(in
DaemonSet
)
defines_score_for_residue_pair()
(in
WaterAdductHBondEnergy
)
DisulfideMatchingEnergyContainerCAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
DaemonSet
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
defines_score_for_residue_pair()
(in
DFIRE_Energy
)
DisulfideMatchingEnergyCreator
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
DaemonSetAP
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
defines_score_for_residue_pair()
(in
OrbitalsScore
)
DisulfideMatchingEnergyCreatorAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
DaemonSetCAP
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
defines_score_for_residue_pair()
(in
RNA_FullAtomStackingEnergy
)
DisulfideMatchingEnergyCreatorCAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
DaemonSetMessage
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
defines_score_for_residue_pair()
(in
RNA_JR_SuiteEnergy
)
DisulfideMatchingNeighborConstIterator
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
DALPHABALL
(in
rosetta.basic
)
defines_score_for_residue_pair()
(in
RNA_LJ_BaseEnergy
)
DisulfideMatchingNeighborConstIteratorAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
DALPHABALL
(in
rosetta.basic._basic_
)
defines_score_for_residue_pair()
(in
RNA_Mg_Energy
)
DisulfideMatchingNeighborConstIteratorCAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
DALPHABALL
(in
ProfTag
)
defines_score_for_residue_pair()
(in
RNA_PairwiseLowResolutionEnergy
)
DisulfideMatchingNeighborIterator
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
DALPHABALL_DERIV
(in
rosetta.basic
)
defines_score_for_residue_pair()
(in
RNA_SuiteEnergy
)
DisulfideMatchingNeighborIteratorAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
DALPHABALL_DERIV
(in
rosetta.basic._basic_
)
defines_score_for_residue_pair()
(in
RNA_TorsionEnergy
)
DisulfideMatchingNeighborIteratorCAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
DALPHABALL_DERIV
(in
ProfTag
)
defines_score_for_residue_pair()
(in
RNA_VDW_Energy
)
DisulfideMatchingPotential
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
DarcParticleSwarmMinimizer
(in
rosetta.protocols.pockets._protocols_pockets_
)
defines_score_for_residue_pair()
(in
StackElecEnergy
)
DisulfideMatchingPotentialAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
DarcParticleSwarmMinimizerAP
(in
rosetta.protocols.pockets._protocols_pockets_
)
defines_score_for_residue_pair()
(in
RNA_DataBackboneEnergy
)
DisulfideMatchingPotentialCAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
DarcParticleSwarmMinimizerCAP
(in
rosetta.protocols.pockets._protocols_pockets_
)
defines_score_for_residue_pair()
(in
symEnergy
)
DisulfideMover
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
data
(in
rosetta.core.scoring.rna
)
defines_score_for_residue_pair()
(in
InterchainPairEnergy
)
DisulfideMoverAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
data()
(in
DiagnosticData
)
definite_terminal_root()
(in
rosetta.protocols.stepwise.modeler._protocols_stepwise_modeler_
)
DisulfideMoverCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
data()
(in
map_indexing_suite_map_Real_Real_entry
)
defs2allowedtypes()
(in
rosetta.protocols.motifs._protocols_motifs_
)
DisulfideMoverCreator
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
data()
(in
map_indexing_suite_map_Real_string_entry
)
defs2BuildPositions()
(in
LigandMotifSearch
)
DisulfideMoverCreatorAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
data()
(in
map_indexing_suite_map_SSize_SSize_entry
)
defs2BuildPositions()
(in
MotifSearch
)
DisulfideMoverCreatorCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
data()
(in
map_indexing_suite_map_SSize_string_entry
)
defs2BuildPositions_findts()
(in
LigandMotifSearch
)
disulfides
(in
rosetta.core.scoring
)
data()
(in
map_indexing_suite_map_Size_Real_entry
)
defs2BuildPositions_findts()
(in
MotifSearch
)
disulfides()
(in
DisulfideFile
)
data()
(in
map_indexing_suite_map_Size_Size_entry
)
defs2map()
(in
rosetta.protocols.motifs._protocols_motifs_
)
disulfides()
(in
ForceDisulfidesMover
)
data()
(in
map_indexing_suite_map_Size_SymDof_entry
)
defs2vector()
(in
rosetta.protocols.motifs._protocols_motifs_
)
DisulfPairing
(in
rosetta.protocols.jumping._protocols_jumping_
)
data()
(in
map_indexing_suite_map_Size_string_entry
)
deg2rad()
(in
NumericTraits_T_double_T
)
DisulfPairingAP
(in
rosetta.protocols.jumping._protocols_jumping_
)
data()
(in
map_indexing_suite_map_char_pair_Size_Size_entry
)
deg2rad()
(in
NumericTraits_T_float_T
)
DisulfPairingCAP
(in
rosetta.protocols.jumping._protocols_jumping_
)
data()
(in
map_indexing_suite_map_int_int_entry
)
deg2rad()
(in
NumericTraits_T_long_double_T
)
DisulfPairingLibrary
(in
rosetta.protocols.jumping._protocols_jumping_
)
data()
(in
map_indexing_suite_map_int_string_entry
)
degree()
(in
Polynomial_1d
)
DisulfPairingLibraryAP
(in
rosetta.protocols.jumping._protocols_jumping_
)
data()
(in
map_indexing_suite_map_string_Real_entry
)
degrees_to_radians()
(in
NumericTraits_T_double_T
)
DisulfPairingLibraryCAP
(in
rosetta.protocols.jumping._protocols_jumping_
)
data()
(in
map_indexing_suite_map_string_SSize_entry
)
degrees_to_radians()
(in
NumericTraits_T_float_T
)
DisulfResNeighbConstIterator
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
data()
(in
map_indexing_suite_map_string_Size_entry
)
degrees_to_radians()
(in
NumericTraits_T_long_double_T
)
DisulfResNeighbConstIteratorAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
data()
(in
map_indexing_suite_map_string_int_entry
)
DELETE
(in
rosetta.protocols.stepwise.monte_carlo.mover
)
DisulfResNeighbConstIteratorCAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
data()
(in
map_indexing_suite_map_string_string_entry
)
DELETE
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
DisulfResNeighbIterator
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
data()
(in
RotamerSetBase
)
DELETE
(in
MoveType
)
DisulfResNeighbIteratorAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
data()
(in
Pose
)
delete_all_intragroup_edges()
(in
rosetta.core.graph._core_graph_
)
DisulfResNeighbIteratorCAP
(in
rosetta.core.scoring.disulfides._core_scoring_disulfides_
)
data()
(in
Energies
)
delete_atom()
(in
ResidueType
)
DisulfTemplate
(in
rosetta.protocols.jumping._protocols_jumping_
)
data()
(in
ElectronDensity
)
delete_atom()
(in
Atom
)
DisulfTemplateAP
(in
rosetta.protocols.jumping._protocols_jumping_
)
data()
(in
KDNode
)
delete_atom()
(in
Atom_
)
DisulfTemplateCAP
(in
rosetta.protocols.jumping._protocols_jumping_
)
data()
(in
KDPoint
)
delete_atom_alias()
(in
ResidueType
)
diversify()
(in
GreedyOptMutationMover
)
data()
(in
PNatAAOptEPositionData
)
delete_chain_ending()
(in
Conformation
)
diversify()
(in
MatDesGreedyOptMutationMover
)
data()
(in
PNatAAOptERotamerData
)
delete_chain_ending()
(in
ProtectedConformation
)
diversify_backbone_only_rotamers()
(in
MatchConstraintFileInfo
)
data()
(in
PNatRotOptEPositionData
)
delete_comment()
(in
rosetta.core.pose._core_pose_
)
diversify_cst_conformers()
(in
ResiduePairJump
)
data_annotations()
(in
RDAT
)
delete_content_only()
(in
FileRemoveFilter
)
diversify_dof_conformers()
(in
ResiduePairJump
)
data_integrity_check()
(in
SequenceAlignment
)
delete_db()
(in
LoopHashLibrary
)
DiversifyCrmsdByClustering
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
data_ptr()
(in
Residue
)
delete_edge()
(in
Graph
)
DiversifyCrmsdByClusteringAP
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
DATA_STORAGE
(in
rosetta.basic
)
delete_edge()
(in
FoldTree
)
DiversifyCrmsdByClusteringCAP
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
DATA_STORAGE
(in
rosetta.basic._basic_
)
delete_edge()
(in
SimpleInteractionGraph
)
DiversifyCrmsdSelector
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
DATA_STORAGE
(in
ProfTag
)
delete_edge()
(in
EnergyGraph
)
DiversifyCrmsdSelectorAP
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
database
(in
rosetta.basic
)
delete_edge()
(in
MinimizationGraph
)
DiversifyCrmsdSelectorCAP
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
database
(in
rosetta.protocols.antibody
)
delete_edge()
(in
TenANeighborGraph
)
DiversifyDihedralsSelector
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
database_directory()
(in
ResidueTypeSet
)
delete_edge()
(in
TwelveANeighborGraph
)
DiversifyDihedralsSelectorAP
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
database_fname()
(in
DatabaseThread
)
delete_edge()
(in
ConstraintGraph
)
DiversifyDihedralsSelectorCAP
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
database_mode_from_name()
(in
rosetta.utility.sql_database._utility_sql_database_
)
delete_extra_vertices()
(in
FoldTree
)
DIVIDE_SYMBOL
(in
rosetta.numeric.expression_parser
)
DATABASE_PROTOCOL_AND_BATCH_ID_TAG
(in
rosetta.basic.message_listening
)
delete_interface_native_sidechains()
(in
AnchoredDesignMover
)
DIVIDE_SYMBOL
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
DATABASE_PROTOCOL_AND_BATCH_ID_TAG
(in
rosetta.basic.message_listening._basic_message_listening_
)
delete_jump_and_intervening_cutpoint()
(in
FoldTree
)
DIVIDE_SYMBOL
(in
TokenType
)
DATABASE_PROTOCOL_AND_BATCH_ID_TAG
(in
listener_tags
)
delete_loop()
(in
Loops
)
DivideExpression
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
database_session()
(in
DatabaseSessionOptions
)
delete_metalbinding_atom()
(in
ResidueType
)
DivideExpressionAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
database_table()
(in
ReadResfileFromDB
)
delete_overhang_residues()
(in
rosetta.protocols.grafting._protocols_grafting_
)
DivideExpressionCAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
DatabaseEntryWorkUnit
(in
rosetta.protocols.wum._protocols_wum_
)
delete_polymer_residue()
(in
Conformation
)
divides_backbone_and_sidechain_energetics()
(in
CarbonHBondEnergy
)
DatabaseEntryWorkUnitAP
(in
rosetta.protocols.wum._protocols_wum_
)
delete_polymer_residue()
(in
Pose
)
divides_backbone_and_sidechain_energetics()
(in
FullatomCustomPairDistanceEnergy
)
DatabaseEntryWorkUnitCAP
(in
rosetta.protocols.wum._protocols_wum_
)
delete_polymer_residue()
(in
ProtectedConformation
)
divides_backbone_and_sidechain_energetics()
(in
DNATorsionEnergy
)
DatabaseFilter
(in
rosetta.protocols.features._protocols_features_
)
delete_pose()
(in
ProteinSilentReport
)
divides_backbone_and_sidechain_energetics()
(in
FA_ElecEnergy
)
DatabaseFilterAP
(in
rosetta.protocols.features._protocols_features_
)
delete_pose_from_tag()
(in
ProteinSilentReport
)
divides_backbone_and_sidechain_energetics()
(in
FA_ElecEnergyAroAll
)
DatabaseFilterCAP
(in
rosetta.protocols.features._protocols_features_
)
delete_position()
(in
ChemicalShiftSequence
)
divides_backbone_and_sidechain_energetics()
(in
FA_ElecEnergyAroAro
)
DatabaseJobInputter
(in
rosetta.protocols.features._protocols_features_
)
delete_position()
(in
CompositeSequence
)
divides_backbone_and_sidechain_energetics()
(in
FA_GrpElecEnergy
)
DatabaseJobInputterAP
(in
rosetta.protocols.features._protocols_features_
)
delete_position()
(in
Sequence
)
divides_backbone_and_sidechain_energetics()
(in
RNA_FA_ElecEnergy
)
DatabaseJobInputterCAP
(in
rosetta.protocols.features._protocols_features_
)
delete_position()
(in
SequenceCoupling
)
divides_backbone_and_sidechain_energetics()
(in
AnalyticEtableEnergy
)
DatabaseJobInputterCreator
(in
rosetta.protocols.features._protocols_features_
)
delete_position()
(in
SequenceProfile
)
divides_backbone_and_sidechain_energetics()
(in
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T
)
DatabaseJobInputterCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
DELETE_PREVIOUS_ROTAMER
(in
rosetta.core.pack.rotamer_set
)
divides_backbone_and_sidechain_energetics()
(in
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T
)
DatabaseJobInputterCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
DELETE_PREVIOUS_ROTAMER
(in
BumpSelectorDecision
)
divides_backbone_and_sidechain_energetics()
(in
TableLookupEtableEnergy
)
DatabaseJobOutputter
(in
rosetta.protocols.features._protocols_features_
)
DELETE_PREVIOUS_ROTAMER
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
divides_backbone_and_sidechain_energetics()
(in
ContextDependentGeometricSolEnergy
)
DatabaseJobOutputterAP
(in
rosetta.protocols.features._protocols_features_
)
delete_property()
(in
ResidueType
)
divides_backbone_and_sidechain_energetics()
(in
ContextIndependentGeometricSolEnergy
)
DatabaseJobOutputterCAP
(in
rosetta.protocols.features._protocols_features_
)
delete_record()
(in
AntibodyFeatures
)
divides_backbone_and_sidechain_energetics()
(in
OccludedHbondSolEnergy
)
DatabaseJobOutputterCreator
(in
rosetta.protocols.features._protocols_features_
)
delete_record()
(in
CDRClusterFeatures
)
divides_backbone_and_sidechain_energetics()
(in
HackAroEnergy
)
DatabaseJobOutputterCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
delete_record()
(in
AtomAtomPairFeatures
)
divides_backbone_and_sidechain_energetics()
(in
HBondEnergy
)
DatabaseJobOutputterCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
delete_record()
(in
AtomInResidueAtomInResiduePairFeatures
)
divides_backbone_and_sidechain_energetics()
(in
DDPscore
)
DatabaseMode
(in
rosetta.utility.sql_database._utility_sql_database_
)
delete_record()
(in
AtomTypesFeatures
)
divides_backbone_and_sidechain_energetics()
(in
FaMPSolvEnergy
)
DatabaseModeAP
(in
rosetta.utility.sql_database._utility_sql_database_
)
delete_record()
(in
BetaTurnDetectionFeatures
)
divides_backbone_and_sidechain_energetics()
(in
MPPairEnergy
)
DatabaseModeCAP
(in
rosetta.utility.sql_database._utility_sql_database_
)
delete_record()
(in
ChargeChargeFeatures
)
divides_backbone_and_sidechain_energetics()
(in
CenHBEnergy
)
DatabaseOccSolEne
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
delete_record()
(in
DdGFeatures
)
divides_backbone_and_sidechain_energetics()
(in
CenPairEnergy
)
DatabaseOccSolEneAP
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
delete_record()
(in
FeaturesReporter
)
divides_backbone_and_sidechain_energetics()
(in
CenRotPairEnergy
)
DatabaseOccSolEneCAP
(in
rosetta.core.scoring.geometric_solvation._core_scoring_geometric_solvation_
)
delete_record()
(in
GeometricSolvationFeatures
)
divides_backbone_and_sidechain_energetics()
(in
ContextDependentTwoBodyEnergy
)
DatabaseResourceLocator
(in
rosetta.basic.resource_manager.locator._basic_resource_manager_locator_
)
delete_record()
(in
HBondFeatures
)
divides_backbone_and_sidechain_energetics()
(in
ContextIndependentTwoBodyEnergy
)
DatabaseResourceLocatorAP
(in
rosetta.basic.resource_manager.locator._basic_resource_manager_locator_
)
delete_record()
(in
HBondParameterFeatures
)
divides_backbone_and_sidechain_energetics()
(in
CustomAtomPairEnergy
)
DatabaseResourceLocatorCAP
(in
rosetta.basic.resource_manager.locator._basic_resource_manager_locator_
)
delete_record()
(in
HelixCapFeatures
)
divides_backbone_and_sidechain_energetics()
(in
DNA_BaseEnergy
)
DatabaseResourceLocatorCreator
(in
rosetta.basic.resource_manager.locator._basic_resource_manager_locator_
)
delete_record()
(in
InterfaceFeatures
)
divides_backbone_and_sidechain_energetics()
(in
Fa_MbsolvEnergy
)
DatabaseResourceLocatorCreatorAP
(in
rosetta.basic.resource_manager.locator._basic_resource_manager_locator_
)
delete_record()
(in
JobDataFeatures
)
divides_backbone_and_sidechain_energetics()
(in
GaussianOverlapEnergy
)
DatabaseResourceLocatorCreatorCAP
(in
rosetta.basic.resource_manager.locator._basic_resource_manager_locator_
)
delete_record()
(in
LoopAnchorFeatures
)
divides_backbone_and_sidechain_energetics()
(in
GoapEnergy
)
DatabaseSessionLoader
(in
rosetta.basic.database._basic_database_
)
delete_record()
(in
OrbitalsFeatures
)
divides_backbone_and_sidechain_energetics()
(in
HybridVDW_Energy
)
DatabaseSessionLoaderAP
(in
rosetta.basic.database._basic_database_
)
delete_record()
(in
PairFeatures
)
divides_backbone_and_sidechain_energetics()
(in
LK_BallEnergy
)
DatabaseSessionLoaderCAP
(in
rosetta.basic.database._basic_database_
)
delete_record()
(in
PdbDataFeatures
)
divides_backbone_and_sidechain_energetics()
(in
LK_PolarNonPolarEnergy
)
DatabaseSessionLoaderCreator
(in
rosetta.basic.database._basic_database_
)
delete_record()
(in
PoseCommentsFeatures
)
divides_backbone_and_sidechain_energetics()
(in
LK_hack
)
DatabaseSessionLoaderCreatorAP
(in
rosetta.basic.database._basic_database_
)
delete_record()
(in
PoseConformationFeatures
)
divides_backbone_and_sidechain_energetics()
(in
MMBondAngleEnergy
)
DatabaseSessionLoaderCreatorCAP
(in
rosetta.basic.database._basic_database_
)
delete_record()
(in
ProteinBackboneAtomAtomPairFeatures
)
divides_backbone_and_sidechain_energetics()
(in
MMBondLengthEnergy
)
DatabaseSessionOptions
(in
rosetta.basic.database._basic_database_
)
delete_record()
(in
ProteinBackboneTorsionAngleFeatures
)
divides_backbone_and_sidechain_energetics()
(in
MMLJEnergyInter
)
DatabaseSessionOptionsAP
(in
rosetta.basic.database._basic_database_
)
delete_record()
(in
ProteinBondGeometryFeatures
)
divides_backbone_and_sidechain_energetics()
(in
MMLJEnergyIntra
)
DatabaseSessionOptionsCAP
(in
rosetta.basic.database._basic_database_
)
delete_record()
(in
ProteinRMSDFeatures
)
divides_backbone_and_sidechain_energetics()
(in
MMTorsionEnergy
)
DatabaseSessionOptionsCreator
(in
rosetta.basic.database._basic_database_
)
delete_record()
(in
ProteinRMSDNoSuperpositionFeatures
)
divides_backbone_and_sidechain_energetics()
(in
MembraneCenPairEnergy
)
DatabaseSessionOptionsCreatorAP
(in
rosetta.basic.database._basic_database_
)
delete_record()
(in
ProteinResidueConformationFeatures
)
divides_backbone_and_sidechain_energetics()
(in
PairEnergy
)
DatabaseSessionOptionsCreatorCAP
(in
rosetta.basic.database._basic_database_
)
delete_record()
(in
RadiusOfGyrationFeatures
)
divides_backbone_and_sidechain_energetics()
(in
PeptideBondEnergy
)
DatabaseThread
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
delete_record()
(in
ResidueBurialFeatures
)
divides_backbone_and_sidechain_energetics()
(in
ProClosureEnergy
)
DatabaseThreadAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
delete_record()
(in
ResidueConformationFeatures
)
divides_backbone_and_sidechain_energetics()
(in
RamachandranEnergy2B
)
DatabaseThreadCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
delete_record()
(in
ResidueFeatures
)
divides_backbone_and_sidechain_energetics()
(in
ShortRangeTwoBodyEnergy
)
DatabaseThreadCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
delete_record()
(in
ResidueGridScoresFeatures
)
divides_backbone_and_sidechain_energetics()
(in
SmoothCenPairEnergy
)
DatabaseThreadCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
delete_record()
(in
ResidueScoresFeatures
)
divides_backbone_and_sidechain_energetics()
(in
SuckerEnergy
)
DatabaseThreadCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
delete_record()
(in
ResidueSecondaryStructureFeatures
)
divides_backbone_and_sidechain_energetics()
(in
WaterAdductHBondEnergy
)
DataBuffer
(in
rosetta.protocols.canonical_sampling.mc_convergence_checks._protocols_canonical_sampling_mc_convergence_checks_
)
delete_record()
(in
ResidueTotalScoresFeatures
)
divides_backbone_and_sidechain_energetics()
(in
OrbitalsScore
)
DataBufferAP
(in
rosetta.protocols.canonical_sampling.mc_convergence_checks._protocols_canonical_sampling_mc_convergence_checks_
)
delete_record()
(in
ResidueTypesFeatures
)
divides_backbone_and_sidechain_energetics()
(in
RNA_FullAtomStackingEnergy
)
DataBufferCAP
(in
rosetta.protocols.canonical_sampling.mc_convergence_checks._protocols_canonical_sampling_mc_convergence_checks_
)
delete_record()
(in
RotamerBoltzmannWeightFeatures
)
divides_backbone_and_sidechain_energetics()
(in
RNA_JR_SuiteEnergy
)
datacache
(in
rosetta.basic
)
delete_record()
(in
RotamerFeatures
)
divides_backbone_and_sidechain_energetics()
(in
RNA_LJ_BaseEnergy
)
datacache
(in
rosetta.core.pose
)
delete_record()
(in
RotamerRecoveryFeatures
)
divides_backbone_and_sidechain_energetics()
(in
RNA_Mg_Energy
)
DataCache_CacheableData
(in
rosetta.basic.datacache._basic_datacache_
)
delete_record()
(in
RuntimeFeatures
)
divides_backbone_and_sidechain_energetics()
(in
RNA_PairwiseLowResolutionEnergy
)
DataCache_CacheableDataAP
(in
rosetta.basic.datacache._basic_datacache_
)
delete_record()
(in
SaltBridgeFeatures
)
divides_backbone_and_sidechain_energetics()
(in
RNA_TorsionEnergy
)
DataCache_CacheableDataCAP
(in
rosetta.basic.datacache._basic_datacache_
)
delete_record()
(in
ScoreFunctionFeatures
)
divides_backbone_and_sidechain_energetics()
(in
RNA_VDW_Energy
)
DataCache_T_basic_datacache_CacheableData_T
(in
rosetta.basic.datacache._basic_datacache_
)
delete_record()
(in
ScoreTypeFeatures
)
divides_backbone_and_sidechain_energetics()
(in
StackElecEnergy
)
DataCache_T_basic_datacache_CacheableData_TAP
(in
rosetta.basic.datacache._basic_datacache_
)
delete_record()
(in
ScreeningFeatures
)
divides_backbone_and_sidechain_energetics()
(in
RNA_DataBackboneEnergy
)
DataCache_T_basic_datacache_CacheableData_TCAP
(in
rosetta.basic.datacache._basic_datacache_
)
delete_record()
(in
SecondaryStructureSegmentFeatures
)
divides_backbone_and_sidechain_energetics()
(in
InterchainPairEnergy
)
DataLoader
(in
rosetta.protocols.jd2.parser._protocols_jd2_parser_
)
delete_record()
(in
SmotifFeatures
)
dixon_eig()
(in
rosetta.numeric.kinematic_closure._numeric_kinematic_closure_
)
DataLoaderAP
(in
rosetta.protocols.jd2.parser._protocols_jd2_parser_
)
delete_record()
(in
StructureFeatures
)
dixon_sturm()
(in
rosetta.numeric.kinematic_closure._numeric_kinematic_closure_
)
DataLoaderCAP
(in
rosetta.protocols.jd2.parser._protocols_jd2_parser_
)
delete_record()
(in
StructureScoresFeatures
)
dk()
(in
OneGaussianScattering
)
DataLoaderCreator
(in
rosetta.protocols.jd2.parser._protocols_jd2_parser_
)
delete_record()
(in
TaskOperationFeatures
)
dK_dphi()
(in
BBDepCartBondedParameters
)
DataLoaderCreatorAP
(in
rosetta.protocols.jd2.parser._protocols_jd2_parser_
)
delete_record()
(in
TotalScoreFeatures
)
dK_dphi()
(in
BBIndepCartBondedParameters
)
DataLoaderCreatorCAP
(in
rosetta.protocols.jd2.parser._protocols_jd2_parser_
)
delete_record()
(in
TrajectoryMapFeatures
)
dK_dphi()
(in
CartBondedParameters
)
DataLoaderFactory
(in
rosetta.protocols.jd2.parser._protocols_jd2_parser_
)
delete_record()
(in
UnrecognizedAtomFeatures
)
dK_dpsi()
(in
BBDepCartBondedParameters
)
DataLoaderFactoryAP
(in
rosetta.protocols.jd2.parser._protocols_jd2_parser_
)
delete_record()
(in
WaterFeatures
)
dK_dpsi()
(in
BBIndepCartBondedParameters
)
DataLoaderFactoryCAP
(in
rosetta.protocols.jd2.parser._protocols_jd2_parser_
)
delete_record()
(in
ConcurrencyTest
)
dK_dpsi()
(in
CartBondedParameters
)
DataMap
(in
rosetta.basic.datacache._basic_datacache_
)
delete_record()
(in
HelixBundleFeatures
)
dljatr()
(in
Etable
)
DataMapAP
(in
rosetta.basic.datacache._basic_datacache_
)
delete_record()
(in
SandwichFeatures
)
dljrep()
(in
Etable
)
DataMapCAP
(in
rosetta.basic.datacache._basic_datacache_
)
delete_record()
(in
StrandBundleFeatures
)
DME_FilterMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
DataPoint
(in
rosetta.protocols.cluster._protocols_cluster_
)
delete_region()
(in
rosetta.protocols.grafting._protocols_grafting_
)
DME_FilterMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
DataPointAP
(in
rosetta.protocols.cluster._protocols_cluster_
)
delete_res()
(in
PDBInfo
)
DME_FilterMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
DataPointCAP
(in
rosetta.protocols.cluster._protocols_cluster_
)
delete_residue()
(in
FragLib
)
DMS
(in
rosetta.core.scoring.rna.data
)
datatype()
(in
WriteableCacheableData
)
delete_residue()
(in
TorsionFragmentLibrary
)
DMS
(in
rosetta.core.scoring.rna.data._core_scoring_rna_data_
)
datatype()
(in
JumpSampleData
)
delete_residue_range_slow()
(in
Conformation
)
DMS
(in
RNA_ReactivityType
)
datatype()
(in
AutoCutData
)
delete_residue_range_slow()
(in
ProtectedConformation
)
DMS_values()
(in
RNA_DMS_Potential
)
date
(in
rosetta.version'
)
delete_residue_slow()
(in
Conformation
)
dmu_dphi()
(in
BBDepCartBondedParameters
)
Dawson()
(in
rosetta.numeric.statistics._numeric_statistics_
)
delete_residue_slow()
(in
ProtectedConformation
)
dmu_dphi()
(in
BBIndepCartBondedParameters
)
db_partition_from_options()
(in
rosetta.basic.database._basic_database_
)
DELETE_ROTAMER
(in
rosetta.core.pack.rotamer_set
)
dmu_dphi()
(in
CartBondedParameters
)
db_session()
(in
RRReporterSQLite
)
DELETE_ROTAMER
(in
BumpSelectorDecision
)
dmu_dpsi()
(in
BBDepCartBondedParameters
)
db_session()
(in
ReadResfileFromDB
)
DELETE_ROTAMER
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
dmu_dpsi()
(in
BBIndepCartBondedParameters
)
DbBigInt
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
delete_segment()
(in
FoldTree
)
dmu_dpsi()
(in
CartBondedParameters
)
DbBigIntAP
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
delete_self_edges()
(in
FoldTree
)
DNA
(in
rosetta
)
DbBigIntCAP
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
delete_seqpos()
(in
AtomTree
)
DNA
(in
rosetta.core.chemical
)
DbDataType
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
delete_seqpos()
(in
FoldTree
)
DNA
(in
rosetta.core.chemical._core_chemical_
)
DbDataTypeAP
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
delete_source_residue()
(in
SequenceMapping
)
DNA
(in
ResidueProperty
)
DbDataTypeCAP
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
delete_target_residue()
(in
SequenceMapping
)
dna
(in
rosetta.core.scoring
)
DbDouble
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
delete_terminal_chi()
(in
ResidueType
)
dna
(in
rosetta.protocols
)
DbDoubleAP
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
delete_this_struct_id()
(in
rosetta.protocols.features.strand_assembly._protocols_features_strand_assembly_
)
dna_base_distance
(in
ScoreType
)
DbDoubleCAP
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
delete_this_sw_can_by_sh_id_from_sw_by_comp()
(in
rosetta.protocols.features.strand_assembly._protocols_features_strand_assembly_
)
dna_base_distance
(in
rosetta.core.scoring._core_scoring_
)
DbInteger
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
delete_unordered_edge()
(in
FoldTree
)
dna_base_distance
(in
rosetta.core.scoring
)
DbIntegerAP
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
delete_virtual_residues()
(in
rosetta.protocols.relax._protocols_relax_
)
dna_base_distance
(in
rosetta
)
DbIntegerCAP
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
DeleteAtom
(in
rosetta.core.chemical._core_chemical_
)
dna_base_partner()
(in
rosetta.protocols.dna._protocols_dna_
)
DbMoverMessageListener
(in
rosetta.basic.message_listening._basic_message_listening_
)
DeleteAtomAP
(in
rosetta.core.chemical._core_chemical_
)
DNA_BaseEnergy
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
DbMoverMessageListenerAP
(in
rosetta.basic.message_listening._basic_message_listening_
)
DeleteAtomCAP
(in
rosetta.core.chemical._core_chemical_
)
DNA_BaseEnergyAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
DbMoverMessageListenerCAP
(in
rosetta.basic.message_listening._basic_message_listening_
)
DeleteChainsMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
DNA_BaseEnergyCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
DbReal
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
DeleteChainsMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
DNA_BaseEnergyCreator
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
DbRealAP
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
DeleteChainsMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
DNA_BaseEnergyCreatorAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
DbRealCAP
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
DeleteChainsMoverCreator
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
DNA_BaseEnergyCreatorCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
DbText
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
DeleteChainsMoverCreatorAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
DNA_BasePotential
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
DbTextAP
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
DeleteChainsMoverCreatorCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
DNA_BasePotentialAP
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
DbTextCAP
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
DeleteMetalbindingAtom
(in
rosetta.core.chemical._core_chemical_
)
DNA_BasePotentialCAP
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
DbTextKey
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
DeleteMetalbindingAtomAP
(in
rosetta.core.chemical._core_chemical_
)
dna_bb_torsion
(in
ScoreType
)
DbTextKeyAP
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
DeleteMetalbindingAtomCAP
(in
rosetta.core.chemical._core_chemical_
)
dna_bb_torsion
(in
rosetta.core.scoring._core_scoring_
)
DbTextKeyCAP
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
DeleteMover
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
dna_bb_torsion
(in
rosetta.core.scoring
)
DbTrajectoryReader
(in
rosetta.protocols.canonical_sampling._protocols_canonical_sampling_
)
DeleteMoverAP
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
dna_bb_torsion
(in
rosetta
)
DbTrajectoryReader
(in
rosetta.protocols.trajectory._protocols_trajectory_
)
DeleteMoverCAP
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
dna_bp
(in
ScoreType
)
DbTrajectoryReaderAP
(in
rosetta.protocols.canonical_sampling._protocols_canonical_sampling_
)
DeleteProperty
(in
rosetta.core.chemical._core_chemical_
)
dna_bp
(in
rosetta.core.scoring._core_scoring_
)
DbTrajectoryReaderAP
(in
rosetta.protocols.trajectory._protocols_trajectory_
)
DeletePropertyAP
(in
rosetta.core.chemical._core_chemical_
)
dna_bp
(in
rosetta.core.scoring
)
DbTrajectoryReaderCAP
(in
rosetta.protocols.canonical_sampling._protocols_canonical_sampling_
)
DeletePropertyCAP
(in
rosetta.core.chemical._core_chemical_
)
dna_bp
(in
rosetta
)
DbTrajectoryReaderCAP
(in
rosetta.protocols.trajectory._protocols_trajectory_
)
DeleteRegionMover
(in
rosetta.protocols.grafting.simple_movers._protocols_grafting_simple_movers_
)
dna_bs
(in
ScoreType
)
DbTrajectoryRecorder
(in
rosetta.protocols.canonical_sampling._protocols_canonical_sampling_
)
DeleteRegionMoverAP
(in
rosetta.protocols.grafting.simple_movers._protocols_grafting_simple_movers_
)
dna_bs
(in
rosetta.core.scoring._core_scoring_
)
DbTrajectoryRecorderAP
(in
rosetta.protocols.canonical_sampling._protocols_canonical_sampling_
)
DeleteRegionMoverCAP
(in
rosetta.protocols.grafting.simple_movers._protocols_grafting_simple_movers_
)
dna_bs
(in
rosetta.core.scoring
)
DbTrajectoryRecorderCAP
(in
rosetta.protocols.canonical_sampling._protocols_canonical_sampling_
)
DeleteRegionMoverCreator
(in
rosetta.protocols.grafting.simple_movers._protocols_grafting_simple_movers_
)
dna_bs
(in
rosetta
)
DbTrajectoryRecorderCreator
(in
rosetta.protocols.canonical_sampling._protocols_canonical_sampling_
)
DeleteRegionMoverCreatorAP
(in
rosetta.protocols.grafting.simple_movers._protocols_grafting_simple_movers_
)
dna_chains()
(in
RestrictDesignToProteinDNAInterface
)
DbTrajectoryRecorderCreatorAP
(in
rosetta.protocols.canonical_sampling._protocols_canonical_sampling_
)
DeleteRegionMoverCreatorCAP
(in
rosetta.protocols.grafting.simple_movers._protocols_grafting_simple_movers_
)
dna_chi
(in
ScoreType
)
DbTrajectoryRecorderCreatorCAP
(in
rosetta.protocols.canonical_sampling._protocols_canonical_sampling_
)
DeleteTerminalChi
(in
rosetta.core.chemical._core_chemical_
)
dna_chi
(in
rosetta.core.scoring._core_scoring_
)
DbTrajectoryWriter
(in
rosetta.protocols.trajectory._protocols_trajectory_
)
DeleteTerminalChiAP
(in
rosetta.core.chemical._core_chemical_
)
dna_chi
(in
rosetta.core.scoring
)
DbTrajectoryWriterAP
(in
rosetta.protocols.trajectory._protocols_trajectory_
)
DeleteTerminalChiCAP
(in
rosetta.core.chemical._core_chemical_
)
dna_chi
(in
rosetta
)
DbTrajectoryWriterCAP
(in
rosetta.protocols.trajectory._protocols_trajectory_
)
DELTA
(in
rosetta.core.chemical.rna
)
dna_comp_name_str()
(in
rosetta.protocols.dna._protocols_dna_
)
DbUUID
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
DELTA
(in
rosetta.core.chemical.rna._core_chemical_rna_
)
dna_dr
(in
ScoreType
)
DbUUIDAP
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
DELTA
(in
RNA_Torsion
)
dna_dr
(in
rosetta.core.scoring._core_scoring_
)
DbUUIDCAP
(in
rosetta.basic.database.schema_generator._basic_database_schema_generator_
)
delta()
(in
Pose
)
dna_dr
(in
rosetta.core.scoring
)
DC
(in
rosetta.core.scoring._core_scoring_
)
delta()
(in
DNABase
)
dna_dr
(in
rosetta
)
dc
(in
ScoreType
)
delta()
(in
PerturbBundleOptions
)
dna_full_name3()
(in
rosetta.protocols.dna._protocols_dna_
)
dc
(in
rosetta.core.scoring._core_scoring_
)
delta()
(in
IteratedConvergenceMover
)
dna_neighbors()
(in
DnaInterfaceFinder
)
dc
(in
rosetta.core.scoring
)
delta()
(in
FilterScanFilter
)
dna_positions()
(in
LigandMotifSearch
)
dc
(in
rosetta
)
delta()
(in
LoopLengthChange
)
dna_positions()
(in
MotifSearch
)
DC_TYPE
(in
DC
)
delta()
(in
ContingentAcceptMover
)
dna_seq_tag()
(in
DnaInterfacePacker
)
DC_TYPE_CC
(in
DC_TYPE
)
delta_atr_score()
(in
ProteinAtrRepChecker
)
dna_sugar_close
(in
ScoreType
)
DC_TYPE_CC
(in
DC
)
delta_atr_score()
(in
RNA_AtrRepChecker
)
dna_sugar_close
(in
rosetta.core.scoring._core_scoring_
)
DC_TYPE_CH
(in
DC_TYPE
)
delta_chi_zz()
(in
PCS_tensor
)
dna_sugar_close
(in
rosetta.core.scoring
)
DC_TYPE_CH
(in
DC
)
delta_chi_zz()
(in
PCS_tensor_Ts1
)
dna_sugar_close
(in
rosetta
)
DC_TYPE_NC
(in
DC_TYPE
)
delta_chi_zz()
(in
PCS_tensor_Ts2
)
DNABase
(in
rosetta.protocols.dna._protocols_dna_
)
DC_TYPE_NC
(in
DC
)
delta_chi_zz()
(in
PCS_tensor_Ts3
)
DNABaseAP
(in
rosetta.protocols.dna._protocols_dna_
)
DC_TYPE_NH
(in
DC_TYPE
)
delta_chi_zz()
(in
PCS_tensor_Ts4
)
DNABaseCAP
(in
rosetta.protocols.dna._protocols_dna_
)
DC_TYPE_NH
(in
DC
)
delta_components()
(in
DNATorsionPotential
)
DNABasepair
(in
rosetta.protocols.dna._protocols_dna_
)
DCAP
(in
rosetta.core.scoring._core_scoring_
)
delta_cutoff()
(in
RNA_FittedTorsionInfo
)
DNABasepairAP
(in
rosetta.protocols.dna._protocols_dna_
)
DCCAP
(in
rosetta.core.scoring._core_scoring_
)
delta_cutoff()
(in
DNATorsionPotential
)
DNABasepairCAP
(in
rosetta.protocols.dna._protocols_dna_
)
dCCdB_fastRes()
(in
ElectronDensity
)
delta_filter_thresholds()
(in
FilterScanFilter
)
DNABasestep
(in
rosetta.protocols.dna._protocols_dna_
)
dCCdBs()
(in
ElectronDensity
)
delta_filters()
(in
GreedyOptMutationMover
)
DNABasestepAP
(in
rosetta.protocols.dna._protocols_dna_
)
dCCdx_aacen()
(in
ElectronDensity
)
delta_filters()
(in
ParetoOptMutationMover
)
DNABasestepCAP
(in
rosetta.protocols.dna._protocols_dna_
)
dCCdx_cen()
(in
ElectronDensity
)
delta_filters()
(in
MatDesGreedyOptMutationMover
)
DNABFormPotential
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
dCCdx_fastRes()
(in
ElectronDensity
)
delta_filters()
(in
FilterScanFilter
)
DNABFormPotentialAP
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
dCCdx_pat()
(in
ElectronDensity
)
delta_north()
(in
RNA_FittedTorsionInfo
)
DNABFormPotentialCAP
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
dCCdx_PointFast()
(in
ElectronDensity
)
delta_omega0()
(in
BundleGridSampler
)
DnaChains
(in
rosetta.protocols.dna._protocols_dna_
)
dCCdx_res()
(in
ElectronDensity
)
delta_omega0()
(in
MakeBundleHelix
)
DnaChainsAP
(in
rosetta.protocols.dna._protocols_dna_
)
DCcomputed()
(in
DC
)
delta_omega0()
(in
PerturbBundle
)
DnaChainsCAP
(in
rosetta.protocols.dna._protocols_dna_
)
DCerr()
(in
DC
)
delta_omega0()
(in
BundleParameters
)
DNAChiEnergy
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
dchidevpen_dbb()
(in
RotamerLibraryScratchSpace
)
delta_omega1()
(in
BundleGridSampler
)
DNAChiEnergyAP
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
dchidevpen_dchi()
(in
RotamerLibraryScratchSpace
)
delta_omega1()
(in
MakeBundleHelix
)
DNAChiEnergyCAP
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
dchimean_dbb()
(in
RotamerLibraryScratchSpace
)
delta_omega1()
(in
PerturbBundle
)
DNAChiEnergyCreator
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
dchimean_domg()
(in
RotamerLibraryScratchSpace
)
delta_omega1()
(in
BundleParameters
)
DNAChiEnergyCreatorAP
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
dchisd_dbb()
(in
RotamerLibraryScratchSpace
)
delta_omega1_all()
(in
MakeBundleHelix
)
DNAChiEnergyCreatorCAP
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
dchisd_domg()
(in
RotamerLibraryScratchSpace
)
delta_omega1_all()
(in
BundleParameters
)
DnaDesignDef
(in
rosetta.protocols.dna._protocols_dna_
)
Dconst()
(in
DC
)
delta_omega1_vect()
(in
MakeBundleHelix
)
DnaDesignDefAP
(in
rosetta.protocols.dna._protocols_dna_
)
Dconst()
(in
RDC
)
delta_omega1_vect()
(in
BundleParameters
)
DnaDesignDefCAP
(in
rosetta.protocols.dna._protocols_dna_
)
DCV_ALREADY_CYCLIZED
(in
rosetta
)
delta_rep_score()
(in
ProteinAtrRepChecker
)
DnaInterfaceFinder
(in
rosetta.protocols.dna._protocols_dna_
)
DCV_ALREADY_CYCLIZED
(in
rosetta.protocols.simple_moves
)
delta_rep_score()
(in
RNA_AtrRepChecker
)
DnaInterfaceFinderAP
(in
rosetta.protocols.dna._protocols_dna_
)
DCV_ALREADY_CYCLIZED
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
delta_south()
(in
RNA_FittedTorsionInfo
)
DnaInterfaceFinderCAP
(in
rosetta.protocols.dna._protocols_dna_
)
DCV_ALREADY_CYCLIZED
(in
DisulfideCyclizationViability
)
delta_t()
(in
BundleGridSampler
)
DnaInterfaceMinMover
(in
rosetta.protocols.dna._protocols_dna_
)
DCV_CYCLIZABLE
(in
rosetta
)
delta_t()
(in
MakeBundleHelix
)
DnaInterfaceMinMoverAP
(in
rosetta.protocols.dna._protocols_dna_
)
DCV_CYCLIZABLE
(in
rosetta.protocols.simple_moves
)
delta_t()
(in
PerturbBundle
)
DnaInterfaceMinMoverCAP
(in
rosetta.protocols.dna._protocols_dna_
)
DCV_CYCLIZABLE
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
delta_t()
(in
BundleParameters
)
DnaInterfaceMinMoverCreator
(in
rosetta.protocols.dna._protocols_dna_
)
DCV_CYCLIZABLE
(in
DisulfideCyclizationViability
)
delta_X_xx()
(in
PCS_tensor
)
DnaInterfaceMinMoverCreatorAP
(in
rosetta.protocols.dna._protocols_dna_
)
DCV_NOT_CYCLIZABLE
(in
rosetta
)
delta_X_xx()
(in
PCS_tensor_Ts1
)
DnaInterfaceMinMoverCreatorCAP
(in
rosetta.protocols.dna._protocols_dna_
)
DCV_NOT_CYCLIZABLE
(in
rosetta.protocols.simple_moves
)
delta_X_xx()
(in
PCS_tensor_Ts2
)
DnaInterfaceMultiStateDesign
(in
rosetta.protocols.dna._protocols_dna_
)
DCV_NOT_CYCLIZABLE
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
delta_X_xx()
(in
PCS_tensor_Ts3
)
DnaInterfaceMultiStateDesignAP
(in
rosetta.protocols.dna._protocols_dna_
)
DCV_NOT_CYCLIZABLE
(in
DisulfideCyclizationViability
)
delta_X_xx()
(in
PCS_tensor_Ts4
)
DnaInterfaceMultiStateDesignCAP
(in
rosetta.protocols.dna._protocols_dna_
)
DCval()
(in
DC
)
delta_X_yy()
(in
PCS_tensor
)
DnaInterfaceMultiStateDesignCreator
(in
rosetta.protocols.dna._protocols_dna_
)
dD_dv1()
(in
rosetta.protocols.pockets._protocols_pockets_
)
delta_X_yy()
(in
PCS_tensor_Ts1
)
DnaInterfaceMultiStateDesignCreatorAP
(in
rosetta.protocols.dna._protocols_dna_
)
dD_dv2()
(in
rosetta.protocols.pockets._protocols_pockets_
)
delta_X_yy()
(in
PCS_tensor_Ts2
)
DnaInterfaceMultiStateDesignCreatorCAP
(in
rosetta.protocols.dna._protocols_dna_
)
dD_dv3()
(in
rosetta.protocols.pockets._protocols_pockets_
)
delta_X_yy()
(in
PCS_tensor_Ts3
)
DnaInterfacePacker
(in
rosetta.protocols.dna._protocols_dna_
)
dD_dv4()
(in
rosetta.protocols.pockets._protocols_pockets_
)
delta_X_yy()
(in
PCS_tensor_Ts4
)
DnaInterfacePackerAP
(in
rosetta.protocols.dna._protocols_dna_
)
dD_dv5()
(in
rosetta.protocols.pockets._protocols_pockets_
)
delta_X_zz()
(in
PCS_tensor
)
DnaInterfacePackerCAP
(in
rosetta.protocols.dna._protocols_dna_
)
dD_dv6()
(in
rosetta.protocols.pockets._protocols_pockets_
)
delta_X_zz()
(in
PCS_tensor_Ts1
)
DnaInterfacePackerCreator
(in
rosetta.protocols.dna._protocols_dna_
)
ddg
(in
rosetta.core.io
)
delta_X_zz()
(in
PCS_tensor_Ts2
)
DnaInterfacePackerCreatorAP
(in
rosetta.protocols.dna._protocols_dna_
)
ddg
(in
rosetta.protocols
)
delta_X_zz()
(in
PCS_tensor_Ts3
)
DnaInterfacePackerCreatorCAP
(in
rosetta.protocols.dna._protocols_dna_
)
ddG
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
delta_X_zz()
(in
PCS_tensor_Ts4
)
DnaNeighbor
(in
rosetta.protocols.dna._protocols_dna_
)
ddG()
(in
ddGMover
)
delta_z1()
(in
MakeBundleHelix
)
DnaNeighborAP
(in
rosetta.protocols.dna._protocols_dna_
)
ddg()
(in
GrowPeptides
)
delta_z1()
(in
BundleParameters
)
DnaNeighborCAP
(in
rosetta.protocols.dna._protocols_dna_
)
ddg_based()
(in
SeedFoldTree
)
delta_z1_vect()
(in
MakeBundleHelix
)
DNAParameters
(in
rosetta.protocols.dna._protocols_dna_
)
ddG_bind_correlation
(in
OptEPositionDataType
)
delta_z1_vect()
(in
BundleParameters
)
DNAParametersAP
(in
rosetta.protocols.dna._protocols_dna_
)
ddG_bind_correlation
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
DeltaFilter
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
DNAParametersCAP
(in
rosetta.protocols.dna._protocols_dna_
)
ddG_bind_correlation
(in
rosetta.protocols.optimize_weights
)
DeltaFilterAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
DnaPosition
(in
rosetta.protocols.dna._protocols_dna_
)
DDG_Bind_File_Index
(in
DDGBindOptEData
)
DeltaFilterCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
DnaPositionAP
(in
rosetta.protocols.dna._protocols_dna_
)
ddG_for_single_residue()
(in
AlaScan
)
DeltaFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
DnaPositionCAP
(in
rosetta.protocols.dna._protocols_dna_
)
ddG_for_single_residue()
(in
DdGScan
)
DeltaFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
DNATorsionEnergy
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
ddG_mover()
(in
DdGScan
)
DeltaFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
DNATorsionEnergyAP
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
ddG_mutation_correlation
(in
OptEPositionDataType
)
deltaG_bind()
(in
DGBindOptEData
)
DNATorsionEnergyCAP
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
ddG_mutation_correlation
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
DemoBase
(in
rosetta.core._core_
)
DNATorsionEnergyCreator
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
ddG_mutation_correlation
(in
rosetta.protocols.optimize_weights
)
DemoDerived
(in
rosetta.core._core_
)
DNATorsionEnergyCreatorAP
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
ddG_mutation_correlation_with_unfolded_energy
(in
OptEPositionDataType
)
DemoTesterFunction()
(in
rosetta.core._core_
)
DNATorsionEnergyCreatorCAP
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
ddG_mutation_correlation_with_unfolded_energy
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
denovo_design
(in
rosetta.protocols
)
DNATorsionPotential
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
ddG_mutation_correlation_with_unfolded_energy
(in
rosetta.protocols.optimize_weights
)
dens_grad()
(in
ElectronDensity
)
DNATorsionPotentialAP
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
ddG_threshold()
(in
HotspotDisjointedFoldTreeMover
)
DenseEnergyContainer
(in
rosetta.core.scoring._core_scoring_
)
DNATorsionPotentialCAP
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
ddG_threshold()
(in
RotamerBoltzmannWeight
)
DenseEnergyContainerAP
(in
rosetta.core.scoring._core_scoring_
)
dneglnrotprob_dbb()
(in
RotamerLibraryScratchSpace
)
ddGAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
DenseEnergyContainerCAP
(in
rosetta.core.scoring._core_scoring_
)
do_apply()
(in
LoopFilter
)
DDGBindOptEData
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
DenseIGRepacker
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
do_caching()
(in
ABEGO_SS_Score
)
DDGBindOptEDataAP
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
DenseIGRepackerAP
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
do_caching()
(in
AmbigCSScore
)
DDGBindOptEDataCAP
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
DenseIGRepackerCAP
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
do_caching()
(in
AtomBasedConstraintsScore
)
ddGCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
DenseNeighborConstIterator
(in
rosetta.core.scoring._core_scoring_
)
do_caching()
(in
AtomPairConstraintsScore
)
ddGCreator
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
DenseNeighborConstIteratorAP
(in
rosetta.core.scoring._core_scoring_
)
do_caching()
(in
CSScore
)
ddGCreatorAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
DenseNeighborConstIteratorCAP
(in
rosetta.core.scoring._core_scoring_
)
do_caching()
(in
CachingScoringMethod
)
ddGCreatorCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
DenseNeighborIterator
(in
rosetta.core.scoring._core_scoring_
)
do_caching()
(in
DihedralConstraintsScore
)
DdGFeatures
(in
rosetta.protocols.features._protocols_features_
)
DenseNeighborIteratorAP
(in
rosetta.core.scoring._core_scoring_
)
do_caching()
(in
DisulfideDistance
)
DdGFeaturesAP
(in
rosetta.protocols.features._protocols_features_
)
DenseNeighborIteratorCAP
(in
rosetta.core.scoring._core_scoring_
)
do_caching()
(in
FragmentCrmsd
)
DdGFeaturesCAP
(in
rosetta.protocols.features._protocols_features_
)
DensePDEdge
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
do_caching()
(in
FragmentCrmsdResDepth
)
DdGFeaturesCreator
(in
rosetta.protocols.features._protocols_features_
)
DensePDEdgeAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
do_caching()
(in
FragmentDME
)
DdGFeaturesCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
DensePDEdgeCAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
do_caching()
(in
FragmentScoreManager
)
DdGFeaturesCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
DensePDInteractionGraph
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
do_caching()
(in
GunnCostScore
)
DdgFilter
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
DensePDInteractionGraphAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
do_caching()
(in
HydrophobicityProfileSimilarity
)
DdgFilterAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
DensePDInteractionGraphCAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
do_caching()
(in
HydrophobicitySimilarity
)
DdgFilterCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
DensePDNode
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
do_caching()
(in
InterbondAngleScore
)
DdgFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
DensePDNodeAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
do_caching()
(in
JCoupling
)
DdgFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
DensePDNodeCAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
do_caching()
(in
LAMBEGO_Similarity
)
DdgFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
density()
(in
FragmentBiasAssigner
)
do_caching()
(in
MidPhiOut
)
ddGMover
(in
rosetta.protocols.ddg._protocols_ddg_
)
density_nbr()
(in
FragmentBiasAssigner
)
do_caching()
(in
MidPsiOut
)
ddGMoverAP
(in
rosetta.protocols.ddg._protocols_ddg_
)
DensityMorphingMover
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
do_caching()
(in
PCS_FragDistance
)
ddGMoverCAP
(in
rosetta.protocols.ddg._protocols_ddg_
)
DensityMorphingMoverAP
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
do_caching()
(in
PartialSecondarySimilarity
)
DDGMutationOptEData
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
DensityMorphingMoverCAP
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
do_caching()
(in
Phi
)
DDGMutationOptEDataAP
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
DensityMorphingMoverCreator
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
do_caching()
(in
PhiPsiRmsd
)
DDGMutationOptEDataCAP
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
DensityMorphingMoverCreatorAP
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
do_caching()
(in
PhiPsiSquareWell
)
DdGScan
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
DensityMorphingMoverCreatorCAP
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
do_caching()
(in
ProfileScore
)
DdGScanAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
DensityScoringClaimer
(in
rosetta.protocols.topology_broker._protocols_topology_broker_'
)
do_caching()
(in
ProfileScoreBlosum62
)
DdGScanCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
DensityScoringClaimerAP
(in
rosetta.protocols.topology_broker._protocols_topology_broker_'
)
do_caching()
(in
ProfileScoreDistWeight
)
DdGScanCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
DensityScoringClaimerCAP
(in
rosetta.protocols.topology_broker._protocols_topology_broker_'
)
do_caching()
(in
ProfileScoreL1
)
DdGScanCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
dentropy_dbb()
(in
RotamerLibraryScratchSpace
)
do_caching()
(in
ProfileScoreStructL1
)
DdGScanCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
DenyPdbIdFilter
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
do_caching()
(in
ProfileScoreSubMatrix
)
DDomainParse
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
DenyPdbIdFilterAP
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
do_caching()
(in
Psi
)
DDomainParseAP
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
DenyPdbIdFilterCAP
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
do_caching()
(in
RDCScore
)
DDomainParseCAP
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
DEOXY_SUGAR
(in
rosetta
)
do_caching()
(in
RamaScore
)
DDPlookup
(in
rosetta.core.scoring.interface_._core_scoring_interface__
)
DEOXY_SUGAR
(in
rosetta.core.chemical
)
do_caching()
(in
ScoreEValuator
)
DDPlookupAP
(in
rosetta.core.scoring.interface_._core_scoring_interface__
)
DEOXY_SUGAR
(in
rosetta.core.chemical._core_chemical_
)
do_caching()
(in
SecondarySimilarity
)
DDPlookupCAP
(in
rosetta.core.scoring.interface_._core_scoring_interface__
)
DEOXY_SUGAR
(in
ResidueProperty
)
do_caching()
(in
SolventAccessibility
)
DDPscore
(in
rosetta.core.scoring.interface_._core_scoring_interface__
)
dependencies()
(in
BuildInstruction
)
do_caching()
(in
TalosSSSimilarity
)
DDPscoreAP
(in
rosetta.core.scoring.interface_._core_scoring_interface__
)
dependencies_exist()
(in
BuildManager
)
do_caching()
(in
TorsionBinSimilarity
)
DDPscoreCAP
(in
rosetta.core.scoring.interface_._core_scoring_interface__
)
dependent()
(in
DOF_Node
)
do_caching_simple()
(in
ProfileScoreL1
)
DDPscoreCreator
(in
rosetta.core.scoring.interface_._core_scoring_interface__
)
dependent_atoms()
(in
SymmetryInfo
)
do_caching_simple()
(in
ProfileScoreStructL1
)
DDPscoreCreatorAP
(in
rosetta.core.scoring.interface_._core_scoring_interface__
)
dependent_begin()
(in
SymMinimizerMap
)
do_caching_simple()
(in
SecondarySimilarity
)
DDPscoreCreatorCAP
(in
rosetta.core.scoring.interface_._core_scoring_interface__
)
dependent_dofs()
(in
SymmetryInfo
)
do_caching_simple()
(in
TalosSSSimilarity
)
ddy()
(in
SimpleInterpolator
)
dependent_end()
(in
SymMinimizerMap
)
do_clustering()
(in
ClusterPhilStyle
)
dE_dbb()
(in
RotamerLibraryScratchSpace
)
dependent_on()
(in
BuildInstruction
)
do_clustering()
(in
ClusterPhilStyle_Loop
)
dE_dbb_dev()
(in
RotamerLibraryScratchSpace
)
dependent_torsions()
(in
SymmetryInfo
)
do_clustering()
(in
ClusterPhilStyle_PoseReporter
)
dE_dbb_dev_perchi()
(in
RotamerLibraryScratchSpace
)
depends_on_polymer_lower()
(in
AtomICoor
)
do_clustering()
(in
ClusterPhilStyle
)
dE_dbb_rot()
(in
RotamerLibraryScratchSpace
)
depends_on_polymer_upper()
(in
AtomICoor
)
do_distributed_rerun()
(in
AbrelaxApplication
)
dE_dbb_semi()
(in
RotamerLibraryScratchSpace
)
depends_on_residue_connection()
(in
AtomICoor
)
do_final_repack()
(in
CentroidRelax
)
dE_dchi()
(in
RotamerLibraryScratchSpace
)
deposition_date()
(in
HeaderInformation
)
do_I_skip()
(in
rosetta.protocols.scoring.methods.pcs2._protocols_scoring_methods_pcs2_
)
dE_dchi_dev()
(in
RotamerLibraryScratchSpace
)
deprecated_eval_atom_derivative()
(in
ConstraintSet
)
do_init()
(in
BasicCmdLineInit
)
dE_dchi_semi()
(in
RotamerLibraryScratchSpace
)
deprecated_eval_atom_derivative()
(in
IgnoreSubsetConstraintSet
)
do_init()
(in
BasicInit
)
deallocate_arraypoolelement()
(in
EnergyGraph
)
deprecated_eval_atom_derivative()
(in
MaxSeqSepConstraintSet
)
do_intrastage_docking()
(in
HybridizeProtocol
)
debug()
(in
HPool_RMSD
)
DEPROTONATED
(in
rosetta
)
do_not_sample_multiple_virtual_sugar()
(in
StepWiseRNA_ModelerOptions
)
debug()
(in
CheckPointer
)
DEPROTONATED
(in
rosetta.core.chemical
)
do_one_line()
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
debug()
(in
LoopRefineInnerCycle
)
DEPROTONATED
(in
rosetta.core.chemical._core_chemical_
)
do_packing()
(in
StepWisePacker
)
debug()
(in
SeqprofConsensusOperation
)
DEPROTONATED
(in
VariantType
)
do_prepack()
(in
StepWiseMasterPacker
)
debug_dump_icoor()
(in
ResidueType
)
depth()
(in
Emitter
)
do_prepack()
(in
StepWisePacker
)
debug_dump_rotamers()
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
depth()
(in
DOF_Node
)
do_prepack()
(in
MultiPhosphateSampler
)
debug_note_accepted_substitution()
(in
OTFFlexbbInteractionGraph
)
depth()
(in
MembraneEmbed
)
do_recursion()
(in
rosetta.numeric.random._numeric_random_
)
debug_note_considered_substitution()
(in
OTFFlexbbInteractionGraph
)
depth()
(in
MembraneTopology
)
do_redistribution()
(in
ClusterPhilStyle
)
debug_note_projected_deltaE_of_considered_substitution()
(in
OTFFlexbbInteractionGraph
)
depth()
(in
VallResidue
)
do_rerun()
(in
AbrelaxApplication
)
debug_note_rejected_substitution()
(in
OTFFlexbbInteractionGraph
)
depth_first_connected_component_counting()
(in
NodeBase
)
do_rotation()
(in
TMalign
)
debug_output()
(in
ddGMover
)
deriv
(in
rosetta.numeric
)
do_score()
(in
DGBindOptEData
)
debug_pause()
(in
Conformation
)
deriv_check()
(in
MinimizerOptions
)
do_score()
(in
PNatLigPoseOptEData
)
debug_pdb()
(in
xyzStripeHash
)
deriv_check()
(in
DnaInterfaceMinMover
)
do_scoring()
(in
rosetta.protocols.toolbox.sample_around._protocols_toolbox_sample_around_
)
debug_print_addresses()
(in
HierarchicalLevel
)
deriv_check()
(in
RNA_Minimizer
)
do_screen()
(in
AlignRMSD_Screener
)
debug_print_hierarchy()
(in
HierarchicalLevel
)
deriv_check()
(in
MinMover
)
do_set_xyz()
(in
rosetta.protocols.stepwise.sampler.protein._protocols_stepwise_sampler_protein_
)
debug_print_size_per_level()
(in
HierarchicalLevel
)
deriv_check()
(in
SymMinMover
)
do_test_move()
(in
StepWiseMasterMover
)
debug_residue_torsions()
(in
Conformation
)
deriv_check_result()
(in
AtomTreeMinimizer
)
do_the_modeler()
(in
VirtualSugarJustInTimeInstantiator
)
DebuggingAnnealer
(in
rosetta.core.pack.annealer._core_pack_annealer_
)
deriv_check_result()
(in
CartesianMinimizer
)
do_the_move()
(in
StepWiseMasterMover
)
DebuggingAnnealerAP
(in
rosetta.core.pack.annealer._core_pack_annealer_
)
deriv_check_result()
(in
NumericalDerivCheckResult
)
do_xy_scan()
(in
rosetta.protocols.toolbox.sample_around._protocols_toolbox_sample_around_
)
DebuggingAnnealerCAP
(in
rosetta.core.pack.annealer._core_pack_annealer_
)
deriv_check_result()
(in
NormalModeMinimizer
)
DOCK_DOMAIN
(in
rosetta.core.pose.full_model_info
)
DebugOut_MpiFileBuffer
(in
rosetta.protocols.jd2._protocols_jd2_
)
deriv_check_to_stdout()
(in
MinimizerOptions
)
DOCK_DOMAIN
(in
rosetta.core.pose.full_model_info._core_pose_full_model_info_
)
DebugOut_MpiFileBufferAP
(in
rosetta.protocols.jd2._protocols_jd2_
)
deriv_check_verbose()
(in
MinimizerOptions
)
DOCK_DOMAIN
(in
FullModelParameterType
)
DebugOut_MpiFileBufferCAP
(in
rosetta.protocols.jd2._protocols_jd2_
)
deriv_multiply()
(in
SymmetryInfo
)
dock_domain_map()
(in
FullModelInfo
)
decide_read_from_binary()
(in
RotamerLibrary
)
deriv_score()
(in
MMLJEnergyTable
)
dock_ens_conf
(in
ScoreType
)
decide_to_keep_pose()
(in
DeleteMover
)
deriv_score()
(in
MMLJScore
)
dock_ens_conf
(in
rosetta.core.scoring._core_scoring_
)
declare_all_rotamers_initialized()
(in
OTFFlexbbNode
)
deriv_type_from_name()
(in
HBondTypeManager
)
dock_ens_conf
(in
rosetta.core.scoring
)
declare_chemical_bond()
(in
Conformation
)
derivative_atom()
(in
DisulfideAtomIndices
)
dock_ens_conf
(in
rosetta
)
declare_chemical_bond()
(in
ProtectedConformation
)
derivative_graph()
(in
SymmetricEnergies
)
DOCK_ENS_CONF1
(in
CacheableDataType
)
declare_edge_energies_final()
(in
PrecomputedPairEnergiesInteractionGraph
)
DerivCheckDataPoint
(in
rosetta.core.optimization._core_optimization_
)
DOCK_ENS_CONF1
(in
Enum
)
declare_energies_final()
(in
DensePDEdge
)
DerivCheckDataPointAP
(in
rosetta.core.optimization._core_optimization_
)
DOCK_ENS_CONF2
(in
CacheableDataType
)
declare_energies_final()
(in
DoubleDensePDEdge
)
DerivCheckDataPointCAP
(in
rosetta.core.optimization._core_optimization_
)
DOCK_ENS_CONF2
(in
Enum
)
declare_energies_final()
(in
DoubleLazyEdge
)
derive_from_src_lib()
(in
TorsionFragmentLibrary
)
dock_high_res()
(in
AntibodyDesignModeler
)
declare_energies_final()
(in
EdgeBase
)
derive_peptide()
(in
PeptideDeriverFilter
)
dock_low_res()
(in
AntibodyDesignModeler
)
declare_energies_final()
(in
FASTEREdge
)
derive_sc_sc_restraints()
(in
rosetta.protocols.relax._protocols_relax_
)
DockAndRetrieveSidechains
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
declare_energies_final()
(in
FixedBBEdge
)
derived_dofs()
(in
WrapperOptEMultifunc
)
DockAndRetrieveSidechainsAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
declare_energies_final()
(in
LazyEdge
)
DerivedSequenceMapping
(in
rosetta.core.sequence._core_sequence_
)
DockAndRetrieveSidechainsCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
declare_energies_final()
(in
LinearMemEdge
)
DerivedSequenceMappingAP
(in
rosetta.core.sequence._core_sequence_
)
DockAndRetrieveSidechainsCreator
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
declare_energies_final()
(in
OnTheFlyEdge
)
DerivedSequenceMappingCAP
(in
rosetta.core.sequence._core_sequence_
)
DockAndRetrieveSidechainsCreatorAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
declare_energies_final()
(in
PDEdge
)
derivs()
(in
HBond
)
DockAndRetrieveSidechainsCreatorCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
declare_energies_final()
(in
PrecomputedPairEnergiesEdge
)
DerivVectorPair
(in
rosetta.core.scoring._core_scoring_
)
DockDesignFilterFactory
(in
rosetta.protocols.protein_interface_design._protocols_protein_interface_design_
)
declare_energies_final()
(in
SymmLinearMemEdge
)
DerivVectorPairAP
(in
rosetta.core.scoring._core_scoring_
)
DockDesignFilterFactoryAP
(in
rosetta.protocols.protein_interface_design._protocols_protein_interface_design_
)
declare_energies_final()
(in
SymmMinimalistEdge
)
DerivVectorPairCAP
(in
rosetta.core.scoring._core_scoring_
)
DockDesignFilterFactoryCAP
(in
rosetta.protocols.protein_interface_design._protocols_protein_interface_design_
)
declare_energies_final()
(in
SymmOnTheFlyEdge
)
DescentDirectionAlgorithm
(in
rosetta.core.optimization._core_optimization_
)
docking
(in
rosetta.protocols
)
declare_energies_final()
(in
FlexbbEdge
)
DescentDirectionAlgorithmAP
(in
rosetta.core.optimization._core_optimization_
)
docking_frequency()
(in
StepWiseMoveSelector
)
declare_energies_final()
(in
MinimalistFlexbbEdge
)
DescentDirectionAlgorithmCAP
(in
rosetta.core.optimization._core_optimization_
)
docking_frequency()
(in
StepWiseMonteCarloOptions
)
declare_energies_final()
(in
OTFFlexbbEdge
)
describe_fragments()
(in
FragmentScoreManager
)
docking_highres_filter()
(in
SymDockProtocol
)
declare_minimization_over()
(in
OptEMultifunc
)
describe_fragments()
(in
PValuedFragmentScoreManager
)
docking_highres_mover()
(in
DockingProtocol
)
DeclareBond
(in
rosetta.protocols.cyclic_peptide._protocols_cyclic_peptide_
)
describe_score()
(in
BFactor
)
docking_lowres_filter()
(in
SymDockProtocol
)
DeclareBondAP
(in
rosetta.protocols.cyclic_peptide._protocols_cyclic_peptide_
)
describe_score()
(in
DisulfideIdentity
)
docking_lowres_mover()
(in
DockingProtocol
)
DeclareBondCAP
(in
rosetta.protocols.cyclic_peptide._protocols_cyclic_peptide_
)
describe_score()
(in
PhiPsiRmsd
)
DockingEnsemble
(in
rosetta.protocols.docking._protocols_docking_
)
DeclareBondCreator
(in
rosetta.protocols.cyclic_peptide._protocols_cyclic_peptide_
)
describe_score()
(in
ProfileScore
)
DockingEnsembleAP
(in
rosetta.protocols.docking._protocols_docking_
)
DeclareBondCreatorAP
(in
rosetta.protocols.cyclic_peptide._protocols_cyclic_peptide_
)
describe_score()
(in
ProlinePhiScore
)
DockingEnsembleCAP
(in
rosetta.protocols.docking._protocols_docking_
)
DeclareBondCreatorCAP
(in
rosetta.protocols.cyclic_peptide._protocols_cyclic_peptide_
)
describe_score()
(in
RamaScore
)
DockingEnsemblePrepackProtocol
(in
rosetta.protocols.docking._protocols_docking_
)
decode6bit()
(in
rosetta.utility._utility_
)
describe_score()
(in
SecondaryIdentity
)
DockingEnsemblePrepackProtocolAP
(in
rosetta.protocols.docking._protocols_docking_
)
decode_32_to_24()
(in
rosetta.utility._utility_
)
describe_score()
(in
SequenceIdentity
)
DockingEnsemblePrepackProtocolCAP
(in
rosetta.protocols.docking._protocols_docking_
)
decompose_bb_hb_into_pair_energies()
(in
HBondOptions
)
deserialize()
(in
CompoundInterpolator
)
DockingHighRes
(in
rosetta.protocols.docking._protocols_docking_
)
DecomposeAndReweightEnergiesCalculator
(in
rosetta.protocols.toolbox.pose_metric_calculators._protocols_toolbox_pose_metric_calculators_
)
deserialize()
(in
Interpolator
)
DockingHighResAP
(in
rosetta.protocols.docking._protocols_docking_
)
DecomposeAndReweightEnergiesCalculatorAP
(in
rosetta.protocols.toolbox.pose_metric_calculators._protocols_toolbox_pose_metric_calculators_
)
deserialize()
(in
SimpleInterpolator
)
DockingHighResCAP
(in
rosetta.protocols.docking._protocols_docking_
)
DecomposeAndReweightEnergiesCalculatorCAP
(in
rosetta.protocols.toolbox.pose_metric_calculators._protocols_toolbox_pose_metric_calculators_
)
deserialize()
(in
WorkUnit_LoopHash
)
DockingHighResFilter
(in
rosetta.protocols.docking._protocols_docking_
)
decoy_tag()
(in
RawStruct
)
deserialize()
(in
WorkUnit_CombinePose
)
DockingHighResFilterAP
(in
rosetta.protocols.docking._protocols_docking_
)
decoy_tag()
(in
SilentStruct
)
deserialize()
(in
WorkUnit_FragInsert
)
DockingHighResFilterCAP
(in
rosetta.protocols.docking._protocols_docking_
)
DecoyFileData
(in
rosetta.core.io.raw_data._core_io_raw_data_
)
deserialize()
(in
WorkUnit_KicCloser
)
DockingHighResLegacy
(in
rosetta.protocols.docking._protocols_docking_
)
DecoyFileDataAP
(in
rosetta.core.io.raw_data._core_io_raw_data_
)
deserialize()
(in
WorkUnit_LoopHash
)
DockingHighResLegacyAP
(in
rosetta.protocols.docking._protocols_docking_
)
DecoyFileDataCAP
(in
rosetta.core.io.raw_data._core_io_raw_data_
)
deserialize()
(in
WorkUnit_MD
)
DockingHighResLegacyCAP
(in
rosetta.protocols.docking._protocols_docking_
)
decoys()
(in
ArchiveBase
)
deserialize()
(in
WorkUnit_NormalMode
)
DockingInitialPerturbation
(in
rosetta.protocols.docking._protocols_docking_
)
decoys()
(in
WorkUnit_SilentStructStore
)
deserialize()
(in
WorkUnit_PartialAbinitio
)
DockingInitialPerturbationAP
(in
rosetta.protocols.docking._protocols_docking_
)
decoys_returned()
(in
Batch
)
deserialize()
(in
WorkUnit_RamaPerturber
)
DockingInitialPerturbationCAP
(in
rosetta.protocols.docking._protocols_docking_
)
DecoySetEvaluation
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
deserialize()
(in
WorkUnit_Relax
)
DockingInitialPerturbationCreator
(in
rosetta.protocols.docking._protocols_docking_
)
DecoySetEvaluationAP
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
deserialize()
(in
WorkUnit_Sampler
)
DockingInitialPerturbationCreatorAP
(in
rosetta.protocols.docking._protocols_docking_
)
DecoySetEvaluationCAP
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
deserialize()
(in
WorkUnit_bbGauss
)
DockingInitialPerturbationCreatorCAP
(in
rosetta.protocols.docking._protocols_docking_
)
DecoyStruct
(in
rosetta.core.io.raw_data._core_io_raw_data_
)
deserialize()
(in
WorkUnit_BatchRelax
)
DockingLowRes
(in
rosetta.protocols.docking._protocols_docking_
)
DecoyStructAP
(in
rosetta.core.io.raw_data._core_io_raw_data_
)
deserialize()
(in
WorkUnit_BatchRelax_and_PostRescore
)
DockingLowResAP
(in
rosetta.protocols.docking._protocols_docking_
)
DecoyStructCAP
(in
rosetta.core.io.raw_data._core_io_raw_data_
)
deserialize()
(in
WorkUnit_MoverWrapper
)
DockingLowResCAP
(in
rosetta.protocols.docking._protocols_docking_
)
decrease_double_lazy_ig_memlimit()
(in
PackerTask
)
deserialize()
(in
WorkUnit_SilentStructStore
)
DockingLowResEnsemble
(in
rosetta.protocols.docking._protocols_docking_
)
decrease_double_lazy_ig_memlimit()
(in
PackerTask_
)
deserialize_data()
(in
DbMoverMessageListener
)
DockingLowResEnsembleAP
(in
rosetta.protocols.docking._protocols_docking_
)
decrease_linmem_ig_history_size()
(in
PackerTask
)
deserialize_db_listener_data()
(in
rosetta.protocols.features._protocols_features_
)
DockingLowResEnsembleCAP
(in
rosetta.protocols.docking._protocols_docking_
)
decrease_linmem_ig_history_size()
(in
PackerTask_
)
deserialize_xyz_coords()
(in
rosetta.protocols.features._protocols_features_
)
DockingLowResFilter
(in
rosetta.protocols.docking._protocols_docking_
)
decreasing()
(in
Loop
)
design
(in
rosetta.protocols.antibody
)
DockingLowResFilterAP
(in
rosetta.protocols.docking._protocols_docking_
)
decrement_from_cached()
(in
RotamerDots
)
DESIGN
(in
LayerDesignOperation
)
DockingLowResFilterCAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_allow_bondangles()
(in
MakeBundle
)
DESIGN
(in
LayerOperationType
)
DockingNoRepack1
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
default_allow_bondangles_set()
(in
MakeBundle
)
design()
(in
CDRGraftDesignOptions
)
DockingNoRepack1AP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
default_allow_bondlengths()
(in
MakeBundle
)
design()
(in
CDRSeqDesignOptions
)
DockingNoRepack1CAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
default_allow_bondlengths_set()
(in
MakeBundle
)
design()
(in
DockingHighResLegacy
)
DockingNoRepack2
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
default_allow_dihedrals()
(in
MakeBundle
)
design()
(in
PlaceSimultaneouslyMover
)
DockingNoRepack2AP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
default_allow_dihedrals_set()
(in
MakeBundle
)
design()
(in
DesignRepackMover
)
DockingNoRepack2CAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
default_commands()
(in
ResfileContents
)
design()
(in
SymDockProtocol
)
DockingPrepackProtocol
(in
rosetta.protocols.docking._protocols_docking_
)
default_crick_params_file()
(in
MakeBundle
)
design()
(in
SymDockingHiRes
)
DockingPrepackProtocolAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_crick_params_file_set()
(in
MakeBundle
)
design_all_aas()
(in
ProteinInterfaceDesignOperation
)
DockingPrepackProtocolCAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_delta_omega0()
(in
BundleGridSampler
)
design_antigen()
(in
AntibodySeqDesignTFCreator
)
DockingProtocol
(in
rosetta.protocols.docking._protocols_docking_
)
default_delta_omega0()
(in
MakeBundle
)
design_any()
(in
PackerTask
)
DockingProtocolAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_delta_omega0()
(in
PerturbBundle
)
design_any()
(in
PackerTask_
)
DockingProtocolCAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_delta_omega0_set()
(in
MakeBundle
)
design_chain1()
(in
ProteinInterfaceDesignOperation
)
DockingProtocolCreator
(in
rosetta.protocols.docking._protocols_docking_
)
default_delta_omega1()
(in
BundleGridSampler
)
design_chain2()
(in
ProteinInterfaceDesignOperation
)
DockingProtocolCreatorAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_delta_omega1()
(in
PerturbBundle
)
design_framework()
(in
AntibodySeqDesignTFCreator
)
DockingProtocolCreatorCAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_delta_omega1_all()
(in
MakeBundle
)
design_layer()
(in
LayerDesignOperation
)
DockingScoreFunction
(in
rosetta.core.scoring._core_scoring_
)
default_delta_omega1_all_set()
(in
MakeBundle
)
design_loop()
(in
RestrictToLoops
)
DockingScoreFunctionAP
(in
rosetta.core.scoring._core_scoring_
)
default_delta_t()
(in
BundleGridSampler
)
design_mover()
(in
MSDMover
)
DockingScoreFunctionCAP
(in
rosetta.core.scoring._core_scoring_
)
default_delta_t()
(in
MakeBundle
)
design_neighbors()
(in
RestrictToLoopsAndNeighbors
)
DockingSlideIntoContact
(in
rosetta.protocols.docking._protocols_docking_
)
default_delta_t()
(in
PerturbBundle
)
design_only_target_residues()
(in
RestrictIdentitiesAtAlignedPositionsOperation
)
DockingSlideIntoContactAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_delta_t_set()
(in
MakeBundle
)
design_opt
(in
rosetta.protocols
)
DockingSlideIntoContactCAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_filename()
(in
ReadResfile
)
design_proline()
(in
AntibodySeqDesignTFCreator
)
DockMCMCycle
(in
rosetta.protocols.docking._protocols_docking_
)
default_helix_length()
(in
MakeBundle
)
design_protocol_to_enum()
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
DockMCMCycleAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_helix_length_set()
(in
MakeBundle
)
design_protocol_to_string()
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
DockMCMCycleCAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_invert()
(in
MakeBundle
)
design_residue()
(in
PackerTask
)
DockMCMProtocol
(in
rosetta.protocols.docking._protocols_docking_
)
default_invert_set()
(in
MakeBundle
)
design_residue()
(in
PackerTask_
)
DockMCMProtocolAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_jump_atom()
(in
rosetta.core.chemical.rna._core_chemical_rna_
)
design_residues_list()
(in
rosetta.protocols.dna._protocols_dna_
)
DockMCMProtocolCAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_master()
(in
WriteUpstreamHitKinemage
)
design_shell()
(in
DesignAroundOperation
)
DockMinMover
(in
rosetta.protocols.docking._protocols_docking_
)
default_omega0()
(in
BundleGridSampler
)
design_strategy()
(in
CDRSeqDesignOptions
)
DockMinMoverAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_omega0()
(in
MakeBundle
)
DESIGNABLE
(in
LayerDesignOperation
)
DockMinMoverCAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_omega0()
(in
PerturbBundle
)
DESIGNABLE
(in
LayerSpecificationType
)
dockPoseIntoMap()
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
default_omega0_set()
(in
MakeBundle
)
designable()
(in
DesignableResiduesFilter
)
DockSetupMover
(in
rosetta.protocols.docking._protocols_docking_
)
default_omega1()
(in
MakeBundle
)
designable()
(in
DatabaseThread
)
DockSetupMoverAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_omega1_set()
(in
MakeBundle
)
designable_only()
(in
SaveResfileToDiskFilter
)
DockSetupMoverCAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_options()
(in
DatabaseSessionLoader
)
designable_only()
(in
TaskAwareSASAFilter
)
DockSetupMoverCreator
(in
rosetta.protocols.docking._protocols_docking_
)
default_options()
(in
ResourceLoader
)
DesignableResiduesFilter
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
DockSetupMoverCreatorAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_options()
(in
ResidueLoader
)
DesignableResiduesFilterAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
DockSetupMoverCreatorCAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_options()
(in
SymmDataLoader
)
DesignableResiduesFilterCAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
DockTaskFactory
(in
rosetta.protocols.docking._protocols_docking_
)
default_options()
(in
PoseFromPDBLoader
)
DesignableResiduesFilterCreator
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
DockTaskFactoryAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_options()
(in
SilentFileLoader
)
DesignableResiduesFilterCreatorAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
DockTaskFactoryCAP
(in
rosetta.protocols.docking._protocols_docking_
)
default_options()
(in
ElectronDensityLoader
)
DesignableResiduesFilterCreatorCAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
DockWithHotspotMover
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
default_options()
(in
FiberDiffractionLoader
)
DesignAroundOperation
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
DockWithHotspotMoverAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
default_options()
(in
LoopHashLibraryLoader
)
DesignAroundOperationAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
DockWithHotspotMoverCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
default_options()
(in
LoopsFileLoader
)
DesignAroundOperationCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
DockWithHotspotMoverCreator
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
default_options()
(in
LipoFileLoader
)
DesignAroundOperationCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
DockWithHotspotMoverCreatorAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
default_options()
(in
SpanFileLoader
)
DesignAroundOperationCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
DockWithHotspotMoverCreatorCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
default_options()
(in
SurfaceVectorLoader
)
DesignAroundOperationCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
DOES_NOT_CONTROL
(in
rosetta.protocols.environment.claims
)
default_r0()
(in
BundleGridSampler
)
DesignContrast
(in
rosetta.core.io.sequence_comparation._core_io_sequence_comparation_
)
DOES_NOT_CONTROL
(in
ClaimStrength
)
default_r0()
(in
MakeBundle
)
DesignContrastAP
(in
rosetta.core.io.sequence_comparation._core_io_sequence_comparation_
)
DOES_NOT_CONTROL
(in
PrioSubtype
)
default_r0()
(in
PerturbBundle
)
DesignContrastCAP
(in
rosetta.core.io.sequence_comparation._core_io_sequence_comparation_
)
DOES_NOT_CONTROL
(in
ControlStrength
)
default_r0_set()
(in
MakeBundle
)
designed_residue()
(in
PDBOutput
)
DOES_NOT_CONTROL
(in
rosetta.protocols.environment.claims._protocols_environment_claims_
)
default_residue_name()
(in
MakeBundle
)
designing_residues()
(in
PackerTask
)
does_overlap()
(in
Circle
)
default_residue_name_set()
(in
MakeBundle
)
designing_residues()
(in
PackerTask_
)
dof()
(in
Conformation
)
default_value()
(in
AtomID_Map_T_bool_T
)
DesignMinimizeHbonds
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
dof()
(in
AtomTree
)
default_value()
(in
AtomID_Map_T_core_id_AtomID_T
)
DesignMinimizeHbondsAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
dof()
(in
Atom
)
default_value()
(in
AtomID_Map_T_double_T
)
DesignMinimizeHbondsCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
dof()
(in
BondedAtom
)
default_value()
(in
AtomID_Map_T_numeric_xyzVector_T_double_T__T
)
DesignMinimizeHbondsCreator
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
dof()
(in
JumpAtom
)
default_value()
(in
NamedAtomID_Map_T_core_id_NamedAtomID_T
)
DesignMinimizeHbondsCreatorAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
dof()
(in
Pose
)
default_value()
(in
PerturbBundleOptions
)
DesignMinimizeHbondsCreatorCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
dof()
(in
RigidBodyDofPerturbMover
)
default_z0_offset()
(in
BundleGridSampler
)
DesignProteinBackboneAroundDNA
(in
rosetta.protocols.dna._protocols_dna_
)
dof_access()
(in
DofPassport
)
default_z0_offset()
(in
MakeBundle
)
DesignProteinBackboneAroundDNAAP
(in
rosetta.protocols.dna._protocols_dna_
)
DOF_bin_size()
(in
rosetta.protocols.stepwise.modeler.rna.rigid_body._protocols_stepwise_modeler_rna_rigid_body_
)
default_z0_offset()
(in
PerturbBundle
)
DesignProteinBackboneAroundDNACAP
(in
rosetta.protocols.dna._protocols_dna_
)
DOF_bin_value()
(in
rosetta.protocols.stepwise.modeler.rna.rigid_body._protocols_stepwise_modeler_rna_rigid_body_
)
default_z0_offset_set()
(in
MakeBundle
)
DesignProteinBackboneAroundDNACreator
(in
rosetta.protocols.dna._protocols_dna_
)
dof_constraint
(in
ScoreType
)
default_z1()
(in
MakeBundle
)
DesignProteinBackboneAroundDNACreatorAP
(in
rosetta.protocols.dna._protocols_dna_
)
dof_constraint
(in
rosetta.core.scoring._core_scoring_
)
default_z1_offset()
(in
BundleGridSampler
)
DesignProteinBackboneAroundDNACreatorCAP
(in
rosetta.protocols.dna._protocols_dna_
)
DOF_Constraint
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
default_z1_offset()
(in
MakeBundle
)
DesignProtocolEnum_total
(in
rosetta.protocols.antibody.design
)
dof_constraint
(in
rosetta.core.scoring
)
default_z1_offset()
(in
PerturbBundle
)
DesignProtocolEnum_total
(in
AntibodyDesignProtocolEnum
)
dof_constraint
(in
rosetta
)
default_z1_offset_set()
(in
MakeBundle
)
DesignProtocolEnum_total
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
DOF_ConstraintAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
default_z1_set()
(in
MakeBundle
)
DesignRepackMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
DOF_ConstraintCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
DefaultCubeHash
(in
rosetta.core.conformation._core_conformation_
)
DesignRepackMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
DOF_DataPoint
(in
rosetta.core.optimization._core_optimization_
)
DefaultCubeHashAP
(in
rosetta.core.conformation._core_conformation_
)
DesignRepackMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
DOF_DataPointAP
(in
rosetta.core.optimization._core_optimization_
)
DefaultCubeHashCAP
(in
rosetta.core.conformation._core_conformation_
)
DesignTask
(in
rosetta.protocols.flxbb._protocols_flxbb_
)
DOF_DataPointCAP
(in
rosetta.core.optimization._core_optimization_
)
define_active_site_from_gridlig_file()
(in
MatcherTask
)
DesignTask_Layer
(in
rosetta.protocols.flxbb._protocols_flxbb_
)
dof_deriv_1benmeths_begin()
(in
MinimizationNode
)
define_active_site_from_residue_radii_list()
(in
MatcherTask
)
DesignTask_LayerAP
(in
rosetta.protocols.flxbb._protocols_flxbb_
)
dof_deriv_1benmeths_end()
(in
MinimizationNode
)
define_chains()
(in
rosetta.protocols.stepwise.setup._protocols_stepwise_setup_
)
DesignTask_LayerCAP
(in
rosetta.protocols.flxbb._protocols_flxbb_
)
dof_deriv_2benmeths_begin()
(in
MinimizationNode
)
define_loops()
(in
DockingHighResLegacy
)
DesignTask_Normal
(in
rosetta.protocols.flxbb._protocols_flxbb_
)
dof_deriv_2benmeths_end()
(in
MinimizationNode
)
define_mainchain_atoms()
(in
rosetta.core.chemical._core_chemical_
)
DesignTask_NormalAP
(in
rosetta.protocols.flxbb._protocols_flxbb_
)
DoF_helix_index()
(in
BundleGridSamplerHelper
)
define_match_by_single_downstream_positioning()
(in
MatcherTask
)
DesignTask_NormalCAP
(in
rosetta.protocols.flxbb._protocols_flxbb_
)
DOF_ID
(in
rosetta.core.id._core_id_
)
define_scorable_core_from_secondary_structure()
(in
rosetta.protocols.loops._protocols_loops_
)
DesignTaskAP
(in
rosetta.protocols.flxbb._protocols_flxbb_
)
dof_id()
(in
DOF_ID_Range
)
define_start_window()
(in
ClassicFragmentMover
)
DesignTaskCAP
(in
rosetta.protocols.flxbb._protocols_flxbb_
)
dof_id()
(in
DOF_DataPoint
)
defined()
(in
MembraneJump
)
desired_entity_history_size()
(in
TopEntitySet
)
dof_id()
(in
DOF_Node
)
defined_adducts()
(in
ResidueType
)
desired_remodelres_in_vicinity()
(in
ResidueVicinityInfo
)
dof_id()
(in
DOF_Constraint
)
defined_positions()
(in
Bridge
)
desired_result()
(in
ResidueSelectorSingle
)
dof_id_begin()
(in
MoveMap
)
defined_positions()
(in
BuildInstruction
)
destination_size()
(in
subset_mapping
)
dof_id_end()
(in
MoveMap
)
defined_positions()
(in
BuildManager
)
DestructionEvent
(in
rosetta.core.pose.signals._core_pose_signals_
)
dof_id_from_torsion_id()
(in
Conformation
)
defined_positions()
(in
ConnectRight
)
DestructionEventAP
(in
rosetta.core.pose.signals._core_pose_signals_
)
DOF_ID_Range
(in
rosetta.core.id._core_id_
)
defined_positions()
(in
GrowLeft
)
DestructionEventCAP
(in
rosetta.core.pose.signals._core_pose_signals_
)
DOF_ID_RangeAP
(in
rosetta.core.id._core_id_
)
defined_positions()
(in
GrowRight
)
desymmeterize()
(in
DunbrackSCSampler
)
DOF_ID_RangeCAP
(in
rosetta.core.id._core_id_
)
defined_positions()
(in
SegmentRebuild
)
desymmeterize_upstream_restype_for_constraint()
(in
Matcher
)
dof_id_ranges()
(in
BackrubMover
)
defined_positions()
(in
SegmentSwap
)
det
(in
xyzMatrix_Real
)
dof_id_ranges()
(in
BackrubSidechainMover
)
defineEnergyMethodCreator()
(in
rosetta
)
det
(in
xyzMatrix_SSize
)
dof_id_ranges()
(in
ThermodynamicMover
)
DefineMovableLoops
(in
rosetta.protocols.seeded_abinitio._protocols_seeded_abinitio_
)
det
(in
xyzMatrix_Size
)
dof_id_ranges()
(in
BalancedKicMover
)
DefineMovableLoopsAP
(in
rosetta.protocols.seeded_abinitio._protocols_seeded_abinitio_
)
det
(in
xyzMatrix_double
)
dof_id_ranges()
(in
RigidBodyDeterministicSpinMover
)
DefineMovableLoopsCAP
(in
rosetta.protocols.seeded_abinitio._protocols_seeded_abinitio_
)
det
(in
xyzMatrix_float
)
dof_id_ranges()
(in
RigidBodyDofPerturbMover
)
DefineMovableLoopsCreator
(in
rosetta.protocols.seeded_abinitio._protocols_seeded_abinitio_
)
det()
(in
xyzMatrix_T_float_T
)
dof_id_ranges()
(in
RigidBodyDofRandomTransMover
)
DefineMovableLoopsCreatorAP
(in
rosetta.protocols.seeded_abinitio._protocols_seeded_abinitio_
)
det3()
(in
rosetta.numeric.model_quality._numeric_model_quality_
)
dof_id_ranges()
(in
RigidBodyDofRandomizeMover
)
DefineMovableLoopsCreatorCAP
(in
rosetta.protocols.seeded_abinitio._protocols_seeded_abinitio_
)
detach()
(in
ObserverCache
)
dof_id_ranges()
(in
RigidBodyDofSeqPerturbMover
)
defines_dof_derivatives()
(in
DunbrackEnergy
)
detach()
(in
PyMolObserver
)
dof_id_ranges()
(in
RigidBodyDofSeqRandomizeMover
)
defines_dof_derivatives()
(in
CenRotDunEnergy
)
detach_after_modify()
(in
BuildInstruction
)
dof_id_ranges()
(in
RigidBodyDofSeqTransMover
)
defines_dof_derivatives()
(in
HPatchEnergy
)
detach_from()
(in
PDBInfo
)
dof_id_ranges()
(in
RigidBodyDofTransMover
)
defines_dof_derivatives()
(in
SurfaceEnergy
)
detach_from()
(in
CacheableObserver
)
dof_id_ranges()
(in
RigidBodyMover
)
defines_dof_derivatives()
(in
DNAChiEnergy
)
detach_from()
(in
PoseMetricContainer
)
dof_id_ranges()
(in
RigidBodyPerturbMover
)
defines_dof_derivatives()
(in
ExactOccludedHbondSolEnergy
)
detach_from()
(in
BuildInstruction
)
dof_id_ranges()
(in
RigidBodyPerturbNoCenterMover
)
defines_dof_derivatives()
(in
OccludedHbondSolEnergy_onebody
)
detach_from_conformation()
(in
ConstraintSet
)
dof_id_ranges()
(in
RigidBodyPerturbRandomJumpMover
)
defines_dof_derivatives()
(in
FaMPEnvEnergy
)
detailed_balance()
(in
CanonicalSamplingMover
)
dof_id_ranges()
(in
RigidBodyRandomizeMover
)
defines_dof_derivatives()
(in
FaMPEnvSmoothEnergy
)
detailed_search()
(in
TMalign
)
dof_id_ranges()
(in
RigidBodySpinMover
)
defines_dof_derivatives()
(in
MPCbetaEnergy
)
detect_base_contacts()
(in
rosetta.protocols.stepwise.modeler.rna.bulge._protocols_stepwise_modeler_rna_bulge_
)
dof_id_ranges()
(in
RigidBodyTransMover
)
defines_dof_derivatives()
(in
MPEnvEnergy
)
detect_bonds()
(in
Conformation
)
dof_id_ranges()
(in
UniformRigidBodyMover
)
defines_dof_derivatives()
(in
MPNonHelixPenalty
)
detect_bonds()
(in
DeleteChainsMover
)
dof_id_ranges()
(in
UniformSphereTransMover
)
defines_dof_derivatives()
(in
MPTerminiPenalty
)
detect_disulfides()
(in
Conformation
)
dof_id_ranges()
(in
BBConRotMover
)
defines_dof_derivatives()
(in
BurialEnergy
)
detect_disulfides()
(in
SymmetricConformation
)
dof_id_ranges()
(in
BBG8T3AMover
)
defines_dof_derivatives()
(in
CenRotEnvEnergy
)
detect_disulfides()
(in
ProtectedConformation
)
dof_id_ranges()
(in
BBGaussianMover
)
defines_dof_derivatives()
(in
ContextDependentOneBodyEnergy
)
detect_phosphate_contacts()
(in
rosetta.protocols.stepwise.modeler.rna.phosphate._protocols_stepwise_modeler_rna_phosphate_
)
dof_id_ranges()
(in
BackboneMover
)
defines_dof_derivatives()
(in
ContextIndependentOneBodyEnergy
)
detect_pseudobonds()
(in
Conformation
)
dof_id_ranges()
(in
ShearMover
)
defines_dof_derivatives()
(in
EnvEnergy
)
detect_pseudobonds()
(in
DeleteChainsMover
)
dof_id_ranges()
(in
SmallMover
)
defines_dof_derivatives()
(in
EnvSmoothEnergy
)
detect_sugar_contacts()
(in
rosetta.protocols.stepwise.modeler.rna.sugar._protocols_stepwise_modeler_rna_sugar_
)
dof_id_ranges()
(in
JumpRotamerSidechainMover
)
defines_dof_derivatives()
(in
Fa_MbenvEnergy
)
DetectSymmetry
(in
rosetta.protocols.simple_moves.symmetry._protocols_simple_moves_symmetry_
)
dof_id_ranges()
(in
PerturbChiSidechainMover
)
defines_dof_derivatives()
(in
FreeDOF_Energy
)
DetectSymmetryAP
(in
rosetta.protocols.simple_moves.symmetry._protocols_simple_moves_symmetry_
)
dof_id_ranges()
(in
PerturbRotamerSidechainMover
)
defines_dof_derivatives()
(in
MembraneCbetaEnergy
)
DetectSymmetryCAP
(in
rosetta.protocols.simple_moves.symmetry._protocols_simple_moves_symmetry_
)
dof_id_ranges()
(in
SidechainMCMover
)
defines_dof_derivatives()
(in
MembraneEnvEnergy
)
DetectSymmetryMoverCreator
(in
rosetta.protocols.simple_moves.symmetry._protocols_simple_moves_symmetry_
)
dof_id_ranges()
(in
SidechainMover
)
defines_dof_derivatives()
(in
MembraneEnvSmoothEnergy
)
DetectSymmetryMoverCreatorAP
(in
rosetta.protocols.simple_moves.symmetry._protocols_simple_moves_symmetry_
)
dof_id_ranges()
(in
SidechainMoverBase
)
defines_dof_derivatives()
(in
NMerPSSMEnergy
)
DetectSymmetryMoverCreatorCAP
(in
rosetta.protocols.simple_moves.symmetry._protocols_simple_moves_symmetry_
)
DOF_IDAP
(in
rosetta.core.id._core_id_
)
defines_dof_derivatives()
(in
NMerRefEnergy
)
determine_atom_inds_for_restype()
(in
EnzCstTemplateRes
)
DOF_IDCAP
(in
rosetta.core.id._core_id_
)
defines_dof_derivatives()
(in
NMerSVMEnergy
)
determine_core_heading_surface_heading_by_distance()
(in
rosetta.protocols.features.strand_assembly._protocols_features_strand_assembly_
)
dof_is_independent()
(in
SymmetryInfo
)
defines_dof_derivatives()
(in
OmegaTetherEnergy
)
determine_cyclization_viability()
(in
DisulfideInsertionMover
)
DoF_name()
(in
BundleGridSamplerHelper
)
defines_dof_derivatives()
(in
OneBodyEnergy
)
determine_dna_interface()
(in
DnaInterfaceFinder
)
DOF_Node
(in
rosetta.core.optimization._core_optimization_
)
defines_dof_derivatives()
(in
P_AA_Energy
)
determine_heading_direction_by_vector()
(in
rosetta.protocols.features.strand_assembly._protocols_features_strand_assembly_
)
dof_node_from_id()
(in
MinimizerMap
)
defines_dof_derivatives()
(in
P_AA_pp_Energy
)
determine_interface()
(in
DnaInterfaceFinder
)
dof_node_from_id()
(in
SymMinimizerMap
)
defines_dof_derivatives()
(in
RamachandranEnergy
)
determine_largest_nbr_atom_distance()
(in
RigidBodyMoveBaseRSO
)
DOF_NodeAP
(in
rosetta.core.optimization._core_optimization_
)
defines_dof_derivatives()
(in
ReferenceEnergy
)
determine_loop()
(in
SlidingWindowLoopClosure
)
DOF_NodeCAP
(in
rosetta.core.optimization._core_optimization_
)
defines_dof_derivatives()
(in
ReferenceEnergyNoncanonical
)
determine_protein_interface()
(in
DnaInterfaceFinder
)
dof_nodes()
(in
MinimizerMap
)
defines_dof_derivatives()
(in
SequenceDependentRefEnergy
)
determine_ramachandran_hash()
(in
BetaTurnDetection
)
dof_nodes()
(in
SymMinimizerMap
)
defines_dof_derivatives()
(in
SmoothEnvEnergy
)
determine_ramachandran_hash_for_residue_with_dihedrals()
(in
BetaTurnDetection
)
DoF_sample_value()
(in
BundleGridSamplerHelper
)
defines_dof_derivatives()
(in
SymmetricLigandEnergy
)
determine_redundant_conformer_groups()
(in
LigandConformerBuilder
)
dof_step_data()
(in
NumDerivCheckData
)
defines_dof_derivatives()
(in
UnfoldedStateEnergy
)
determine_redundant_upstream_matchres()
(in
OutputWriter
)
dof_type
(in
rosetta.core.conformation.symmetry._core_conformation_symmetry_
)
defines_dof_derivatives()
(in
WaterAdductIntraEnergy
)
determine_res_cb_deviation()
(in
FlexbbRotamerSets
)
DOF_Type
(in
rosetta.core.id._core_id_
)
defines_dof_derivatives()
(in
YHHPlanarityEnergy
)
determine_residue_connection()
(in
CountPairFactory
)
DoF_type()
(in
BundleGridSamplerHelper
)
defines_dof_derivatives()
(in
pHEnergy
)
determine_score_variations()
(in
NormalizedEvaluatedArchive
)
dof_type_begin()
(in
MoveMap
)
defines_dof_derivatives()
(in
SugarBackboneEnergy
)
deterministic_graft
(in
AntibodyDesignProtocolEnum
)
dof_type_end()
(in
MoveMap
)
defines_dof_derivatives()
(in
NVscore
)
deterministic_graft
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
DOF_type_is_rb()
(in
rosetta.core.id._core_id_
)
defines_dof_derivatives()
(in
RNA_BulgeEnergy
)
deterministic_graft
(in
rosetta.protocols.antibody.design
)
dof_val()
(in
DOF_DataPoint
)
defines_dof_derivatives()
(in
RNA_FullAtomVDW_BasePhosphate
)
deviation()
(in
CCDLoopClosureMover
)
dof_val()
(in
DerivCheckDataPoint
)
defines_dof_derivatives()
(in
RNA_SugarCloseEnergy
)
dexponential()
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
DofClaim
(in
rosetta.protocols.topology_broker.claims._protocols_topology_broker_claims_
)
defines_dof_derivatives()
(in
AACompositionEnergy
)
dF()
(in
CubicSpline
)
DofClaimAP
(in
rosetta.protocols.topology_broker.claims._protocols_topology_broker_claims_
)
defines_dof_derivatives()
(in
InterchainEnvEnergy
)
dFdall()
(in
PolycubicSpline
)
DofClaimCAP
(in
rosetta.protocols.topology_broker.claims._protocols_topology_broker_claims_
)
defines_dof_derivatives()
(in
SpecialRotamerEnergy
)
dFdx()
(in
BicubicSpline
)
DOFElement
(in
rosetta.protocols.environment.claims._protocols_environment_claims_
)
defines_high_order_terms()
(in
DunbrackEnergy
)
dFdx()
(in
TricubicSpline
)
DOFElementAP
(in
rosetta.protocols.environment.claims._protocols_environment_claims_
)
defines_high_order_terms()
(in
CenRotDunEnergy
)
dFdxi()
(in
PolycubicSpline
)
DOFElementCAP
(in
rosetta.protocols.environment.claims._protocols_environment_claims_
)
defines_high_order_terms()
(in
HPatchEnergy
)
dFdy()
(in
BicubicSpline
)
DOFHistogramRecorder
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
defines_high_order_terms()
(in
SurfaceEnergy
)
dFdy()
(in
TricubicSpline
)
DOFHistogramRecorderAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
defines_high_order_terms()
(in
CarbonHBondEnergy
)
dFdz()
(in
TricubicSpline
)
DOFHistogramRecorderCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
defines_high_order_terms()
(in
ConstraintsEnergy
)
DFIRE
(in
rosetta
)
dofmover_compresses()
(in
SymmetrySlider
)
defines_high_order_terms()
(in
XtalMLEnergy
)
DFIRE
(in
rosetta.core.scoring
)
DofPassport
(in
rosetta.core.environment._core_environment_
)
defines_high_order_terms()
(in
FullatomCustomPairDistanceEnergy
)
DFIRE
(in
rosetta.core.scoring._core_scoring_
)
DofPassportAP
(in
rosetta.core.environment._core_environment_
)
defines_high_order_terms()
(in
CentroidDisulfideEnergy
)
DFIRE
(in
ScoreType
)
DofPassportCAP
(in
rosetta.core.environment._core_environment_
)
defines_high_order_terms()
(in
DisulfideMatchingEnergy
)
DFIRE
(in
rosetta.core.scoring.methods
)
dofs()
(in
RigidBodyDofSeqPerturbMover
)
defines_high_order_terms()
(in
FullatomDisulfideEnergy
)
DFIRE
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
dofs()
(in
DOFHistogramRecorder
)
defines_high_order_terms()
(in
DNAChiEnergy
)
DFIRE
(in
LongRangeEnergyType
)
dofs_to_vars()
(in
NormalModeMultifunc
)
defines_high_order_terms()
(in
DNATorsionEnergy
)
dfire
(in
rosetta.core.scoring.methods
)
DoFType
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
defines_high_order_terms()
(in
FA_ElecEnergy
)
DFIRE_Energy
(in
rosetta.core.scoring.methods.dfire._core_scoring_methods_dfire_
)
dofType
(in
rosetta.protocols.jumping._protocols_jumping_
)
defines_high_order_terms()
(in
FA_ElecEnergyAroAll
)
DFIRE_EnergyAP
(in
rosetta.core.scoring.methods.dfire._core_scoring_methods_dfire_
)
DofUnlock
(in
rosetta.protocols.environment._protocols_environment_
)
defines_high_order_terms()
(in
FA_ElecEnergyAroAro
)
DFIRE_EnergyCAP
(in
rosetta.core.scoring.methods.dfire._core_scoring_methods_dfire_
)
DofUnlockAP
(in
rosetta.protocols.environment._protocols_environment_
)
defines_high_order_terms()
(in
FA_GrpElecEnergy
)
DFIRE_EnergyCreator
(in
rosetta.core.scoring.methods.dfire._core_scoring_methods_dfire_
)
DofUnlockCAP
(in
rosetta.protocols.environment._protocols_environment_
)
defines_high_order_terms()
(in
RNA_FA_ElecEnergy
)
DFIRE_EnergyCreatorAP
(in
rosetta.core.scoring.methods.dfire._core_scoring_methods_dfire_
)
domain_assembly
(in
rosetta.protocols
)
defines_high_order_terms()
(in
ElecDensAllAtomCenEnergy
)
DFIRE_EnergyCreatorCAP
(in
rosetta.core.scoring.methods.dfire._core_scoring_methods_dfire_
)
domain_map()
(in
MinimizerMapBase
)
defines_high_order_terms()
(in
ElecDensCenEnergy
)
DFIRE_Potential
(in
rosetta.core.scoring.methods.dfire._core_scoring_methods_dfire_
)
domain_map()
(in
CartesianMinimizerMap
)
defines_high_order_terms()
(in
ElecDensEnergy
)
DFIRE_PotentialAP
(in
rosetta.core.scoring.methods.dfire._core_scoring_methods_dfire_
)
domain_map()
(in
MinimizerMap
)
defines_high_order_terms()
(in
FastDensEnergy
)
DFIRE_PotentialCAP
(in
rosetta.core.scoring.methods.dfire._core_scoring_methods_dfire_
)
domain_map()
(in
SymMinimizerMap
)
defines_high_order_terms()
(in
PattersonCorrEnergy
)
dfour1_plan()
(in
rosetta.core.scoring.fiber_diffraction._core_scoring_fiber_diffraction_
)
domain_map()
(in
Energies
)
defines_high_order_terms()
(in
ElecDensAtomwiseEnergy
)
DFPMinConvergedAbsolute
(in
rosetta.core.optimization._core_optimization_
)
domain_map()
(in
NeighborList
)
defines_high_order_terms()
(in
AnalyticEtableEnergy
)
DFPMinConvergedAbsoluteAP
(in
rosetta.core.optimization._core_optimization_
)
domain_parse_templates()
(in
HybridizeProtocol
)
defines_high_order_terms()
(in
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T
)
DFPMinConvergedAbsoluteCAP
(in
rosetta.core.optimization._core_optimization_
)
DomainAssembly
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
defines_high_order_terms()
(in
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T
)
DFPMinConvergedFractional
(in
rosetta.core.optimization._core_optimization_
)
DomainAssembly
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
defines_high_order_terms()
(in
TableLookupEtableEnergy
)
DFPMinConvergedFractionalAP
(in
rosetta.core.optimization._core_optimization_
)
DomainAssemblyAP
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
defines_high_order_terms()
(in
FiberDiffractionEnergy
)
DFPMinConvergedFractionalCAP
(in
rosetta.core.optimization._core_optimization_
)
DomainAssemblyAP
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
defines_high_order_terms()
(in
FiberDiffractionEnergyDens
)
DFr
(in
rosetta.protocols.fldsgn.topology
)
DomainAssemblyCAP
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
defines_high_order_terms()
(in
ContextDependentGeometricSolEnergy
)
DFr
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
DomainAssemblyCAP
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
defines_high_order_terms()
(in
ContextIndependentGeometricSolEnergy
)
DFr
(in
SheetFoldType
)
DomainAssemblyCreator
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
defines_high_order_terms()
(in
ExactOccludedHbondSolEnergy
)
DFr_BAB
(in
rosetta.protocols.fldsgn.topology
)
DomainAssemblyCreatorAP
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
defines_high_order_terms()
(in
OccludedHbondSolEnergy
)
DFr_BAB
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
DomainAssemblyCreatorCAP
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
defines_high_order_terms()
(in
OccludedHbondSolEnergy_onebody
)
DFr_BAB
(in
SheetFoldType
)
DomainInterfaceFilter
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
defines_high_order_terms()
(in
HackAroEnergy
)
DFr_HPN
(in
rosetta.protocols.fldsgn.topology
)
DomainInterfaceFilterAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
defines_high_order_terms()
(in
HBondEnergy
)
DFr_HPN
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
DomainInterfaceFilterCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
defines_high_order_terms()
(in
DDPscore
)
DFr_HPN
(in
SheetFoldType
)
doMD()
(in
MolecularDynamics
)
defines_high_order_terms()
(in
LoopCloseEnergy
)
dfs()
(in
Atom
)
dominant()
(in
ResidueKinWriter
)
defines_high_order_terms()
(in
FaMPEnvEnergy
)
dfs()
(in
Atom_
)
dominant()
(in
ResidueKinemageWriter
)
defines_high_order_terms()
(in
FaMPEnvSmoothEnergy
)
dfs()
(in
BondedAtom
)
dominant()
(in
WriteUpstreamHitKinemage
)
defines_high_order_terms()
(in
FaMPSolvEnergy
)
dfs()
(in
JumpAtom
)
doMinimising()
(in
MolecularDynamics
)
defines_high_order_terms()
(in
MPCbetaEnergy
)
DFUNC
(in
rosetta.basic
)
don_bbg_in_bb_bb_hbond()
(in
HBondSet
)
defines_high_order_terms()
(in
MPEnvEnergy
)
DFUNC
(in
rosetta.basic._basic_
)
don_chem_type_from_name()
(in
HBondTypeManager
)
defines_high_order_terms()
(in
MPLipoEnergy
)
DFUNC
(in
ProfTag
)
don_dist_cutoff()
(in
WaterFeatures
)
defines_high_order_terms()
(in
MPNonHelixPenalty
)
dfunc()
(in
AtomTreeMultifunc
)
don_hatm()
(in
HBond
)
defines_high_order_terms()
(in
MPPairEnergy
)
dfunc()
(in
CartesianMultifunc
)
don_hatm_is_backbone()
(in
HBond
)
defines_high_order_terms()
(in
MPTMProjPenalty
)
dfunc()
(in
Multifunc
)
don_hatm_is_protein_backbone()
(in
HBond
)
defines_high_order_terms()
(in
MPTerminiPenalty
)
dfunc()
(in
SingleResidueMultifunc
)
don_res()
(in
HBond
)
defines_high_order_terms()
(in
BurialEnergy
)
dfunc()
(in
func_1d
)
don_res_is_dna()
(in
HBond
)
defines_high_order_terms()
(in
CartesianBondedEnergy
)
dfunc()
(in
SymAtomTreeMultifunc
)
don_res_is_protein()
(in
HBond
)
defines_high_order_terms()
(in
CenHBEnergy
)
dfunc()
(in
CenHBPotential
)
don_strength()
(in
HBondDatabase
)
defines_high_order_terms()
(in
CenPairEnergy
)
dfunc()
(in
SmoothScoreTermCoeffs
)
don_type()
(in
HBEvalTuple
)
defines_high_order_terms()
(in
CenRotEnvEnergy
)
dfunc()
(in
AngleConstraint
)
dont_be_lenient()
(in
FilteredSolutions
)
defines_high_order_terms()
(in
CenRotPairEnergy
)
dfunc()
(in
BoundFunc
)
dont_check_overlap()
(in
FilteredSolutions
)
defines_high_order_terms()
(in
ChainbreakEnergy
)
dfunc()
(in
DOF_Constraint
)
dont_check_rama()
(in
FilteredSolutions
)
defines_high_order_terms()
(in
ChemicalShiftAnisotropyEnergy
)
dfunc()
(in
OffsetPeriodicBoundFunc
)
dot()
(in
EMapVector
)
defines_high_order_terms()
(in
ContactOrderEnergy
)
dfunc()
(in
PeriodicBoundFunc
)
dot()
(in
EnergyEdge
)
defines_high_order_terms()
(in
ContextDependentLRTwoBodyEnergy
)
dfunc()
(in
DistanceFunc
)
dot()
(in
Quaternion_Real
)
defines_high_order_terms()
(in
ContextDependentOneBodyEnergy
)
dfunc()
(in
CBSG_Dihedral_Func
)
dot()
(in
Quaternion_double
)
defines_high_order_terms()
(in
ContextDependentTwoBodyEnergy
)
dfunc()
(in
CB_Angle_Func
)
dot()
(in
Quaternion_float
)
defines_high_order_terms()
(in
ContextIndependentLRTwoBodyEnergy
)
dfunc()
(in
CaCbCbCa_Dihedral_Func
)
dot()
(in
xyzTriple_Real
)
defines_high_order_terms()
(in
ContextIndependentOneBodyEnergy
)
dfunc()
(in
CaCbCb_Angle_Func
)
dot()
(in
xyzTriple_SSize
)
defines_high_order_terms()
(in
ContextIndependentTwoBodyEnergy
)
dfunc()
(in
Cb_Distance_Func
)
dot()
(in
xyzTriple_Size
)
defines_high_order_terms()
(in
CustomAtomPairEnergy
)
dfunc()
(in
Cen_Distance_Func
)
dot()
(in
xyzTriple_double
)
defines_high_order_terms()
(in
D2H_SA_Energy
)
dfunc()
(in
NCaCaC_Dihedral_Func
)
dot()
(in
xyzTriple_float
)
defines_high_order_terms()
(in
DNA_BaseEnergy
)
dfunc()
(in
SGSG_Dihedral_Func
)
dot()
(in
xyzVector_Real
)
defines_high_order_terms()
(in
DipolarCouplingEnergy
)
dfunc()
(in
SG_Dist_Func
)
dot()
(in
xyzVector_SSize
)
defines_high_order_terms()
(in
DirectReadoutEnergy
)
dfunc()
(in
AmberPeriodicFunc
)
dot()
(in
xyzVector_Size
)
defines_high_order_terms()
(in
DistanceChainbreakEnergy
)
dfunc()
(in
CharmmPeriodicFunc
)
dot()
(in
xyzVector_double
)
defines_high_order_terms()
(in
EnergyMethod
)
dfunc()
(in
CircularGeneral1D_Func
)
dot()
(in
xyzVector_float
)
defines_high_order_terms()
(in
EnvEnergy
)
dfunc()
(in
CircularHarmonicFunc
)
dot()
(in
rosetta.numeric.kinematic_closure._numeric_kinematic_closure_
)
defines_high_order_terms()
(in
EnvSmoothEnergy
)
dfunc()
(in
CircularPowerFunc
)
dot_coord()
(in
RotamerDots
)
defines_high_order_terms()
(in
Fa_MbenvEnergy
)
dfunc()
(in
CircularSigmoidalFunc
)
dot_exposed()
(in
InvRotamerDots
)
defines_high_order_terms()
(in
Fa_MbsolvEnergy
)
dfunc()
(in
CircularSplineFunc
)
dot_product()
(in
Quaternion_Real
)
defines_high_order_terms()
(in
FreeDOF_Energy
)
dfunc()
(in
ConstantFunc
)
dot_product()
(in
Quaternion_double
)
defines_high_order_terms()
(in
GaussianOverlapEnergy
)
dfunc()
(in
CountViolFunc
)
dot_product()
(in
Quaternion_float
)
defines_high_order_terms()
(in
GenBornEnergy
)
dfunc()
(in
EtableFunc
)
dot_product()
(in
xyzTriple_Real
)
defines_high_order_terms()
(in
GoapEnergy
)
dfunc()
(in
FadeFunc
)
dot_product()
(in
xyzTriple_SSize
)
defines_high_order_terms()
(in
HybridVDW_Energy
)
dfunc()
(in
FlatHarmonicFunc
)
dot_product()
(in
xyzTriple_Size
)
defines_high_order_terms()
(in
IntermolEnergy
)
dfunc()
(in
Func
)
dot_product()
(in
xyzTriple_double
)
defines_high_order_terms()
(in
LK_BallEnergy
)
dfunc()
(in
GaussianChainDoubleFunc
)
dot_product()
(in
xyzTriple_float
)
defines_high_order_terms()
(in
LK_PolarNonPolarEnergy
)
dfunc()
(in
GaussianChainFunc
)
dot_product()
(in
xyzVector_Real
)
defines_high_order_terms()
(in
LK_hack
)
dfunc()
(in
GaussianChainQuadrupleFunc
)
dot_product()
(in
xyzVector_SSize
)
defines_high_order_terms()
(in
LinearChainbreakEnergy
)
dfunc()
(in
GaussianChainSingleFunc
)
dot_product()
(in
xyzVector_Size
)
defines_high_order_terms()
(in
LongRangeTwoBodyEnergy
)
dfunc()
(in
GaussianChainTripleFunc
)
dot_product()
(in
xyzVector_double
)
defines_high_order_terms()
(in
MMBondAngleEnergy
)
dfunc()
(in
GaussianFunc
)
dot_product()
(in
xyzVector_float
)
defines_high_order_terms()
(in
MMBondLengthEnergy
)
dfunc()
(in
HarmonicFunc
)
DotSphere
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
MMLJEnergyInter
)
dfunc()
(in
IdentityFunc
)
DotSphereAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
MMLJEnergyIntra
)
dfunc()
(in
KarplusFunc
)
DotSphereCAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
MMTorsionEnergy
)
dfunc()
(in
LinearPenaltyFunction
)
double_lazy_ig()
(in
PackerTask
)
defines_high_order_terms()
(in
MembraneCbetaEnergy
)
dfunc()
(in
MinMultiHarmonicFunc
)
double_lazy_ig()
(in
PackerTask_
)
defines_high_order_terms()
(in
MembraneCenPairEnergy
)
dfunc()
(in
MixtureFunc
)
double_lazy_ig_memlimit()
(in
PackerTask
)
defines_high_order_terms()
(in
MembraneEnvEnergy
)
dfunc()
(in
PeriodicFunc
)
double_lazy_ig_memlimit()
(in
PackerTask_
)
defines_high_order_terms()
(in
MembraneEnvPenalties
)
dfunc()
(in
SOGFunc
)
double_msg()
(in
SimulateMPIMessage
)
defines_high_order_terms()
(in
MembraneEnvSmoothEnergy
)
dfunc()
(in
SOGFunc_Impl
)
DoubleBond
(in
rosetta
)
defines_high_order_terms()
(in
MembraneLipo
)
dfunc()
(in
ScalarWeightedFunc
)
DoubleBond
(in
rosetta.core.chemical
)
defines_high_order_terms()
(in
MissingEnergy
)
dfunc()
(in
SigmoidFunc
)
DoubleBond
(in
BondName
)
defines_high_order_terms()
(in
NMerPSSMEnergy
)
dfunc()
(in
SkipViolFunc
)
DoubleBond
(in
rosetta.core.chemical._core_chemical_
)
defines_high_order_terms()
(in
NMerRefEnergy
)
dfunc()
(in
SoedingFunc
)
DoubleBondOrder
(in
rosetta
)
defines_high_order_terms()
(in
NMerSVMEnergy
)
dfunc()
(in
SplineFunc
)
DoubleBondOrder
(in
rosetta.core.chemical
)
defines_high_order_terms()
(in
OmegaTetherEnergy
)
dfunc()
(in
SquareWell2Func
)
DoubleBondOrder
(in
BondOrder
)
defines_high_order_terms()
(in
OneBodyEnergy
)
dfunc()
(in
SquareWellFunc
)
DoubleBondOrder
(in
rosetta.core.chemical._core_chemical_
)
defines_high_order_terms()
(in
OtherPoseEnergy
)
dfunc()
(in
SumFunc
)
DoubleDenseIGRepacker
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
defines_high_order_terms()
(in
P_AA_Energy
)
dfunc()
(in
TopOutFunc
)
DoubleDenseIGRepackerAP
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
defines_high_order_terms()
(in
P_AA_pp_Energy
)
dfunc()
(in
USOGFunc
)
DoubleDenseIGRepackerCAP
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
defines_high_order_terms()
(in
PackStatEnergy
)
dfunc()
(in
BfactorMultifunc
)
DoubleDensePDEdge
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
PairEnergy
)
dfunc()
(in
FitSimpleHelixMultiFunc
)
DoubleDensePDEdgeAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
PeptideBondEnergy
)
dfunc()
(in
NormalModeMultifunc
)
DoubleDensePDEdgeCAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
PoissonBoltzmannEnergy
)
dfunc()
(in
OptEMultifunc
)
DoubleDensePDInteractionGraph
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
ProClosureEnergy
)
dfunc()
(in
WrapperOptEMultifunc
)
DoubleDensePDInteractionGraphAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
ProQ_Energy
)
dfunc()
(in
FingerprintMultifunc
)
DoubleDensePDInteractionGraphCAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
RG_Energy_Fast
)
dfunc()
(in
PocketExemplarMultifunc
)
DoubleDensePDNode
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
RG_LocalEnergy
)
dfunc()
(in
TensorsOptimizer
)
DoubleDensePDNodeAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
RMS_Energy
)
dfunc()
(in
TensorsOptimizer
)
DoubleDensePDNodeCAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
Rama2BOffsetEnergy
)
dfunc()
(in
TensorsOptimizerFix
)
DoubleLayerKinematicAbinitio
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
defines_high_order_terms()
(in
RamachandranEnergy
)
dfunc()
(in
TensorsOptimizerSvd
)
DoubleLayerKinematicAbinitioAP
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
defines_high_order_terms()
(in
RamachandranEnergy2B
)
dfunc()
(in
TensorsOptimizer_Ts1
)
DoubleLayerKinematicAbinitioCAP
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
defines_high_order_terms()
(in
ReferenceEnergy
)
dfunc()
(in
TensorsOptimizer_Ts2
)
DoubleLazyEdge
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
ReferenceEnergyNoncanonical
)
dfunc()
(in
TensorsOptimizer_Ts3
)
DoubleLazyEdgeAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
ResidualDipolarCouplingEnergy
)
dfunc()
(in
TensorsOptimizer_Ts4
)
DoubleLazyEdgeCAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
ResidualDipolarCouplingEnergy_Rohl
)
dfunc_component()
(in
MixtureFunc
)
DoubleLazyInteractionGraph
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
SA_Energy
)
dfunc_exact()
(in
TensorsOptimizer
)
DoubleLazyInteractionGraphAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
SecondaryStructureEnergy
)
dfunc_exact()
(in
TensorsOptimizerFix
)
DoubleLazyInteractionGraphCAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
SequenceDependentRefEnergy
)
dfunc_exact()
(in
TensorsOptimizerSvd
)
DoubleLazyNode
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
ShortRangeTwoBodyEnergy
)
dfunc_numeric()
(in
TensorsOptimizer
)
DoubleLazyNodeAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
SmoothCenPairEnergy
)
dfunc_numeric()
(in
TensorsOptimizerFix
)
DoubleLazyNodeCAP
(in
rosetta.core.pack.interaction_graph._core_pack_interaction_graph_
)
defines_high_order_terms()
(in
SmoothEnvEnergy
)
dfunc_numeric()
(in
TensorsOptimizerSvd
)
doubles_msg()
(in
SimulateMPIMessage
)
defines_high_order_terms()
(in
SuckerEnergy
)
dG_binding_correlation
(in
OptEPositionDataType
)
DownJumpSRFD
(in
rosetta.core.fragment._core_fragment_
)
defines_high_order_terms()
(in
SymmetricLigandEnergy
)
dG_binding_correlation
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
DownJumpSRFDAP
(in
rosetta.core.fragment._core_fragment_
)
defines_high_order_terms()
(in
TwoBodyEnergy
)
dG_binding_correlation
(in
rosetta.protocols.optimize_weights
)
DownJumpSRFDCAP
(in
rosetta.core.fragment._core_fragment_
)
defines_high_order_terms()
(in
UnfoldedStateEnergy
)
dgaussian()
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
downsample_pfront_poses()
(in
GreedyOptMutationMover
)
defines_high_order_terms()
(in
WaterAdductHBondEnergy
)
DGBindOptEData
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
downstream
(in
rosetta.protocols.match
)
defines_high_order_terms()
(in
WaterAdductIntraEnergy
)
DGBindOptEDataAP
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
downstream()
(in
Atom
)
defines_high_order_terms()
(in
WholeStructureEnergy
)
DGBindOptEDataCAP
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
downstream()
(in
Atom_
)
defines_high_order_terms()
(in
YHHPlanarityEnergy
)
diag()
(in
xyzMatrix_Real
)
downstream_algorithms()
(in
Matcher
)
defines_high_order_terms()
(in
pHEnergy
)
diag()
(in
xyzMatrix_SSize
)
downstream_atom()
(in
Edge
)
defines_high_order_terms()
(in
SugarBackboneEnergy
)
diag()
(in
xyzMatrix_Size
)
downstream_atom()
(in
FoldTree
)
defines_high_order_terms()
(in
DFIRE_Energy
)
diag()
(in
xyzMatrix_T_float_T
)
downstream_atoms_required_inside_active_site()
(in
MatcherTask
)
defines_high_order_terms()
(in
NVscore
)
diag()
(in
xyzMatrix_double
)
downstream_builder()
(in
Matcher
)
defines_high_order_terms()
(in
OrbitalsScore
)
diag()
(in
xyzMatrix_float
)
downstream_builders()
(in
Matcher
)
defines_high_order_terms()
(in
HolesEnergy
)
DiagnosticData
(in
rosetta.basic.datacache._basic_datacache_
)
downstream_combine()
(in
SequenceMapping
)
defines_high_order_terms()
(in
HolesEnergyRes
)
DiagnosticDataAP
(in
rosetta.basic.datacache._basic_datacache_
)
downstream_conf_id()
(in
Hit
)
defines_high_order_terms()
(in
SurfEnergy
)
DiagnosticDataCAP
(in
rosetta.basic.datacache._basic_datacache_
)
downstream_conf_id()
(in
downstream_hit
)
defines_high_order_terms()
(in
SurfVolEnergy
)
diagonal
(in
AlignMove
)
downstream_hit
(in
rosetta.protocols.match._protocols_match_
)
defines_high_order_terms()
(in
RG_Energy_RNA
)
diagonal
(in
rosetta.core.sequence._core_sequence_
)
downstream_hitAP
(in
rosetta.protocols.match._protocols_match_
)
defines_high_order_terms()
(in
RNA_BulgeEnergy
)
diagonal
(in
rosetta.core.sequence
)
downstream_hitCAP
(in
rosetta.protocols.match._protocols_match_
)
defines_high_order_terms()
(in
RNA_FullAtomStackingEnergy
)
DID_NOT_ADD_STRUCTURE
(in
rosetta.protocols.optimize_weights
)
downstream_jump_residue()
(in
FoldTree
)
defines_high_order_terms()
(in
RNA_FullAtomVDW_BasePhosphate
)
DID_NOT_ADD_STRUCTURE
(in
AddStatus
)
downstream_jump_stub()
(in
Conformation
)
defines_high_order_terms()
(in
RNA_JR_SuiteEnergy
)
DID_NOT_ADD_STRUCTURE
(in
rosetta.protocols.optimize_weights._protocols_optimize_weights_
)
downstream_orientation_atoms()
(in
MatcherTask
)
defines_high_order_terms()
(in
RNA_LJ_BaseEnergy
)
die()
(in
Coulomb
)
downstream_pose()
(in
Matcher
)
defines_high_order_terms()
(in
RNA_Mg_Energy
)
die_for_unaccessed_options()
(in
Tag
)
downstream_pose()
(in
MatcherTask
)
defines_high_order_terms()
(in
RNA_PairwiseLowResolutionEnergy
)
die_for_unaccessed_options_recursively()
(in
Tag
)
downstream_pose_from_hit()
(in
DownstreamBuilder
)
defines_high_order_terms()
(in
RNA_SugarCloseEnergy
)
difference_from()
(in
GasteigerAtomTypeData
)
downstream_pose_from_hit()
(in
LigandConformerBuilder
)
defines_high_order_terms()
(in
RNA_SuiteEnergy
)
differentiate()
(in
AbsoluteValueExpression
)
downstream_pose_from_hit()
(in
RigidLigandBuilder
)
defines_high_order_terms()
(in
RNA_TorsionEnergy
)
differentiate()
(in
AddExpression
)
downstream_res()
(in
MatchConstraintFileInfo
)
defines_high_order_terms()
(in
RNA_VDW_Energy
)
differentiate()
(in
AndExpression
)
downstream_res_nr()
(in
JumpSample
)
defines_high_order_terms()
(in
StackElecEnergy
)
differentiate()
(in
BinaryExpression
)
downstream_residues_from_jump()
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
defines_high_order_terms()
(in
RNA_ChemicalShiftEnergy
)
differentiate()
(in
DivideExpression
)
DownstreamAlgorithm
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
defines_high_order_terms()
(in
RNA_ChemicalMappingEnergy
)
differentiate()
(in
EqualsExpression
)
DownstreamAlgorithmAP
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
defines_high_order_terms()
(in
RNA_DataBackboneEnergy
)
differentiate()
(in
Expression
)
DownstreamAlgorithmCAP
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
defines_high_order_terms()
(in
FastSAXSEnergy
)
differentiate()
(in
GTE_Expression
)
DownstreamBuilder
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
defines_high_order_terms()
(in
SAXSEnergy
)
differentiate()
(in
GT_Expression
)
DownstreamBuilderAP
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
defines_high_order_terms()
(in
symEnergy
)
differentiate()
(in
ITEExpression
)
DownstreamBuilderCAP
(in
rosetta.protocols.match.downstream._protocols_match_downstream_
)
defines_high_order_terms()
(in
AACompositionEnergy
)
differentiate()
(in
LTE_Expression
)
DownstreamCoordinateKinemageWriter
(in
rosetta.protocols.match.output._protocols_match_output_
)
defines_high_order_terms()
(in
NatbiasSecondaryStructureEnergy
)
differentiate()
(in
LT_Expression
)
DownstreamCoordinateKinemageWriterAP
(in
rosetta.protocols.match.output._protocols_match_output_
)
defines_high_order_terms()
(in
EnsembleEnergy
)
differentiate()
(in
LiteralExpression
)
DownstreamCoordinateKinemageWriterCAP
(in
rosetta.protocols.match.output._protocols_match_output_
)
defines_high_order_terms()
(in
InterchainEnvEnergy
)
differentiate()
(in
MaxExpression
)
DownstreamRMSEvaluator
(in
rosetta.protocols.match.output._protocols_match_output_
)
defines_high_order_terms()
(in
InterchainPairEnergy
)
differentiate()
(in
MetaMaxExpression
)
DownstreamRMSEvaluatorAP
(in
rosetta.protocols.match.output._protocols_match_output_
)
defines_high_order_terms()
(in
ResidualDipolarCouplingEnergyRigidSegments
)
differentiate()
(in
MetaMinExpression
)
DownstreamRMSEvaluatorCAP
(in
rosetta.protocols.match.output._protocols_match_output_
)
defines_high_order_terms()
(in
SpecialRotamerEnergy
)
differentiate()
(in
MinExpression
)
dp()
(in
DimerPairing
)
defines_high_order_terms()
(in
PCS_Energy
)
differentiate()
(in
MultiplyExpression
)
DP_iter()
(in
TMalign
)
defines_high_order_terms()
(in
PcsEnergy
)
differentiate()
(in
NotExpression
)
DP_Matrix
(in
rosetta.core.sequence._core_sequence_
)
defines_high_order_terms()
(in
PCS_Energy_Ts1
)
differentiate()
(in
OrExpression
)
DP_MatrixAP
(in
rosetta.core.sequence._core_sequence_
)
defines_high_order_terms()
(in
PCS_Energy_Ts2
)
differentiate()
(in
SquarerootExpression
)
DP_MatrixCAP
(in
rosetta.core.sequence._core_sequence_
)
defines_high_order_terms()
(in
PCS_Energy_Ts3
)
differentiate()
(in
SubtractExpression
)
DPScoringScheme
(in
rosetta.core.sequence._core_sequence_
)
defines_high_order_terms()
(in
PCS_Energy_Ts4
)
differentiate()
(in
UnaryExpression
)
DPScoringSchemeAP
(in
rosetta.core.sequence._core_sequence_
)
defines_high_order_terms()
(in
PDDFEnergy
)
differentiate()
(in
VariableExpression
)
DPScoringSchemeCAP
(in
rosetta.core.sequence._core_sequence_
)
defines_intrares_dof_derivatives()
(in
CarbonHBondEnergy
)
differentiate()
(in
ExpExpression
)
dr_cycles()
(in
BDR
)
defines_intrares_dof_derivatives()
(in
ConstraintsEnergy
)
differentiate()
(in
InSetExpression
)
drawn_out_heavyatom_hydrogenatom_energy()
(in
HBondEnergy
)
defines_intrares_dof_derivatives()
(in
FullatomCustomPairDistanceEnergy
)
differentiate()
(in
IterativeVectorExpression
)
drift()
(in
GenericMonteCarloMover
)
defines_intrares_dof_derivatives()
(in
CentroidDisulfideEnergy
)
differentiate()
(in
LnExpression
)
drop_aa_submatrix()
(in
DoubleLazyEdge
)
defines_intrares_dof_derivatives()
(in
DisulfideMatchingEnergy
)
differentiate()
(in
PowExpression
)
drop_all_edges()
(in
UpperEdgeGraph_T_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_T
)
defines_intrares_dof_derivatives()
(in
FullatomDisulfideEnergy
)
differentiate()
(in
SurrogateVariableExpression
)
drop_all_edges()
(in
Graph
)
defines_intrares_dof_derivatives()
(in
DNATorsionEnergy
)
differentiate()
(in
VMax
)
drop_all_edges()
(in
Node
)
defines_intrares_dof_derivatives()
(in
FA_ElecEnergy
)
differentiate()
(in
VMaxBy
)
drop_all_edges()
(in
NodeBase
)
defines_intrares_dof_derivatives()
(in
FA_ElecEnergyAroAll
)
differentiate()
(in
VMin
)
drop_all_edges_for_node()
(in
Graph
)
defines_intrares_dof_derivatives()
(in
FA_ElecEnergyAroAro
)
differentiate()
(in
VMinBy
)
drop_all_edges_for_node()
(in
InteractionGraphBase
)
defines_intrares_dof_derivatives()
(in
FA_GrpElecEnergy
)
differentiate()
(in
VariableVectorExpression
)
drop_constraints()
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
defines_intrares_dof_derivatives()
(in
RNA_FA_ElecEnergy
)
differentiate()
(in
VectorExpression
)
drop_edge()
(in
Node
)
defines_intrares_dof_derivatives()
(in
ElecDensAllAtomCenEnergy
)
dihedral()
(in
ResidueType
)
drop_edge()
(in
NodeBase
)
defines_intrares_dof_derivatives()
(in
ElecDensCenEnergy
)
dihedral()
(in
CentroidRotamerSampleData
)
drop_rotamer()
(in
RotamerSet
)
defines_intrares_dof_derivatives()
(in
ElecDensEnergy
)
dihedral()
(in
rosetta.numeric._numeric_
)
drop_rotamer()
(in
RotamerSet_
)
defines_intrares_dof_derivatives()
(in
FastDensEnergy
)
dihedral_between_bonded_children()
(in
Atom
)
drop_rotamer()
(in
RotamerSubset
)
defines_intrares_dof_derivatives()
(in
PattersonCorrEnergy
)
dihedral_between_bonded_children()
(in
Atom_
)
drop_rotamer()
(in
SymmetricRotamerSet_
)
defines_intrares_dof_derivatives()
(in
ElecDensAtomwiseEnergy
)
dihedral_constraint
(in
ScoreType
)
drop_rotamer()
(in
FlexbbRotamerSet
)
defines_intrares_dof_derivatives()
(in
AnalyticEtableEnergy
)
dihedral_constraint
(in
rosetta.core.scoring._core_scoring_
)
drop_rotamers()
(in
RotamerSet
)
defines_intrares_dof_derivatives()
(in
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T
)
dihedral_constraint
(in
rosetta.core.scoring
)
drop_rotamers()
(in
RotamerSet_
)
defines_intrares_dof_derivatives()
(in
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T
)
dihedral_constraint
(in
rosetta
)
drop_rotamers()
(in
RotamerSubset
)
defines_intrares_dof_derivatives()
(in
TableLookupEtableEnergy
)
dihedral_constraint_energy()
(in
ConstraintEdge
)
drop_rotamers()
(in
SymmetricRotamerSet_
)
defines_intrares_dof_derivatives()
(in
ContextDependentGeometricSolEnergy
)
dihedral_degrees()
(in
rosetta.numeric._numeric_
)
drop_rotamers()
(in
FlexbbRotamerSet
)
defines_intrares_dof_derivatives()
(in
ContextIndependentGeometricSolEnergy
)
dihedral_degrees_double()
(in
rosetta.numeric._numeric_
)
drop_rotamers_by_index()
(in
RotamerSet
)
defines_intrares_dof_derivatives()
(in
OccludedHbondSolEnergy
)
dihedral_distance()
(in
rosetta.protocols.idealize._protocols_idealize_
)
drop_rotamers_by_index()
(in
RotamerSet_
)
defines_intrares_dof_derivatives()
(in
HackAroEnergy
)
dihedral_double()
(in
rosetta.numeric._numeric_
)
drop_rotamers_by_index()
(in
RotamerSubset
)
defines_intrares_dof_derivatives()
(in
HBondEnergy
)
dihedral_radians()
(in
rosetta.numeric._numeric_
)
drop_rotamers_by_index()
(in
SymmetricRotamerSet_
)
defines_intrares_dof_derivatives()
(in
DDPscore
)
dihedral_radians_double()
(in
rosetta.numeric._numeric_
)
drop_rotamers_by_index()
(in
FlexbbRotamerSet
)
defines_intrares_dof_derivatives()
(in
FaMPSolvEnergy
)
dihedral_rmsd()
(in
DiversifyDihedralsSelector
)
drop_small_submatrices_where_possible()
(in
AminoAcidNeighborSparseMatrix_T_float_T
)
defines_intrares_dof_derivatives()
(in
MPPairEnergy
)
dihedralA
(in
cstType
)
drop_strand_pairs()
(in
StrandPairingSet
)
defines_intrares_dof_derivatives()
(in
CartesianBondedEnergy
)
dihedralA
(in
rosetta.protocols.jumping._protocols_jumping_
)
drop_unsatisfied_voxels()
(in
OccupiedSpaceHash
)
defines_intrares_dof_derivatives()
(in
CenHBEnergy
)
dihedralA
(in
rosetta.protocols.jumping
)
drop_zero_submatrices_where_possible()
(in
AminoAcidNeighborSparseMatrix_T_float_T
)
defines_intrares_dof_derivatives()
(in
CenPairEnergy
)
dihedralAB
(in
cstType
)
drotprob_dbb()
(in
RotamerLibraryScratchSpace
)
defines_intrares_dof_derivatives()
(in
CenRotPairEnergy
)
dihedralAB
(in
rosetta.protocols.jumping._protocols_jumping_
)
dround()
(in
rosetta.core.scoring.rna.chemical_shift._core_scoring_rna_chemical_shift_
)
defines_intrares_dof_derivatives()
(in
ContextDependentLRTwoBodyEnergy
)
dihedralAB
(in
rosetta.protocols.jumping
)
dry_run()
(in
RelaxProtocolBase
)
defines_intrares_dof_derivatives()
(in
ContextDependentTwoBodyEnergy
)
dihedralB
(in
cstType
)
ds_find()
(in
DisjointSets
)
defines_intrares_dof_derivatives()
(in
ContextIndependentLRTwoBodyEnergy
)
dihedralB
(in
rosetta.protocols.jumping._protocols_jumping_
)
ds_hitset_end_its()
(in
CloudPDBWriter
)
defines_intrares_dof_derivatives()
(in
ContextIndependentTwoBodyEnergy
)
dihedralB
(in
rosetta.protocols.jumping
)
ds_hitset_its()
(in
CloudPDBWriter
)
defines_intrares_dof_derivatives()
(in
CustomAtomPairEnergy
)
DihedralConstraint
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
ds_make_set()
(in
DisjointSets
)
defines_intrares_dof_derivatives()
(in
DNA_BaseEnergy
)
DihedralConstraintAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
DS_Node
(in
rosetta.core.graph._core_graph_
)
defines_intrares_dof_derivatives()
(in
Fa_MbsolvEnergy
)
DihedralConstraintCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
DS_NodeAP
(in
rosetta.core.graph._core_graph_
)
defines_intrares_dof_derivatives()
(in
GaussianOverlapEnergy
)
DihedralConstraintCreator
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
DS_NodeCAP
(in
rosetta.core.graph._core_graph_
)
defines_intrares_dof_derivatives()
(in
GenBornEnergy
)
DihedralConstraintCreatorAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
ds_union()
(in
DisjointSets
)
defines_intrares_dof_derivatives()
(in
GoapEnergy
)
DihedralConstraintCreatorCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
dscore()
(in
MMBondAngleScore
)
defines_intrares_dof_derivatives()
(in
HybridVDW_Energy
)
DihedralConstraintsScore
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
dscore()
(in
MMBondLengthScore
)
defines_intrares_dof_derivatives()
(in
LK_BallEnergy
)
DihedralConstraintsScoreAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
dscore()
(in
MMTorsionScore
)
defines_intrares_dof_derivatives()
(in
LK_PolarNonPolarEnergy
)
DihedralConstraintsScoreCAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
dslf_ca_dih
(in
ScoreType
)
defines_intrares_dof_derivatives()
(in
LK_hack
)
DihedralPairConstraint
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
dslf_ca_dih
(in
rosetta.core.scoring._core_scoring_
)
defines_intrares_dof_derivatives()
(in
LongRangeTwoBodyEnergy
)
DihedralPairConstraintAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
dslf_ca_dih
(in
rosetta.core.scoring
)
defines_intrares_dof_derivatives()
(in
MMBondAngleEnergy
)
DihedralPairConstraintCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
dslf_ca_dih
(in
rosetta
)
defines_intrares_dof_derivatives()
(in
MMBondLengthEnergy
)
DihedralPairConstraintCreator
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
dslf_ca_dih()
(in
FullatomDisulfideEnergyComponents
)
defines_intrares_dof_derivatives()
(in
MMLJEnergyInter
)
DihedralPairConstraintCreatorAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
dslf_cbs_ds
(in
ScoreType
)
defines_intrares_dof_derivatives()
(in
MMLJEnergyIntra
)
DihedralPairConstraintCreatorCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
dslf_cbs_ds
(in
rosetta.core.scoring._core_scoring_
)
defines_intrares_dof_derivatives()
(in
MMTorsionEnergy
)
dihedrals_for_atom()
(in
ResidueType
)
dslf_cbs_ds
(in
rosetta.core.scoring
)
defines_intrares_dof_derivatives()
(in
MembraneCenPairEnergy
)
DIIODINATION
(in
rosetta
)
dslf_cbs_ds
(in
rosetta
)
defines_intrares_dof_derivatives()
(in
PairEnergy
)
DIIODINATION
(in
rosetta.core.chemical
)
dslf_cbs_ds()
(in
FullatomDisulfideEnergyComponents
)
defines_intrares_dof_derivatives()
(in
PeptideBondEnergy
)
DIIODINATION
(in
rosetta.core.chemical._core_chemical_
)
dslf_cs_ang
(in
ScoreType
)
defines_intrares_dof_derivatives()
(in
PoissonBoltzmannEnergy
)
DIIODINATION
(in
VariantType
)
dslf_cs_ang
(in
rosetta.core.scoring._core_scoring_
)
defines_intrares_dof_derivatives()
(in
ProClosureEnergy
)
dijkstras()
(in
ResidueNetwork
)
dslf_cs_ang
(in
rosetta.core.scoring
)
defines_intrares_dof_derivatives()
(in
Rama2BOffsetEnergy
)
dim()
(in
PocketGrid
)
dslf_cs_ang
(in
rosetta
)
defines_intrares_dof_derivatives()
(in
RamachandranEnergy2B
)
dim()
(in
ClusterBase
)
dslf_cs_ang()
(in
FullatomDisulfideEnergyComponents
)
defines_intrares_dof_derivatives()
(in
ShortRangeTwoBodyEnergy
)
dim_labels()
(in
MultiDimensionalHistogram
)
dslf_fa13
(in
ScoreType
)
defines_intrares_dof_derivatives()
(in
SmoothCenPairEnergy
)
DimerPairing
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
dslf_fa13
(in
rosetta.core.scoring._core_scoring_
)
defines_intrares_dof_derivatives()
(in
SuckerEnergy
)
DimerPairingAP
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
dslf_fa13
(in
rosetta.core.scoring
)
defines_intrares_dof_derivatives()
(in
TwoBodyEnergy
)
DimerPairingCAP
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
dslf_fa13
(in
rosetta
)
defines_intrares_dof_derivatives()
(in
WaterAdductHBondEnergy
)
DimerPairings
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
dslf_fa13()
(in
FullatomDisulfideEnergyComponents
)
defines_intrares_dof_derivatives()
(in
DFIRE_Energy
)
DimerPairingsAP
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
dslf_ss_dih
(in
ScoreType
)
defines_intrares_dof_derivatives()
(in
OrbitalsScore
)
DimerPairingsCAP
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
dslf_ss_dih
(in
rosetta.core.scoring._core_scoring_
)
defines_intrares_dof_derivatives()
(in
RNA_FullAtomStackingEnergy
)
DIMETHYLATION
(in
rosetta
)
dslf_ss_dih
(in
rosetta.core.scoring
)
defines_intrares_dof_derivatives()
(in
RNA_JR_SuiteEnergy
)
DIMETHYLATION
(in
rosetta.core.chemical
)
dslf_ss_dih
(in
rosetta
)
defines_intrares_dof_derivatives()
(in
RNA_LJ_BaseEnergy
)
DIMETHYLATION
(in
rosetta.core.chemical._core_chemical_
)
dslf_ss_dih()
(in
FullatomDisulfideEnergyComponents
)
defines_intrares_dof_derivatives()
(in
RNA_Mg_Energy
)
DIMETHYLATION
(in
VariantType
)
dslf_ss_dst
(in
ScoreType
)
defines_intrares_dof_derivatives()
(in
RNA_PairwiseLowResolutionEnergy
)
dimOther()
(in
kiss_fftndr_state
)
dslf_ss_dst
(in
rosetta.core.scoring._core_scoring_
)
defines_intrares_dof_derivatives()
(in
RNA_SuiteEnergy
)
dimprod()
(in
kiss_fftnd_state
)
dslf_ss_dst
(in
rosetta.core.scoring
)
defines_intrares_dof_derivatives()
(in
RNA_TorsionEnergy
)
dimReal()
(in
kiss_fftndr_state
)
dslf_ss_dst
(in
rosetta
)
defines_intrares_dof_derivatives()
(in
RNA_VDW_Energy
)
dims_v()
(in
kiss_fftnd_state
)
dslf_ss_dst()
(in
FullatomDisulfideEnergyComponents
)
defines_intrares_dof_derivatives()
(in
StackElecEnergy
)
dimsize()
(in
LexicographicalIterator
)
dslfc_ang
(in
ScoreType
)
defines_intrares_dof_derivatives()
(in
RNA_DataBackboneEnergy
)
dimsizes()
(in
SixDCoordinateBinner
)
dslfc_ang
(in
rosetta.core.scoring._core_scoring_
)
defines_intrares_dof_derivatives()
(in
symEnergy
)
dimsizes()
(in
Bool3DGrid
)
dslfc_ang
(in
rosetta.core.scoring
)
defines_intrares_dof_derivatives()
(in
InterchainPairEnergy
)
DipolarCoupling
(in
rosetta.core.scoring._core_scoring_
)
dslfc_ang
(in
rosetta
)
defines_intrares_energy()
(in
CarbonHBondEnergy
)
DipolarCouplingAP
(in
rosetta.core.scoring._core_scoring_
)
dslfc_ang()
(in
CentroidDisulfideEnergyComponents
)
defines_intrares_energy()
(in
ConstraintsEnergy
)
DipolarCouplingCAP
(in
rosetta.core.scoring._core_scoring_
)
dslfc_bb_dih
(in
ScoreType
)
defines_intrares_energy()
(in
FullatomCustomPairDistanceEnergy
)
DipolarCouplingEnergy
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
dslfc_bb_dih
(in
rosetta.core.scoring._core_scoring_
)
defines_intrares_energy()
(in
CentroidDisulfideEnergy
)
DipolarCouplingEnergyAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
dslfc_bb_dih
(in
rosetta.core.scoring
)
defines_intrares_energy()
(in
DisulfideMatchingEnergy
)
DipolarCouplingEnergyCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
dslfc_bb_dih
(in
rosetta
)
defines_intrares_energy()
(in
FullatomDisulfideEnergy
)
DipolarCouplingEnergyCreator
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
dslfc_bb_dih()
(in
CentroidDisulfideEnergyComponents
)
defines_intrares_energy()
(in
DNATorsionEnergy
)
DipolarCouplingEnergyCreatorAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
dslfc_cb_dih
(in
ScoreType
)
defines_intrares_energy()
(in
FA_ElecEnergy
)
DipolarCouplingEnergyCreatorCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
dslfc_cb_dih
(in
rosetta.core.scoring._core_scoring_
)
defines_intrares_energy()
(in
FA_ElecEnergyAroAll
)
dir()
(in
Batch
)
dslfc_cb_dih
(in
rosetta.core.scoring
)
defines_intrares_energy()
(in
FA_ElecEnergyAroAro
)
Direction
(in
rosetta.protocols.rigid._protocols_rigid_
)
dslfc_cb_dih
(in
rosetta
)
defines_intrares_energy()
(in
FA_GrpElecEnergy
)
directory()
(in
AtomTypeSet
)
dslfc_cb_dih()
(in
CentroidDisulfideEnergyComponents
)
defines_intrares_energy()
(in
RNA_FA_ElecEnergy
)
DirectReadoutEnergy
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
dslfc_cb_dst
(in
ScoreType
)
defines_intrares_energy()
(in
ElecDensAllAtomCenEnergy
)
DirectReadoutEnergyAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
dslfc_cb_dst
(in
rosetta.core.scoring._core_scoring_
)
defines_intrares_energy()
(in
ElecDensCenEnergy
)
DirectReadoutEnergyCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
dslfc_cb_dst
(in
rosetta.core.scoring
)
defines_intrares_energy()
(in
ElecDensEnergy
)
DirectReadoutEnergyCreator
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
dslfc_cb_dst
(in
rosetta
)
defines_intrares_energy()
(in
FastDensEnergy
)
DirectReadoutEnergyCreatorAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
dslfc_cb_dst()
(in
CentroidDisulfideEnergyComponents
)
defines_intrares_energy()
(in
PattersonCorrEnergy
)
DirectReadoutEnergyCreatorCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
dslfc_cen_dst
(in
ScoreType
)
defines_intrares_energy()
(in
ElecDensAtomwiseEnergy
)
DirectReadoutPotential
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
dslfc_cen_dst
(in
rosetta.core.scoring._core_scoring_
)
defines_intrares_energy()
(in
AnalyticEtableEnergy
)
DirectReadoutPotentialAP
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
dslfc_cen_dst
(in
rosetta.core.scoring
)
defines_intrares_energy()
(in
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T
)
DirectReadoutPotentialCAP
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
dslfc_cen_dst
(in
rosetta
)
defines_intrares_energy()
(in
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T
)
dis()
(in
ResidueVicinityInfo
)
dslfc_cen_dst()
(in
CentroidDisulfideEnergyComponents
)
defines_intrares_energy()
(in
TableLookupEtableEnergy
)
dis()
(in
ResInteractions
)
dslfc_rot
(in
ScoreType
)
defines_intrares_energy()
(in
ContextDependentGeometricSolEnergy
)
dis_U1D1()
(in
MatchConstraintFileInfo
)
dslfc_rot
(in
rosetta.core.scoring._core_scoring_
)
defines_intrares_energy()
(in
ContextIndependentGeometricSolEnergy
)
dis_U1D1_samples()
(in
ExternalGeomSampler
)
dslfc_rot
(in
rosetta.core.scoring
)
defines_intrares_energy()
(in
ExactOccludedHbondSolEnergy
)
disAB
(in
cstType
)
dslfc_rot
(in
rosetta
)
defines_intrares_energy()
(in
OccludedHbondSolEnergy
)
disAB
(in
rosetta.protocols.jumping._protocols_jumping_
)
dslfc_rot()
(in
DisulfideMatchingEnergyComponents
)
defines_intrares_energy()
(in
OccludedHbondSolEnergy_onebody
)
disAB
(in
rosetta.protocols.jumping
)
dslfc_RT
(in
ScoreType
)
defines_intrares_energy()
(in
HackAroEnergy
)
disable()
(in
ResidueTorsionRestraints
)
dslfc_RT
(in
rosetta.core.scoring._core_scoring_
)
defines_intrares_energy()
(in
HBondEnergy
)
disable_auto_update()
(in
NeighborList
)
dslfc_RT
(in
rosetta.core.scoring
)
defines_intrares_energy()
(in
DDPscore
)
disable_autotemp()
(in
RationalMonteCarlo
)
dslfc_RT
(in
rosetta
)
defines_intrares_energy()
(in
FaMPSolvEnergy
)
disable_build_stage()
(in
LoopModeler
)
dslfc_RT()
(in
DisulfideMatchingEnergyComponents
)
defines_intrares_energy()
(in
MPPairEnergy
)
disable_centroid_stage()
(in
LoopModeler
)
dslfc_trans
(in
ScoreType
)
defines_intrares_energy()
(in
CartesianBondedEnergy
)
disable_conserved_framework_positions()
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
dslfc_trans
(in
rosetta.core.scoring._core_scoring_
)
defines_intrares_energy()
(in
CenHBEnergy
)
disable_design_antigen()
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
dslfc_trans
(in
rosetta.core.scoring
)
defines_intrares_energy()
(in
CenPairEnergy
)
disable_design_cdr()
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
dslfc_trans
(in
rosetta
)
defines_intrares_energy()
(in
CenRotPairEnergy
)
disable_design_cdrs()
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
dslfc_trans()
(in
DisulfideMatchingEnergyComponents
)
defines_intrares_energy()
(in
ContextDependentLRTwoBodyEnergy
)
disable_design_for_non_designing_cdrs()
(in
AntibodySeqDesignTFCreator
)
dsolv()
(in
Etable
)
defines_intrares_energy()
(in
ContextDependentTwoBodyEnergy
)
disable_design_framework()
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
dsolv1()
(in
Etable
)
defines_intrares_energy()
(in
ContextIndependentLRTwoBodyEnergy
)
disable_design_region()
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
dspos1_mode()
(in
BestMatchesCollection
)
defines_intrares_energy()
(in
ContextIndependentTwoBodyEnergy
)
disable_fullatom_stage()
(in
LoopModeler
)
dsq()
(in
PointGraphEdgeData
)
defines_intrares_energy()
(in
CustomAtomPairEnergy
)
disable_h3_stem_positions()
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
dssp
(in
rosetta.core.scoring
)
defines_intrares_energy()
(in
DNA_BaseEnergy
)
disable_ignorefinished()
(in
BaseJobDistributor
)
Dssp
(in
rosetta.core.scoring.dssp._core_scoring_dssp_
)
defines_intrares_energy()
(in
Fa_MbsolvEnergy
)
disable_inprogress()
(in
BaseJobDistributor
)
dssp()
(in
Dssp
)
defines_intrares_energy()
(in
GaussianOverlapEnergy
)
disable_output()
(in
BaseJobDistributor
)
dssp()
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
defines_intrares_energy()
(in
GenBornEnergy
)
disable_proline_design()
(in
AntibodySeqDesignTFCreator
)
dssp1()
(in
ResPairMotif
)
defines_intrares_energy()
(in
GoapEnergy
)
disable_sampling_of_loop_takeoff()
(in
StepWiseProteinModelerOptions
)
dssp2()
(in
ResPairMotif
)
defines_intrares_energy()
(in
HybridVDW_Energy
)
DisableAntibodyRegionOperation
(in
rosetta.protocols.antibody.task_operations._protocols_antibody_task_operations_
)
dssp_featurizer()
(in
Dssp
)
defines_intrares_energy()
(in
LK_BallEnergy
)
DisableAntibodyRegionOperationAP
(in
rosetta.protocols.antibody.task_operations._protocols_antibody_task_operations_
)
dssp_phi()
(in
VallResidue
)
defines_intrares_energy()
(in
LK_PolarNonPolarEnergy
)
DisableAntibodyRegionOperationCAP
(in
rosetta.protocols.antibody.task_operations._protocols_antibody_task_operations_
)
dssp_psi()
(in
VallResidue
)
defines_intrares_energy()
(in
LK_hack
)
DisableCDRsOperation
(in
rosetta.protocols.antibody.task_operations._protocols_antibody_task_operations_
)
dssp_reduced()
(in
Dssp
)
defines_intrares_energy()
(in
LongRangeTwoBodyEnergy
)
DisableCDRsOperationAP
(in
rosetta.protocols.antibody.task_operations._protocols_antibody_task_operations_
)
dssp_reduced_IG_as_L()
(in
Dssp
)
defines_intrares_energy()
(in
MMBondAngleEnergy
)
DisableCDRsOperationCAP
(in
rosetta.protocols.antibody.task_operations._protocols_antibody_task_operations_
)
dssp_reduced_IG_as_L_if_adjcent_H()
(in
Dssp
)
defines_intrares_energy()
(in
MMBondLengthEnergy
)
disallow_aas()
(in
DisallowIfNonnative
)
dssp_state()
(in
StrandPairingSet
)
defines_intrares_energy()
(in
MMLJEnergyInter
)
disallow_aas()
(in
DisallowIfNonnativeRLT
)
DsspAP
(in
rosetta.core.scoring.dssp._core_scoring_dssp_
)
defines_intrares_energy()
(in
MMLJEnergyIntra
)
disallow_current_slide()
(in
SymmetrySlider
)
DsspCAP
(in
rosetta.core.scoring.dssp._core_scoring_dssp_
)
defines_intrares_energy()
(in
MMTorsionEnergy
)
disallow_noncanonical_aas()
(in
ResidueLevelTask
)
DsspDesignOperation
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
defines_intrares_energy()
(in
MembraneCenPairEnergy
)
disallow_noncanonical_aas()
(in
ResidueLevelTask_
)
DsspDesignOperationAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
defines_intrares_energy()
(in
PairEnergy
)
disallow_quench()
(in
PackerTask
)
DsspDesignOperationCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
defines_intrares_energy()
(in
PeptideBondEnergy
)
disallow_quench()
(in
PackerTask_
)
DsspDesignOperationCreator
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
defines_intrares_energy()
(in
PoissonBoltzmannEnergy
)
disallow_realign()
(in
StepWiseBasicModelerOptions
)
DsspDesignOperationCreatorAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
defines_intrares_energy()
(in
ProClosureEnergy
)
disallow_resid()
(in
OptH
)
DsspDesignOperationCreatorCAP
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
defines_intrares_energy()
(in
Rama2BOffsetEnergy
)
DisallowIfNonnative
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
DsspMover
(in
rosetta.protocols.moves._protocols_moves_
)
defines_intrares_energy()
(in
RamachandranEnergy2B
)
DisallowIfNonnativeAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
DsspMoverAP
(in
rosetta.protocols.moves._protocols_moves_
)
defines_intrares_energy()
(in
ShortRangeTwoBodyEnergy
)
DisallowIfNonnativeCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
DsspMoverCAP
(in
rosetta.protocols.moves._protocols_moves_
)
defines_intrares_energy()
(in
SmoothCenPairEnergy
)
DisallowIfNonnativeCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
DsspMoverCreator
(in
rosetta.protocols.moves._protocols_moves_
)
defines_intrares_energy()
(in
SuckerEnergy
)
DisallowIfNonnativeCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
DsspMoverCreatorAP
(in
rosetta.protocols.moves._protocols_moves_
)
defines_intrares_energy()
(in
TwoBodyEnergy
)
DisallowIfNonnativeCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
DsspMoverCreatorCAP
(in
rosetta.protocols.moves._protocols_moves_
)
defines_intrares_energy()
(in
WaterAdductHBondEnergy
)
DisallowIfNonnativeRLT
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
dst()
(in
SimulateMPIMessage
)
defines_intrares_energy()
(in
DFIRE_Energy
)
DisallowIfNonnativeRLTAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
dt()
(in
MDBase
)
defines_intrares_energy()
(in
OrbitalsScore
)
DisallowIfNonnativeRLTCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
dtest_cutoff()
(in
LigandMotifSearch
)
defines_intrares_energy()
(in
RNA_FullAtomStackingEnergy
)
DisallowIfNonnativeRLTCreator
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
dtest_cutoff()
(in
MotifSearch
)
defines_intrares_energy()
(in
RNA_JR_SuiteEnergy
)
DisallowIfNonnativeRLTCreatorAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
DualMonteCarlo
(in
rosetta.protocols.moves._protocols_moves_
)
defines_intrares_energy()
(in
RNA_LJ_BaseEnergy
)
DisallowIfNonnativeRLTCreatorCAP
(in
rosetta.core.pack.task.operation._core_pack_task_operation_
)
DualMonteCarloAP
(in
rosetta.protocols.moves._protocols_moves_
)
defines_intrares_energy()
(in
RNA_Mg_Energy
)
discard_conformation_domain_map()
(in
Energies
)
DualMonteCarloCAP
(in
rosetta.protocols.moves._protocols_moves_
)
defines_intrares_energy()
(in
RNA_PairwiseLowResolutionEnergy
)
discard_old_entity
(in
DaemonSetMessage
)
dualspace
(in
MinTypeEnum
)
defines_intrares_energy()
(in
RNA_SuiteEnergy
)
discard_old_entity
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
dualspace
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
defines_intrares_energy()
(in
RNA_TorsionEnergy
)
discard_old_entity
(in
rosetta.protocols.pack_daemon
)
dualspace
(in
rosetta.protocols.antibody.design
)
defines_intrares_energy()
(in
RNA_VDW_Energy
)
DISCONNECT
(in
ConnectionEvent
)
dualspace()
(in
FastRelax
)
defines_intrares_energy()
(in
StackElecEnergy
)
DISCONNECT
(in
Tag
)
dummy_modify()
(in
BuildManager
)
defines_intrares_energy()
(in
RNA_DataBackboneEnergy
)
discontinued_lower()
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
dummy_score_type
(in
ScoreType
)
defines_intrares_energy()
(in
symEnergy
)
discontinued_upper()
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
dummy_score_type
(in
rosetta.core.scoring._core_scoring_
)
defines_intrares_energy()
(in
InterchainPairEnergy
)
DiscreteRandomizer
(in
rosetta.protocols.genetic_algorithm._protocols_genetic_algorithm_
)
dummy_score_type
(in
rosetta.core.scoring
)
defines_intrares_energy_for_residue()
(in
CarbonHBondEnergy
)
DiscreteRandomizerAP
(in
rosetta.protocols.genetic_algorithm._protocols_genetic_algorithm_
)
dummy_score_type
(in
rosetta
)
defines_intrares_energy_for_residue()
(in
ConstraintsEnergy
)
DiscreteRandomizerCAP
(in
rosetta.protocols.genetic_algorithm._protocols_genetic_algorithm_
)
DummyClass
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
defines_intrares_energy_for_residue()
(in
FullatomCustomPairDistanceEnergy
)
disjoint_set_sizes()
(in
DisjointSets
)
DummyClassAP
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
defines_intrares_energy_for_residue()
(in
CentroidDisulfideEnergy
)
DisjointSets
(in
rosetta.core.graph._core_graph_
)
DummyClassCAP
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
defines_intrares_energy_for_residue()
(in
DisulfideMatchingEnergy
)
DisjointSetsAP
(in
rosetta.core.graph._core_graph_
)
dump()
(in
AtomTreeMultifunc
)
defines_intrares_energy_for_residue()
(in
FullatomDisulfideEnergy
)
DisjointSetsCAP
(in
rosetta.core.graph._core_graph_
)
dump()
(in
CartesianMultifunc
)
defines_intrares_energy_for_residue()
(in
DNATorsionEnergy
)
display_constraint_residues()
(in
AntibodyModelerProtocol
)
dump()
(in
Multifunc
)
defines_intrares_energy_for_residue()
(in
FA_ElecEnergy
)
display_constraint_residues()
(in
GraftCDRLoopsProtocol
)
dump()
(in
SingleResidueMultifunc
)
defines_intrares_energy_for_residue()
(in
FA_ElecEnergyAroAll
)
display_constraint_residues()
(in
AntibodyModeler
)
dump()
(in
func_1d
)
defines_intrares_energy_for_residue()
(in
FA_ElecEnergyAroAro
)
dist()
(in
ShortestPathInFoldTree
)
dump()
(in
SymAtomTreeMultifunc
)
defines_intrares_energy_for_residue()
(in
FA_GrpElecEnergy
)
dist()
(in
DunbrackConstraint
)
dump()
(in
FileBuffer
)
defines_intrares_energy_for_residue()
(in
RNA_FA_ElecEnergy
)
dist()
(in
RotamerConstraint
)
dump()
(in
BfactorMultifunc
)
defines_intrares_energy_for_residue()
(in
ElecDensAllAtomCenEnergy
)
dist()
(in
AmbiguousConstraint
)
dump()
(in
FitSimpleHelixMultiFunc
)
defines_intrares_energy_for_residue()
(in
ElecDensCenEnergy
)
dist()
(in
AmbiguousNMRConstraint
)
dump()
(in
NormalModeMultifunc
)
defines_intrares_energy_for_residue()
(in
ElecDensEnergy
)
dist()
(in
AmbiguousNMRDistanceConstraint
)
dump()
(in
OptEMultifunc
)
defines_intrares_energy_for_residue()
(in
FastDensEnergy
)
dist()
(in
AngleConstraint
)
dump()
(in
WrapperOptEMultifunc
)
defines_intrares_energy_for_residue()
(in
PattersonCorrEnergy
)
dist()
(in
AtomPairConstraint
)
dump()
(in
FingerprintMultifunc
)
defines_intrares_energy_for_residue()
(in
ElecDensAtomwiseEnergy
)
dist()
(in
BackboneStubConstraint
)
dump()
(in
PocketExemplarMultifunc
)
defines_intrares_energy_for_residue()
(in
AnalyticEtableEnergy
)
dist()
(in
BackboneStubLinearConstraint
)
dump()
(in
TensorsOptimizer
)
defines_intrares_energy_for_residue()
(in
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T
)
dist()
(in
BigBinConstraint
)
dump()
(in
TensorsOptimizer
)
defines_intrares_energy_for_residue()
(in
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T
)
dist()
(in
ConstantConstraint
)
dump()
(in
TensorsOptimizerFix
)
defines_intrares_energy_for_residue()
(in
TableLookupEtableEnergy
)
dist()
(in
Constraint
)
dump()
(in
TensorsOptimizerSvd
)
defines_intrares_energy_for_residue()
(in
ContextDependentGeometricSolEnergy
)
dist()
(in
CoordinateConstraint
)
dump()
(in
TensorsOptimizer_Ts1
)
defines_intrares_energy_for_residue()
(in
ContextIndependentGeometricSolEnergy
)
dist()
(in
DihedralConstraint
)
dump()
(in
TensorsOptimizer_Ts2
)
defines_intrares_energy_for_residue()
(in
OccludedHbondSolEnergy
)
dist()
(in
DihedralPairConstraint
)
dump()
(in
TensorsOptimizer_Ts3
)
defines_intrares_energy_for_residue()
(in
HackAroEnergy
)
dist()
(in
DistancePairConstraint
)
dump()
(in
TensorsOptimizer_Ts4
)
defines_intrares_energy_for_residue()
(in
HBondEnergy
)
dist()
(in
FabConstraint
)
dump()
(in
StepWiseBasicModelerOptions
)
defines_intrares_energy_for_residue()
(in
DDPscore
)
dist()
(in
KofNConstraint
)
dump_aligned_motif()
(in
ResPairMotif
)
defines_intrares_energy_for_residue()
(in
FaMPSolvEnergy
)
dist()
(in
LocalCoordinateConstraint
)
dump_as_pdb()
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
defines_intrares_energy_for_residue()
(in
MPPairEnergy
)
dist()
(in
MultiConstraint
)
dump_atom_tree_diff()
(in
rosetta.core.import_pose.atom_tree_diffs._core_import_pose_atom_tree_diffs_
)
defines_intrares_energy_for_residue()
(in
CartesianBondedEnergy
)
dist()
(in
NamedAngleConstraint
)
dump_bfactor_pdb()
(in
rosetta.core.io.pdb._core_io_pdb_
)
defines_intrares_energy_for_residue()
(in
CenHBEnergy
)
dist()
(in
NamedAtomPairConstraint
)
dump_comment_pdb()
(in
rosetta.core.pose._core_pose_
)
defines_intrares_energy_for_residue()
(in
CenPairEnergy
)
dist()
(in
NonResidueTypeConstraint
)
dump_connect_info()
(in
rosetta.core.io.pdb._core_io_pdb_
)
defines_intrares_energy_for_residue()
(in
CenRotPairEnergy
)
dist()
(in
ResidueTypeConstraint
)
dump_debug_pdb()
(in
ImplicitFastClashCheck
)
defines_intrares_energy_for_residue()
(in
ContextDependentLRTwoBodyEnergy
)
dist()
(in
ResidueTypeLinkingConstraint
)
dump_eggshell()
(in
EggshellGrid
)
defines_intrares_energy_for_residue()
(in
ContextDependentTwoBodyEnergy
)
dist()
(in
SequenceProfileConstraint
)
dump_file()
(in
EvaluatedTrialMover
)
defines_intrares_energy_for_residue()
(in
ContextIndependentLRTwoBodyEnergy
)
dist()
(in
SiteConstraint
)
dump_frames_as_pdb()
(in
rosetta.core.fragment._core_fragment_
)
defines_intrares_energy_for_residue()
(in
ContextIndependentTwoBodyEnergy
)
dist()
(in
SiteConstraintResidues
)
dump_graph()
(in
rosetta.core.chemical.sdf._core_chemical_sdf_
)
defines_intrares_energy_for_residue()
(in
CustomAtomPairEnergy
)
dist()
(in
AmbiguousMultiConstraint
)
dump_gws()
(in
rosetta.core.io.carbohydrates._core_io_carbohydrates_
)
defines_intrares_energy_for_residue()
(in
DNA_BaseEnergy
)
dist()
(in
BindingSiteConstraint
)
dump_gws_chain()
(in
rosetta.core.io.carbohydrates._core_io_carbohydrates_
)
defines_intrares_energy_for_residue()
(in
Fa_MbsolvEnergy
)
dist()
(in
COMCoordinateConstraint
)
dump_invrots_tree_as_multimodel_pdbs()
(in
InvrotTree
)
defines_intrares_energy_for_residue()
(in
GaussianOverlapEnergy
)
dist()
(in
SequenceCoupling1BDConstraint
)
dump_linkers()
(in
LinkerScore
)
defines_intrares_energy_for_residue()
(in
GenBornEnergy
)
dist()
(in
SequenceCouplingConstraint
)
dump_loophash_linkers()
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
defines_intrares_energy_for_residue()
(in
GoapEnergy
)
dist()
(in
DimerPairing
)
dump_matching_motifs()
(in
MotifHashRigidScore
)
defines_intrares_energy_for_residue()
(in
HybridVDW_Energy
)
dist()
(in
HelixPairing
)
dump_minimal_pdb()
(in
Rose
)
defines_intrares_energy_for_residue()
(in
LK_BallEnergy
)
dist()
(in
Contact
)
dump_motif_hit()
(in
MotifHit
)
defines_intrares_energy_for_residue()
(in
LK_PolarNonPolarEnergy
)
dist()
(in
PhiPsiTalosIO
)
dump_motifs_pdb()
(in
MotifHits
)
defines_intrares_energy_for_residue()
(in
LK_hack
)
dist()
(in
TMalign
)
dump_oriented_pose_and_fp_to_pdb()
(in
PlaidFingerprint
)
defines_intrares_energy_for_residue()
(in
LongRangeTwoBodyEnergy
)
dist()
(in
PocketConstraint
)
dump_packertask()
(in
DesignTask
)
defines_intrares_energy_for_residue()
(in
MMBondAngleEnergy
)
dist()
(in
AlaScan
)
dump_PCS_info()
(in
PCS_Energy
)
defines_intrares_energy_for_residue()
(in
MMBondLengthEnergy
)
dist()
(in
ClusterBase
)
dump_PCS_info()
(in
PcsEnergy
)
defines_intrares_energy_for_residue()
(in
MMLJEnergyInter
)
dist2()
(in
ResPairMotif
)
dump_PCS_info()
(in
PCS_Energy_Ts1
)
defines_intrares_energy_for_residue()
(in
MMLJEnergyIntra
)
dist2_cut()
(in
NormalMode
)
dump_PCS_info()
(in
PCS_Energy_Ts2
)
defines_intrares_energy_for_residue()
(in
MMTorsionEnergy
)
dist_cutoff()
(in
InterGroupNeighborsCalculator
)
dump_PCS_info()
(in
PCS_Energy_Ts3
)
defines_intrares_energy_for_residue()
(in
MembraneCenPairEnergy
)
dist_cutoff()
(in
NeighborhoodByDistanceCalculator
)
dump_PCS_info()
(in
PCS_Energy_Ts4
)
defines_intrares_energy_for_residue()
(in
PairEnergy
)
dist_cutoff()
(in
NeighborsByDistanceCalculator
)
dump_pdb()
(in
FileData
)
defines_intrares_energy_for_residue()
(in
PeptideBondEnergy
)
dist_square()
(in
KClusterData
)
dump_pdb()
(in
rosetta.core.io.pdb._core_io_pdb_
)
defines_intrares_energy_for_residue()
(in
PoissonBoltzmannEnergy
)
dist_squared()
(in
Contact
)
dump_pdb()
(in
RotamerSets
)
defines_intrares_energy_for_residue()
(in
ProClosureEnergy
)
dist_squared()
(in
RNA_ChainClosableGeometryChecker
)
dump_pdb()
(in
Pose
)
defines_intrares_energy_for_residue()
(in
Rama2BOffsetEnergy
)
distance()
(in
Bond
)
dump_pdb()
(in
ResPairMotif
)
defines_intrares_energy_for_residue()
(in
RamachandranEnergy2B
)
distance()
(in
ICoorOrbitalData
)
dump_pdb()
(in
GreedyOptMutationMover
)
defines_intrares_energy_for_residue()
(in
ShortRangeTwoBodyEnergy
)
distance()
(in
OrbitalType
)
dump_pdb()
(in
ParetoOptMutationMover
)
defines_intrares_energy_for_residue()
(in
SmoothCenPairEnergy
)
distance()
(in
Extent_T__core_fragment_picking_old_vall_VallSection_PageConstIterator__T
)
dump_pdb()
(in
PointMutationCalculator
)
defines_intrares_energy_for_residue()
(in
SuckerEnergy
)
distance()
(in
VallFragmentScore
)
dump_pdb()
(in
MatDesGreedyOptMutationMover
)
defines_intrares_energy_for_residue()
(in
TwoBodyEnergy
)
distance()
(in
rosetta.core.kinematics._core_kinematics_
)
dump_pdb()
(in
MatDesPointMutationCalculator
)
defines_intrares_energy_for_residue()
(in
WaterAdductHBondEnergy
)
distance()
(in
Atom
)
dump_pdb()
(in
FilterScanFilter
)
defines_intrares_energy_for_residue()
(in
DFIRE_Energy
)
distance()
(in
Atom_
)
dump_pdb()
(in
Rose
)
defines_intrares_energy_for_residue()
(in
OrbitalsScore
)
distance()
(in
rosetta.core.kinematics.tree._core_kinematics_tree_
)
dump_pdb_name()
(in
FilterScanFilter
)
defines_intrares_energy_for_residue()
(in
RNA_FullAtomStackingEnergy
)
distance()
(in
CentroidRotamerSampleData
)
dump_pdb_residue()
(in
rosetta.core.io.pdb._core_io_pdb_
)
defines_intrares_energy_for_residue()
(in
RNA_JR_SuiteEnergy
)
distance()
(in
DistanceHistogram
)
dump_pdb_to_file()
(in
HelixNCapperMover
)
defines_intrares_energy_for_residue()
(in
RNA_LJ_BaseEnergy
)
distance()
(in
ClusteringTreeNode
)
dump_pdb_to_file()
(in
VIP_Mover
)
defines_intrares_energy_for_residue()
(in
RNA_Mg_Energy
)
distance()
(in
xyzTransform_T_double_T
)
dump_pdb_when_fail()
(in
BluePrintBDR
)
defines_intrares_energy_for_residue()
(in
RNA_PairwiseLowResolutionEnergy
)
distance()
(in
xyzTransform_T_float_T
)
dump_pdbs()
(in
ddGMover
)
defines_intrares_energy_for_residue()
(in
RNA_SuiteEnergy
)
distance()
(in
xyzTriple_Real
)
dump_pdbs()
(in
FlexbbRotamerSets
)
defines_intrares_energy_for_residue()
(in
RNA_TorsionEnergy
)
distance()
(in
xyzTriple_SSize
)
dump_points_pdb()
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
defines_intrares_energy_for_residue()
(in
RNA_VDW_Energy
)
distance()
(in
xyzTriple_Size
)
dump_pose()
(in
AtomTreeDiffJobDistributor
)
defines_intrares_energy_for_residue()
(in
StackElecEnergy
)
distance()
(in
xyzTriple_double
)
dump_pose()
(in
PlainSilentFileJobDistributor
)
defines_intrares_energy_for_residue()
(in
RNA_DataBackboneEnergy
)
distance()
(in
xyzTriple_float
)
dump_pose_and_map()
(in
BaseJobDistributor
)
defines_intrares_energy_for_residue()
(in
symEnergy
)
distance()
(in
xyzVector_Real
)
dump_pose_and_map()
(in
PlainPdbJobDistributor
)
defines_intrares_energy_for_residue()
(in
InterchainPairEnergy
)
distance()
(in
xyzVector_SSize
)
dump_pose_and_map()
(in
PlainRawJobDistributor
)
defines_residue_pair_energy()
(in
ConstraintsEnergy
)
distance()
(in
xyzVector_Size
)
dump_pose_fname()
(in
RelativePoseFilter
)
defines_residue_pair_energy()
(in
CentroidDisulfideEnergy
)
distance()
(in
xyzVector_double
)
dump_poses()
(in
CartesianMD
)
defines_residue_pair_energy()
(in
DisulfideMatchingEnergy
)
distance()
(in
xyzVector_float
)
dump_pymol()
(in
JumpSample
)
defines_residue_pair_energy()
(in
FullatomDisulfideEnergy
)
distance()
(in
KDNode
)
dump_reference_pose()
(in
rosetta.core.import_pose.atom_tree_diffs._core_import_pose_atom_tree_diffs_
)
defines_residue_pair_energy()
(in
DNATorsionEnergy
)
distance()
(in
KDPoint
)
dump_resfile()
(in
MotifHits
)
defines_residue_pair_energy()
(in
ElecDensAllAtomCenEnergy
)
distance()
(in
CDRCluster
)
dump_score_line()
(in
rosetta.core.import_pose.atom_tree_diffs._core_import_pose_atom_tree_diffs_
)
defines_residue_pair_energy()
(in
ElecDensCenEnergy
)
distance()
(in
Interface
)
dump_scored_pdb()
(in
Pose
)
defines_residue_pair_energy()
(in
ElecDensEnergy
)
distance()
(in
InterfaceInfo
)
dump_scoring_table()
(in
GreedyOptMutationMover
)
defines_residue_pair_energy()
(in
FastDensEnergy
)
distance()
(in
RestrictToInterface
)
dump_scoring_table()
(in
MatDesGreedyOptMutationMover
)
defines_residue_pair_energy()
(in
PattersonCorrEnergy
)
distance_chainbreak
(in
ScoreType
)
dump_silent()
(in
PlainSilentFileJobDistributor
)
defines_residue_pair_energy()
(in
ElecDensAtomwiseEnergy
)
distance_chainbreak
(in
rosetta.core.scoring._core_scoring_
)
dump_table()
(in
GreedyOptMutationMover
)
defines_residue_pair_energy()
(in
CartesianBondedEnergy
)
distance_chainbreak
(in
rosetta.core.scoring
)
dump_table()
(in
ParetoOptMutationMover
)
defines_residue_pair_energy()
(in
ContextDependentLRTwoBodyEnergy
)
distance_chainbreak
(in
rosetta
)
dump_table()
(in
MatDesGreedyOptMutationMover
)
defines_residue_pair_energy()
(in
ContextIndependentLRTwoBodyEnergy
)
distance_cutoff()
(in
NumNeighborsSelector
)
dump_trisbpy()
(in
TrisBpyScore
)
defines_residue_pair_energy()
(in
GenBornEnergy
)
distance_cutoff()
(in
KDPointList
)
dump_vall_fasta()
(in
rosetta.protocols.frags._protocols_frags_
)
defines_residue_pair_energy()
(in
LongRangeTwoBodyEnergy
)
distance_cutoff()
(in
ChargeChargeFeatures
)
dump_vd_info()
(in
ResidueType
)
defines_residue_pair_energy()
(in
PoissonBoltzmannEnergy
)
distance_cutoff()
(in
SaltBridgeFeatures
)
dumpExemplarToFile()
(in
PocketGrid
)
defines_residue_pair_energy()
(in
Rama2BOffsetEnergy
)
distance_cutoff()
(in
InterfacePackingFilter
)
dumpGridToFile()
(in
PocketGrid
)
defines_residue_pair_energy()
(in
DFIRE_Energy
)
distance_matrix()
(in
ClusterBase
)
DumpPdb
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
defines_residue_pair_energy()
(in
RNA_JR_SuiteEnergy
)
distance_pair()
(in
SetupNCSMover
)
DumpPdbAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
defines_residue_pair_energy()
(in
RNA_SuiteEnergy
)
distance_squared
(in
AtomPairEnergy
)
DumpPdbCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
defines_residue_pair_energy()
(in
RNA_TorsionEnergy
)
distance_squared()
(in
RT
)
DumpPdbCreator
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
defines_residue_pair_energy()
(in
symEnergy
)
distance_squared()
(in
Atom
)
DumpPdbCreatorAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
defines_score_for_residue()
(in
DunbrackEnergy
)
distance_squared()
(in
Atom_
)
DumpPdbCreatorCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
defines_score_for_residue()
(in
CenRotDunEnergy
)
distance_squared()
(in
rosetta.core.kinematics.tree._core_kinematics_tree_
)
dumpTargetPocketsToFile()
(in
PocketGrid
)
defines_score_for_residue()
(in
HPatchEnergy
)
distance_squared()
(in
xyzTransform_T_double_T
)
dumpTargetPocketsToPDB()
(in
PocketGrid
)
defines_score_for_residue()
(in
SurfaceEnergy
)
distance_squared()
(in
xyzTransform_T_float_T
)
dumpTargetPocketsToPDB()
(in
TargetPocketGrid
)
defines_score_for_residue()
(in
DNAChiEnergy
)
distance_squared()
(in
xyzTriple_Real
)
dunbrack
(in
rosetta.core.pack
)
defines_score_for_residue()
(in
ExactOccludedHbondSolEnergy
)
distance_squared()
(in
xyzTriple_SSize
)
dunbrack_constraint
(in
ScoreType
)
defines_score_for_residue()
(in
OccludedHbondSolEnergy_onebody
)
distance_squared()
(in
xyzTriple_Size
)
dunbrack_constraint
(in
rosetta.core.scoring._core_scoring_
)
defines_score_for_residue()
(in
FaMPEnvEnergy
)
distance_squared()
(in
xyzTriple_double
)
dunbrack_constraint
(in
rosetta.core.scoring
)
defines_score_for_residue()
(in
FaMPEnvSmoothEnergy
)
distance_squared()
(in
xyzTriple_float
)
dunbrack_constraint
(in
rosetta
)
defines_score_for_residue()
(in
MPCbetaEnergy
)
distance_squared()
(in
xyzVector_Real
)
dunbrack_method
(in
EnergyMethods
)
defines_score_for_residue()
(in
MPEnvEnergy
)
distance_squared()
(in
xyzVector_SSize
)
dunbrack_method
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
defines_score_for_residue()
(in
MPNonHelixPenalty
)
distance_squared()
(in
xyzVector_Size
)
dunbrack_method
(in
rosetta.core.scoring.methods
)
defines_score_for_residue()
(in
MPTerminiPenalty
)
distance_squared()
(in
xyzVector_double
)
dunbrack_print()
(in
rosetta.protocols.make_rot_lib._protocols_make_rot_lib_
)
defines_score_for_residue()
(in
BurialEnergy
)
distance_squared()
(in
xyzVector_float
)
DunbrackConstraint
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
defines_score_for_residue()
(in
CenRotEnvEnergy
)
distance_squared()
(in
VallResidue
)
DunbrackConstraintAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
defines_score_for_residue()
(in
ContextDependentOneBodyEnergy
)
distance_squared_cb()
(in
VallResidue
)
DunbrackConstraintCAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
defines_score_for_residue()
(in
ContextIndependentOneBodyEnergy
)
distance_squared_cen()
(in
VallResidue
)
DunbrackConstraintCreator
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
defines_score_for_residue()
(in
EnvEnergy
)
distance_threshold()
(in
OligomericAverageDegreeFilter
)
DunbrackConstraintCreatorAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
defines_score_for_residue()
(in
EnvSmoothEnergy
)
distance_threshold()
(in
AverageDegreeFilter
)
DunbrackConstraintCreatorCAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
defines_score_for_residue()
(in
Fa_MbenvEnergy
)
distance_threshold()
(in
NonSequentialNeighborsFilter
)
DunbrackEnergy
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
defines_score_for_residue()
(in
FreeDOF_Energy
)
distance_threshold()
(in
ResidueBurialFilter
)
DunbrackEnergyAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
defines_score_for_residue()
(in
MembraneCbetaEnergy
)
DistanceChainbreakEnergy
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
DunbrackEnergyCAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
defines_score_for_residue()
(in
MembraneEnvEnergy
)
DistanceChainbreakEnergyAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
DunbrackEnergyCreator
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
defines_score_for_residue()
(in
MembraneEnvSmoothEnergy
)
DistanceChainbreakEnergyCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
DunbrackEnergyCreatorAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
defines_score_for_residue()
(in
NMerPSSMEnergy
)
DistanceChainbreakEnergyCreator
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
DunbrackEnergyCreatorCAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
defines_score_for_residue()
(in
NMerRefEnergy
)
DistanceChainbreakEnergyCreatorAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
DunbrackRotamerSampleData
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
defines_score_for_residue()
(in
NMerSVMEnergy
)
DistanceChainbreakEnergyCreatorCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
DunbrackRotamerSampleDataAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
defines_score_for_residue()
(in
OmegaTetherEnergy
)
DistanceFunc
(in
rosetta.core.scoring.custom_pair_distance._core_scoring_custom_pair_distance_
)
DunbrackRotamerSampleDataCAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
defines_score_for_residue()
(in
OneBodyEnergy
)
DistanceFuncAP
(in
rosetta.core.scoring.custom_pair_distance._core_scoring_custom_pair_distance_
)
DunbrackSCSampler
(in
rosetta.protocols.match.upstream._protocols_match_upstream_
)
defines_score_for_residue()
(in
P_AA_Energy
)
DistanceFuncCAP
(in
rosetta.core.scoring.custom_pair_distance._core_scoring_custom_pair_distance_
)
DunbrackSCSamplerAP
(in
rosetta.protocols.match.upstream._protocols_match_upstream_
)
defines_score_for_residue()
(in
P_AA_pp_Energy
)
DistanceHistogram
(in
rosetta.core.scoring.saxs._core_scoring_saxs_
)
DunbrackSCSamplerCAP
(in
rosetta.protocols.match.upstream._protocols_match_upstream_
)
defines_score_for_residue()
(in
RamachandranEnergy
)
DistanceHistogramAP
(in
rosetta.core.scoring.saxs._core_scoring_saxs_
)
dw_dr()
(in
FAElecContextData
)
defines_score_for_residue()
(in
ReferenceEnergy
)
DistanceHistogramCAP
(in
rosetta.core.scoring.saxs._core_scoring_saxs_
)
dweight()
(in
MinimizationEdge
)
defines_score_for_residue()
(in
ReferenceEnergyNoncanonical
)
DistancePairConstraint
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
dweight()
(in
MinimizationNode
)
defines_score_for_residue()
(in
SequenceDependentRefEnergy
)
DistancePairConstraintAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
Dx2y2
(in
AtomicOrbitalTypes
)
defines_score_for_residue()
(in
SmoothEnvEnergy
)
DistancePairConstraintCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
Dx2y2
(in
GasteigerAtomTypeData
)
defines_score_for_residue()
(in
SymmetricLigandEnergy
)
DistanceResidueNetwork
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
dx_ddelta_omega1()
(in
rosetta.numeric.crick_equations._numeric_crick_equations_
)
defines_score_for_residue()
(in
UnfoldedStateEnergy
)
DistanceResidueNetworkAP
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
dx_ddelta_z1()
(in
rosetta.numeric.crick_equations._numeric_crick_equations_
)
defines_score_for_residue()
(in
WaterAdductIntraEnergy
)
DistanceResidueNetworkCAP
(in
rosetta.protocols.toolbox._protocols_toolbox_
)
dx_ddz1()
(in
rosetta.numeric.crick_equations._numeric_crick_equations_
)
defines_score_for_residue()
(in
YHHPlanarityEnergy
)
distbin_map()
(in
GoapEnergy
)
dx_domega1()
(in
rosetta.numeric.crick_equations._numeric_crick_equations_
)
defines_score_for_residue()
(in
pHEnergy
)
distinguish_backbone_and_sidechain()
(in
OnTheFlyNode
)
dx_dr1()
(in
rosetta.numeric.crick_equations._numeric_crick_equations_
)
defines_score_for_residue()
(in
SugarBackboneEnergy
)
distinguish_backbone_and_sidechain()
(in
SymmOnTheFlyNode
)
Dxy
(in
AtomicOrbitalTypes
)
defines_score_for_residue()
(in
NVscore
)
distinguish_backbone_and_sidechain_for_node()
(in
OnTheFlyInteractionGraph
)
Dxy
(in
GasteigerAtomTypeData
)
defines_score_for_residue()
(in
RNA_BulgeEnergy
)
distinguish_backbone_and_sidechain_for_node()
(in
SymmOnTheFlyInteractionGraph
)
Dxz
(in
AtomicOrbitalTypes
)
defines_score_for_residue()
(in
RNA_FullAtomVDW_BasePhosphate
)
distinguish_pucker()
(in
StepWiseRNA_ModelerOptions
)
Dxz
(in
GasteigerAtomTypeData
)
defines_score_for_residue()
(in
RNA_SugarCloseEnergy
)
Distribution
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
dy_ddelta_omega1()
(in
rosetta.numeric.crick_equations._numeric_crick_equations_
)
defines_score_for_residue()
(in
AACompositionEnergy
)
DistributionMap
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
dy_ddelta_z1()
(in
rosetta.numeric.crick_equations._numeric_crick_equations_
)
defines_score_for_residue()
(in
InterchainEnvEnergy
)
DistributionMapAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
dy_ddz1()
(in
rosetta.numeric.crick_equations._numeric_crick_equations_
)
defines_score_for_residue()
(in
SpecialRotamerEnergy
)
DistributionMapCAP
(in
rosetta.protocols.ligand_docking._protocols_ligand_docking_
)
dy_domega1()
(in
rosetta.numeric.crick_equations._numeric_crick_equations_
)
defines_score_for_residue_pair()
(in
CarbonHBondEnergy
)
disulf_atom_index()
(in
DisulfideAtomIndices
)
dy_dr1()
(in
rosetta.numeric.crick_equations._numeric_crick_equations_
)
defines_score_for_residue_pair()
(in
ConstraintsEnergy
)
DISULFIDE
(in
rosetta
)
dynamic_grid_refinement()
(in
MatcherTask
)
defines_score_for_residue_pair()
(in
FullatomCustomPairDistanceEnergy
)
DISULFIDE
(in
rosetta.core.chemical
)
dynamic_memory_usage()
(in
recent_history_queue
)
defines_score_for_residue_pair()
(in
CentroidDisulfideEnergy
)
DISULFIDE
(in
rosetta.core.chemical._core_chemical_
)
DynamicAggregateFunction
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
defines_score_for_residue_pair()
(in
DisulfideMatchingEnergy
)
DISULFIDE
(in
VariantType
)
DynamicAggregateFunctionAP
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
defines_score_for_residue_pair()
(in
FullatomDisulfideEnergy
)
DISULFIDE
(in
rosetta.core.pose.full_model_info
)
DynamicAggregateFunctionCAP
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
defines_score_for_residue_pair()
(in
DNATorsionEnergy
)
DISULFIDE
(in
rosetta.core.pose.full_model_info._core_pose_full_model_info_
)
DynamicAggregateFunctionDriver
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
defines_score_for_residue_pair()
(in
FA_ElecEnergy
)
DISULFIDE
(in
FullModelParameterType
)
DynamicAggregateFunctionDriverAP
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
defines_score_for_residue_pair()
(in
FA_ElecEnergyAroAll
)
disulfide_atom_indices()
(in
CentroidDisulfideEnergyContainer
)
DynamicAggregateFunctionDriverCAP
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
defines_score_for_residue_pair()
(in
FA_ElecEnergyAroAro
)
disulfide_atom_indices()
(in
DisulfideMatchingEnergyContainer
)
DynamicProfileThis
(in
rosetta.basic._basic_
)
defines_score_for_residue_pair()
(in
FA_GrpElecEnergy
)
disulfide_atom_indices()
(in
FullatomDisulfideEnergyContainer
)
DynamicProfileThisAP
(in
rosetta.basic._basic_
)
defines_score_for_residue_pair()
(in
RNA_FA_ElecEnergy
)
DISULFIDE_BONDED
(in
rosetta
)
DynamicProfileThisCAP
(in
rosetta.basic._basic_
)
defines_score_for_residue_pair()
(in
ElecDensAllAtomCenEnergy
)
DISULFIDE_BONDED
(in
rosetta.core.chemical
)
Dyz
(in
AtomicOrbitalTypes
)
defines_score_for_residue_pair()
(in
ElecDensCenEnergy
)
DISULFIDE_BONDED
(in
rosetta.core.chemical._core_chemical_
)
Dyz
(in
GasteigerAtomTypeData
)
defines_score_for_residue_pair()
(in
ElecDensEnergy
)
DISULFIDE_BONDED
(in
ResidueProperty
)
Dz2
(in
AtomicOrbitalTypes
)
defines_score_for_residue_pair()
(in
FastDensEnergy
)
disulfide_bonded()
(in
CentroidDisulfideEnergyContainer
)
Dz2
(in
GasteigerAtomTypeData
)
defines_score_for_residue_pair()
(in
PattersonCorrEnergy
)
disulfide_bonded()
(in
DisulfideMatchingEnergyContainer
)
dz_ddelta_omega1()
(in
rosetta.numeric.crick_equations._numeric_crick_equations_
)
defines_score_for_residue_pair()
(in
ElecDensAtomwiseEnergy
)
disulfide_bonded()
(in
FullatomDisulfideEnergyContainer
)
dz_ddelta_z1()
(in
rosetta.numeric.crick_equations._numeric_crick_equations_
)
defines_score_for_residue_pair()
(in
AnalyticEtableEnergy
)
disulfide_bonds()
(in
rosetta.core.conformation._core_conformation_
)
dz_ddz1()
(in
rosetta.numeric.crick_equations._numeric_crick_equations_
)
defines_score_for_residue_pair()
(in
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T
)
disulfide_list()
(in
DisulfideMover
)
dz_domega1()
(in
rosetta.numeric.crick_equations._numeric_crick_equations_
)
defines_score_for_residue_pair()
(in
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T
)
disulfide_matching_energy
(in
LongRangeEnergyType
)
dz_dr1()
(in
rosetta.numeric.crick_equations._numeric_crick_equations_
)
defines_score_for_residue_pair()
(in
TableLookupEtableEnergy
)
disulfide_matching_energy
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
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