Home
Trees
Indices
Help
[
hide private
]
[
frames
] |
no frames
]
Identifier Index
[
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
_
]
B
B
(in
rosetta.protocols.comparative_modeling.features
)
BB_PH
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
BOTH_SC_AND_BB
(in
FlexbbInteractionGraph
)
B
(in
rosetta.protocols.comparative_modeling.features._protocols_comparative_modeling_features_
)
BB_PH
(in
RPM_Type
)
BOTH_SC_AND_BB
(in
Subsitution
)
B
(in
TorsionBin
)
BB_PO
(in
rosetta.core.scoring.motif
)
bottom()
(in
DnaPosition
)
B
(in
rosetta.protocols.features
)
BB_PO
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
bound()
(in
NonSequentialNeighborsFilter
)
B
(in
rosetta.protocols.features._protocols_features_
)
BB_PO
(in
RPM_Type
)
bound_struct()
(in
DGBindOptEData
)
B
(in
RamachandranHash
)
BB_Pos
(in
rosetta.core.scoring._core_scoring_
)
bound_width()
(in
AddConstraintsToCurrentConformationMover
)
B()
(in
CrystInfo
)
BB_Pos
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
boundary_left()
(in
FoldTree
)
B()
(in
OneGaussianScattering
)
bb_pos()
(in
SS_Info
)
boundary_neighs()
(in
FAElecContextData
)
b1_b2_Ktheta()
(in
BranchParam2
)
bb_pos()
(in
SS_Info2
)
boundary_right()
(in
FoldTree
)
b1_b2_theta0()
(in
BranchParam2
)
BB_PosAP
(in
rosetta.core.scoring._core_scoring_
)
bounded()
(in
AtomCoordinateCstMover
)
b1_bond_angle_A()
(in
BranchCoef1
)
BB_PosAP
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
bounded_loops_from_alignment()
(in
rosetta.protocols.comparative_modeling._protocols_comparative_modeling_
)
b1_bond_angle_B()
(in
BranchCoef1
)
BB_PosCAP
(in
rosetta.core.scoring._core_scoring_
)
bounded_protocol()
(in
FragmentPicker
)
b1_bond_angle_C()
(in
BranchCoef1
)
BB_PosCAP
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
BoundedCollector_CompareTotalScore
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
b1_torsion_offset_A()
(in
BranchCoef1
)
bb_radius()
(in
SimpleNode
)
BoundedCollector_CompareTotalScoreAP
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
b1_torsion_offset_B()
(in
BranchCoef1
)
bb_rmsd()
(in
rosetta.core.scoring._core_scoring_
)
BoundedCollector_CompareTotalScoreCAP
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
b1_torsion_offset_C()
(in
BranchCoef1
)
bb_rmsd_including_O()
(in
rosetta.core.scoring._core_scoring_
)
BoundedCollector_T_protocols_frag_picker_CompareTotalScore_T
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
b2_bond_angle_A()
(in
BranchCoef2
)
bb_stats()
(in
OrbitalsStatistics
)
BoundedCollector_T_protocols_frag_picker_CompareTotalScore_TAP
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
b2_bond_angle_B()
(in
BranchCoef2
)
BBClaim
(in
rosetta.protocols.topology_broker.claims._protocols_topology_broker_claims_
)
BoundedCollector_T_protocols_frag_picker_CompareTotalScore_TCAP
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
b2_bond_angle_C()
(in
BranchCoef2
)
BBClaimAP
(in
rosetta.protocols.topology_broker.claims._protocols_topology_broker_claims_
)
BoundFunc
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
b2_torsion_offset_A()
(in
BranchCoef2
)
BBClaimCAP
(in
rosetta.protocols.topology_broker.claims._protocols_topology_broker_claims_
)
BoundFuncAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
b2_torsion_offset_B()
(in
BranchCoef2
)
bbconf_for_rotamer()
(in
FlexbbRotamerSets
)
BoundFuncCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
b2_torsion_offset_C()
(in
BranchCoef2
)
bbconf_for_rotamer_on_moltenres()
(in
FlexbbRotamerSets
)
bounding_box()
(in
SixDCoordinateBinner
)
b_is_full_motif_bb_alignment()
(in
MotifMatch
)
BBConRotMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
bounding_box()
(in
ActiveSiteGrid
)
BAB_CFr
(in
rosetta.protocols.fldsgn.topology
)
BBConRotMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
bounding_radius_for_rotamers()
(in
OTFFlexbbNode
)
BAB_CFr
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
BBConRotMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
bounding_volume_from_index()
(in
SixDCoordinateBinner
)
BAB_CFr
(in
SheetFoldType
)
BBData
(in
rosetta.protocols.loophash._protocols_loophash_
)
bounds()
(in
KDTree
)
bab_motif()
(in
BetaAlphaBetaMotifSet
)
BBDataAP
(in
rosetta.protocols.loophash._protocols_loophash_
)
bp_motifhits()
(in
MotifSearch
)
bab_motifs()
(in
BetaAlphaBetaMotifSet
)
BBDataCAP
(in
rosetta.protocols.loophash._protocols_loophash_
)
bp_rotamers()
(in
LigandMotifSearch
)
BABx1
(in
rosetta.protocols.fldsgn.topology
)
bbdb_range()
(in
LoopHashMap
)
bp_rotamers()
(in
MotifSearch
)
BABx1
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
bbdep_angle_parameters()
(in
ResidueCartBondedParameters
)
bpdefs2map()
(in
rosetta.protocols.motifs._protocols_motifs_
)
BABx1
(in
SheetFoldType
)
bbdep_bond_devs()
(in
IdealParametersDatabase
)
bQuickTest()
(in
ClassicAbinitio
)
BABx2
(in
rosetta.protocols.fldsgn.topology
)
bbdep_bond_params()
(in
IdealParametersDatabase
)
bQuickTest()
(in
FragmentSampler
)
BABx2
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
bbdep_length_parameters()
(in
ResidueCartBondedParameters
)
bQuickTest()
(in
MembraneAbinitio
)
BABx2
(in
SheetFoldType
)
BBDepCartBondedParameters
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
branch_angle
(in
rosetta.protocols
)
BABx3
(in
rosetta.protocols.fldsgn.topology
)
BBDepCartBondedParametersAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
BRANCH_LOWER_TERMINUS
(in
rosetta
)
BABx3
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
BBDepCartBondedParametersCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
BRANCH_LOWER_TERMINUS
(in
rosetta.core.chemical
)
BABx3
(in
SheetFoldType
)
BBDepNRChiSample_T_double_T
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
BRANCH_LOWER_TERMINUS
(in
rosetta.core.chemical._core_chemical_
)
back()
(in
ChainedSolutionList
)
BBDepNRChiSample_T_double_TAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
BRANCH_LOWER_TERMINUS
(in
ResidueProperty
)
backbone_aa()
(in
ResidueType
)
BBDepNRChiSample_T_double_TCAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
BRANCH_LOWER_TERMINUS_VARIANT
(in
rosetta
)
backbone_aa()
(in
Residue
)
BBDepNRChiSample_T_float_T
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
BRANCH_LOWER_TERMINUS_VARIANT
(in
rosetta.core.chemical
)
backbone_backbone_energy()
(in
CarbonHBondEnergy
)
BBDepNRChiSample_T_float_TAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
BRANCH_LOWER_TERMINUS_VARIANT
(in
rosetta.core.chemical._core_chemical_
)
backbone_backbone_energy()
(in
ConstraintsEnergy
)
BBDepNRChiSample_T_float_TCAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
BRANCH_LOWER_TERMINUS_VARIANT
(in
VariantType
)
backbone_backbone_energy()
(in
FullatomCustomPairDistanceEnergy
)
BBExtraData
(in
rosetta.protocols.loophash._protocols_loophash_
)
BRANCH_POINT
(in
rosetta
)
backbone_backbone_energy()
(in
CentroidDisulfideEnergy
)
BBExtraDataAP
(in
rosetta.protocols.loophash._protocols_loophash_
)
BRANCH_POINT
(in
rosetta.core.chemical
)
backbone_backbone_energy()
(in
DisulfideMatchingEnergy
)
BBExtraDataCAP
(in
rosetta.protocols.loophash._protocols_loophash_
)
BRANCH_POINT
(in
rosetta.core.chemical._core_chemical_
)
backbone_backbone_energy()
(in
FullatomDisulfideEnergy
)
BBG8T3AMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
BRANCH_POINT
(in
ResidueProperty
)
backbone_backbone_energy()
(in
DNATorsionEnergy
)
BBG8T3AMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
branch_point()
(in
CarbohydrateInfo
)
backbone_backbone_energy()
(in
FA_ElecEnergy
)
BBG8T3AMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
BranchAngleOptimizer
(in
rosetta.protocols.branch_angle._protocols_branch_angle_
)
backbone_backbone_energy()
(in
FA_ElecEnergyAroAll
)
BBGaussianMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
BranchAngleOptimizerAP
(in
rosetta.protocols.branch_angle._protocols_branch_angle_
)
backbone_backbone_energy()
(in
FA_ElecEnergyAroAro
)
BBGaussianMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
BranchAngleOptimizerCAP
(in
rosetta.protocols.branch_angle._protocols_branch_angle_
)
backbone_backbone_energy()
(in
FA_GrpElecEnergy
)
BBGaussianMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
BranchCoef1
(in
rosetta.protocols.branch_angle._protocols_branch_angle_
)
backbone_backbone_energy()
(in
RNA_FA_ElecEnergy
)
BBGaussianMoverCreator
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
BranchCoef1AP
(in
rosetta.protocols.branch_angle._protocols_branch_angle_
)
backbone_backbone_energy()
(in
ElecDensAllAtomCenEnergy
)
BBGaussianMoverCreatorAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
BranchCoef1CAP
(in
rosetta.protocols.branch_angle._protocols_branch_angle_
)
backbone_backbone_energy()
(in
ElecDensCenEnergy
)
BBGaussianMoverCreatorCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
BranchCoef2
(in
rosetta.protocols.branch_angle._protocols_branch_angle_
)
backbone_backbone_energy()
(in
ElecDensEnergy
)
BBIndepCartBondedParameters
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
BranchCoef2AP
(in
rosetta.protocols.branch_angle._protocols_branch_angle_
)
backbone_backbone_energy()
(in
FastDensEnergy
)
BBIndepCartBondedParametersAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
BranchCoef2CAP
(in
rosetta.protocols.branch_angle._protocols_branch_angle_
)
backbone_backbone_energy()
(in
PattersonCorrEnergy
)
BBIndepCartBondedParametersCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
branching_atomid1()
(in
rosetta.protocols.branch_angle._protocols_branch_angle_
)
backbone_backbone_energy()
(in
ElecDensAtomwiseEnergy
)
BBIndNRChiSample_T_float_T
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
branching_atomids2()
(in
rosetta.protocols.branch_angle._protocols_branch_angle_
)
backbone_backbone_energy()
(in
AnalyticEtableEnergy
)
BBIndNRChiSample_T_float_TAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
branchopt()
(in
BackrubMover
)
backbone_backbone_energy()
(in
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T
)
BBIndNRChiSample_T_float_TCAP
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
BranchParam1
(in
rosetta.protocols.branch_angle._protocols_branch_angle_
)
backbone_backbone_energy()
(in
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T
)
bbpos_is_set()
(in
SS_Info2
)
BranchParam1AP
(in
rosetta.protocols.branch_angle._protocols_branch_angle_
)
backbone_backbone_energy()
(in
TableLookupEtableEnergy
)
bbs_appropriate_for_definitions()
(in
MakeRotLibMover
)
BranchParam1CAP
(in
rosetta.protocols.branch_angle._protocols_branch_angle_
)
backbone_backbone_energy()
(in
ContextDependentGeometricSolEnergy
)
bbtorsion_srfd()
(in
VallResidue
)
BranchParam2
(in
rosetta.protocols.branch_angle._protocols_branch_angle_
)
backbone_backbone_energy()
(in
ContextIndependentGeometricSolEnergy
)
bbtorsion_srfd()
(in
VallResidue
)
BranchParam2AP
(in
rosetta.protocols.branch_angle._protocols_branch_angle_
)
backbone_backbone_energy()
(in
OccludedHbondSolEnergy
)
BBTorsionAndAnglesSRFD
(in
rosetta.core.fragment._core_fragment_
)
BranchParam2CAP
(in
rosetta.protocols.branch_angle._protocols_branch_angle_
)
backbone_backbone_energy()
(in
HackAroEnergy
)
BBTorsionAndAnglesSRFDAP
(in
rosetta.core.fragment._core_fragment_
)
BRENT()
(in
BrentLineMinimization
)
backbone_backbone_energy()
(in
HBondEnergy
)
BBTorsionAndAnglesSRFDCAP
(in
rosetta.core.fragment._core_fragment_
)
brent_abs_tolerance()
(in
MinimizerOptions
)
backbone_backbone_energy()
(in
DDPscore
)
BBTorsionSRFD
(in
rosetta.core.fragment._core_fragment_
)
BrentLineMinimization
(in
rosetta.core.optimization._core_optimization_
)
backbone_backbone_energy()
(in
FaMPSolvEnergy
)
BBTorsionSRFDAP
(in
rosetta.core.fragment._core_fragment_
)
BrentLineMinimizationAP
(in
rosetta.core.optimization._core_optimization_
)
backbone_backbone_energy()
(in
MPPairEnergy
)
BBTorsionSRFDCAP
(in
rosetta.core.fragment._core_fragment_
)
BrentLineMinimizationCAP
(in
rosetta.core.optimization._core_optimization_
)
backbone_backbone_energy()
(in
CartesianBondedEnergy
)
BDR
(in
rosetta.protocols.forge.components._protocols_forge_components_
)
Bridge
(in
rosetta.protocols.forge.build._protocols_forge_build_'
)
backbone_backbone_energy()
(in
CenHBEnergy
)
BDRAP
(in
rosetta.protocols.forge.components._protocols_forge_components_
)
bridge_res()
(in
StepWiseProteinModelerOptions
)
backbone_backbone_energy()
(in
CenPairEnergy
)
BDRCAP
(in
rosetta.protocols.forge.components._protocols_forge_components_
)
BridgeAP
(in
rosetta.protocols.forge.build._protocols_forge_build_'
)
backbone_backbone_energy()
(in
CenRotPairEnergy
)
be_lenient()
(in
FilteredSolutions
)
BridgeCAP
(in
rosetta.protocols.forge.build._protocols_forge_build_'
)
backbone_backbone_energy()
(in
ContextDependentLRTwoBodyEnergy
)
bead_bead_interaction
(in
AtomPairEnergy
)
bridgeObjects()
(in
rosetta.numeric.kinematic_closure._numeric_kinematic_closure_
)
backbone_backbone_energy()
(in
ContextDependentTwoBodyEnergy
)
BEFr
(in
rosetta.protocols.fldsgn.topology
)
broker()
(in
Environment
)
backbone_backbone_energy()
(in
ContextIndependentLRTwoBodyEnergy
)
BEFr
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
broker()
(in
TopologyClaimer
)
backbone_backbone_energy()
(in
ContextIndependentTwoBodyEnergy
)
BEFr
(in
SheetFoldType
)
broker_file()
(in
Batch
)
backbone_backbone_energy()
(in
CustomAtomPairEnergy
)
begin()
(in
DataMap
)
Broker_main()
(in
rosetta.protocols.abinitio._protocols_abinitio_
)
backbone_backbone_energy()
(in
DNA_BaseEnergy
)
begin()
(in
WriteableCacheableMap
)
broking_finished()
(in
AbscriptLoopCloserCM
)
backbone_backbone_energy()
(in
Fa_MbsolvEnergy
)
begin()
(in
DofPassport
)
brute_move_large()
(in
ClassicAbinitio
)
backbone_backbone_energy()
(in
GaussianOverlapEnergy
)
begin()
(in
ConstantLengthFragSet
)
brute_move_large()
(in
MembraneAbinitio
)
backbone_backbone_energy()
(in
GenBornEnergy
)
begin()
(in
FragSet
)
brute_move_small()
(in
ClassicAbinitio
)
backbone_backbone_energy()
(in
GoapEnergy
)
begin()
(in
FragSetCollection
)
brute_move_small()
(in
MembraneAbinitio
)
backbone_backbone_energy()
(in
HybridVDW_Energy
)
begin()
(in
OrderedFragSet
)
brute_move_small_top25()
(in
MembraneAbinitio
)
backbone_backbone_energy()
(in
LK_BallEnergy
)
begin()
(in
Book_T_core_fragment_picking_old_vall_VallResidues_T
)
BruteFunGroupTK
(in
rosetta.protocols.kinmatch._protocols_kinmatch_
)
backbone_backbone_energy()
(in
LK_PolarNonPolarEnergy
)
begin()
(in
Library_T_core_fragment_picking_old_vall_VallSections_T
)
BruteFunGroupTKAP
(in
rosetta.protocols.kinmatch._protocols_kinmatch_
)
backbone_backbone_energy()
(in
LK_hack
)
begin()
(in
EdgeList
)
BruteFunGroupTKCAP
(in
rosetta.protocols.kinmatch._protocols_kinmatch_
)
backbone_backbone_energy()
(in
LongRangeTwoBodyEnergy
)
begin()
(in
RawFileData
)
BT_ALPHA_AA
(in
rosetta.core.scoring.bin_transitions
)
backbone_backbone_energy()
(in
MMBondAngleEnergy
)
begin()
(in
SilentFileData
)
BT_ALPHA_AA
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_backbone_energy()
(in
MMBondLengthEnergy
)
begin()
(in
FoldTree
)
BT_ALPHA_AA
(in
BT_PROPERTIES
)
backbone_backbone_energy()
(in
MMLJEnergyInter
)
begin()
(in
MinimizerMap
)
BT_AROMATIC
(in
rosetta.core.scoring.bin_transitions
)
backbone_backbone_energy()
(in
MMLJEnergyIntra
)
begin()
(in
SymMinimizerMap
)
BT_AROMATIC
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_backbone_energy()
(in
MMTorsionEnergy
)
begin()
(in
FixbbRotamerSets
)
BT_AROMATIC
(in
BT_PROPERTIES
)
backbone_backbone_energy()
(in
MembraneCenPairEnergy
)
begin()
(in
RotamerSet
)
BT_BETA_AA
(in
rosetta.core.scoring.bin_transitions
)
backbone_backbone_energy()
(in
PairEnergy
)
begin()
(in
RotamerSet_
)
BT_BETA_AA
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_backbone_energy()
(in
PeptideBondEnergy
)
begin()
(in
RotamerSets
)
BT_BETA_AA
(in
BT_PROPERTIES
)
backbone_backbone_energy()
(in
PoissonBoltzmannEnergy
)
begin()
(in
RotamerSubset
)
BT_CHARGED
(in
rosetta.core.scoring.bin_transitions
)
backbone_backbone_energy()
(in
ProClosureEnergy
)
begin()
(in
RotamerSubsets
)
BT_CHARGED
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_backbone_energy()
(in
Rama2BOffsetEnergy
)
begin()
(in
SymmetricRotamerSet_
)
BT_CHARGED
(in
BT_PROPERTIES
)
backbone_backbone_energy()
(in
RamachandranEnergy2B
)
begin()
(in
TaskFactory
)
BT_CYCLIC
(in
rosetta.core.scoring.bin_transitions
)
backbone_backbone_energy()
(in
ShortRangeTwoBodyEnergy
)
begin()
(in
Constraints
)
BT_CYCLIC
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_backbone_energy()
(in
SmoothCenPairEnergy
)
begin()
(in
ResidueConstraints
)
BT_CYCLIC
(in
BT_PROPERTIES
)
backbone_backbone_energy()
(in
SuckerEnergy
)
begin()
(in
StrandPairingSet
)
BT_D_AA
(in
rosetta.core.scoring.bin_transitions
)
backbone_backbone_energy()
(in
TwoBodyEnergy
)
begin()
(in
xyzStripeHash
)
BT_D_AA
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_backbone_energy()
(in
WaterAdductHBondEnergy
)
begin()
(in
KDPointList
)
BT_D_AA
(in
BT_PROPERTIES
)
backbone_backbone_energy()
(in
DFIRE_Energy
)
begin()
(in
PairingStatistics
)
BT_DISULFIDE_BONDED
(in
rosetta.core.scoring.bin_transitions
)
backbone_backbone_energy()
(in
OrbitalsScore
)
begin()
(in
Templates
)
BT_DISULFIDE_BONDED
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_backbone_energy()
(in
RNA_FullAtomStackingEnergy
)
begin()
(in
DnaChains
)
BT_DISULFIDE_BONDED
(in
BT_PROPERTIES
)
backbone_backbone_energy()
(in
RNA_JR_SuiteEnergy
)
begin()
(in
CompoundFilter
)
BT_END_OF_LIST
(in
rosetta.core.scoring.bin_transitions
)
backbone_backbone_energy()
(in
RNA_LJ_BaseEnergy
)
begin()
(in
HSSTripletSet
)
BT_END_OF_LIST
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_backbone_energy()
(in
RNA_Mg_Energy
)
begin()
(in
SS_Base
)
BT_END_OF_LIST
(in
BT_PROPERTIES
)
backbone_backbone_energy()
(in
RNA_PairwiseLowResolutionEnergy
)
begin()
(in
StrandPairingSet
)
BT_FORMS_DISULFIDE_BOND
(in
rosetta.core.scoring.bin_transitions
)
backbone_backbone_energy()
(in
RNA_SuiteEnergy
)
begin()
(in
FlexbbRotamerSet
)
BT_FORMS_DISULFIDE_BOND
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_backbone_energy()
(in
RNA_TorsionEnergy
)
begin()
(in
BuildManager
)
BT_FORMS_DISULFIDE_BOND
(in
BT_PROPERTIES
)
backbone_backbone_energy()
(in
RNA_VDW_Energy
)
begin()
(in
HotspotStubSet
)
BT_L_AA
(in
rosetta.core.scoring.bin_transitions
)
backbone_backbone_energy()
(in
StackElecEnergy
)
begin()
(in
JumpSelector
)
BT_L_AA
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_backbone_energy()
(in
RNA_DataBackboneEnergy
)
begin()
(in
JumpSetup
)
BT_L_AA
(in
BT_PROPERTIES
)
backbone_backbone_energy()
(in
symEnergy
)
begin()
(in
ResiduePairJumpSetup
)
BT_METALBINDING
(in
rosetta.core.scoring.bin_transitions
)
backbone_backbone_energy()
(in
InterchainPairEnergy
)
begin()
(in
ChainedSolutionList
)
BT_METALBINDING
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_bin
(in
rosetta.protocols.generalized_kinematic_closure.filter._protocols_generalized_kinematic_closure_filter_
)
begin()
(in
MinimizeLigand
)
BT_METALBINDING
(in
BT_PROPERTIES
)
backbone_bin
(in
filter_type
)
begin()
(in
Loops
)
BT_POLAR
(in
rosetta.core.scoring.bin_transitions
)
backbone_bin
(in
rosetta.protocols.generalized_kinematic_closure.filter
)
begin()
(in
MotifLibrary
)
BT_POLAR
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_burial()
(in
RNA_DataInfo
)
begin()
(in
PlacementAuctionMover
)
BT_POLAR
(in
BT_PROPERTIES
)
backbone_database()
(in
LoopHashLibrary
)
begin()
(in
TryRotamers
)
BT_PROPERTIES
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_exposed()
(in
RNA_DataInfo
)
begin()
(in
ParsedProtocol
)
BT_PROTEIN
(in
rosetta.core.scoring.bin_transitions
)
backbone_for_moltenres_bbconf()
(in
FlexbbRotamerSets
)
begin()
(in
FragQualCalculator
)
BT_PROTEIN
(in
BT_PROPERTIES
)
backbone_for_resid_bbconf()
(in
FlexbbRotamerSets
)
begin()
(in
SilentStructStore
)
BT_PROTEIN
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_only()
(in
BuildSet
)
begin()
(in
WorkUnitQueue
)
BT_UNKNOWN_PROPERTY
(in
rosetta.core.scoring.bin_transitions
)
backbone_sidechain_energy()
(in
CarbonHBondEnergy
)
begin()
(in
LexicographicalIterator
)
BT_UNKNOWN_PROPERTY
(in
BT_PROPERTIES
)
backbone_sidechain_energy()
(in
ConstraintsEnergy
)
begin()
(in
LuaObject
)
BT_UNKNOWN_PROPERTY
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_sidechain_energy()
(in
FullatomCustomPairDistanceEnergy
)
begin1()
(in
StrandPairing
)
BTSB_D_AA
(in
rosetta.core.scoring.bin_transitions
)
backbone_sidechain_energy()
(in
CentroidDisulfideEnergy
)
begin1()
(in
StrandPairing
)
BTSB_D_AA
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_sidechain_energy()
(in
DisulfideMatchingEnergy
)
begin2()
(in
StrandPairing
)
BTSB_D_AA
(in
BTSB_SUBBIN_TYPE
)
backbone_sidechain_energy()
(in
FullatomDisulfideEnergy
)
begin_const()
(in
RawFileData
)
BTSB_D_PRO
(in
rosetta.core.scoring.bin_transitions
)
backbone_sidechain_energy()
(in
DNATorsionEnergy
)
begin_critical_section()
(in
BaseJobDistributor
)
BTSB_D_PRO
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_sidechain_energy()
(in
FA_ElecEnergy
)
begin_processing()
(in
MatchConsolidator
)
BTSB_D_PRO
(in
BTSB_SUBBIN_TYPE
)
backbone_sidechain_energy()
(in
FA_ElecEnergyAroAll
)
begin_processing()
(in
MatchOutputter
)
BTSB_END_OF_LIST
(in
rosetta.core.scoring.bin_transitions
)
backbone_sidechain_energy()
(in
FA_ElecEnergyAroAro
)
begin_processing()
(in
MatchProcessor
)
BTSB_END_OF_LIST
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_sidechain_energy()
(in
FA_GrpElecEnergy
)
begin_receptor_partner_pair()
(in
PeptideDeriverBasicStreamOutputter
)
BTSB_END_OF_LIST
(in
BTSB_SUBBIN_TYPE
)
backbone_sidechain_energy()
(in
RNA_FA_ElecEnergy
)
begin_receptor_partner_pair()
(in
PeptideDeriverMarkdownStreamOutputter
)
BTSB_GLY
(in
rosetta.core.scoring.bin_transitions
)
backbone_sidechain_energy()
(in
ElecDensAllAtomCenEnergy
)
begin_receptor_partner_pair()
(in
PeptideDeriverOutputter
)
BTSB_GLY
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_sidechain_energy()
(in
ElecDensCenEnergy
)
begin_receptor_partner_pair()
(in
PeptideDeriverOutputterContainer
)
BTSB_GLY
(in
BTSB_SUBBIN_TYPE
)
backbone_sidechain_energy()
(in
ElecDensEnergy
)
begin_receptor_partner_pair()
(in
PeptideDeriverPoseOutputter
)
BTSB_L_AA
(in
rosetta.core.scoring.bin_transitions
)
backbone_sidechain_energy()
(in
FastDensEnergy
)
begin_structure()
(in
PeptideDeriverBasicStreamOutputter
)
BTSB_L_AA
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_sidechain_energy()
(in
PattersonCorrEnergy
)
begin_structure()
(in
PeptideDeriverMarkdownStreamOutputter
)
BTSB_L_AA
(in
BTSB_SUBBIN_TYPE
)
backbone_sidechain_energy()
(in
ElecDensAtomwiseEnergy
)
begin_structure()
(in
PeptideDeriverOutputter
)
BTSB_L_PRO
(in
rosetta.core.scoring.bin_transitions
)
backbone_sidechain_energy()
(in
AnalyticEtableEnergy
)
begin_structure()
(in
PeptideDeriverOutputterContainer
)
BTSB_L_PRO
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_sidechain_energy()
(in
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T
)
begin_structure()
(in
PeptideDeriverPoseOutputter
)
BTSB_L_PRO
(in
BTSB_SUBBIN_TYPE
)
backbone_sidechain_energy()
(in
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T
)
being_designed()
(in
PackerTask
)
BTSB_NONE
(in
rosetta.core.scoring.bin_transitions
)
backbone_sidechain_energy()
(in
TableLookupEtableEnergy
)
being_designed()
(in
PackerTask_
)
BTSB_NONE
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_sidechain_energy()
(in
ContextDependentGeometricSolEnergy
)
being_designed()
(in
ResidueLevelTask
)
BTSB_NONE
(in
BTSB_SUBBIN_TYPE
)
backbone_sidechain_energy()
(in
ContextIndependentGeometricSolEnergy
)
being_designed()
(in
ResidueLevelTask_
)
BTSB_SUBBIN_TYPE
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_sidechain_energy()
(in
OccludedHbondSolEnergy
)
being_packed()
(in
PackerTask
)
BTSB_UNKNOWN
(in
rosetta.core.scoring.bin_transitions
)
backbone_sidechain_energy()
(in
HackAroEnergy
)
being_packed()
(in
PackerTask_
)
BTSB_UNKNOWN
(in
BTSB_SUBBIN_TYPE
)
backbone_sidechain_energy()
(in
HBondEnergy
)
being_packed()
(in
ResidueLevelTask
)
BTSB_UNKNOWN
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
backbone_sidechain_energy()
(in
DDPscore
)
being_packed()
(in
ResidueLevelTask_
)
buckle()
(in
DNABasepair
)
backbone_sidechain_energy()
(in
FaMPSolvEnergy
)
being_packed()
(in
GenBornPoseInfo
)
buf()
(in
PyTracer
)
backbone_sidechain_energy()
(in
MPPairEnergy
)
bend()
(in
Helix
)
buf_to_address()
(in
DataBuffer
)
backbone_sidechain_energy()
(in
CartesianBondedEnergy
)
bessel_roots()
(in
rosetta.core.scoring.fiber_diffraction._core_scoring_fiber_diffraction_
)
BUFFER
(in
rosetta.core.io.serialization._core_io_serialization_
)
backbone_sidechain_energy()
(in
CenHBEnergy
)
best_abs_log_norm_ratio()
(in
SimpleDerivCheckResult
)
buffer_signals()
(in
Conformation
)
backbone_sidechain_energy()
(in
CenPairEnergy
)
best_assignment()
(in
PackDaemon
)
BUFFERAP
(in
rosetta.core.io.serialization._core_io_serialization_
)
backbone_sidechain_energy()
(in
CenRotPairEnergy
)
best_bbcst_residues()
(in
rosetta.protocols.protein_interface_design._protocols_protein_interface_design_
)
BUFFERCAP
(in
rosetta.core.io.serialization._core_io_serialization_
)
backbone_sidechain_energy()
(in
ContextDependentLRTwoBodyEnergy
)
best_by_ala_scan()
(in
SeedFoldTree
)
buffering_signals()
(in
Conformation
)
backbone_sidechain_energy()
(in
ContextDependentTwoBodyEnergy
)
best_cos_theta()
(in
SimpleDerivCheckResult
)
build
(in
rosetta.protocols.forge
)
backbone_sidechain_energy()
(in
ContextIndependentLRTwoBodyEnergy
)
best_cutpoint()
(in
rosetta.protocols.protein_interface_design._protocols_protein_interface_design_
)
build()
(in
AtomICoor
)
backbone_sidechain_energy()
(in
ContextIndependentTwoBodyEnergy
)
best_entities()
(in
GeneticAlgorithm
)
build()
(in
ICoorOrbitalData
)
backbone_sidechain_energy()
(in
CustomAtomPairEnergy
)
best_entities()
(in
GeneticAlgorithmBase
)
build()
(in
WaterBuilder
)
backbone_sidechain_energy()
(in
DNA_BaseEnergy
)
best_fitness_from_current_generation()
(in
GeneticAlgorithm
)
build()
(in
InterfaceBuilder
)
backbone_sidechain_energy()
(in
Fa_MbsolvEnergy
)
best_fitness_from_current_generation()
(in
GeneticAlgorithmBase
)
build()
(in
MoveMapBuilder
)
backbone_sidechain_energy()
(in
GaussianOverlapEnergy
)
best_motifhits()
(in
BuildPosition
)
build()
(in
ClassicMatchAlgorithm
)
backbone_sidechain_energy()
(in
GenBornEnergy
)
best_motifs()
(in
BuildPosition
)
build()
(in
DownstreamAlgorithm
)
backbone_sidechain_energy()
(in
GoapEnergy
)
best_norm_analytic()
(in
SimpleDerivCheckResult
)
build()
(in
DownstreamBuilder
)
backbone_sidechain_energy()
(in
HybridVDW_Energy
)
best_norm_numeric()
(in
SimpleDerivCheckResult
)
build()
(in
LigandConformerBuilder
)
backbone_sidechain_energy()
(in
LK_BallEnergy
)
best_rotamer_energy()
(in
RotamerLibrary
)
build()
(in
RigidLigandBuilder
)
backbone_sidechain_energy()
(in
LK_PolarNonPolarEnergy
)
best_rotamer_energy()
(in
SingleLigandRotamerLibrary
)
build()
(in
SecondaryMatcherToDownstreamResidue
)
backbone_sidechain_energy()
(in
LK_hack
)
best_rotamer_energy()
(in
SingleResidueRotamerLibrary
)
build()
(in
SecondaryMatcherToUpstreamResidue
)
backbone_sidechain_energy()
(in
LongRangeTwoBodyEnergy
)
best_rotamer_energy()
(in
SingleResidueCenrotLibrary
)
build()
(in
WriteUpstreamCoordinateKinemage
)
backbone_sidechain_energy()
(in
MMBondAngleEnergy
)
best_rotamers()
(in
BuildPosition
)
build()
(in
ProteinUpstreamBuilder
)
backbone_sidechain_energy()
(in
MMBondLengthEnergy
)
BestHotspotCstMover
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
build()
(in
UpstreamBuilder
)
backbone_sidechain_energy()
(in
MMLJEnergyInter
)
BestHotspotCstMoverAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
build_and_discard_first_round_hits_at_all_positions()
(in
ClassicMatchAlgorithm
)
backbone_sidechain_energy()
(in
MMLJEnergyIntra
)
BestHotspotCstMoverCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
build_atom_ideal()
(in
Residue
)
backbone_sidechain_energy()
(in
MMTorsionEnergy
)
BestHotspotCstMoverCreator
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
build_centroid_loop()
(in
CDRH3Modeler
)
backbone_sidechain_energy()
(in
MembraneCenPairEnergy
)
BestHotspotCstMoverCreatorAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
build_chemical_edge()
(in
rosetta.core.conformation._core_conformation_
)
backbone_sidechain_energy()
(in
PairEnergy
)
BestHotspotCstMoverCreatorCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
build_combined_pose_with_zinc_overlay()
(in
MatchGrafter
)
backbone_sidechain_energy()
(in
PeptideBondEnergy
)
BestMatchesCollection
(in
rosetta.protocols.match.output._protocols_match_output_
)
build_constraints()
(in
AlternativePairings
)
backbone_sidechain_energy()
(in
PoissonBoltzmannEnergy
)
BestMatchesCollectionAP
(in
rosetta.protocols.match.output._protocols_match_output_
)
build_constraints()
(in
StrandConstraints
)
backbone_sidechain_energy()
(in
ProClosureEnergy
)
BestMatchesCollectionCAP
(in
rosetta.protocols.match.output._protocols_match_output_
)
build_cst_conformer_jumps()
(in
ResiduePairJump
)
backbone_sidechain_energy()
(in
Rama2BOffsetEnergy
)
BestTotalScoreSelector
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
build_dependent_rotamers()
(in
RotamerSet
)
backbone_sidechain_energy()
(in
RamachandranEnergy2B
)
BestTotalScoreSelectorAP
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
build_dependent_rotamers()
(in
RotamerSet_
)
backbone_sidechain_energy()
(in
ShortRangeTwoBodyEnergy
)
BestTotalScoreSelectorCAP
(in
rosetta.protocols.frag_picker._protocols_frag_picker_
)
build_dependent_rotamers()
(in
RotamerSubset
)
backbone_sidechain_energy()
(in
SmoothCenPairEnergy
)
BETA
(in
rosetta.core.chemical.rna
)
build_dependent_rotamers()
(in
SymmetricRotamerSet_
)
backbone_sidechain_energy()
(in
SuckerEnergy
)
BETA
(in
rosetta.core.chemical.rna._core_chemical_rna_
)
build_dependent_rotamers()
(in
FlexbbRotamerSet
)
backbone_sidechain_energy()
(in
TwoBodyEnergy
)
BETA
(in
RNA_Torsion
)
build_dependent_water_rotamers()
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
backbone_sidechain_energy()
(in
WaterAdductHBondEnergy
)
beta
(in
rosetta.protocols.stepwise.modeler.protein
)
build_dna_rotamers()
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
backbone_sidechain_energy()
(in
DFIRE_Energy
)
beta()
(in
CrystInfo
)
build_fake_xyz()
(in
Stub
)
backbone_sidechain_energy()
(in
OrbitalsScore
)
beta()
(in
Pose
)
build_fold_tree()
(in
FoldandDockClaimer
)
backbone_sidechain_energy()
(in
RNA_FullAtomStackingEnergy
)
beta()
(in
CSA
)
build_fold_tree()
(in
MembraneTopologyClaimer
)
backbone_sidechain_energy()
(in
RNA_JR_SuiteEnergy
)
beta()
(in
DNABase
)
build_fold_tree()
(in
TopologyClaimer
)
backbone_sidechain_energy()
(in
RNA_LJ_BaseEnergy
)
beta()
(in
EulerAngles
)
build_from_three_coords()
(in
ClassicMatchAlgorithm
)
backbone_sidechain_energy()
(in
RNA_Mg_Energy
)
BETA_AA
(in
rosetta
)
build_full_model()
(in
rosetta.protocols.stepwise.monte_carlo._protocols_stepwise_monte_carlo_
)
backbone_sidechain_energy()
(in
RNA_PairwiseLowResolutionEnergy
)
BETA_AA
(in
rosetta.core.chemical
)
build_full_model()
(in
StepWiseMasterMover
)
backbone_sidechain_energy()
(in
RNA_SuiteEnergy
)
BETA_AA
(in
rosetta.core.chemical._core_chemical_
)
build_fullatom_loop()
(in
CDRH3Modeler
)
backbone_sidechain_energy()
(in
RNA_TorsionEnergy
)
BETA_AA
(in
ResidueProperty
)
build_helix()
(in
RNA_HelixAssembler
)
backbone_sidechain_energy()
(in
RNA_VDW_Energy
)
beta_aform()
(in
RNA_FittedTorsionInfo
)
build_hits_at_all_positions()
(in
ClassicMatchAlgorithm
)
backbone_sidechain_energy()
(in
StackElecEnergy
)
beta_components()
(in
DNATorsionPotential
)
build_hits_at_all_positions()
(in
DownstreamAlgorithm
)
backbone_sidechain_energy()
(in
RNA_DataBackboneEnergy
)
BETA_LINKS
(in
rosetta.core.scoring.carbohydrates
)
build_hits_at_all_positions()
(in
SecondaryMatcherToDownstreamResidue
)
backbone_sidechain_energy()
(in
symEnergy
)
BETA_LINKS
(in
rosetta.core.scoring.carbohydrates._core_scoring_carbohydrates_
)
build_hits_at_all_positions()
(in
SecondaryMatcherToUpstreamResidue
)
backbone_sidechain_energy()
(in
InterchainPairEnergy
)
BETA_LINKS
(in
LinkageType
)
build_hits_at_all_positions()
(in
WriteUpstreamCoordinateKinemage
)
backbone_stub_constraint
(in
rosetta
)
BETA_SUGAR
(in
rosetta
)
build_independent_water_rotamers()
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
backbone_stub_constraint
(in
ScoreType
)
BETA_SUGAR
(in
rosetta.core.chemical
)
build_init_pose()
(in
RNA_HelixAssembler
)
backbone_stub_constraint
(in
rosetta.core.scoring._core_scoring_
)
BETA_SUGAR
(in
rosetta.core.chemical._core_chemical_
)
build_inverted_rotamers()
(in
Motif
)
backbone_stub_constraint
(in
rosetta.core.scoring
)
BETA_SUGAR
(in
ResidueProperty
)
build_jump_edge()
(in
rosetta.core.conformation._core_conformation_
)
backbone_stub_constraint_energy()
(in
ConstraintEdge
)
beta_turn_distance_cutoff()
(in
BetaTurnDetection
)
build_lib_dna_rotamers()
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
backbone_stub_linear_constraint
(in
rosetta
)
beta_turn_length()
(in
BetaTurnDetection
)
build_loops()
(in
MultiThreadingMover
)
backbone_stub_linear_constraint
(in
ScoreType
)
beta_turn_present()
(in
BetaTurnDetection
)
build_loops()
(in
ThreadingMover
)
backbone_stub_linear_constraint
(in
rosetta.core.scoring._core_scoring_
)
beta_turn_type()
(in
BetaTurnDetection
)
build_orbital_xyz()
(in
Residue
)
backbone_stub_linear_constraint
(in
rosetta.core.scoring
)
BetaAlphaBetaMotif
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
build_point()
(in
Matcher
)
backbone_stub_linear_constraint_energy()
(in
ConstraintEdge
)
BetaAlphaBetaMotifAP
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
build_polymer_edge()
(in
rosetta.core.conformation._core_conformation_
)
backbone_stub_match()
(in
rosetta.protocols.motifs._protocols_motifs_
)
BetaAlphaBetaMotifCAP
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
build_pose()
(in
rosetta.core.import_pose._core_import_pose_
)
BackboneDB
(in
rosetta.protocols.loophash._protocols_loophash_
)
BetaAlphaBetaMotifSet
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
build_pose_as_is()
(in
rosetta.core.import_pose._core_import_pose_
)
BackboneDBAP
(in
rosetta.protocols.loophash._protocols_loophash_
)
BetaAlphaBetaMotifSetAP
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
build_pose_as_is1()
(in
rosetta.core.io.pdb._core_io_pdb_
)
BackboneDBCAP
(in
rosetta.protocols.loophash._protocols_loophash_
)
BetaAlphaBetaMotifSetCAP
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
build_pose_from_pdb_as_is()
(in
rosetta.core.io.pdb._core_io_pdb_
)
BackboneGridSampler
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BetaTurnDetection
(in
rosetta.protocols.features._protocols_features_
)
build_positionOPs()
(in
LigandMotifSearch
)
BackboneGridSamplerAP
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BetaTurnDetectionAP
(in
rosetta.protocols.features._protocols_features_
)
build_positionOPs()
(in
MotifSearch
)
BackboneGridSamplerCAP
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BetaTurnDetectionCAP
(in
rosetta.protocols.features._protocols_features_
)
build_random_dna_rotamers()
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
BackboneGridSamplerCreator
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BetaTurnDetectionFeatures
(in
rosetta.protocols.features._protocols_features_
)
build_receptor_peptide_pose()
(in
PeptideDeriverFilter
)
BackboneGridSamplerCreatorAP
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BetaTurnDetectionFeaturesAP
(in
rosetta.protocols.features._protocols_features_
)
build_residue_tree()
(in
rosetta.core.conformation._core_conformation_
)
BackboneGridSamplerCreatorCAP
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BetaTurnDetectionFeaturesCAP
(in
rosetta.protocols.features._protocols_features_
)
build_rna_rotamers()
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
BackboneGridSamplerHelper
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BetaTurnDetectionFeaturesCreator
(in
rosetta.protocols.features._protocols_features_
)
build_rotamer()
(in
MotifHit
)
BackboneGridSamplerHelperAP
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BetaTurnDetectionFeaturesCreatorAP
(in
rosetta.protocols.features._protocols_features_
)
build_rotamer_list()
(in
PerturbRotamerSidechainMover
)
BackboneGridSamplerHelperCAP
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BetaTurnDetectionFeaturesCreatorCAP
(in
rosetta.protocols.features._protocols_features_
)
build_rotamers()
(in
ContinuousRotamerSet
)
BackboneMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
bF()
(in
VallResidue
)
build_rotamers()
(in
RotamerSet
)
BackboneMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
bfac()
(in
Xfrag
)
build_rotamers()
(in
RotamerSet_
)
BackboneMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
bfac()
(in
PoseBalls
)
build_rotamers()
(in
RotamerSets
)
BackboneSegment
(in
rosetta.protocols.loophash._protocols_loophash_
)
bfac1()
(in
ResPairMotif
)
build_rotamers()
(in
RotamerSubset
)
BackboneSegmentAP
(in
rosetta.protocols.loophash._protocols_loophash_
)
bfac2()
(in
ResPairMotif
)
build_rotamers()
(in
SymmetricRotamerSet_
)
BackboneSegmentCAP
(in
rosetta.protocols.loophash._protocols_loophash_
)
BFactor
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
build_rotamers()
(in
FlexbbRotamerSet
)
BackboneStubConstraint
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
BFactorAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
build_rotamers()
(in
FlexbbRotamerSets
)
BackboneStubConstraintAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
BFactorCAP
(in
rosetta.protocols.frag_picker.scores._protocols_frag_picker_scores_
)
build_rotamers()
(in
Motif
)
BackboneStubConstraintCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
BfactorFittingMover
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
build_rotamers_from_rotamer_bins()
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
BackboneStubLinearConstraint
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
BfactorFittingMoverAP
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
build_rotamers_lite()
(in
rosetta.protocols.motifs._protocols_motifs_
)
BackboneStubLinearConstraintAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
BfactorFittingMoverCAP
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
build_round1_hits_twice()
(in
MatcherTask
)
BackboneStubLinearConstraintCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
BfactorFittingMoverCreator
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
build_sc_only_rotamer()
(in
DoubleLazyEdge
)
BackboneTorsionPerturbation
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
BfactorFittingMoverCreatorAP
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
build_sc_only_rotamer()
(in
LazyEdge
)
BackboneTorsionPerturbationAP
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
BfactorFittingMoverCreatorCAP
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
build_set()
(in
ProteinUpstreamBuilder
)
BackboneTorsionPerturbationCAP
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
BfactorMPM
(in
rosetta.protocols.match._protocols_match_
)
build_sidechain_rotamers()
(in
ResiduePairJump
)
BackboneTorsionPerturbationCreator
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
BfactorMPMAP
(in
rosetta.protocols.match._protocols_match_
)
build_stage()
(in
LoopModeler
)
BackboneTorsionPerturbationCreatorAP
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
BfactorMPMCAP
(in
rosetta.protocols.match._protocols_match_
)
build_structures()
(in
LoopHashSampler
)
BackboneTorsionPerturbationCreatorCAP
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
BfactorMultifunc
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
build_temperature_list()
(in
ReplicaExchangeMC
)
BackboneTorsionSampler
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
BfactorMultifuncAP
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
build_tree()
(in
rosetta.core.conformation._core_conformation_
)
BackboneTorsionSamplerAP
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
BfactorMultifuncCAP
(in
rosetta.protocols.electron_density._protocols_electron_density_
)
build_waters()
(in
LKB_ResidueInfo
)
BackboneTorsionSamplerCAP
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
bfactors()
(in
FragmentBiasAssigner
)
BuildAlaPose
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
BackboneTorsionSamplerCreator
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
BFr
(in
rosetta.protocols.fldsgn.topology
)
BuildAlaPoseAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
BackboneTorsionSamplerCreatorAP
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
BFr
(in
rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_
)
BuildAlaPoseCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
BackboneTorsionSamplerCreatorCAP
(in
rosetta.protocols.hybridization._protocols_hybridization_
)
BFr
(in
SheetFoldType
)
BuildAlaPoseCreator
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
backrub
(in
rosetta.protocols
)
bgsh_delta_omega0
(in
DoFType
)
BuildAlaPoseCreatorAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
backrub_cdrs()
(in
AntibodyDesignModeler
)
bgsh_delta_omega0
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BuildAlaPoseCreatorCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
BACKRUB_MOVER
(in
rosetta.basic
)
bgsh_delta_omega0
(in
rosetta.protocols.helical_bundle
)
BuildingBlockInterfaceOperation
(in
rosetta.protocols.matdes._protocols_matdes_
)
BACKRUB_MOVER
(in
rosetta.basic._basic_
)
bgsh_delta_omega1
(in
DoFType
)
BuildingBlockInterfaceOperationAP
(in
rosetta.protocols.matdes._protocols_matdes_
)
BACKRUB_MOVER
(in
ProfTag
)
bgsh_delta_omega1
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BuildingBlockInterfaceOperationCAP
(in
rosetta.protocols.matdes._protocols_matdes_
)
backrub_protocol
(in
MinTypeEnum
)
bgsh_delta_omega1
(in
rosetta.protocols.helical_bundle
)
BuildingBlockInterfaceOperationCreator
(in
rosetta.protocols.matdes._protocols_matdes_
)
backrub_protocol
(in
rosetta.protocols.antibody.design._protocols_antibody_design_
)
bgsh_delta_t
(in
DoFType
)
BuildingBlockInterfaceOperationCreatorAP
(in
rosetta.protocols.matdes._protocols_matdes_
)
backrub_protocol
(in
rosetta.protocols.antibody.design
)
bgsh_delta_t
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BuildingBlockInterfaceOperationCreatorCAP
(in
rosetta.protocols.matdes._protocols_matdes_
)
backrub_rotation_angles()
(in
rosetta.protocols.backrub._protocols_backrub_
)
bgsh_delta_t
(in
rosetta.protocols.helical_bundle
)
BuildInstruction
(in
rosetta.protocols.forge.build._protocols_forge_build_'
)
backrub_rotation_constants()
(in
rosetta.protocols.backrub._protocols_backrub_
)
bgsh_omega0
(in
DoFType
)
BuildInstructionAP
(in
rosetta.protocols.forge.build._protocols_forge_build_'
)
BackrubDDMover
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
bgsh_omega0
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BuildInstructionCAP
(in
rosetta.protocols.forge.build._protocols_forge_build_'
)
BackrubDDMoverAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
bgsh_omega0
(in
rosetta.protocols.helical_bundle
)
BuildManager
(in
rosetta.protocols.forge.build._protocols_forge_build_'
)
BackrubDDMoverCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
bgsh_r0
(in
DoFType
)
BuildManagerAP
(in
rosetta.protocols.forge.build._protocols_forge_build_'
)
BackrubDDMoverCreator
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
bgsh_r0
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BuildManagerCAP
(in
rosetta.protocols.forge.build._protocols_forge_build_'
)
BackrubDDMoverCreatorAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
bgsh_r0
(in
rosetta.protocols.helical_bundle
)
BuildPosition
(in
rosetta.protocols.motifs._protocols_motifs_
)
BackrubDDMoverCreatorCAP
(in
rosetta.protocols.protein_interface_design.movers._protocols_protein_interface_design_movers_
)
bgsh_undefined_dof
(in
DoFType
)
BuildPosition_from_Size()
(in
LigandMotifSearch
)
BackrubMover
(in
rosetta.protocols.backrub._protocols_backrub_
)
bgsh_undefined_dof
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BuildPosition_from_Size()
(in
MotifSearch
)
BackrubMoverAP
(in
rosetta.protocols.backrub._protocols_backrub_
)
bgsh_undefined_dof
(in
rosetta.protocols.helical_bundle
)
BuildPositionAP
(in
rosetta.protocols.motifs._protocols_motifs_
)
BackrubMoverCAP
(in
rosetta.protocols.backrub._protocols_backrub_
)
bgsh_z0_offset
(in
DoFType
)
BuildPositionCAP
(in
rosetta.protocols.motifs._protocols_motifs_
)
BackrubMoverCreator
(in
rosetta.protocols.backrub._protocols_backrub_
)
bgsh_z0_offset
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BuildSet
(in
rosetta.protocols.match.upstream._protocols_match_upstream_
)
BackrubMoverCreatorAP
(in
rosetta.protocols.backrub._protocols_backrub_
)
bgsh_z0_offset
(in
rosetta.protocols.helical_bundle
)
BuildSetAP
(in
rosetta.protocols.match.upstream._protocols_match_upstream_
)
BackrubMoverCreatorCAP
(in
rosetta.protocols.backrub._protocols_backrub_
)
bgsh_z1_offset
(in
DoFType
)
BuildSetCAP
(in
rosetta.protocols.match.upstream._protocols_match_upstream_
)
BackrubProtocol
(in
rosetta.protocols.backrub._protocols_backrub_
)
bgsh_z1_offset
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
buildsturm()
(in
rosetta.numeric.kinematic_closure._numeric_kinematic_closure_
)
BackrubProtocolAP
(in
rosetta.protocols.backrub._protocols_backrub_
)
bgsh_z1_offset
(in
rosetta.protocols.helical_bundle
)
buildtype()
(in
BluePrint
)
BackrubProtocolCAP
(in
rosetta.protocols.backrub._protocols_backrub_
)
bias_energy()
(in
BiasedMonteCarlo
)
built_atom_vertex()
(in
AtomICoor
)
BackrubProtocolCreator
(in
rosetta.protocols.backrub._protocols_backrub_
)
BiasedMonteCarlo
(in
rosetta.protocols.canonical_sampling._protocols_canonical_sampling_
)
BULGE
(in
rosetta
)
BackrubProtocolCreatorAP
(in
rosetta.protocols.backrub._protocols_backrub_
)
BiasedMonteCarloAP
(in
rosetta.protocols.canonical_sampling._protocols_canonical_sampling_
)
BULGE
(in
rosetta.core.chemical
)
BackrubProtocolCreatorCAP
(in
rosetta.protocols.backrub._protocols_backrub_
)
BiasedMonteCarloCAP
(in
rosetta.protocols.canonical_sampling._protocols_canonical_sampling_
)
BULGE
(in
rosetta.core.chemical._core_chemical_
)
BackrubSegment
(in
rosetta.protocols.backrub._protocols_backrub_
)
BiasEnergy
(in
rosetta.protocols.canonical_sampling._protocols_canonical_sampling_
)
BULGE
(in
VariantType
)
BackrubSegmentAP
(in
rosetta.protocols.backrub._protocols_backrub_
)
BiasEnergyAP
(in
rosetta.protocols.canonical_sampling._protocols_canonical_sampling_
)
bulge
(in
rosetta.protocols.stepwise.modeler.rna
)
BackrubSegmentCAP
(in
rosetta.protocols.backrub._protocols_backrub_
)
BiasEnergyCAP
(in
rosetta.protocols.canonical_sampling._protocols_canonical_sampling_
)
BULGE_APPLIER
(in
rosetta.protocols.stepwise.screener
)
BackrubSidechainMover
(in
rosetta.protocols.backrub._protocols_backrub_
)
bicubic_interpolation()
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
BULGE_APPLIER
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
BackrubSidechainMoverAP
(in
rosetta.protocols.backrub._protocols_backrub_
)
BicubicSpline
(in
rosetta.numeric.interpolation.spline._numeric_interpolation_spline_
)
BULGE_APPLIER
(in
StepWiseScreenerType
)
BackrubSidechainMoverCAP
(in
rosetta.protocols.backrub._protocols_backrub_
)
BicubicSplineAP
(in
rosetta.numeric.interpolation.spline._numeric_interpolation_spline_
)
BulgeApplier
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
BackrubSidechainMoverCreator
(in
rosetta.protocols.backrub._protocols_backrub_
)
BicubicSplineCAP
(in
rosetta.numeric.interpolation.spline._numeric_interpolation_spline_
)
BulgeApplierAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
BackrubSidechainMoverCreatorAP
(in
rosetta.protocols.backrub._protocols_backrub_
)
bIdealLoopClosing()
(in
SlidingWindowLoopClosure
)
BulgeApplierCAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
BackrubSidechainMoverCreatorCAP
(in
rosetta.protocols.backrub._protocols_backrub_
)
big_bin_constraint
(in
rosetta
)
BulgeApplyMover
(in
rosetta.protocols.stepwise.modeler.rna.bulge._protocols_stepwise_modeler_rna_bulge_
)
backward
(in
ChainDirection
)
big_bin_constraint
(in
ScoreType
)
BulgeApplyMoverAP
(in
rosetta.protocols.stepwise.modeler.rna.bulge._protocols_stepwise_modeler_rna_bulge_
)
backward
(in
rosetta.protocols.loops.loop_closure.ccd._protocols_loops_loop_closure_ccd_
)
big_bin_constraint
(in
rosetta.core.scoring._core_scoring_
)
BulgeApplyMoverCAP
(in
rosetta.protocols.stepwise.modeler.rna.bulge._protocols_stepwise_modeler_rna_bulge_
)
backward
(in
rosetta.protocols.loops.loop_closure.ccd
)
big_bin_constraint
(in
rosetta.core.scoring
)
BulgeUnApplyMover
(in
rosetta.protocols.stepwise.modeler.rna.bulge._protocols_stepwise_modeler_rna_bulge_
)
backward_check()
(in
Motif
)
bigbin()
(in
VallData
)
BulgeUnApplyMoverAP
(in
rosetta.protocols.stepwise.modeler.rna.bulge._protocols_stepwise_modeler_rna_bulge_
)
backward_jump()
(in
Motif
)
BigBinConstraint
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
BulgeUnApplyMoverCAP
(in
rosetta.protocols.stepwise.modeler.rna.bulge._protocols_stepwise_modeler_rna_bulge_
)
bad()
(in
xyzTransform_T_double_T
)
BigBinConstraintAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
bump_check()
(in
RotamerSet_
)
bad()
(in
xyzTransform_T_float_T
)
BigBinConstraintCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
bump_check()
(in
SymmetricRotamerSet_
)
bad()
(in
InnerJob
)
BigBinConstraintCreator
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
bump_check()
(in
PackerTask
)
bad()
(in
Job
)
BigBinConstraintCreatorAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
bump_check()
(in
PackerTask_
)
BAD_INPUT_TAG
(in
rosetta.protocols.jd2
)
BigBinConstraintCreatorCAP
(in
rosetta.core.scoring.constraints._core_scoring_constraints_
)
bump_check_backbone()
(in
ScoreFunction
)
BAD_INPUT_TAG
(in
rosetta.protocols.jd2._protocols_jd2_
)
bin()
(in
BigBinConstraint
)
bump_check_full()
(in
ScoreFunction
)
BAD_INPUT_TAG
(in
mpi_tags
)
bin()
(in
GeneralizedKICperturber
)
bump_energy_backbone()
(in
CarbonHBondEnergy
)
BAD_RT6()
(in
xyzTransform_T_double_T
)
bin0_of_real()
(in
ResPairMotifMetaBinner
)
bump_energy_backbone()
(in
ConstraintsEnergy
)
BAD_RT6()
(in
xyzTransform_T_float_T
)
bin6()
(in
SixDCoordinateBinner
)
bump_energy_backbone()
(in
FullatomCustomPairDistanceEnergy
)
bad_tree()
(in
EXCN_InvalidFoldTree
)
bin_angle()
(in
SingleResidueDunbrackLibrary
)
bump_energy_backbone()
(in
CentroidDisulfideEnergy
)
BAD_XFORM()
(in
xyzTransform_T_double_T
)
bin_angle()
(in
SingleResiduePeptoidLibrary
)
bump_energy_backbone()
(in
DisulfideMatchingEnergy
)
BAD_XFORM()
(in
xyzTransform_T_float_T
)
bin_boundaries_i()
(in
BinTransitionData
)
bump_energy_backbone()
(in
FullatomDisulfideEnergy
)
badfast()
(in
xyzTransform_T_double_T
)
bin_boundaries_iplus1()
(in
BinTransitionData
)
bump_energy_backbone()
(in
DNATorsionEnergy
)
badfast()
(in
xyzTransform_T_float_T
)
bin_center()
(in
Bool3DGrid
)
bump_energy_backbone()
(in
FA_ElecEnergy
)
bah_chi_compute_energy_sp2()
(in
rosetta.core.scoring.hbonds._core_scoring_hbonds_
)
bin_center_point()
(in
SixDCoordinateBinner
)
bump_energy_backbone()
(in
FA_ElecEnergyAroAll
)
bah_chi_compute_energy_sp3()
(in
rosetta.core.scoring.hbonds._core_scoring_hbonds_
)
bin_extrema()
(in
Bool3DGrid
)
bump_energy_backbone()
(in
FA_ElecEnergyAroAro
)
BalancedKicMover
(in
rosetta.protocols.kinematic_closure._protocols_kinematic_closure_
)
bin_from_index()
(in
SixDCoordinateBinner
)
bump_energy_backbone()
(in
FA_GrpElecEnergy
)
BalancedKicMoverAP
(in
rosetta.protocols.kinematic_closure._protocols_kinematic_closure_
)
bin_index()
(in
MotifHash
)
bump_energy_backbone()
(in
RNA_FA_ElecEnergy
)
BalancedKicMoverCAP
(in
rosetta.protocols.kinematic_closure._protocols_kinematic_closure_
)
bin_index()
(in
XformScore
)
bump_energy_backbone()
(in
ElecDensAllAtomCenEnergy
)
Ball
(in
rosetta.core.scoring.packing._core_scoring_packing_
)
bin_index()
(in
SixDCoordinateBinner
)
bump_energy_backbone()
(in
ElecDensCenEnergy
)
Ball
(in
rosetta.numeric.geometry.hashing._numeric_geometry_hashing_
)
bin_index_hasher
(in
rosetta.numeric.geometry.hashing._numeric_geometry_hashing_
)
bump_energy_backbone()
(in
ElecDensEnergy
)
ball()
(in
PoseBalls
)
bin_index_hasherAP
(in
rosetta.numeric.geometry.hashing._numeric_geometry_hashing_
)
bump_energy_backbone()
(in
FastDensEnergy
)
ball()
(in
PoseBallsLite
)
bin_index_hasherCAP
(in
rosetta.numeric.geometry.hashing._numeric_geometry_hashing_
)
bump_energy_backbone()
(in
PattersonCorrEnergy
)
ball()
(in
xyzStripeHash
)
bin_params_loaded()
(in
BinTransitionCalculator
)
bump_energy_backbone()
(in
ElecDensAtomwiseEnergy
)
BallAP
(in
rosetta.core.scoring.packing._core_scoring_packing_
)
bin_rotameric_chi()
(in
SingleResidueDunbrackLibrary
)
bump_energy_backbone()
(in
AnalyticEtableEnergy
)
BallAP
(in
rosetta.numeric.geometry.hashing._numeric_geometry_hashing_
)
bin_rotameric_chi()
(in
SingleResiduePeptoidLibrary
)
bump_energy_backbone()
(in
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T
)
BallCAP
(in
rosetta.core.scoring.packing._core_scoring_packing_
)
bin_transitions
(in
rosetta.core.scoring
)
bump_energy_backbone()
(in
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T
)
BallCAP
(in
rosetta.numeric.geometry.hashing._numeric_geometry_hashing_
)
bin_transitions
(in
rosetta.protocols.simple_moves
)
bump_energy_backbone()
(in
TableLookupEtableEnergy
)
balls()
(in
PoseBalls
)
bin_width()
(in
Bool3DGrid
)
bump_energy_backbone()
(in
ContextDependentGeometricSolEnergy
)
BANGLE_MIN()
(in
KinematicMover
)
bin_widths()
(in
SixDCoordinateBinner
)
bump_energy_backbone()
(in
ContextIndependentGeometricSolEnergy
)
BANGLE_SD()
(in
KinematicMover
)
BinaryExpression
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
bump_energy_backbone()
(in
OccludedHbondSolEnergy
)
bare_name()
(in
FileName
)
BinaryExpressionAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
bump_energy_backbone()
(in
HackAroEnergy
)
Base
(in
rosetta.core._core_
)
BinaryExpressionCAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
bump_energy_backbone()
(in
HBondEnergy
)
Base
(in
rosetta.utility.py._utility_py_
)
BinaryFragmentStoreBackend
(in
rosetta.core.indexed_structure_store._core_indexed_structure_store_
)
bump_energy_backbone()
(in
DDPscore
)
base()
(in
DNAParameters
)
BinaryFragmentStoreBackendAP
(in
rosetta.core.indexed_structure_store._core_indexed_structure_store_
)
bump_energy_backbone()
(in
FaMPSolvEnergy
)
base()
(in
FileName
)
BinaryFragmentStoreBackendCAP
(in
rosetta.core.indexed_structure_store._core_indexed_structure_store_
)
bump_energy_backbone()
(in
MPPairEnergy
)
base2_xyz()
(in
HBAtom
)
BinarySilentStruct
(in
rosetta.core.io.silent._core_io_silent_
)
bump_energy_backbone()
(in
CartesianBondedEnergy
)
base_atoms_square_deviation()
(in
rosetta.protocols.stepwise.modeler.rna._protocols_stepwise_modeler_rna_
)
BinarySilentStructAP
(in
rosetta.core.io.silent._core_io_silent_
)
bump_energy_backbone()
(in
CenHBEnergy
)
base_atr_score()
(in
ProteinAtrRepChecker
)
BinarySilentStructCAP
(in
rosetta.core.io.silent._core_io_silent_
)
bump_energy_backbone()
(in
CenPairEnergy
)
base_atr_score()
(in
RNA_AtrRepChecker
)
BinarySilentStructCreator
(in
rosetta.core.io.silent._core_io_silent_
)
bump_energy_backbone()
(in
CenRotPairEnergy
)
base_axis_array()
(in
RNA_RawBaseBaseInfo
)
BinarySilentStructCreatorAP
(in
rosetta.core.io.silent._core_io_silent_
)
bump_energy_backbone()
(in
ContextDependentLRTwoBodyEnergy
)
base_backbone_distance_cutoff()
(in
RNA_LowResolutionPotential
)
BinarySilentStructCreatorCAP
(in
rosetta.core.io.silent._core_io_silent_
)
bump_energy_backbone()
(in
ContextDependentTwoBodyEnergy
)
base_backbone_rho_cutoff()
(in
RNA_LowResolutionPotential
)
bind_data()
(in
RowDataBase
)
bump_energy_backbone()
(in
ContextIndependentLRTwoBodyEnergy
)
base_backbone_z_cutoff()
(in
RNA_LowResolutionPotential
)
BindingSiteConstraint
(in
rosetta.protocols.constraints_additional._protocols_constraints_additional_
)
bump_energy_backbone()
(in
ContextIndependentTwoBodyEnergy
)
BASE_BIN_MAP
(in
rosetta.protocols.stepwise.screener
)
BindingSiteConstraintAP
(in
rosetta.protocols.constraints_additional._protocols_constraints_additional_
)
bump_energy_backbone()
(in
CustomAtomPairEnergy
)
BASE_BIN_MAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
BindingSiteConstraintCAP
(in
rosetta.protocols.constraints_additional._protocols_constraints_additional_
)
bump_energy_backbone()
(in
DNA_BaseEnergy
)
BASE_BIN_MAP
(in
StepWiseScreenerType
)
BindingSiteConstraintCreator
(in
rosetta.protocols.constraints_additional._protocols_constraints_additional_
)
bump_energy_backbone()
(in
Fa_MbsolvEnergy
)
BASE_CENTROID
(in
rosetta.protocols.stepwise.screener
)
BindingSiteConstraintCreatorAP
(in
rosetta.protocols.constraints_additional._protocols_constraints_additional_
)
bump_energy_backbone()
(in
GaussianOverlapEnergy
)
BASE_CENTROID
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
BindingSiteConstraintCreatorCAP
(in
rosetta.protocols.constraints_additional._protocols_constraints_additional_
)
bump_energy_backbone()
(in
GenBornEnergy
)
BASE_CENTROID
(in
StepWiseScreenerType
)
BindingStrainFilter
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
bump_energy_backbone()
(in
GoapEnergy
)
base_centroids()
(in
RNA_CentroidInfo
)
BindingStrainFilterAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
bump_energy_backbone()
(in
HybridVDW_Energy
)
base_geometry_height_array()
(in
RNA_RawBaseBaseInfo
)
BindingStrainFilterCAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
bump_energy_backbone()
(in
LK_BallEnergy
)
base_geometry_orientation_array()
(in
RNA_RawBaseBaseInfo
)
BindingStrainFilterCreator
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
bump_energy_backbone()
(in
LK_PolarNonPolarEnergy
)
base_name()
(in
CarbohydrateInfo
)
BindingStrainFilterCreatorAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
bump_energy_backbone()
(in
LK_hack
)
base_name()
(in
RNA_CS_residue_parameters
)
BindingStrainFilterCreatorCAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
bump_energy_backbone()
(in
LongRangeTwoBodyEnergy
)
base_name()
(in
rosetta.protocols.vip._protocols_vip_
)
binname()
(in
GeneralizedKICfilter
)
bump_energy_backbone()
(in
MMBondAngleEnergy
)
base_only()
(in
RestrictDesignToProteinDNAInterface
)
binname_index_from_string_i()
(in
BinTransitionData
)
bump_energy_backbone()
(in
MMBondLengthEnergy
)
base_pair_array()
(in
RNA_RawBaseBaseInfo
)
binname_index_from_string_iplus1()
(in
BinTransitionData
)
bump_energy_backbone()
(in
MMLJEnergyInter
)
base_pair_score()
(in
DNA_BasePotential
)
binner()
(in
HitHasher
)
bump_energy_backbone()
(in
MMLJEnergyIntra
)
BASE_PARTNER
(in
CacheableDataType
)
binsums_i()
(in
BinTransitionData
)
bump_energy_backbone()
(in
MMTorsionEnergy
)
BASE_PARTNER
(in
Enum
)
binsums_iplus1()
(in
BinTransitionData
)
bump_energy_backbone()
(in
MembraneCenPairEnergy
)
base_rep_score()
(in
ProteinAtrRepChecker
)
BinTransitionCalculator
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
bump_energy_backbone()
(in
PairEnergy
)
base_rep_score()
(in
RNA_AtrRepChecker
)
BinTransitionCalculatorAP
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
bump_energy_backbone()
(in
PeptideBondEnergy
)
base_restype_name()
(in
ResidueType
)
BinTransitionCalculatorCAP
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
bump_energy_backbone()
(in
PoissonBoltzmannEnergy
)
base_stack_array()
(in
RNA_RawBaseBaseInfo
)
BinTransitionData
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
bump_energy_backbone()
(in
ProClosureEnergy
)
base_stack_axis_array()
(in
RNA_RawBaseBaseInfo
)
BinTransitionDataAP
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
bump_energy_backbone()
(in
Rama2BOffsetEnergy
)
base_stagger_array()
(in
RNA_RawBaseBaseInfo
)
BinTransitionDataCAP
(in
rosetta.core.scoring.bin_transitions._core_scoring_bin_transitions_
)
bump_energy_backbone()
(in
RamachandranEnergy2B
)
base_state()
(in
RNA_ChiStepWiseSampler
)
bit_is_set()
(in
rosetta.core.pack.dunbrack._core_pack_dunbrack_
)
bump_energy_backbone()
(in
ShortRangeTwoBodyEnergy
)
base_step_score()
(in
DNA_BasePotential
)
blank_atom_id_domain_map()
(in
rosetta.core.pose.copydofs._core_pose_copydofs_
)
bump_energy_backbone()
(in
SmoothCenPairEnergy
)
base_stubs()
(in
RNA_CentroidInfo
)
blanket_assign_state_0()
(in
DensePDInteractionGraph
)
bump_energy_backbone()
(in
SuckerEnergy
)
base_xyz()
(in
HBAtom
)
blanket_assign_state_0()
(in
DoubleDensePDInteractionGraph
)
bump_energy_backbone()
(in
TwoBodyEnergy
)
BaseAP
(in
rosetta.utility.py._utility_py_
)
blanket_assign_state_0()
(in
DoubleLazyInteractionGraph
)
bump_energy_backbone()
(in
WaterAdductHBondEnergy
)
BaseArchiveManager
(in
rosetta.protocols.jd2.archive._protocols_jd2_archive_
)
blanket_assign_state_0()
(in
FASTERInteractionGraph
)
bump_energy_backbone()
(in
DFIRE_Energy
)
BaseArchiveManagerAP
(in
rosetta.protocols.jd2.archive._protocols_jd2_archive_
)
blanket_assign_state_0()
(in
InteractionGraphBase
)
bump_energy_backbone()
(in
OrbitalsScore
)
BaseArchiveManagerCAP
(in
rosetta.protocols.jd2.archive._protocols_jd2_archive_
)
blanket_assign_state_0()
(in
LazyInteractionGraph
)
bump_energy_backbone()
(in
RNA_FullAtomStackingEnergy
)
BaseBin
(in
rosetta.protocols.stepwise.modeler.rna.rigid_body._protocols_stepwise_modeler_rna_rigid_body_
)
blanket_assign_state_0()
(in
LinearMemoryInteractionGraph
)
bump_energy_backbone()
(in
RNA_JR_SuiteEnergy
)
BaseBinAP
(in
rosetta.protocols.stepwise.modeler.rna.rigid_body._protocols_stepwise_modeler_rna_rigid_body_
)
blanket_assign_state_0()
(in
PDInteractionGraph
)
bump_energy_backbone()
(in
RNA_LJ_BaseEnergy
)
BaseBinCAP
(in
rosetta.protocols.stepwise.modeler.rna.rigid_body._protocols_stepwise_modeler_rna_rigid_body_
)
blanket_assign_state_0()
(in
SymmLinearMemoryInteractionGraph
)
bump_energy_backbone()
(in
RNA_Mg_Energy
)
BaseBinMapUpdater
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
blanket_assign_state_0()
(in
SymmMinimalistInteractionGraph
)
bump_energy_backbone()
(in
RNA_PairwiseLowResolutionEnergy
)
BaseBinMapUpdaterAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
blanket_assign_state_0()
(in
MinimalistFlexbbInteractionGraph
)
bump_energy_backbone()
(in
RNA_SuiteEnergy
)
BaseBinMapUpdaterCAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
blanket_set()
(in
AminoAcidNeighborSparseMatrix_T_float_T
)
bump_energy_backbone()
(in
RNA_TorsionEnergy
)
BaseCacheUnit
(in
rosetta.core.fragment._core_fragment_
)
BlankMatrixMult()
(in
rosetta.numeric.model_quality._numeric_model_quality_
)
bump_energy_backbone()
(in
RNA_VDW_Energy
)
BaseCacheUnitAP
(in
rosetta.core.fragment._core_fragment_
)
block()
(in
SingleFileBuffer
)
bump_energy_backbone()
(in
StackElecEnergy
)
BaseCacheUnitCAP
(in
rosetta.core.fragment._core_fragment_
)
block()
(in
WriteFileSFB
)
bump_energy_backbone()
(in
RNA_DataBackboneEnergy
)
BaseCAP
(in
rosetta.utility.py._utility_py_
)
block()
(in
Link
)
bump_energy_backbone()
(in
symEnergy
)
BaseCentroidScreener
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
block_file()
(in
MpiFileBuffer
)
bump_energy_backbone()
(in
InterchainPairEnergy
)
BaseCentroidScreenerAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
block_signals()
(in
Conformation
)
bump_energy_full()
(in
CarbonHBondEnergy
)
BaseCentroidScreenerCAP
(in
rosetta.protocols.stepwise.screener._protocols_stepwise_screener_
)
blocked()
(in
Link
)
bump_energy_full()
(in
ConstraintsEnergy
)
BaseDisulfPairingLibrary
(in
rosetta.protocols.jumping._protocols_jumping_
)
blocking_signals()
(in
Conformation
)
bump_energy_full()
(in
FullatomCustomPairDistanceEnergy
)
BaseDisulfPairingLibraryAP
(in
rosetta.protocols.jumping._protocols_jumping_
)
BluePrint
(in
rosetta.protocols.jd2.parser._protocols_jd2_parser_
)
bump_energy_full()
(in
CentroidDisulfideEnergy
)
BaseDisulfPairingLibraryCAP
(in
rosetta.protocols.jumping._protocols_jumping_
)
BluePrintAP
(in
rosetta.protocols.jd2.parser._protocols_jd2_parser_
)
bump_energy_full()
(in
DisulfideMatchingEnergy
)
BaseEdge
(in
rosetta.core.chemical.rna._core_chemical_rna_
)
BluePrintBDR
(in
rosetta.protocols.fldsgn._protocols_fldsgn_
)
bump_energy_full()
(in
FullatomDisulfideEnergy
)
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T
(in
rosetta.core.scoring.etable._core_scoring_etable_
)
BluePrintBDRAP
(in
rosetta.protocols.fldsgn._protocols_fldsgn_
)
bump_energy_full()
(in
DNATorsionEnergy
)
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_TAP
(in
rosetta.core.scoring.etable._core_scoring_etable_
)
BluePrintBDRCAP
(in
rosetta.protocols.fldsgn._protocols_fldsgn_
)
bump_energy_full()
(in
FA_ElecEnergy
)
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_TCAP
(in
rosetta.core.scoring.etable._core_scoring_etable_
)
BluePrintBDRCreator
(in
rosetta.protocols.fldsgn._protocols_fldsgn_
)
bump_energy_full()
(in
FA_ElecEnergyAroAll
)
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T
(in
rosetta.core.scoring.etable._core_scoring_etable_
)
BluePrintBDRCreatorAP
(in
rosetta.protocols.fldsgn._protocols_fldsgn_
)
bump_energy_full()
(in
FA_ElecEnergyAroAro
)
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_TAP
(in
rosetta.core.scoring.etable._core_scoring_etable_
)
BluePrintBDRCreatorCAP
(in
rosetta.protocols.fldsgn._protocols_fldsgn_
)
bump_energy_full()
(in
FA_GrpElecEnergy
)
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_TCAP
(in
rosetta.core.scoring.etable._core_scoring_etable_
)
BluePrintCAP
(in
rosetta.protocols.jd2.parser._protocols_jd2_parser_
)
bump_energy_full()
(in
RNA_FA_ElecEnergy
)
BaseJobDistributor
(in
rosetta.protocols.jobdist._protocols_jobdist_
)
boinc
(in
rosetta.protocols
)
bump_energy_full()
(in
ElecDensAllAtomCenEnergy
)
BaseJobDistributorAP
(in
rosetta.protocols.jobdist._protocols_jobdist_
)
boinc
(in
rosetta.utility
)
bump_energy_full()
(in
ElecDensCenEnergy
)
BaseJobDistributorCAP
(in
rosetta.protocols.jobdist._protocols_jobdist_
)
BOINCJobDistributor
(in
rosetta.protocols.jd2._protocols_jd2_
)
bump_energy_full()
(in
ElecDensEnergy
)
BaseJumpSetup
(in
rosetta.protocols.jumping._protocols_jumping_
)
BOINCJobDistributorAP
(in
rosetta.protocols.jd2._protocols_jd2_
)
bump_energy_full()
(in
FastDensEnergy
)
BaseJumpSetupAP
(in
rosetta.protocols.jumping._protocols_jumping_
)
BOINCJobDistributorCAP
(in
rosetta.protocols.jd2._protocols_jd2_
)
bump_energy_full()
(in
PattersonCorrEnergy
)
BaseJumpSetupCAP
(in
rosetta.protocols.jumping._protocols_jumping_
)
boltz_rank()
(in
GenericMonteCarloMover
)
bump_energy_full()
(in
ElecDensAtomwiseEnergy
)
baseline()
(in
DeltaFilter
)
boltzmann()
(in
BiasedMonteCarlo
)
bump_energy_full()
(in
AnalyticEtableEnergy
)
baseline()
(in
RelativePoseFilter
)
boltzmann()
(in
DualMonteCarlo
)
bump_energy_full()
(in
BaseEtableEnergy_T_core_scoring_etable_AnalyticEtableEnergy_T
)
baseline_checkpointing_filename()
(in
Sigmoid
)
boltzmann()
(in
MonteCarlo
)
bump_energy_full()
(in
BaseEtableEnergy_T_core_scoring_etable_TableLookupEtableEnergy_T
)
baseline_val()
(in
RelativePoseFilter
)
boltzmann()
(in
ReplicaExchangeMC
)
bump_energy_full()
(in
TableLookupEtableEnergy
)
BasePair
(in
rosetta.core.pose.rna._core_pose_rna_
)
boltzmann()
(in
SimulatedTempering
)
bump_energy_full()
(in
ContextDependentGeometricSolEnergy
)
basepair()
(in
DNAParameters
)
boltzmann()
(in
GenericMonteCarloMover
)
bump_energy_full()
(in
ContextIndependentGeometricSolEnergy
)
basepair_axis_stagger_scaling()
(in
RNA_FilteredBaseBaseInfo
)
boltzmann_accept_probability()
(in
rosetta.numeric._numeric_
)
bump_energy_full()
(in
OccludedHbondSolEnergy
)
BasePairAP
(in
rosetta.core.pose.rna._core_pose_rna_
)
boltzmann_energy_selector
(in
rosetta.protocols.generalized_kinematic_closure.selector._protocols_generalized_kinematic_closure_selector_
)
bump_energy_full()
(in
HackAroEnergy
)
BasePairCAP
(in
rosetta.core.pose.rna._core_pose_rna_
)
boltzmann_energy_selector
(in
selector_type
)
bump_energy_full()
(in
HBondEnergy
)
BasePairingLibrary
(in
rosetta.protocols.jumping._protocols_jumping_
)
boltzmann_energy_selector
(in
rosetta.protocols.generalized_kinematic_closure.selector
)
bump_energy_full()
(in
DDPscore
)
BasePairingLibraryAP
(in
rosetta.protocols.jumping._protocols_jumping_
)
BoltzmannFilter
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
bump_energy_full()
(in
FaMPSolvEnergy
)
BasePairingLibraryCAP
(in
rosetta.protocols.jumping._protocols_jumping_
)
BoltzmannFilterAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
bump_energy_full()
(in
MPPairEnergy
)
basepairs_begin()
(in
DNAParameters
)
BoltzmannFilterCAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
bump_energy_full()
(in
CartesianBondedEnergy
)
basepairs_end()
(in
DNAParameters
)
BoltzmannFilterCreator
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
bump_energy_full()
(in
CenHBEnergy
)
BasePairStep
(in
rosetta.protocols.farna._protocols_farna_
)
BoltzmannFilterCreatorAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
bump_energy_full()
(in
CenPairEnergy
)
BasePairStepAP
(in
rosetta.protocols.farna._protocols_farna_
)
BoltzmannFilterCreatorCAP
(in
rosetta.protocols.protein_interface_design.filters._protocols_protein_interface_design_filters_
)
bump_energy_full()
(in
CenRotPairEnergy
)
BasePairStepCAP
(in
rosetta.protocols.farna._protocols_farna_
)
BoltzmannRotamerMover
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
bump_energy_full()
(in
ContextDependentLRTwoBodyEnergy
)
BasePairStepLibrary
(in
rosetta.protocols.farna._protocols_farna_
)
BoltzmannRotamerMoverAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
bump_energy_full()
(in
ContextDependentTwoBodyEnergy
)
BasePairStepLibraryAP
(in
rosetta.protocols.farna._protocols_farna_
)
BoltzmannRotamerMoverCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
bump_energy_full()
(in
ContextIndependentLRTwoBodyEnergy
)
BasePairStepLibraryCAP
(in
rosetta.protocols.farna._protocols_farna_
)
BoltzmannRotamerMoverCreator
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
bump_energy_full()
(in
ContextIndependentTwoBodyEnergy
)
BasePairStepSequence
(in
rosetta.protocols.farna._protocols_farna_
)
BoltzmannRotamerMoverCreatorAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
bump_energy_full()
(in
CustomAtomPairEnergy
)
BasePairStepSequenceAP
(in
rosetta.protocols.farna._protocols_farna_
)
BoltzmannRotamerMoverCreatorCAP
(in
rosetta.protocols.simple_moves._protocols_simple_moves_
)
bump_energy_full()
(in
DNA_BaseEnergy
)
BasePairStepSequenceCAP
(in
rosetta.protocols.farna._protocols_farna_
)
Bond
(in
rosetta.core.chemical._core_chemical_
)
bump_energy_full()
(in
Fa_MbsolvEnergy
)
BasePairType
(in
rosetta.protocols.farna._protocols_farna_
)
bond()
(in
ResidueType
)
bump_energy_full()
(in
GaussianOverlapEnergy
)
BasePairTypeAP
(in
rosetta.protocols.farna._protocols_farna_
)
bond_angle()
(in
Conformation
)
bump_energy_full()
(in
GenBornEnergy
)
BasePairTypeCAP
(in
rosetta.protocols.farna._protocols_farna_
)
bond_angle()
(in
AtomTree
)
bump_energy_full()
(in
GoapEnergy
)
BasePartner
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
bond_angle_atoms()
(in
BackrubSegment
)
bump_energy_full()
(in
HybridVDW_Energy
)
BasePartnerAP
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
bond_angle_central_atoms_to_score()
(in
EnergyMethodOptions
)
bump_energy_full()
(in
LK_BallEnergy
)
BasePartnerCAP
(in
rosetta.core.scoring.dna._core_scoring_dna_
)
bond_angle_dof_id()
(in
AtomTree
)
bump_energy_full()
(in
LK_PolarNonPolarEnergy
)
baserotamer_data()
(in
ContinuousRotamerSet
)
bond_angle_residue_type_param_set()
(in
EnergyMethodOptions
)
bump_energy_full()
(in
LK_hack
)
bases_begin()
(in
DNAParameters
)
bond_angle_residue_type_param_set()
(in
BranchAngleOptimizer
)
bump_energy_full()
(in
LongRangeTwoBodyEnergy
)
bases_end()
(in
DNAParameters
)
bond_geometry
(in
rosetta
)
bump_energy_full()
(in
MMBondAngleEnergy
)
BaseStack
(in
rosetta.core.pose.rna._core_pose_rna_
)
bond_geometry
(in
ScoreType
)
bump_energy_full()
(in
MMBondLengthEnergy
)
basestack_axis_scaling()
(in
RNA_FilteredBaseBaseInfo
)
bond_geometry
(in
rosetta.core.scoring._core_scoring_
)
bump_energy_full()
(in
MMLJEnergyInter
)
BaseStackAP
(in
rosetta.core.pose.rna._core_pose_rna_
)
bond_geometry
(in
rosetta.core.scoring
)
bump_energy_full()
(in
MMLJEnergyIntra
)
BaseStackCAP
(in
rosetta.core.pose.rna._core_pose_rna_
)
bond_geometry_energy()
(in
ConstraintEdge
)
bump_energy_full()
(in
MMTorsionEnergy
)
basestep()
(in
DNAParameters
)
bond_iterators()
(in
ResidueType
)
bump_energy_full()
(in
MembraneCenPairEnergy
)
basesteps_begin()
(in
DNAParameters
)
bond_length()
(in
Conformation
)
bump_energy_full()
(in
PairEnergy
)
basesteps_end()
(in
DNAParameters
)
bond_length()
(in
AtomTree
)
bump_energy_full()
(in
PeptideBondEnergy
)
BaseTabooPerturber
(in
rosetta.protocols.loops.loop_closure.kinematic_closure._protocols_loops_loop_closure_kinematic_closure_
)
bond_length()
(in
CutChainMover
)
bump_energy_full()
(in
PoissonBoltzmannEnergy
)
BaseTabooPerturberAP
(in
rosetta.protocols.loops.loop_closure.kinematic_closure._protocols_loops_loop_closure_kinematic_closure_
)
bond_length_dof_id()
(in
AtomTree
)
bump_energy_full()
(in
ProClosureEnergy
)
BaseTabooPerturberCAP
(in
rosetta.protocols.loops.loop_closure.kinematic_closure._protocols_loops_loop_closure_kinematic_closure_
)
bond_name()
(in
Bond
)
bump_energy_full()
(in
Rama2BOffsetEnergy
)
basic
(in
rosetta
)
BOND_TO_NEXT
(in
rosetta.protocols.stepwise.monte_carlo.mover
)
bump_energy_full()
(in
RamachandranEnergy2B
)
basic_idealize()
(in
rosetta.protocols.idealize._protocols_idealize_
)
BOND_TO_NEXT
(in
AttachmentType
)
bump_energy_full()
(in
ShortRangeTwoBodyEnergy
)
basic_otstream_T_char_std_char_traits_T_char_T__T
(in
rosetta.basic._basic_
)
BOND_TO_NEXT
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
bump_energy_full()
(in
SmoothCenPairEnergy
)
basic_otstream_T_char_std_char_traits_T_char_T__TAP
(in
rosetta.basic._basic_
)
BOND_TO_PREVIOUS
(in
rosetta.protocols.stepwise.monte_carlo.mover
)
bump_energy_full()
(in
SuckerEnergy
)
basic_otstream_T_char_std_char_traits_T_char_T__TCAP
(in
rosetta.basic._basic_
)
BOND_TO_PREVIOUS
(in
AttachmentType
)
bump_energy_full()
(in
TwoBodyEnergy
)
BasicCDRClusterSet
(in
rosetta.protocols.antibody.clusters._protocols_antibody_clusters_
)
BOND_TO_PREVIOUS
(in
rosetta.protocols.stepwise.monte_carlo.mover._protocols_stepwise_monte_carlo_mover_
)
bump_energy_full()
(in
WaterAdductHBondEnergy
)
BasicCDRClusterSetAP
(in
rosetta.protocols.antibody.clusters._protocols_antibody_clusters_
)
bondangle()
(in
ResidueType
)
bump_energy_full()
(in
DFIRE_Energy
)
BasicCDRClusterSetCAP
(in
rosetta.protocols.antibody.clusters._protocols_antibody_clusters_
)
bondangle()
(in
MMBondAngleResidueTypeParam
)
bump_energy_full()
(in
OrbitalsScore
)
BasicCmdLineInit
(in
rosetta.protocols.rpc._protocols_rpc_
)
bondangle()
(in
rosetta.numeric.kinematic_closure._numeric_kinematic_closure_
)
bump_energy_full()
(in
RNA_FullAtomStackingEnergy
)
BasicCmdLineInitAP
(in
rosetta.protocols.rpc._protocols_rpc_
)
bondangle_index()
(in
MMBondAngleResidueTypeParam
)
bump_energy_full()
(in
RNA_JR_SuiteEnergy
)
BasicCmdLineInitCAP
(in
rosetta.protocols.rpc._protocols_rpc_
)
BondAnglePerturber
(in
rosetta.protocols.kinematic_closure.perturbers._protocols_kinematic_closure_perturbers_
)
bump_energy_full()
(in
RNA_LJ_BaseEnergy
)
BasicDataCache
(in
rosetta.basic.datacache._basic_datacache_
)
BondAnglePerturberAP
(in
rosetta.protocols.kinematic_closure.perturbers._protocols_kinematic_closure_perturbers_
)
bump_energy_full()
(in
RNA_Mg_Energy
)
BasicDataCacheAP
(in
rosetta.basic.datacache._basic_datacache_
)
BondAnglePerturberCAP
(in
rosetta.protocols.kinematic_closure.perturbers._protocols_kinematic_closure_perturbers_
)
bump_energy_full()
(in
RNA_PairwiseLowResolutionEnergy
)
BasicDataCacheCAP
(in
rosetta.basic.datacache._basic_datacache_
)
bondangles_for_atom()
(in
ResidueType
)
bump_energy_full()
(in
RNA_SuiteEnergy
)
BasicInit
(in
rosetta.protocols.rpc._protocols_rpc_
)
bondangles_for_atom()
(in
MMBondAngleResidueTypeParam
)
bump_energy_full()
(in
RNA_TorsionEnergy
)
BasicInitAP
(in
rosetta.protocols.rpc._protocols_rpc_
)
BondAP
(in
rosetta.core.chemical._core_chemical_
)
bump_energy_full()
(in
RNA_VDW_Energy
)
BasicInitCAP
(in
rosetta.protocols.rpc._protocols_rpc_
)
BondAromaticity
(in
rosetta.core.chemical._core_chemical_
)
bump_energy_full()
(in
StackElecEnergy
)
BasicJob
(in
rosetta.protocols.jobdist._protocols_jobdist_
)
BondCAP
(in
rosetta.core.chemical._core_chemical_
)
bump_energy_full()
(in
RNA_DataBackboneEnergy
)
BasicJobAP
(in
rosetta.protocols.jobdist._protocols_jobdist_
)
BondConjugability
(in
rosetta.core.chemical._core_chemical_
)
bump_energy_full()
(in
symEnergy
)
BasicJobCAP
(in
rosetta.protocols.jobdist._protocols_jobdist_
)
BondData
(in
rosetta.core.chemical.sdf._core_chemical_sdf_
)
bump_energy_full()
(in
InterchainPairEnergy
)
BasicSimAnnealerRepacker
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
BondDataAP
(in
rosetta.core.chemical.sdf._core_chemical_sdf_
)
bump_grid()
(in
MatchCollisionFilter
)
BasicSimAnnealerRepackerAP
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
BondDataCAP
(in
rosetta.core.chemical.sdf._core_chemical_sdf_
)
bump_grid_to_enclose_pose()
(in
rosetta.protocols.match._protocols_match_
)
BasicSimAnnealerRepackerCAP
(in
rosetta.protocols.pack_daemon._protocols_pack_daemon_
)
bonded_neighbor()
(in
ResidueType
)
bump_grid_to_enclose_residue()
(in
rosetta.protocols.match._protocols_match_
)
Batch
(in
rosetta.protocols.jd2.archive._protocols_jd2_archive_
)
bonded_neighbor()
(in
Residue
)
bump_grid_to_enclose_residue_backbone()
(in
rosetta.protocols.match._protocols_match_
)
batch()
(in
Batch
)
bonded_neighbor_all_res()
(in
Conformation
)
bump_parameter()
(in
RNA_AtomVDW
)
batch_apply()
(in
FastRelax
)
bonded_neighbor_iterators()
(in
ResidueType
)
BumpGrid
(in
rosetta.protocols.match._protocols_match_
)
batch_get_xyz()
(in
Conformation
)
bonded_neighbor_types()
(in
ResidueType
)
BumpGridAP
(in
rosetta.protocols.match._protocols_match_
)
batch_get_xyz()
(in
SymmetricConformation
)
bonded_orbitals()
(in
Atom
)
BumpGridCAP
(in
rosetta.protocols.match._protocols_match_
)
batch_get_xyz()
(in
Pose
)
bonded_orbitals()
(in
ResidueType
)
BumpSelector
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
batch_get_xyz()
(in
ProtectedConformation
)
bonded_orbitals()
(in
Residue
)
BumpSelectorAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
batch_set_xyz()
(in
Conformation
)
BondedAtom
(in
rosetta.core.kinematics.tree._core_kinematics_tree_
)
BumpSelectorCAP
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
batch_set_xyz()
(in
SymmetricConformation
)
BondedAtomAP
(in
rosetta.core.kinematics.tree._core_kinematics_tree_
)
BumpSelectorDecision
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
batch_set_xyz()
(in
AtomTree
)
BondedAtomCAP
(in
rosetta.core.kinematics.tree._core_kinematics_tree_
)
bundle_parameters()
(in
MakeBundleHelix
)
batch_set_xyz()
(in
Pose
)
BondID
(in
rosetta.core.id._core_id_
)
bundle_symmetry()
(in
BundleParametersSet
)
batch_set_xyz()
(in
ProtectedConformation
)
BondIDAP
(in
rosetta.core.id._core_id_
)
bundle_symmetry_copies()
(in
BundleParametersSet
)
BatchAP
(in
rosetta.protocols.jd2.archive._protocols_jd2_archive_
)
BondIDCAP
(in
rosetta.core.id._core_id_
)
BundleGridSampler
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BatchCAP
(in
rosetta.protocols.jd2.archive._protocols_jd2_archive_
)
bonding_distance_threshold()
(in
rosetta.core.io.pdb._core_io_pdb_
)
BundleGridSamplerAP
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
batches()
(in
BaseArchiveManager
)
BondInRing
(in
rosetta
)
BundleGridSamplerCAP
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BatchEvaluator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
BondInRing
(in
rosetta.core.chemical
)
BundleGridSamplerCreator
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BatchEvaluatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
BondInRing
(in
rosetta.core.chemical._core_chemical_
)
BundleGridSamplerCreatorAP
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BatchEvaluatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
BondInRing
(in
BondRingness
)
BundleGridSamplerCreatorCAP
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BatchFeatures
(in
rosetta.protocols.features._protocols_features_
)
BondIsometry
(in
rosetta.core.chemical._core_chemical_
)
BundleGridSamplerHelper
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BatchFeaturesAP
(in
rosetta.protocols.features._protocols_features_
)
BondName
(in
rosetta.core.chemical._core_chemical_
)
BundleGridSamplerHelperAP
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BatchFeaturesCAP
(in
rosetta.protocols.features._protocols_features_
)
BondNotInRing
(in
rosetta
)
BundleGridSamplerHelperCAP
(in
rosetta.protocols.helical_bundle._protocols_helical_bundle_
)
BatchJobInputter
(in
rosetta.protocols.jd2._protocols_jd2_
)
BondNotInRing
(in
rosetta.core.chemical
)
BundleParameters
(in
rosetta.protocols.helical_bundle.parameters._protocols_helical_bundle_parameters_
)
BatchJobInputterAP
(in
rosetta.protocols.jd2._protocols_jd2_
)
BondNotInRing
(in
rosetta.core.chemical._core_chemical_
)
BundleParametersAP
(in
rosetta.protocols.helical_bundle.parameters._protocols_helical_bundle_parameters_
)
BatchJobInputterCAP
(in
rosetta.protocols.jd2._protocols_jd2_
)
BondNotInRing
(in
BondRingness
)
BundleParametersCAP
(in
rosetta.protocols.helical_bundle.parameters._protocols_helical_bundle_parameters_
)
BatchNrEvaluator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
BondOrder
(in
rosetta.core.chemical._core_chemical_
)
BundleParametersSet
(in
rosetta.protocols.helical_bundle.parameters._protocols_helical_bundle_parameters_
)
BatchNrEvaluatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
BondRingness
(in
rosetta.core.chemical._core_chemical_
)
bundleparametersset_index()
(in
PerturbBundle
)
BatchNrEvaluatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
bonus_value()
(in
HotspotStub
)
BundleParametersSetAP
(in
rosetta.protocols.helical_bundle.parameters._protocols_helical_bundle_parameters_
)
BB
(in
rosetta
)
Book_T_core_fragment_picking_old_vall_VallResidues_T
(in
rosetta.core.fragment.picking_old.concepts._core_fragment_picking_old_concepts_
)
BundleParametersSetCAP
(in
rosetta.protocols.helical_bundle.parameters._protocols_helical_bundle_parameters_
)
BB
(in
rosetta.core.id
)
Book_T_core_fragment_picking_old_vall_VallResidues_TAP
(in
rosetta.core.fragment.picking_old.concepts._core_fragment_picking_old_concepts_
)
burial
(in
rosetta
)
BB
(in
rosetta.core.id._core_id_
)
Book_T_core_fragment_picking_old_vall_VallResidues_TCAP
(in
rosetta.core.fragment.picking_old.concepts._core_fragment_picking_old_concepts_
)
burial
(in
ScoreType
)
BB
(in
TorsionType
)
Book_VallResidues
(in
rosetta.core.fragment.picking_old.concepts._core_fragment_picking_old_concepts_
)
burial
(in
rosetta.core.scoring._core_scoring_
)
bb()
(in
DnaInterfaceMinMover
)
Book_VallResiduesAP
(in
rosetta.core.fragment.picking_old.concepts._core_fragment_picking_old_concepts_
)
burial
(in
rosetta.core.scoring
)
bb()
(in
TaskAwareMinMover
)
Book_VallResiduesCAP
(in
rosetta.core.fragment.picking_old.concepts._core_fragment_picking_old_concepts_
)
burial()
(in
Xfrag
)
bb()
(in
SetupNCSMover
)
Bool3DGrid
(in
rosetta.protocols.match._protocols_match_
)
BurialEnergy
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
BB_BB
(in
rosetta.core.scoring.motif
)
Bool3DGridAP
(in
rosetta.protocols.match._protocols_match_
)
BurialEnergyAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
BB_BB
(in
rosetta.core.scoring.motif._core_scoring_motif_
)
Bool3DGridCAP
(in
rosetta.protocols.match._protocols_match_
)
BurialEnergyCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
BB_BB
(in
RPM_Type
)
Bool3DGridKinemageWriter
(in
rosetta.protocols.match._protocols_match_
)
BurialEnergyCreator
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
bb_bb()
(in
EnergyPerResidueFilter
)
Bool3DGridKinemageWriterAP
(in
rosetta.protocols.match._protocols_match_
)
BurialEnergyCreatorAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
bb_bb()
(in
TaskAwareScoreTypeFilter
)
Bool3DGridKinemageWriterCAP
(in
rosetta.protocols.match._protocols_match_
)
BurialEnergyCreatorCAP
(in
rosetta.core.scoring.methods._core_scoring_methods_
)
bb_bins_from_pose()
(in
RotamerRecovery
)
boolean_operations
(in
rosetta.protocols.filters._protocols_filters_
)
BuriedPolarScore
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
bb_bounding_sphere()
(in
SymmOnTheFlyNode
)
boolean_operations
(in
rosetta.protocols.toolbox.task_operations._protocols_toolbox_task_operations_
)
BuriedPolarScoreAP
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
bb_C_index()
(in
ResidueCartBondedParameters
)
BOOLEAN_OR
(in
rosetta.protocols.simple_filters
)
BuriedPolarScoreCAP
(in
rosetta.protocols.sic_dock._protocols_sic_dock_
)
bb_CA_index()
(in
ResidueCartBondedParameters
)
BOOLEAN_OR
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
BuriedUnsatHbondFilter
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
bb_centroid()
(in
SimpleNode
)
BOOLEAN_OR
(in
Operation
)
BuriedUnsatHbondFilterAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
bb_clones()
(in
SymmetryInfo
)
BooleanExpressionCreator
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
BuriedUnsatHbondFilterCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
bb_donor_acceptor_check()
(in
HBondOptions
)
BooleanExpressionCreatorAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
BuriedUnsatHbondFilterCreator
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
bb_follows()
(in
SymmetryInfo
)
BooleanExpressionCreatorCAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
BuriedUnsatHbondFilterCreatorAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
bb_H_index()
(in
ResidueCartBondedParameters
)
BooleanExpressionScanner
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
BuriedUnsatHbondFilterCreatorCAP
(in
rosetta.protocols.simple_filters._protocols_simple_filters_
)
bb_independent_rotamers()
(in
rosetta.core.pack.rotamer_set._core_pack_rotamer_set_
)
BooleanExpressionScannerAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
BuriedUnsatisfiedPolarsCalculator
(in
rosetta.protocols.toolbox.pose_metric_calculators._protocols_toolbox_pose_metric_calculators_
)
bb_is_independent()
(in
SymmetryInfo
)
BooleanExpressionScannerCAP
(in
rosetta.numeric.expression_parser._numeric_expression_parser_
)
BuriedUnsatisfiedPolarsCalculatorAP
(in
rosetta.protocols.toolbox.pose_metric_calculators._protocols_toolbox_pose_metric_calculators_
)
bb_N_index()
(in
ResidueCartBondedParameters
)
bools_from_sizes()
(in
rosetta.protocols.motifs._protocols_motifs_
)
BuriedUnsatisfiedPolarsCalculatorCAP
(in
rosetta.protocols.toolbox.pose_metric_calculators._protocols_toolbox_pose_metric_calculators_
)
bb_O_index()
(in
ResidueCartBondedParameters
)
boost
(in
rosetta.utility.pointer
)
burunsat_atoms()
(in
SHOBuriedUnsatisfiedPolarsCalculator
)
bb_only()
(in
AddConstraintsToCurrentConformationMover
)
bootstrapCATrace()
(in
FragInsertAndAlignMover
)
bx_init()
(in
MinimizerOptions
)
bb_pair_score()
(in
Dssp
)
BorderFlag
(in
rosetta.numeric.interpolation.spline._numeric_interpolation_spline_
)
by_aln()
(in
RmsdFilter
)
BB_PH
(in
rosetta.core.scoring.motif
)
born_radius()
(in
GenBornResidueInfo
)
Home
Trees
Indices
Help
Generated by Epydoc 3.0.1 on Sat Jun 6 00:09:41 2015
http://epydoc.sourceforge.net