- b -

• B() : core::pose::CrystInfo , core::scoring::electron_density::OneGaussianScattering
• b1() : core::scoring::FACTSRsdTypeInfo
• b2() : core::scoring::FACTSRsdTypeInfo
• backbone_aa() : core::chemical::ResidueType , core::conformation::Residue
• backbone_backbone_energy() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::methods::TwoBodyEnergy
• backbone_burial() : core::scoring::rna::data::RNA_DataInfo
• backbone_exposed() : core::scoring::rna::data::RNA_DataInfo
• backbone_sidechain_energy() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::methods::TwoBodyEnergy
• backbone_stub_constraint_energy() : core::scoring::constraints::ConstraintEdge
• backbone_stub_linear_constraint_energy() : core::scoring::constraints::ConstraintEdge
• backbone_torsion_angle_atoms() : core::conformation::Conformation
• BackboneStubConstraint() : core::scoring::constraints::BackboneStubConstraint
• BackboneStubLinearConstraint() : core::scoring::constraints::BackboneStubLinearConstraint
• BackgroundNode() : core::pack::interaction_graph::BackgroundNode< V, E, G >
• BackgroundToFirstClassEdge() : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• bad_tree() : core::kinematics::EXCN_InvalidFoldTree
• Ball() : core::scoring::packing::Ball
• ball() : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• balls() : core::scoring::packing::PoseBalls
• base2_xyz() : core::scoring::hbonds::hbtrie::HBAtom
• base_axis_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_backbone_distance_cutoff() : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_rho_cutoff() : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_z_cutoff() : core::scoring::rna::RNA_LowResolutionPotential
• base_centroids() : core::scoring::rna::RNA_CentroidInfo
• base_geometry_height_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_geometry_orientation_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_name() : core::chemical::carbohydrates::CarbohydrateInfo , core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• base_pair_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_pair_score() : core::scoring::dna::DNA_BasePotential
• base_restype_name() : core::chemical::ResidueType
• base_score() : core::scoring::dna::DNA_BasePotential
• base_stack_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_stack_axis_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_stagger_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_step_score() : core::scoring::dna::DNA_BasePotential
• base_string() : core::scoring::dna::DNA_BasePotential
• base_stubs() : core::scoring::rna::RNA_CentroidInfo
• base_xyz() : core::scoring::hbonds::hbtrie::HBAtom
• BaseEtableEnergy() : core::scoring::etable::BaseEtableEnergy< Derived >
• BasePair() : core::pose::rna::BasePair
• basepair_axis_stagger_scaling() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• BasePartner() : core::scoring::dna::BasePartner
• baserotamer_data() : core::pack::rotamer_set::ContinuousRotamerSet
• BaseStack() : core::pose::rna::BaseStack
• basestack_axis_scaling() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• batch_get_xyz() : core::conformation::Conformation , core::pose::Pose
• batch_set_xyz() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree , core::pose::Pose
• bb_acc_avail() : core::scoring::hbonds::HBondResidueMinData
• bb_bb_boundaries() : core::pack::interaction_graph::SimpleEdge
• bb_bb_carbon_hbond_one_way() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• BB_BB_EnergyInvoker() : core::scoring::etable::BB_BB_EnergyInvoker< Evaluator >
• bb_bbE() : core::pack::interaction_graph::SimpleEdge
• bb_bbE_calced() : core::pack::interaction_graph::SimpleEdge
• bb_bounding_sphere() : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• bb_C_index() : core::scoring::methods::ResidueCartBondedParameters
• bb_CA_index() : core::scoring::methods::ResidueCartBondedParameters
• bb_centroid() : core::pack::interaction_graph::SimpleNode
• bb_clones() : core::conformation::symmetry::SymmetryInfo
• bb_don_avail() : core::scoring::hbonds::HBondResidueMinData
• bb_donor_acceptor_check() : core::scoring::hbonds::HBondOptions
• bb_follows() : core::conformation::symmetry::SymmetryInfo
• bb_H_index() : core::scoring::methods::ResidueCartBondedParameters
• bb_is_independent() : core::conformation::symmetry::SymmetryInfo
• bb_N_index() : core::scoring::methods::ResidueCartBondedParameters
• bb_O_index() : core::scoring::methods::ResidueCartBondedParameters
• bb_pair_score() : core::scoring::dssp::Dssp
• bb_pos() : core::scoring::SS_Info
• bb_radius() : core::pack::interaction_graph::SimpleNode
• bb_sc_carbon_hbond_one_way() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• bb_stats() : core::scoring::orbitals::OrbitalsStatistics
• bbdep_angle_parameters() : core::scoring::methods::ResidueCartBondedParameters
• bbdep_bond_devs() : core::scoring::methods::IdealParametersDatabase
• bbdep_bond_params() : core::scoring::methods::IdealParametersDatabase
• bbdep_chisamples_for_rotamer_chi() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• bbdep_length_parameters() : core::scoring::methods::ResidueCartBondedParameters
• bbdep_nrchi_sample() : core::pack::dunbrack::BBDepSemiRotamericData< T, N >
• bbdep_nrchi_score() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• BBDepCartBondedParameters() : core::scoring::methods::BBDepCartBondedParameters
• BBDepNRChiSample() : core::pack::dunbrack::BBDepNRChiSample< P >
• BBDepScoreInterpData() : core::pack::dunbrack::BBDepScoreInterpData< N >
• BBDepSemiRotamericData() : core::pack::dunbrack::BBDepSemiRotamericData< T, N >
• bbind_chisamples_for_rotamer_chi() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• bbind_nrchi_sample() : core::pack::dunbrack::BBIndSemiRotamericData< T, N >
• bbind_nrchi_score() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• BBIndepCartBondedParameters() : core::scoring::methods::BBIndepCartBondedParameters
• bbindices_up_to_date() : core::scoring::BB_Pos
• BBIndNRChiSample() : core::pack::dunbrack::BBIndNRChiSample< P >
• BBIndSemiRotamericData() : core::pack::dunbrack::BBIndSemiRotamericData< T, N >
• bbtorsion_srfd() : core::fragment::picking_old::vall::VallResidue
• BBTorsionAndAnglesSRFD() : core::fragment::BBTorsionAndAnglesSRFD
• BBTorsionSRFD() : core::fragment::BBTorsionSRFD
• begin() : core::environment::DofPassport , core::fragment::ConstantLengthFragSet , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::OrderedFragSet , core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Library< Books > , core::graph::EdgeList , core::io::raw_data::RawFileData , core::io::silent::SilentFileData , core::kinematics::FoldTree , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap , core::pack::rotamer_set::FixbbRotamerSets , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubset , core::pack::rotamer_set::RotamerSubsets , core::pack::task::TaskFactory , core::scoring::constraints::Constraints , core::scoring::constraints::ResidueConstraints , core::scoring::dssp::StrandPairingSet , core::scoring::EMapVector
• begin1() : core::scoring::dssp::StrandPairing
• begin_const() : core::io::raw_data::RawFileData
• being_designed() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• being_packed() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_ , core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo
• BesselI0() : core::scoring::CenHBPotential
• best_abs_log_norm_ratio() : core::optimization::SimpleDerivCheckResult
• best_cos_theta() : core::optimization::SimpleDerivCheckResult
• best_norm_analytic() : core::optimization::SimpleDerivCheckResult
• best_norm_numeric() : core::optimization::SimpleDerivCheckResult
• best_rotamer_energy() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N > , core::pack::dunbrack::RotamerLibrary , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleLigandRotamerLibrary , core::pack::dunbrack::SingleResidueRotamerLibrary
• bestenergy() : core::pack::annealer::SimAnnealerBase
• bestrotamer_at_seqpos() : core::pack::annealer::SimAnnealerBase
• beta() : core::pose::CrystInfo , core::pose::Pose , core::scoring::CSA
• beta_aform() : core::chemical::rna::RNA_FittedTorsionInfo
• beta_components() : core::scoring::dna::DNATorsionPotential
• bfac() : core::scoring::motif::Xfrag , core::scoring::packing::PoseBalls
• bfac1() : core::scoring::motif::ResPairMotif
• bfac2() : core::scoring::motif::ResPairMotif
• bg_node_2_resid() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• Bi() : core::scoring::FACTSResidueInfo
• biased_mainchain_torsions() : core::scoring::bin_transitions::BinTransitionCalculator
• BigBinConstraint() : core::scoring::constraints::BigBinConstraint
• BigBinConstraintCreator() : core::scoring::constraints::BigBinConstraintCreator
• bin() : core::scoring::constraints::BigBinConstraint
• bin0_of_real() : core::scoring::motif::ResPairMotifMetaBinner
• bin_angle() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• bin_boundaries_i() : core::scoring::bin_transitions::BinTransitionData
• bin_boundaries_iplus1() : core::scoring::bin_transitions::BinTransitionData
• bin_index() : core::scoring::motif::MotifHash , core::scoring::motif::XformScore
• bin_params_loaded() : core::scoring::bin_transitions::BinTransitionCalculator
• bin_rotameric_chi() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• bin_transition_data() : core::scoring::bin_transitions::BinTransitionCalculator
• binary_is_up_to_date() : core::pack::dunbrack::RotamerLibrary
• binary_is_up_to_date_02() : core::pack::dunbrack::RotamerLibrary
• binary_is_up_to_date_10() : core::pack::dunbrack::RotamerLibrary
• BinaryFragmentStoreBackend() : core::indexed_structure_store::BinaryFragmentStoreBackend
• BinarySilentStruct() : core::io::silent::BinarySilentStruct
• BinarySilentStructCreator() : core::io::silent::BinarySilentStructCreator
• binsums_i() : core::scoring::bin_transitions::BinTransitionData
• binsums_iplus1() : core::scoring::bin_transitions::BinTransitionData
• BinTransitionCalculator() : core::scoring::bin_transitions::BinTransitionCalculator
• BinTransitionData() : core::scoring::bin_transitions::BinTransitionData
• blanket_assign_state_0() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph
• blanket_reset_alt_state_total_hASAs() : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• blanket_set() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• block_signals() : core::conformation::Conformation
• block_size() : core::graph::ArrayPool< T >
• blocking_signals() : core::conformation::Conformation
• Bond() : core::chemical::Bond
• bond() : core::chemical::ResidueType
• bond_angle() : core::conformation::Conformation , core::kinematics::AtomTree
• bond_angle_central_atoms_to_score() : core::scoring::methods::EnergyMethodOptions
• bond_angle_dof_id() : core::kinematics::AtomTree
• bond_angle_residue_type_param_set() : core::scoring::methods::EnergyMethodOptions
• bond_geometry_energy() : core::scoring::constraints::ConstraintEdge
• bond_iterators() : core::chemical::ResidueType
• bond_length() : core::conformation::Conformation , core::kinematics::AtomTree
• bond_length_dof_id() : core::kinematics::AtomTree
• bond_name() : core::chemical::Bond
• bondangle() : core::chemical::ResidueType , core::scoring::mm::MMBondAngleResidueTypeParam
• bondangle_index() : core::scoring::mm::MMBondAngleResidueTypeParam
• bondangles_for_atom() : core::chemical::ResidueType , core::scoring::mm::MMBondAngleResidueTypeParam
• BondData() : core::chemical::sdf::BondData
• bonded() : core::chemical::AutomorphismIterator
• bonded2() : core::chemical::AutomorphismIterator
• bonded_neighbor() : core::chemical::ResidueType , core::conformation::Residue
• bonded_neighbor_all_res() : core::conformation::Conformation
• bonded_neighbor_iterators() : core::chemical::ResidueType
• bonded_neighbor_types() : core::chemical::ResidueType
• bonded_orbitals() : core::chemical::Atom , core::chemical::ResidueType , core::conformation::Residue
• BondedAtom() : core::kinematics::tree::BondedAtom
• BondID() : core::id::BondID
• Book() : core::fragment::picking_old::concepts::Book< Pages >
• bookmarks() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• books() : core::fragment::picking_old::concepts::Library< Books >
• born_radius() : core::scoring::GenBornResidueInfo
• boundary_left() : core::kinematics::FoldTree
• boundary_neighs() : core::scoring::elec::FAElecContextData
• boundary_right() : core::kinematics::FoldTree
• BoundFunc() : core::scoring::constraints::BoundFunc
• bounds_check() : core::graph::Array0< T >
• BR() : core::scoring::FACTSResidueInfo
• branch_point() : core::chemical::carbohydrates::CarbohydrateInfo
• BRENT() : core::optimization::BrentLineMinimization
• brent_abs_tolerance() : core::optimization::MinimizerOptions
• BrentLineMinimization() : core::optimization::BrentLineMinimization
• BUFFER() : core::io::serialization::BUFFER
• buffer_signals() : core::conformation::Conformation
• buffering_signals() : core::conformation::Conformation
• build() : core::chemical::AtomICoor , core::chemical::orbitals::ICoorOrbitalData , core::scoring::methods::WaterBuilder
• build_atom_ideal() : core::conformation::Residue
• build_bbdep_rotamers() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• build_bbind_rotamers() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• build_dependent_rotamers() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• build_dependent_rotamers_for_concrete() : core::pack::rotamer_set::RotamerSet_
• build_fake_xyz() : core::kinematics::Stub
• build_groupinfo() : core::scoring::elec::GroupElec
• build_jumpres_distmap() : core::kinematics::ShortestPathInFoldTree
• build_optimize_H_rotamers() : core::pack::rotamer_set::RotamerSet_
• build_orbital_xyz() : core::conformation::Residue
• build_peptide_table() : core::kinematics::ShortestPathInFoldTree
• build_placeholders() : core::scoring::GenBornPotential
• build_rotamers() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N > , core::pack::rotamer_set::ContinuousRotamerSet , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubset
• build_rotamers_for_concrete() : core::pack::rotamer_set::RotamerSet_
• build_rotamers_for_concrete_virt() : core::pack::rotamer_set::RotamerSet_
• build_sc_only_rotamer() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge
• build_tp3_water_rotamers() : core::pack::rotamer_set::RotamerSet_
• build_waters() : core::scoring::methods::LKB_ResidueInfo
• built_atom_vertex() : core::chemical::AtomICoor
• bump_check() : core::pack::rotamer_set::RotamerSet_ , core::pack::task::PackerTask , core::pack::task::PackerTask_
• bump_check_backbone() : core::scoring::ScoreFunction
• bump_check_full() : core::scoring::ScoreFunction
• bump_energy_backbone() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::ProClosureEnergy , core::scoring::methods::TwoBodyEnergy
• bump_energy_full() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::ProClosureEnergy , core::scoring::methods::TwoBodyEnergy
• bump_parameter() : core::scoring::rna::RNA_AtomVDW
• BumpSelector() : core::pack::rotamer_set::BumpSelector
• burial() : core::scoring::motif::Xfrag
• burial_deriv() : core::scoring::elec::FA_GrpElecEnergy
• burial_weight() : core::scoring::elec::FA_GrpElecEnergy
• BurialEnergy() : core::scoring::methods::BurialEnergy
• bx_init() : core::optimization::MinimizerOptions