- b -

• b : core::scoring::packstat::PointPair
• b1_ : core::scoring::FACTSRsdTypeInfo
• b2_ : core::scoring::FACTSRsdTypeInfo
• B_ : core::pose::CrystInfo
• b_ : core::scoring::electron_density::KromerMann
• B_ : core::scoring::electron_density::poseCoord , core::scoring::func::KarplusFunc
• b_ : core::scoring::ProQPotential
• b_flag_is_present_ : core::chemical::Selector_CMDFLAG
• b_proq2_ : core::scoring::ProQPotential
• backbone1_2_target_ : core::scoring::constraints::BackboneStubConstraint
• backbone1_target_ : core::scoring::constraints::BackboneStubConstraint
• backbone2_target_ : core::scoring::constraints::BackboneStubConstraint
• backbone_aa_ : core::chemical::ResidueType
• backbone_atom1_id_ : core::scoring::constraints::BackboneStubConstraint
• backbone_atom2_id_ : core::scoring::constraints::BackboneStubConstraint
• backbone_backbone_acceptor_ : core::scoring::hbonds::HBondSet
• backbone_backbone_bin_width_ : core::scoring::rna::RNA_LowResolutionPotential
• backbone_backbone_distance_cutoff_ : core::scoring::rna::RNA_LowResolutionPotential
• backbone_backbone_donor_ : core::scoring::hbonds::HBondSet
• backbone_backbone_num_bins_ : core::scoring::rna::RNA_LowResolutionPotential
• backbone_burial_ : core::scoring::rna::data::RNA_DataInfo
• backbone_burial_res_ : core::io::rna::RNA_DataReader
• backbone_dihedral_scores_ : core::scoring::disulfides::NCaCaC_Dihedral_Func
• backbone_exposed_ : core::scoring::rna::data::RNA_DataInfo
• backbone_exposed_res_ : core::io::rna::RNA_DataReader
• backbone_stub_constraint_energy_ : core::scoring::constraints::ConstraintEdge
• backbone_stub_linear_constraint_energy_ : core::scoring::constraints::ConstraintEdge
• background_node_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• background_node_index_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• background_prob : core::scoring::func::USOGFunc
• backptr_ : core::sequence::Cell
• bad_tree_ : core::kinematics::EXCN_InvalidFoldTree
• balls_ : core::pose::xyzStripeHashPose , core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• band : core::scoring::sc::MolecularSurfaceCalculator
• bAnnotate_ : core::fragment::FragmentIO
• barea : core::scoring::packstat::LR_MP_AtomData
• base2_xyz_ : core::scoring::hbonds::hbtrie::HBAtom
• base_ : core::scoring::PeptideBondedNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator
• BASE_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• base_atom_list_ : core::chemical::rna::RNA_ResidueType
• base_axis_array_ : core::scoring::rna::RNA_RawBaseBaseInfo
• base_backbone_atom_dist_cutoff_ : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_bin_width_ : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_check_atom_neighbor_ : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_distance_cutoff_ : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_num_bins_ : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_rho_cutoff_ : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_rho_fade_zone_ : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_table_size_ : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_z_cutoff_ : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_z_fade_zone_ : core::scoring::rna::RNA_LowResolutionPotential
• base_base_only_ : core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::StackElecEnergy
• 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_pair_array_ : core::scoring::rna::RNA_RawBaseBaseInfo
• base_pseudo_atom_centers_ : core::scoring::methods::LK_hack
• base_pseudo_atom_f1_f2s_ : core::scoring::methods::LK_hack
• base_restype_name_ : core::chemical::ResidueType
• base_score_ : core::scoring::disulfides::Cb_Distance_Func
• base_stack_array_ : core::scoring::rna::RNA_RawBaseBaseInfo
• base_stack_axis_array_ : core::scoring::rna::RNA_RawBaseBaseInfo
• base_stack_max_height_ : core::scoring::rna::RNA_LowResolutionPotential
• base_stack_min_height_ : core::scoring::rna::RNA_LowResolutionPotential
• base_stack_radius2_ : core::scoring::rna::RNA_LowResolutionPotential
• base_stack_radius_ : core::scoring::rna::RNA_LowResolutionPotential
• base_stack_rho_fade_zone_ : core::scoring::rna::RNA_LowResolutionPotential
• base_stack_z_fade_zone_ : core::scoring::rna::RNA_LowResolutionPotential
• base_stagger_array_ : core::scoring::rna::RNA_RawBaseBaseInfo
• base_stubs_ : core::scoring::rna::RNA_CentroidInfo
• base_xyz_ : core::scoring::hbonds::hbtrie::HBAtom
• basepair_axis_stagger_scaling_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• basepair_xy_bin_width_ : core::scoring::rna::RNA_LowResolutionPotential
• basepair_xy_num_bins_ : core::scoring::rna::RNA_LowResolutionPotential
• basepair_xy_table_size_ : core::scoring::rna::RNA_LowResolutionPotential
• basepair_xy_z_fade_zone_ : core::scoring::rna::RNA_LowResolutionPotential
• baserots_offsets_ : core::pack::rotamer_set::ContinuousRotamerSet
• basestack_axis_scaling_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• bb_acc_avail_ : core::scoring::hbonds::HBondResidueMinData
• 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_fourier_data : core::scoring::dna::DNABFormPotential
• bb_H_index_ : core::scoring::methods::ResidueCartBondedParameters
• bb_N_index_ : core::scoring::methods::ResidueCartBondedParameters
• bb_O_index_ : core::scoring::methods::ResidueCartBondedParameters
• bb_pos_ : core::scoring::SS_Info
• bb_radius_ : core::pack::interaction_graph::SimpleNode
• bbC_ : core::scoring::methods::ProClosureEnergy
• bbdep_angle_params_ : core::scoring::methods::ResidueCartBondedParameters
• bbdep_bond_devs_ : core::scoring::methods::IdealParametersDatabase
• bbdep_bond_params_ : core::scoring::methods::IdealParametersDatabase
• bbdep_length_params_ : core::scoring::methods::ResidueCartBondedParameters
• bbdep_nrc_interpdata_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbdep_nrchi_binsize_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbdep_nrchi_nbins_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbdep_nrchi_sample_ : core::pack::dunbrack::BBDepSemiRotamericData< T >
• bbdep_rotamers_to_sample_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbdep_rotsample_sorted_order_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbind_non_rotameric_chi_scores_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbind_nrchi_binsize_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbind_nrchi_nbins_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbind_nrchi_sample_ : core::pack::dunbrack::BBIndSemiRotamericData< T >
• bbind_nrchi_sampling_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbind_nrchi_scoring_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbind_rotamers_sorted_by_probability_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbind_rotamers_to_sample_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbN_ : core::scoring::methods::ProClosureEnergy
• bbO_ : core::scoring::methods::ProClosureEnergy
• bcfl : core::scoring::APBSConfig::I_PARAM
• bdx : core::scoring::packstat::LR_MP_AtomData
• bdy : core::scoring::packstat::LR_MP_AtomData
• bead_bead_interaction : core::scoring::etable::AtomPairEnergy
• bead_names_ : core::coarse::Translator
• beads_ : core::coarse::Translator
• begin : core::fragment::picking_old::concepts::Extent< PageIterator >
• begin1_ : core::scoring::dssp::StrandPairing
• begin2_ : core::scoring::dssp::StrandPairing
• behavior_ : core::pack::task::operation::AddBehaviorRLT
• behaviors_ : core::pack::task::ResidueLevelTask_
• being_packed_ : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo
• best_ : core::optimization::GA_Minimizer
• best_abs_log_norm_ratio : core::optimization::symmetry::MinDebug
• best_abs_log_norm_ratio_ : core::optimization::SimpleDerivCheckResult
• best_cos_theta : core::optimization::symmetry::MinDebug
• best_cos_theta_ : core::optimization::SimpleDerivCheckResult
• best_norm_analytic : core::optimization::symmetry::MinDebug
• best_norm_analytic_ : core::optimization::SimpleDerivCheckResult
• best_norm_numeric : core::optimization::symmetry::MinDebug
• best_norm_numeric_ : core::optimization::SimpleDerivCheckResult
• best_rot_bumpenergy_ : core::pack::rotamer_set::BumpSelector
• best_score_ : core::io::pdb::GeometricRenameIsomorphismCallback
• best_valid_ : core::optimization::Particle
• bestenergy_ : core::pack::annealer::SimAnnealerBase
• bestrotamer_at_seqpos_ : core::pack::annealer::SimAnnealerBase
• beta_ : core::pose::CrystInfo , core::scoring::CSA
• beta_atom_names_ : core::scoring::dna::DNATorsionPotential
• beta_barrel_ : core::scoring::MembraneTopology
• beta_components_ : core::scoring::dna::DNATorsionPotential
• beta_potential_ : core::scoring::rna::RNA_TorsionPotential
• betamax : core::pose::rna::RNA_SuiteName
• betamin : core::pose::rna::RNA_SuiteName
• bfac : core::scoring::packstat::SimplePDB_Atom
• bfac1_ : core::scoring::motif::ResPairMotif
• bfac2_ : core::scoring::motif::ResPairMotif
• bfac_ : core::scoring::motif::Xfrag , core::scoring::packing::PoseBalls
• bfactors_set : core::scoring::electron_density::FastDensEnergy
• bg_bg_atom_atom_overlaps_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• bg_bg_respairs_w_hphobe_olap_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• bg_edge_list_ : core::pack::interaction_graph::FirstClassNode< V, E, G >
• bg_edge_vector_ : core::pack::interaction_graph::FirstClassNode< V, E, G >
• bg_edge_vector_up_to_date_ : core::pack::interaction_graph::FirstClassNode< V, E, G >
• bg_exp_hphobe_djs_offsets_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• bg_mean_ : core::scoring::func::MixtureFunc
• bg_n_exp_hphobes_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• bg_neighbor_map : core::pack::interaction_graph::SurfaceNode< V, E, G >
• bg_node_vector_ : core::pack::interaction_graph::FirstClassNode< V, E, G >
• bg_nodes_ : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• bg_nodes_near_rotsub_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• bg_nodes_near_rotsub_bool_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• bg_res_num_atoms_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• bg_residues_ : core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc
• bg_sd_ : core::scoring::func::MixtureFunc
• bg_to_fc_edge_list_ : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• bgenumeration_2_resid_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• Bi_ : core::scoring::FACTSResidueInfo
• BIG_BULGE_LIMIT : core::scoring::dssp::StrandPairing
• big_polar_h_ : core::scoring::sasa::SasaCalc
• bin_ : core::scoring::constraints::BigBinConstraint
• bin_dist_ : core::scoring::mm::MMLJEnergyTable
• bin_size_ : core::scoring::func::SplineFunc
• bin_width_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• binding_energy_values_ : core::scoring::rna::data::RNA_DMS_Potential
• bins_per_A2 : core::scoring::etable::Etable , core::scoring::etable::EtableOptions , core::scoring::etable::MembEtable
• bins_per_angstrom_squared_ : core::scoring::mm::MMLJEnergyTable
• bins_vect_ : core::scoring::func::SplineFunc
• bins_vect_size_ : core::scoring::func::SplineFunc
• binw_ : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• binwidth_dist : core::scoring::sc::MolecularSurfaceCalculator
• binwidth_norm : core::scoring::sc::MolecularSurfaceCalculator
• bJumps_use_IntraResStub_ : core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• bKeepStubInResidue_ : core::kinematics::Edge
• block_size_ : core::graph::ArrayPool< T >
• bond_angle_central_atoms_to_score_ : core::scoring::methods::EnergyMethodOptions
• bond_angle_residue_type_param_set_ : core::scoring::methods::EnergyMethodOptions
• bond_geometry_energy_ : core::scoring::constraints::ConstraintEdge
• bond_lengths_ : core::chemical::IdealBondLengthSet
• bond_name_ : core::chemical::Bond
• bond_sd_ : core::scoring::rna::RNA_SugarCloseEnergy
• bond_type_ : core::chemical::AddBondType
• bondangle_atom_sets_ : core::chemical::ResidueType , core::scoring::mm::MMBondAngleResidueTypeParam
• bondangle_index_ : core::scoring::mm::MMBondAngleResidueTypeParam
• bondangles_bbdep_def_ : core::scoring::methods::IdealParametersDatabase
• bondangles_bbdep_gly_ : core::scoring::methods::IdealParametersDatabase
• bondangles_bbdep_prepro_ : core::scoring::methods::IdealParametersDatabase
• bondangles_bbdep_pro_ : core::scoring::methods::IdealParametersDatabase
• bondangles_bbdep_valile_ : core::scoring::methods::IdealParametersDatabase
• bondangles_for_atom_ : core::chemical::ResidueType , core::scoring::mm::MMBondAngleResidueTypeParam
• bondangles_indep_ : core::scoring::methods::IdealParametersDatabase
• bonded_neighbor_ : core::chemical::ResidueType
• bonded_neighbor_type_ : core::chemical::ResidueType
• bonded_orbitals_ : core::chemical::Atom
• bondlengths_bbdep_def_ : core::scoring::methods::IdealParametersDatabase
• bondlengths_bbdep_gly_ : core::scoring::methods::IdealParametersDatabase
• bondlengths_bbdep_prepro_ : core::scoring::methods::IdealParametersDatabase
• bondlengths_bbdep_pro_ : core::scoring::methods::IdealParametersDatabase
• bondlengths_bbdep_valile_ : core::scoring::methods::IdealParametersDatabase
• bondlengths_indep_ : core::scoring::methods::IdealParametersDatabase
• bondType : core::chemical::sdf::BondData
• bonus_ : core::pack::dunbrack::DunbrackConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint
• 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_neighs_ : core::scoring::elec::FAElecContextData
• BR_ : core::scoring::FACTSResidueInfo
• branch_atom_ : core::scoring::methods::GoapRsdType
• branch_points_ : core::chemical::carbohydrates::CarbohydrateInfo
• brent_abs_tolerance_ : core::optimization::MinimizerOptions
• brief : update_ResidueType_enum_files.EnumInfo
• bucket_counts : core::scoring::electron_density::ElectronDensity
• bucket_id : core::scoring::electron_density::ElectronDensity
• buf_ : core::io::serialization::BUFFER
• built_vd_ : core::chemical::AtomICoor
• bulge_bonus_ : core::scoring::rna::RNA_BulgeEnergy
• bump_check_ : core::pack::task::PackerTask_
• bump_overlap_factor_ : core::pack::task::residue_selector::ClashBasedRepackShellSelector
• bump_selector_ : core::pack::rotamer_set::RotamerSet_
• burial_ : core::scoring::motif::Xfrag
• burial_function_ : core::scoring::rna::data::RNA_DataBackboneEnergy
• buried : core::scoring::sc::_DOT , core::scoring::sc::Atom
• buried_area : core::scoring::packstat::AreaAccumulator
• BURIED_RESIDUE_NO_HSASA_CUTOFF : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfacePotential
• bX_ : core::grid::CartGrid< T >
• bx_init_ : core::optimization::MinimizerOptions
• bY_ : core::grid::CartGrid< T >
• bZ_ : core::grid::CartGrid< T >