- 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::RNA_DataInfo
backbone_dihedral_scores_ : core::scoring::disulfides::NCaCaC_Dihedral_Func
backbone_exposed_ : core::scoring::rna::RNA_DataInfo
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::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_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
bfac_ : 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
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_lengths_ : core::chemical::IdealBondLengthSet
bond_name_ : core::chemical::Bond
bond_sd_ : core::scoring::rna::RNA_SugarCloseEnergy
bond_type_data_set_ : core::chemical::sdf::CtabBase
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_atom_name : core::chemical::sdf::addedH
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
BR_ : core::scoring::FACTSResidueInfo
branch_atom_ : core::scoring::methods::GoapRsdType
branch_points_ : core::chemical::carbohydrates::CarbohydrateInfo
brent_abs_tolerance_ : core::optimization::MinimizerOptions
bucket_counts : core::scoring::electron_density::ElectronDensity
bucket_id : core::scoring::electron_density::ElectronDensity
buf_ : core::io::serialization::BUFFER
bump_check_ : core::pack::task::PackerTask_
bump_selector_ : core::pack::rotamer_set::RotamerSet_
burial_function_ : core::scoring::rna::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 >