- b -

• backbone_stub_match() : protocols::motifs
• backrub_rotation_angles() : protocols::backrub
• backrub_rotation_constants() : protocols::backrub
• bad_anchorfile() : protocols::anchored_design
• bad_inner_job_exception() : protocols::jd3::chunk_library , protocols::jd3::full_model
• bah_chi_compute_energy_sp2() : core::scoring::hbonds
• bah_chi_compute_energy_sp3() : core::scoring::hbonds
• base_atoms_square_deviation() : protocols::stepwise::modeler::rna
• base_name() : protocols::vip
• base_pair_moving() : core::pose::rna
• base_pair_step_moving() : core::pose::rna
• basename_for_score_function() : core::scoring
• bases_are_coplanar() : core::pose::rna
• bases_form_a_hydrogen_bond() : core::pose::rna
• basic_idealize() : protocols::idealize
• bb_independent_rotamers() : core::pack::rotamer_set
• bb_rmsd() : core::scoring
• bb_rmsd_including_O() : core::scoring
• bessel_roots() : core::scoring::fiber_diffraction
• best_bbcst_residues() : protocols::protein_interface_design
• best_cutpoint() : protocols::protein_interface_design
• BETA_GENPOT() : core::scoring
• BETA_JULY15() : core::scoring
• BETA_NOV15() : core::scoring
• BETA_NOV16() : core::scoring
• biggest_residue_deviation_no_super() : core::scoring
• biggest_residue_deviation_no_super_subset() : core::scoring
• bin_by_seq_separation() : core::scoring::constraints
• bin_from_bond() : core::scoring
• bind_pose_utility() : protocols::indexed_structure_store
• bind_QueryDatabase() : protocols::indexed_structure_store::search
• bind_StructureStore() : protocols::indexed_structure_store
• bit_is_set() : core::pack::dunbrack
• BOGUS_ENERGY() : core::scoring
• boincOutputFilter() : protocols::boinc
• Boltzmann() : protocols::md
• bond_angles() : protocols::environment
• bond_lengths() : protocols::environment
• bond_order_to_property() : core::chemical
• bond_torsions() : protocols::environment
• bonding_distance_threshold() : core::io::pose_from_sfr
• bondorders_map() : core::scoring
• bool_mask_from_resnums() : core::pack::task::residue_selector
• bool_mask_from_task() : core::pack::task::residue_selector
• bools_from_sizes() : protocols::motifs
• bounded_loops_from_alignment() : protocols::comparative_modeling
• bpdefs2map() : protocols::motifs
• bpybb() : protocols::sic_dock::scores
• branching_atomid1() : protocols::branch_angle
• branching_atomids2() : protocols::branch_angle
• break_disulfide() : core::conformation
• Broker_main() : protocols::abinitio
• brute_mindis() : protocols::sic_dock
• build_acceptor_acceptor_waters() : core::pack::rotamer_set
• build_anchorless_water_rotamers() : core::pack::rotamer_set
• build_and_score_disulfide() : protocols::forge::remodel
• build_chemical_edge() : core::conformation
• build_dependent_water_rotamers() : core::pack::rotamer_set
• build_dna_rotamers() : core::pack::rotamer_set
• build_donor_acceptor_waters() : core::pack::rotamer_set
• build_donor_donor_waters() : core::pack::rotamer_set
• build_five_prime_phosphate_rotamers() : core::pack::rotamer_set
• build_fixed_O_water_rotamers_independent() : core::pack::rotamer_set
• build_full_model() : protocols::stepwise::monte_carlo
• build_independent_water_rotamers() : core::pack::rotamer_set
• build_jump_edge() : core::conformation
• build_lib_dna_rotamers() : core::pack::rotamer_set
• build_moving_O_bridge_waters() : core::pack::rotamer_set
• build_moving_O_water_rotamers_dependent() : core::pack::rotamer_set
• build_moving_O_water_rotamers_independent() : core::pack::rotamer_set
• build_optimal_hyp_H_for_acceptor() : core::pack::rotamer_set
• build_optimal_hyp_H_for_donor() : core::pack::rotamer_set
• build_optimal_water_O_on_donor() : core::pack::rotamer_set , core::scoring::lkball
• build_optimal_water_Os_on_acceptor() : core::pack::rotamer_set , core::scoring::lkball
• build_polymer_edge() : core::conformation
• build_pose() : core::import_pose
• build_pose_as_is() : core::import_pose
• build_pose_as_is2() : core::import_pose
• build_pose_from_pdb_as_is() : core::io::pdb
• build_proton_chi_rotamers() : core::pack::rotamer_set
• build_random_dna_rotamers() : core::pack::rotamer_set
• build_residue_tree() : core::conformation
• build_rna_chi_rotamers() : core::pack::rotamer_set
• build_rna_rotamers() : core::pack::rotamer_set
• build_rotamers_from_rotamer_bins() : core::pack::rotamer_set
• build_rotamers_lite() : protocols::motifs
• build_rotated_water_rotamers() : core::pack::rotamer_set
• build_sew_waters_to_acceptor() : core::pack::rotamer_set
• build_sew_waters_to_donor() : core::pack::rotamer_set
• build_single_anchor_water_rotamers_independet() : core::pack::rotamer_set
• build_single_edge_waters() : core::pack::rotamer_set
• build_three_prime_phosphate_rotamers() : core::pack::rotamer_set
• build_tree() : core::conformation
• build_water_O_on_donor() : core::pack::rotamer_set
• bulge_residues() : protocols::denovo_design::architects
• bump_check() : core::pack::rotamer_set , protocols::nmr , protocols::rna::movers
• bump_grid_to_enclose_pose() : protocols::match
• bump_grid_to_enclose_residue() : protocols::match
• bump_grid_to_enclose_residue_backbone() : protocols::match
• burial3class_weight_initializer() : core::scoring::hbonds
• burial_weight() : core::scoring::hbonds
• buried_unsat_hbond_filter_tracer() : protocols::simple_filters