- b -

• b() : score::fiber_diffraction
• b_factor() : score::fiber_diffraction
• b_factor_solv() : score::fiber_diffraction
• b_factor_solv_K() : score::fiber_diffraction
• backbone_mover() : coupled_moves
• backbone_only1() : stepwise
• backbone_only2() : stepwise
• background_weight() : mh::score
• backrub() : backrub , canonical_sampling::probabilities
• backrub_peptide() : flexPepDocking
• backrub_trials() : loops
• bad_nter() : antibody
• base64_decode() : utility::io
• base64_encode() : utility::io
• base_cdr_instructions() : antibody::design
• base_contacts_only() : dna::design
• base_default_default_constructor_available() : binder
• base_namespace() : binder
• base_native_bonus() : legacy_sewing
• base_pair() : recces::base_pair
• basename() : ProQ
• basic_array_to_structured() : pyrosetta::utility::array
• batch_relax() : batch_relax
• batch_size() : batch_relax , hotspot
• batches() : run
• bb_average_weight() : mean_field
• bb_boltz_probs() : mean_field
• bb_bump_cutoff() : enzdes
• bb_list() : mean_field
• bb_min() : enzdes
• bb_min_allowed_dev() : enzdes
• bb_min_res() : docking
• bb_move() : relax
• bb_moves() : jumps
• bb_stats() : orbitals
• bb_stdev() : recces::thermal_sampling
• bbdep_bond_devs() : corrections::score
• bbdep_bond_params() : corrections::score
• bbdep_omega() : corrections::score
• bbg() : bbg
• bbnbrs() : ddg
• begin() : ObjexxFCL
• begins_with() : binder
• benchmark() : hotspot , mp::benchmark , run
• beta() : corrections
• beta_cart() : corrections
• beta_cdr1_template_id() : tcrmodel
• beta_cdr1_template_pdb() : tcrmodel
• beta_cdr2_template_id() : tcrmodel
• beta_cdr2_template_pdb() : tcrmodel
• beta_cdr3_template_id() : tcrmodel
• beta_cdr3_template_pdb() : tcrmodel
• beta_framework_template_id() : tcrmodel
• beta_framework_template_pdb() : tcrmodel
• beta_germline_template_id() : tcrmodel
• beta_germline_template_pdb() : tcrmodel
• beta_july15() : corrections
• beta_july15_cart() : corrections
• beta_nov16() : corrections
• beta_nov16_cart() : corrections
• beta_orientation_template_id() : tcrmodel
• beta_orientation_template_pdb() : tcrmodel
• bGDT() : abinitio
• bias_design_search_to_native() : hydrate
• bias_sampling() : coupled_moves
• biased_dist_all_gen() : mean_field
• big_frag_insertion_weight() : cm::hybridize
• bilinearly_interpolated() : numeric::interpolation , numeric::interpolation::periodic_range::full , numeric::interpolation::periodic_range::half
• bin() : fmt , lh::fragpdb , numeric::interpolation::periodic_range::full , numeric::interpolation::periodic_range::half
• binary_chk() : in::file
• binary_output() : rna::denovo::out
• binary_search_cdf() : numeric::random
• binary_search_ranges() : utility
• bind_classmethod() : pyrosetta::bindings::utility
• bind_constructor() : binder
• bind_copy_constructor() : binder
• bind_data_member() : binder
• bind_default_constructor() : binder
• bind_enum() : binder
• bind_forward_declaration() : binder
• bind_function() : binder
• bind_member_functions_for_call_back() : binder
• bind_method() : pyrosetta::bindings::utility
• bind_property() : pyrosetta::bindings::utility
• bind_rmsd_calc() : numeric::alignment
• binding() : dna::design
• binding_public_data_members() : binder
• binding_public_member_functions() : binder
• binding_score() : pepspec
• binding_template_bases() : binder
• biounit() : mh::path
• biounit_ideal() : mh::path
• bit_and() : ObjexxFCL::bit
• bit_clr() : ObjexxFCL::bit
• bit_not() : ObjexxFCL::bit
• bit_or() : ObjexxFCL::bit
• bit_set() : ObjexxFCL::bit
• bit_test() : ObjexxFCL::bit
• bit_xor() : ObjexxFCL::bit
• bite() : ObjexxFCL::format
• blank() : ObjexxFCL
• BlankMatrixMult() : numeric::model_quality
• blastp() : antibody
• blastp_identity_cutoff() : tcrmodel
• blivens() : blivens
• block() : cloud
• block_allocation_error_message() : utility::graph
• block_stack() : recces::base_pair
• block_stack_above_res() : full_model::rna
• block_stack_below_res() : full_model::rna
• blueprint() : flxbb , remodel
• boinc() : boinc
• boinc_wu_zip() : in::file
• Boltz_temp() : dna::design , ms
• boltzmann_accept_probability() : numeric
• boltzmann_choice_post_enumerated_minimize() : stepwise
• boltzmann_kt() : coupled_moves , nmr::spinlabel
• bond_angle_sd_polar_hydrogen() : stepwise::polar_hydrogens
• bond_torsion_sd_polar_hydrogen() : stepwise::polar_hydrogens
• bondangle() : numeric::kinematic_closure , numeric::kinematic_closure::radians
• bonded_params() : score
• bonded_params_dir() : score
• boost_closure_cycles() : remodel::RemodelLoopMover
• boost_fa_atr() : flexPepDocking
• bot() : loodo
• boundary_cutoff() : remodel
• boundaryAA() : remodel
• bounded_protocol() : frags
• box_length() : legacy_sewing , sewing
• BPData() : motifs
• bps_database() : rna::denovo::db
• bps_moves() : rna::denovo
• breadth_first_search_prune() : utility::graph
• breadth_first_visit_prune() : utility::graph
• bridge_objects() : numeric::kinematic_closure::radians
• bridge_res() : stepwise::protein
• bridgeObjects() : numeric::kinematic_closure
• bridgeObjects_nonredundant() : numeric::kinematic_closure
• broker() : broker
• Bsol() : patterson
• bss() : lh
• buffer_flush_frequency() : jd2
• buffer_silent_output() : jd2
• build_all_loops() : loops
• build_attempts() : loops
• build_disulf() : remodel
• build_dixon_matrices() : numeric::kinematic_closure
• build_generated_bindings() : build
• build_initial() : loops
• build_residue_file() : motifs
• build_round1_hits_twice() : match
• build_sin_and_cos() : numeric::kinematic_closure
• build_specific_loops() : loops
• buildsturm() : numeric::kinematic_closure
• built_in_rdc() : evaluation
• bulge_res() : full_model::rna
• bump_check() : coupled_moves
• bump_tolerance() : match
• bunsat_calc2() : bunsat_calc2
• burial() : in::file
• buried_unsatisfied_penalty_burial_threshold() : score
• buried_unsatisfied_penalty_cone_angle_exponent() : score
• buried_unsatisfied_penalty_cone_angle_shift_factor() : score
• buried_unsatisfied_penalty_cone_dist_exponent() : score
• buried_unsatisfied_penalty_cone_dist_midpoint() : score
• buried_unsatisfied_penalty_hbond_energy_threshold() : score
• bypass_closure() : remodel::RemodelLoopMover
• bypass_fragments() : remodel