- b -

• backbone_only1() : stepwise
• backbone_only2() : stepwise
• backrub() : backrub , basic::options::OptionKeys::backrub , basic::options::OptionKeys::canonical_sampling::probabilities , canonical_sampling::probabilities , remodel
• backrub_peptide() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• backrub_trials() : basic::options::OptionKeys::loops , loops
• bad_nter() : antibody , basic::options::OptionKeys::antibody
• base_contacts_only() : basic::options::OptionKeys::dna::design , dna::design
• basename() : ProQ
• batch_relax() : basic::options::OptionKeys::batch_relax , batch_relax
• batch_size() : basic::options::OptionKeys::batch_relax , batch_relax
• batches() : run
• bb_bump_cutoff() : basic::options::OptionKeys::enzdes , enzdes
• bb_min() : basic::options::OptionKeys::enzdes , enzdes
• bb_min_allowed_dev() : basic::options::OptionKeys::enzdes , enzdes
• bb_min_res() : basic::options::OptionKeys::docking , docking
• bb_move() : relax
• bb_moves() : basic::options::OptionKeys::dna::design , basic::options::OptionKeys::jumps , dna::design , jumps
• bb_stats() : orbitals
• bbdep_bond_devs() : basic::options::OptionKeys::corrections::score , corrections::score
• bbdep_bond_params() : basic::options::OptionKeys::corrections::score , corrections::score
• bbdep_omega() : basic::options::OptionKeys::corrections::score , corrections::score
• bbg() : basic::options::OptionKeys::bbg , bbg
• benchmark() : basic::options::OptionKeys::hotspot , hotspot , run
• benchmark_basic_design() : antibody::design , basic::options::OptionKeys::antibody::design
• beta() : basic::options::OptionKeys::corrections , corrections
• bGDT() : abinitio , basic::options::OptionKeys::abinitio
• big_frag_insertion_weight() : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• bilinearly_interpolated() : numeric::interpolation , numeric::interpolation::periodic_range::full , numeric::interpolation::periodic_range::half , numeric::interpolation::periodic_range::periodic_value::full , numeric::interpolation::periodic_range::periodic_value::half
• bin() : basic::options::OptionKeys::lh::fragpdb , lh::fragpdb , numeric::interpolation::periodic_range::full , numeric::interpolation::periodic_range::half , numeric::interpolation::periodic_range::periodic_value::full , numeric::interpolation::periodic_range::periodic_value::half
• binary_chk() : basic::options::OptionKeys::in::file , in::file
• binding() : basic::options::OptionKeys::dna::design , dna::design
• binding_score() : pepspec
• BlankMatrixMult() : numeric::model_quality
• blivens() : basic::options::OptionKeys::blivens , blivens
• blueprint() : basic::options::OptionKeys::fldsgn , basic::options::OptionKeys::flxbb , basic::options::OptionKeys::loops::loop_closure , fldsgn , flxbb , loops::loop_closure , remodel
• boinc() : basic::options::OptionKeys::boinc , boinc
• boinc_wu_zip() : basic::options::OptionKeys::in::file , in::file
• Boltz_temp() : basic::options::OptionKeys::dna::design , basic::options::OptionKeys::ms , dna::design , ms
• boltzmann_accept_probability() : numeric
• bondangle() : numeric::kinematic_closure , numeric::kinematic_closure::radians
• bonded_params() : score
• bonded_params_dir() : score
• boost_closure_cycles() : remodel::RemodelLoopMover
• boost_fa_atr() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• bound_delta() : basic::options::OptionKeys::cm::sanitize , cm::sanitize
• bound_sd() : basic::options::OptionKeys::cm::sanitize , cm::sanitize
• boundary_cutoff() : remodel
• bounded_protocol() : basic::options::OptionKeys::frags , frags
• BPData() : basic::options::OptionKeys::motifs , motifs
• bps_database() : rna
• 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
• broker() : basic::options::OptionKeys::broker , broker
• Bsol() : patterson
• bss() : basic::options::OptionKeys::lh , lh
• buffer_flush_frequency() : basic::options::OptionKeys::jd2 , jd2
• buffer_silent_output() : basic::options::OptionKeys::jd2 , jd2
• build_all_loops() : basic::options::OptionKeys::loops , loops
• build_attempts() : basic::options::OptionKeys::loops , loops
• build_disulf() : remodel
• build_dixon_matrices() : numeric::kinematic_closure
• build_initial() : basic::options::OptionKeys::loops , loops
• build_residue_file() : basic::options::OptionKeys::motifs , motifs
• build_round1_hits_twice() : basic::options::OptionKeys::match , match
• build_sin_and_cos() : numeric::kinematic_closure
• build_specific_loops() : basic::options::OptionKeys::loops , loops
• builder() : basic::options::OptionKeys::nonlocal , nonlocal
• buildsturm() : numeric::kinematic_closure
• built_in_rdc() : basic::options::OptionKeys::evaluation , evaluation
• bulge_res() : stepwise::rna
• bump_tolerance() : basic::options::OptionKeys::match , match
• bunsat_calc2() : basic::options::OptionKeys::bunsat_calc2 , bunsat_calc2
• burial() : basic::options::OptionKeys::flxbb::layer , basic::options::OptionKeys::in::file , flxbb::layer , in::file
• bypass_closure() : remodel::RemodelLoopMover
• bypass_fragments() : remodel