- b -

• b : basic::options::OptionKeys::score::fiber_diffraction , compute_difference , test.T850_SubClassing
• b1 : docking
• b2 : docking
• b3 : docking
• b3aa : b3a_distro
• b53_12_pose : evaluate_beta_mutants
• b53_12_score : evaluate_beta_mutants
• b53_12b_pose : evaluate_beta_mutants
• b53_12b_score : evaluate_beta_mutants
• b53_13_pose : evaluate_beta_mutants
• b53_13_score : evaluate_beta_mutants
• b53_14_pose : evaluate_beta_mutants
• b53_14_score : evaluate_beta_mutants
• b53_15_pose : evaluate_beta_mutants
• b53_15_score : evaluate_beta_mutants
• b53_16_pose : evaluate_beta_mutants
• b53_16_score : evaluate_beta_mutants
• b53_17_pose : evaluate_beta_mutants
• b53_17_score : evaluate_beta_mutants
• b53_18_pose : evaluate_beta_mutants
• b53_18_score : evaluate_beta_mutants
• b53_8_score : evaluate_beta_mutants
• b_factor : basic::options::OptionKeys::score::fiber_diffraction
• b_factor_solv : basic::options::OptionKeys::score::fiber_diffraction
• b_factor_solv_K : basic::options::OptionKeys::score::fiber_diffraction
• backbone : internal_coordinates , make_comparison
• backbone_angle_max : demo.D070_Refinement
• backbone_minimization_mode : basic::options::OptionKeys::trRosetta
• backbone_mover : basic::options::OptionKeys::coupled_moves
• backbone_only1 : basic::options::OptionKeys::stepwise
• backbone_only2 : basic::options::OptionKeys::stepwise
• backbone_randomization_mode : basic::options::OptionKeys::trRosetta
• backbones : internal_coordinates
• background : execute , kic_runner , run_backbone , run_sidechain
• background_weight : basic::options::OptionKeys::mh::score
• backrub : basic::options::OptionKeys::backrub , basic::options::OptionKeys::canonical_sampling::probabilities
• backrub_peptide : basic::options::OptionKeys::flexPepDocking
• backrub_trials : basic::options::OptionKeys::loops
• bad_calls : basic
• Base : schema
• base : test.T005_Bindings
• base64_chars : utility::io
• base_cdr_instructions : basic::options::OptionKeys::antibody::design
• base_contacts_only : basic::options::OptionKeys::dna::design
• base_dir : rna_rosetta_ready_set
• base_native_bonus : basic::options::OptionKeys::legacy_sewing
• base_pair : basic::options::OptionKeys::recces::base_pair
• basename : basic::options::OptionKeys::ProQ
• basic_data< void > : detail
• basic_init : nacl_rosetta
• batch_relax : basic::options::OptionKeys::batch_relax
• batch_size : basic::options::OptionKeys::batch_relax , basic::options::OptionKeys::hotspot
• batches : basic::options::OptionKeys::run
• bb_average_weight : basic::options::OptionKeys::mean_field
• bb_boltz_probs : basic::options::OptionKeys::mean_field
• bb_bump_cutoff : basic::options::OptionKeys::enzdes
• bb_list : basic::options::OptionKeys::mean_field
• bb_min : basic::options::OptionKeys::enzdes , local
• bb_min_allowed_dev : basic::options::OptionKeys::enzdes
• bb_min_res : basic::options::OptionKeys::docking
• bb_move : basic::options::OptionKeys::relax
• bb_moves : basic::options::OptionKeys::jumps
• bb_stats : basic::options::OptionKeys::orbitals
• bb_stdev : basic::options::OptionKeys::recces::thermal_sampling
• bbdep_bond_devs : basic::options::OptionKeys::corrections::score
• bbdep_bond_params : basic::options::OptionKeys::corrections::score
• bbdep_omega : basic::options::OptionKeys::corrections::score
• bbg : basic::options::OptionKeys::bbg
• bblist : kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib , kmeans_common , spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• bbnbrs : basic::options::OptionKeys::ddg
• bcl : basic::options::OptionKeys::in::path
• before_score : test_terpenes
• benchmark : basic::options::OptionKeys::hotspot , basic::options::OptionKeys::mp::benchmark , basic::options::OptionKeys::run
• best_angles : oop_conformations
• best_pdbs_to_keep : basic::options::OptionKeys::motifs
• best_pose : create_a3b_hbs , oop_conformations
• best_score : create_a3b_hbs , pna
• beta : basic::options::OptionKeys::corrections
• beta_cart : basic::options::OptionKeys::corrections
• beta_cdr1_template_id : basic::options::OptionKeys::tcrmodel
• beta_cdr1_template_pdb : basic::options::OptionKeys::tcrmodel
• beta_cdr2_template_id : basic::options::OptionKeys::tcrmodel
• beta_cdr2_template_pdb : basic::options::OptionKeys::tcrmodel
• beta_cdr3_template_id : basic::options::OptionKeys::tcrmodel
• beta_cdr3_template_pdb : basic::options::OptionKeys::tcrmodel
• beta_framework_template_id : basic::options::OptionKeys::tcrmodel
• beta_framework_template_pdb : basic::options::OptionKeys::tcrmodel
• beta_germline_template_id : basic::options::OptionKeys::tcrmodel
• beta_germline_template_pdb : basic::options::OptionKeys::tcrmodel
• beta_july15 : basic::options::OptionKeys::corrections
• beta_july15_cart : basic::options::OptionKeys::corrections
• beta_nov16 : basic::options::OptionKeys::corrections
• beta_nov16_cart : basic::options::OptionKeys::corrections
• beta_orientation_template_id : basic::options::OptionKeys::tcrmodel
• beta_orientation_template_pdb : basic::options::OptionKeys::tcrmodel
• betaphi : create_a3b_hbs
• betapsi : create_a3b_hbs
• betatht : create_a3b_hbs
• bfactor_cutoff : basic::options::OptionKeys::antibody
• bGDT : basic::options::OptionKeys::abinitio
• bias_design_search_to_native : basic::options::OptionKeys::hydrate
• bias_sampling : basic::options::OptionKeys::coupled_moves
• biased_dist_all_gen : basic::options::OptionKeys::mean_field
• bicelle_radius : basic::options::OptionKeys::mp::geo
• big_frag_insertion_weight : basic::options::OptionKeys::cm::hybridize
• big_pert_dock_rbpm : pna
• bin : basic::options::OptionKeys::lh::fragpdb , create_a3b_hbs
• bin_size : a3b_test , b3a_distro , ss_finder
• binary_chk : basic::options::OptionKeys::in::file
• binary_output : basic::options::OptionKeys::rna::denovo::out
• binder_executable : make_bindings_via_cmake
• binder_source : make_bindings_via_cmake
• binding : basic::options::OptionKeys::dna::design
• binding_pocket_center_sf : basic::options::OptionKeys::motifs
• binding_pocket_dimensions_sf : basic::options::OptionKeys::motifs
• binding_score : basic::options::OptionKeys::pepspec
• bindings_dir : make_bindings_via_cmake
• bins : 3d_histogram , bin_torsions , compute_difference , hist2d , plot , solution_counts
• biounit : basic::options::OptionKeys::mh::path
• biounit_ideal : basic::options::OptionKeys::mh::path
• black : subloop_histogram
• blastp : basic::options::OptionKeys::antibody
• blastp_identity_cutoff : basic::options::OptionKeys::tcrmodel
• blivens : basic::options::OptionKeys::blivens
• block : basic::options::OptionKeys::cloud
• block_stack : basic::options::OptionKeys::recces::base_pair
• block_stack_above_res : basic::options::OptionKeys::full_model::rna
• block_stack_below_res : basic::options::OptionKeys::full_model::rna
• blosc : pyrosetta.distributed.utility.pickle
• blueprint : basic::options::OptionKeys::flxbb , basic::options::OptionKeys::remodel
• bn : docking
• boinc : basic::options::OptionKeys::boinc
• boinc_wu_zip : basic::options::OptionKeys::in::file
• Boltz_temp : basic::options::OptionKeys::dna::design , basic::options::OptionKeys::ms
• boltzmann_choice_post_enumerated_minimize : basic::options::OptionKeys::stepwise
• boltzmann_kt : basic::options::OptionKeys::coupled_moves , basic::options::OptionKeys::nmr::spinlabel
• bond1 : erraser_analysis
• bond2 : erraser_analysis
• bond_angle_sd_polar_hydrogen : basic::options::OptionKeys::stepwise::polar_hydrogens
• bond_torsion_sd_polar_hydrogen : basic::options::OptionKeys::stepwise::polar_hydrogens
• bondangle_perturbation_magnitude : basic::options::OptionKeys::cyclic_peptide
• bonded_params : basic::options::OptionKeys::score
• bonded_params_dir : basic::options::OptionKeys::score
• bondlength_perturbation_magnitude : basic::options::OptionKeys::cyclic_peptide
• bool : enumerate_junctions
• boost_closure_cycles : basic::options::OptionKeys::remodel::RemodelLoopMover
• boost_fa_atr : basic::options::OptionKeys::flexPepDocking
• bot : basic::options::OptionKeys::loodo
• bottom_label_locations : subloop_histogram
• bottom_labels : subloop_histogram
• boundary_cutoff : basic::options::OptionKeys::remodel
• boundaryAA : basic::options::OptionKeys::remodel
• bounded_protocol : basic::options::OptionKeys::frags
• box_length : basic::options::OptionKeys::legacy_sewing , basic::options::OptionKeys::sewing
• BPData : basic::options::OptionKeys::motifs
• bps_database : basic::options::OptionKeys::rna::denovo::db
• bps_moves : basic::options::OptionKeys::rna::denovo
• breadth_moves : run_backbone
• bridge_res : basic::options::OptionKeys::stepwise::protein
• bridgehead_gly : a3b_hbs_creator
• broker : basic::options::OptionKeys::broker
• Bsol : basic::options::OptionKeys::patterson
• bss : basic::options::OptionKeys::lh
• buf : cal_vdw_radius_pool
• buffer_flush_frequency : basic::options::OptionKeys::jd2
• buffer_silent_output : basic::options::OptionKeys::jd2
• build_all_loops : basic::options::OptionKeys::loops
• build_attempts : basic::options::OptionKeys::loops
• build_disulf : basic::options::OptionKeys::remodel
• build_flags : app_runner
• build_initial : basic::options::OptionKeys::loops
• build_residue_file : basic::options::OptionKeys::motifs
• build_round1_hits_twice : basic::options::OptionKeys::match
• build_specific_loops : basic::options::OptionKeys::loops
• built_in_rdc : basic::options::OptionKeys::evaluation
• BuiltinFunctionType : pyrosetta.distributed.cluster.hkdf
• bulge_res : basic::options::OptionKeys::full_model::rna
• bump_check : basic::options::OptionKeys::coupled_moves
• bump_tolerance : basic::options::OptionKeys::match
• bunsat_calc2 : basic::options::OptionKeys::bunsat_calc2
• burial : basic::options::OptionKeys::in::file
• buried_unsatisfied_penalty_burial_threshold : basic::options::OptionKeys::score
• buried_unsatisfied_penalty_cone_angle_exponent : basic::options::OptionKeys::score
• buried_unsatisfied_penalty_cone_angle_shift_factor : basic::options::OptionKeys::score
• buried_unsatisfied_penalty_cone_dist_exponent : basic::options::OptionKeys::score
• buried_unsatisfied_penalty_cone_dist_midpoint : basic::options::OptionKeys::score
• buried_unsatisfied_penalty_hbond_energy_threshold : basic::options::OptionKeys::score
• bypass_closure : basic::options::OptionKeys::remodel::RemodelLoopMover
• bypass_fragments : basic::options::OptionKeys::remodel
• bytes : pyrosetta.distributed.cluster.hkdf