Here is a list of all namespace members with links to the namespace documentation for each member:

- b -

• B : core::chemical::element , protocols::comparative_modeling::features , protocols::features
• b : protocols::match::upstream
• Ba : core::chemical::element
• BAB_CFr : protocols::fldsgn::topology
• BABx1 : protocols::fldsgn::topology
• BABx2 : protocols::fldsgn::topology
• BABx3 : protocols::fldsgn::topology
• BACKBONE : protocols::noesy_assign
• backbone_bin : protocols::generalized_kinematic_closure::filter
• backbone_stub_constraint : core::scoring
• backbone_stub_linear_constraint : core::scoring
• backbone_stub_match() : protocols::motifs
• BackboneGridSamplerCOP : protocols::helical_bundle
• BackboneGridSamplerCOPs : protocols::helical_bundle
• BackboneGridSamplerHelperAP : protocols::helical_bundle
• BackboneGridSamplerHelperCAP : protocols::helical_bundle
• BackboneGridSamplerHelperCAPs : protocols::helical_bundle
• BackboneGridSamplerHelperCOP : protocols::helical_bundle
• BackboneGridSamplerHelperCOPs : protocols::helical_bundle
• BackboneGridSamplerHelperOP : protocols::helical_bundle
• BackboneGridSamplerHelperOPs : protocols::helical_bundle
• BackboneGridSamplerOP : protocols::helical_bundle
• BackboneGridSamplerOPs : protocols::helical_bundle
• BackboneIndexMap : protocols::loophash
• BackboneMoverCOP : protocols::simple_moves
• BackboneMoverOP : protocols::simple_moves
• BackboneStubConstraintCOP : core::scoring::constraints
• BackboneStubConstraintCOPs : core::scoring::constraints
• BackboneStubConstraintOP : core::scoring::constraints
• BackboneStubConstraintOPs : core::scoring::constraints
• BackboneStubLinearConstraintCOP : core::scoring::constraints
• BackboneStubLinearConstraintCOPs : core::scoring::constraints
• BackboneStubLinearConstraintOP : core::scoring::constraints
• BackboneStubLinearConstraintOPs : core::scoring::constraints
• backrub_protocol : protocols::antibody::design
• backrub_rotation_angles() : protocols::backrub
• backrub_rotation_constants() : protocols::backrub
• BackrubMoverCOP : protocols::backrub
• BackrubMoverOP : protocols::backrub
• BackrubProtocolCOP : protocols::backrub
• BackrubProtocolOP : protocols::backrub
• BackrubSidechainMoverCOP : protocols::backrub
• BackrubSidechainMoverOP : protocols::backrub
• backward : protocols::loops::loop_closure::ccd
• bad_anchorfile() : protocols::anchored_design
• BAD_INPUT : protocols::jd2
• BAD_INPUT_TAG : protocols::jd2
• bah_chi_compute_energy_sp2() : core::scoring::hbonds
• bah_chi_compute_energy_sp3() : core::scoring::hbonds
• bailout_mutex : protocols::boinc::watchdog
• bailout_silent_structure : protocols::boinc::watchdog
• bailout_silent_structure_header : protocols::boinc::watchdog
• BalancedKicMoverCOP : protocols::kinematic_closure
• BalancedKicMoverOP : protocols::kinematic_closure
• base_atoms_square_deviation() : protocols::stepwise::modeler::rna
• BASE_BIN_MAP : protocols::stepwise::screener
• BASE_CENTROID : protocols::stepwise::screener
• base_name() : protocols::vip
• BaseArchiveManagerAP : protocols::jd2::archive
• BaseBinMap : protocols::stepwise::modeler::rna::rigid_body
• BaseBinMapUpdaterCOP : protocols::stepwise::screener
• BaseBinMapUpdaterOP : protocols::stepwise::screener
• BaseCacheUnitAP : core::fragment
• BaseCacheUnitOP : core::fragment
• BaseCentroidScreenerCOP : protocols::stepwise::screener
• BaseCentroidScreenerOP : protocols::stepwise::screener
• BaseDoubletOrientation : core::chemical::rna
• BaseEdge : core::chemical::rna
• BaseJobDistributorOP : protocols::jobdist
• BaseJumpSetupCOP : protocols::jumping
• BaseJumpSetupOP : protocols::jumping
• BasePairCOP : core::pose::rna
• BasePairingLibraryCOP : protocols::jumping
• BasePairingLibraryOP : protocols::jumping
• BasePairOP : core::pose::rna
• BasePairStepCOP : protocols::farna::base_pairs
• BasePairStepLibraryCOP : protocols::farna::libraries
• BasePairStepLibraryOP : protocols::farna::libraries
• BasePairStepOP : protocols::farna::base_pairs
• BasePartnerOP : core::scoring::dna
• bases_are_coplanar() : core::pose::rna
• bases_form_a_hydrogen_bond() : core::pose::rna
• BaseStackCOP : core::pose::rna
• BaseStackOP : core::pose::rna
• BaseStackWhichSide : core::chemical::rna
• basic_idealize() : protocols::idealize
• BasicCDRClusterSetCOP : protocols::antibody::clusters
• BasicCDRClusterSetOP : protocols::antibody::clusters
• BasicJobCOP : protocols::jobdist
• BasicJobOP : protocols::jobdist
• BasicJumpClaimerAP : protocols::topology_broker
• BasicJumpClaimerCAP : protocols::topology_broker
• BasicJumpClaimerCOP : protocols::topology_broker
• BasicJumpClaimerOP : protocols::topology_broker
• BasicRotamerLibrarySpecificationCOP : core::chemical::rotamers
• BasicRotamerLibrarySpecificationCreator_registrator : core::init
• BasicRotamerLibrarySpecificationOP : core::chemical::rotamers
• BasicSimAnnealerRepackerCOP : protocols::pack_daemon
• BasicSimAnnealerRepackerOP : protocols::pack_daemon
• BasisPair : protocols::sewing
• BATCH_SYNC : protocols::jd2::archive
• BatchFeaturesCOP : protocols::features
• BatchFeaturesOP : protocols::features
• BatchJobInputterOP : protocols::jd2
• BB : core::id
• BB_BB : core::scoring::motif
• bb_independent_rotamers() : core::pack::rotamer_set
• BB_PH : core::scoring::motif
• BB_PO : core::scoring::motif
• bb_rmsd() : core::scoring
• bb_rmsd_including_O() : core::scoring
• BBClaimAP : protocols::topology_broker::claims
• BBClaimCAP : protocols::topology_broker::claims
• BBClaimCOP : protocols::topology_broker::claims
• BBClaimOP : protocols::topology_broker::claims
• BBConRotMoverCOP : protocols::simple_moves
• BBConRotMoverOP : protocols::simple_moves
• BBDihedralSampler2DCOP : protocols::simple_moves::bb_sampler
• BBDihedralSampler2DOP : protocols::simple_moves::bb_sampler
• BBDihedralSampler3DCOP : protocols::simple_moves::bb_sampler
• BBDihedralSampler3DOP : protocols::simple_moves::bb_sampler
• BBDihedralSamplerBaseCOP : protocols::simple_moves::bb_sampler
• BBDihedralSamplerBaseOP : protocols::simple_moves::bb_sampler
• BBDihedralSamplerCOP : protocols::simple_moves::bb_sampler
• BBDihedralSamplerMoverCOP : protocols::simple_moves
• BBDihedralSamplerMoverOP : protocols::simple_moves
• BBDihedralSamplerNDCOP : protocols::simple_moves::bb_sampler
• BBDihedralSamplerNDOP : protocols::simple_moves::bb_sampler
• BBDihedralSamplerOP : protocols::simple_moves::bb_sampler
• BBdisplayState : protocols::viewer::graphics_states_param
• BBG8T3AMoverCOP : protocols::simple_moves
• BBG8T3AMoverOP : protocols::simple_moves
• BBGaussianMoverCOP : protocols::simple_moves
• BBGaussianMoverOP : protocols::simple_moves
• BBSampleType : protocols::simple_moves::bb_sampler
• BBTorsionSRFDCOP : core::fragment
• BBTorsionSRFDOP : core::fragment
• BDR_AP : protocols::forge::components
• BDR_CAP : protocols::forge::components
• BDR_COP : protocols::forge::components
• BDR_OP : protocols::forge::components
• Be : core::chemical::element
• BEFr : protocols::fldsgn::topology
• BELOW : core::chemical::rna
• bessel_roots() : core::scoring::fiber_diffraction
• best_bbcst_residues() : protocols::protein_interface_design
• best_cutpoint() : protocols::protein_interface_design
• BestMatchesCollectionCOP : protocols::match::output
• BestMatchesCollectionOP : protocols::match::output
• BestTotalScoreSelectorCOP : protocols::frag_picker
• BestTotalScoreSelectorOP : protocols::frag_picker
• BETA : core::chemical::rna , core::scoring::dna
• BETA_AA : core::chemical
• BETA_ATOM : core::chemical
• BETA_LINKS : core::chemical::carbohydrates
• BETA_NON_METHYL : protocols::noesy_assign
• BETA_SUGAR : core::chemical
• BetaAlphaBetaMotifCOP : protocols::fldsgn::topology
• BetaAlphaBetaMotifOP : protocols::fldsgn::topology
• BetaAlphaBetaMotifs : protocols::fldsgn::topology
• BetaAlphaBetaMotifSetCOP : protocols::fldsgn::topology
• BetaAlphaBetaMotifSetOP : protocols::fldsgn::topology
• BetaTurnDetectionCOP : protocols::features
• BetaTurnDetectionFeaturesCOP : protocols::features
• BetaTurnDetectionFeaturesOP : protocols::features
• BetaTurnDetectionOP : protocols::features
• BFr : protocols::fldsgn::topology
• bgsh_delta_omega0 : protocols::helical_bundle
• bgsh_delta_omega1 : protocols::helical_bundle
• bgsh_delta_t : protocols::helical_bundle
• bgsh_omega0 : protocols::helical_bundle
• bgsh_r0 : protocols::helical_bundle
• bgsh_undefined_dof : protocols::helical_bundle
• bgsh_z0_offset : protocols::helical_bundle
• bgsh_z1_offset : protocols::helical_bundle
• Bh : core::chemical::element
• Bi : core::chemical::element
• BiasedFragmentMoverCOP : protocols::nonlocal
• BiasedFragmentMoverOP : protocols::nonlocal
• BiasedMonteCarloCOP : protocols::canonical_sampling
• BiasedMonteCarloOP : protocols::canonical_sampling
• BiasEnergyAP : protocols::canonical_sampling
• BiasEnergyCAP : protocols::canonical_sampling
• BiasEnergyCOP : protocols::canonical_sampling
• BiasEnergyOP : protocols::canonical_sampling
• big_bin_constraint : core::scoring
• BigBinConstraintCOP : core::scoring::constraints
• BigBinConstraintCreator_registrator : core::init
• BigBinConstraintOP : core::scoring::constraints
• biggest_residue_deviation_no_super() : core::scoring
• biggest_residue_deviation_no_super_subset() : core::scoring
• bin_by_seq_separation() : core::scoring::constraints
• BinarySilentStructCreator_registrator : core::init
• BinarySilentStructOP : core::io::silent
• BindingStrainFilterCOP : protocols::protein_interface_design::filters
• BindingStrainFilterOP : protocols::protein_interface_design::filters
• BinTransitionCalculatorCOP : core::scoring::bin_transitions
• BinTransitionCalculatorCOPs : core::scoring::bin_transitions
• BinTransitionCalculatorOP : core::scoring::bin_transitions
• BinTransitionCalculatorOPs : core::scoring::bin_transitions
• BinTransitionDataCOP : core::scoring::bin_transitions
• BinTransitionDataCOPs : core::scoring::bin_transitions
• BinTransitionDataOP : core::scoring::bin_transitions
• BinTransitionDataOPs : core::scoring::bin_transitions
• bisector : core::scoring
• bit_count : core::scoring , core::scoring::packstat::old
• bit_is_set() : core::pack::dunbrack
• Bk : core::chemical::element
• blank_atom_id_domain_map() : core::pose::copydofs
• block_allocation_error_message() : core::graph
• BLOCK_STACK_ABOVE : core::chemical
• BLOCK_STACK_BELOW : core::chemical
• BlosumScorerCOP : protocols::sewing::scoring
• BlosumScorerOP : protocols::sewing::scoring
• BluePrintBDR_AP : protocols::fldsgn
• BluePrintBDR_CAP : protocols::fldsgn
• BluePrintBDR_COP : protocols::fldsgn
• BluePrintBDR_OP : protocols::fldsgn
• BluePrintCOP : protocols::jd2::parser
• BluePrintOP : protocols::flxbb , protocols::jd2::parser
• BOGUS_ASSIGNMENT : protocols::noesy_assign
• BOGUS_ATOM_ID : core::id
• BOGUS_DOF_ID : core::id
• BOGUS_ENERGY() : core::scoring
• BOGUS_JUMP : core::kinematics::tree
• BOGUS_NAMED_ATOM_ID : core::id
• BOGUS_STUB_ID : core::id
• BOGUS_TORSION_ID : core::id
• BoincCurrentPoseObserverOP : protocols::boinc
• boincOutputFilter() : protocols::boinc
• Boltzmann() : protocols::md
• boltzmann_energy_selector : protocols::generalized_kinematic_closure::selector
• BoltzmannFilterCOP : protocols::protein_interface_design::filters
• BoltzmannFilterOP : protocols::protein_interface_design::filters
• BoltzmannRotamerMoverCOP : protocols::simple_moves
• BoltzmannRotamerMoverOP : protocols::simple_moves
• bond_angles() : protocols::environment
• bond_geometry : core::scoring
• bond_lengths() : protocols::environment
• bond_order_to_property() : core::chemical
• BOND_TO_NEXT : protocols::stepwise::monte_carlo::mover
• BOND_TO_PREVIOUS : protocols::stepwise::monte_carlo::mover
• bond_torsions() : protocols::environment
• bondangle_atom_set : core::chemical
• BondAngleDatabaseOP : protocols::features
• BondAnglePerturberCOP : protocols::kinematic_closure::perturbers
• BondAnglePerturberOP : protocols::kinematic_closure::perturbers
• BondAromaticity : core::chemical
• BondConjugability : core::chemical
• BondedAtomAP : core::kinematics::tree
• BondedAtomCAP : core::kinematics::tree
• BondedAtomCOP : core::kinematics::tree
• BondedAtomOP : core::kinematics::tree
• BondIndex : core::chemical::sdf
• bonding_distance_threshold() : core::io::pose_from_sfr
• BondInRing : core::chemical
• BondIsometry : core::chemical
• BondLength : core::chemical
• BondName : core::chemical
• BondNotInRing : core::chemical
• BondOrder : core::chemical
• BondRingness : core::chemical
• Bool3DGridCOP : protocols::match
• Bool3DGridOP : protocols::match
• boolean_operations : protocols::filters , protocols::toolbox::task_operations
• BOOLEAN_OR : protocols::simple_filters
• Bools : core::scoring::motif
• bools_from_sizes() : protocols::motifs
• bounded_loops_from_alignment() : protocols::comparative_modeling
• BoundedQuotaContainer : protocols::frag_picker::quota
• BoundedQuotaContainerOP : protocols::frag_picker::quota
• BoundFuncCOP : core::scoring::constraints
• BoundFuncOP : core::scoring::constraints
• BoundingBox : protocols::loophash
• bpdefs2map() : protocols::motifs
• bpybb() : protocols::sic_dock::scores
• Br : core::chemical::element
• BRANCH : core::id
• BRANCH_LOWER_TERMINUS : core::chemical
• BRANCH_LOWER_TERMINUS_VARIANT : core::chemical
• BRANCH_POINT : core::chemical
• branching_atomid1() : protocols::branch_angle
• branching_atomids2() : protocols::branch_angle
• break_disulfide() : core::conformation
• brf_always_false : protocols::helical_bundle
• brf_always_true : protocols::helical_bundle
• brf_filter_by_energy : protocols::helical_bundle
• brf_undefined : protocols::helical_bundle
• BridgeAP : protocols::forge::build
• BridgeCAP : protocols::forge::build
• BridgeChainsAP : protocols::denovo_design::connection
• BridgeChainsCAP : protocols::denovo_design::connection
• BridgeChainsCOP : protocols::denovo_design::connection
• BridgeChainsOP : protocols::denovo_design::connection
• BridgeCOP : protocols::forge::build
• BridgeOP : protocols::forge::build
• BridgeTomponentsAP : protocols::denovo_design::connection
• BridgeTomponentsCAP : protocols::denovo_design::connection
• BridgeTomponentsCOP : protocols::denovo_design::connection
• BridgeTomponentsOP : protocols::denovo_design::connection
• Broker_main() : protocols::abinitio
• brute_mindis() : protocols::sic_dock
• BT_ALPHA_AA : core::scoring::bin_transitions
• BT_AROMATIC : core::scoring::bin_transitions
• BT_BETA_AA : core::scoring::bin_transitions
• BT_CHARGED : core::scoring::bin_transitions
• BT_CYCLIC : core::scoring::bin_transitions
• BT_D_AA : core::scoring::bin_transitions
• BT_DISULFIDE_BONDED : core::scoring::bin_transitions
• BT_END_OF_LIST : core::scoring::bin_transitions
• BT_L_AA : core::scoring::bin_transitions
• BT_METALBINDING : core::scoring::bin_transitions
• BT_POLAR : core::scoring::bin_transitions
• BT_PROPERTIES : core::scoring::bin_transitions
• BT_PROTEIN : core::scoring::bin_transitions
• BT_SIDECHAIN_THIOL : core::scoring::bin_transitions
• BT_UNKNOWN_PROPERTY : core::scoring::bin_transitions
• BTSB_D_AA : core::scoring::bin_transitions
• BTSB_D_PRO : core::scoring::bin_transitions
• BTSB_END_OF_LIST : core::scoring::bin_transitions
• BTSB_GLY : core::scoring::bin_transitions
• BTSB_L_AA : core::scoring::bin_transitions
• BTSB_L_PRO : core::scoring::bin_transitions
• BTSB_NONE : core::scoring::bin_transitions
• BTSB_SUBBIN_TYPE : core::scoring::bin_transitions
• BTSB_UNKNOWN : core::scoring::bin_transitions
• build_acceptor_acceptor_waters() : 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_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_three_prime_phosphate_rotamers() : core::pack::rotamer_set
• build_tree() : core::conformation
• BuildAlaPoseCOP : protocols::protein_interface_design::movers
• BuildAlaPoseOP : protocols::protein_interface_design::movers
• BuildingBlockInterfaceOperationCOP : protocols::matdes
• BuildingBlockInterfaceOperationOP : protocols::matdes
• BuildInstructionAP : protocols::forge::build
• BuildInstructionCAP : protocols::forge::build
• BuildInstructionCOP : protocols::forge::build
• BuildInstructionOP : protocols::forge::build
• BuildManagerAP : protocols::forge::build
• BuildManagerCAP : protocols::forge::build
• BuildManagerCOP : protocols::forge::build
• BuildManagerOP : protocols::forge::build
• BuildPositionCOP : protocols::motifs
• BuildPositionCOPs : protocols::motifs
• BuildPositionOP : protocols::motifs
• BuildPositionOPs : protocols::motifs
• BULGE : core::chemical
• BULGE_APPLIER : protocols::stepwise::screener
• BulgeApplierCOP : protocols::stepwise::screener
• BulgeApplierOP : protocols::stepwise::screener
• BulgeApplyMoverCOP : protocols::stepwise::modeler::rna::bulge
• BulgeApplyMoverOP : protocols::stepwise::modeler::rna::bulge
• BulgeUnApplyMoverCOP : protocols::stepwise::modeler::rna::bulge
• BulgeUnApplyMoverOP : protocols::stepwise::modeler::rna::bulge
• bump_grid_to_enclose_pose() : protocols::match
• bump_grid_to_enclose_residue() : protocols::match
• bump_grid_to_enclose_residue_backbone() : protocols::match
• BumpGridCOP : protocols::match
• BumpGridOP : protocols::match
• BumpSelectorDecision : core::pack::rotamer_set
• BundleGridSamplerCOP : protocols::helical_bundle
• BundleGridSamplerCOPs : protocols::helical_bundle
• BundleGridSamplerHelperAP : protocols::helical_bundle
• BundleGridSamplerHelperCAP : protocols::helical_bundle
• BundleGridSamplerHelperCAPs : protocols::helical_bundle
• BundleGridSamplerHelperCOP : protocols::helical_bundle
• BundleGridSamplerHelperCOPs : protocols::helical_bundle
• BundleGridSamplerHelperOP : protocols::helical_bundle
• BundleGridSamplerHelperOPs : protocols::helical_bundle
• BundleGridSamplerOP : protocols::helical_bundle
• BundleGridSamplerOPs : protocols::helical_bundle
• BundleParametersAP : protocols::helical_bundle::parameters
• BundleParametersCAP : protocols::helical_bundle::parameters
• BundleParametersCAPs : protocols::helical_bundle::parameters
• BundleParametersCOP : protocols::helical_bundle::parameters
• BundleParametersCOPs : protocols::helical_bundle::parameters
• BundleParametersOP : protocols::helical_bundle::parameters
• BundleParametersOPs : protocols::helical_bundle::parameters
• BundleParametersSetAP : protocols::helical_bundle::parameters
• BundleParametersSetCAP : protocols::helical_bundle::parameters
• BundleParametersSetCAPs : protocols::helical_bundle::parameters
• BundleParametersSetCOP : protocols::helical_bundle::parameters
• BundleParametersSetCOPs : protocols::helical_bundle::parameters
• BundleParametersSetOP : protocols::helical_bundle::parameters
• BundleParametersSetOPs : protocols::helical_bundle::parameters
• BundleReporterFilterBehaviour : protocols::helical_bundle
• burial : core::scoring
• burial3class_weight_initializer() : core::scoring::hbonds
• burial_weight() : core::scoring::hbonds
• BurialCreator_registrator : core::init
• buried_unsat_hbond_filter_tracer() : protocols::simple_filters