- b -

• b1_b2_Ktheta() : protocols::branch_angle::BranchParam2
• b1_b2_theta0() : protocols::branch_angle::BranchParam2
• b1_bond_angle_A() : protocols::branch_angle::BranchCoef1
• b1_bond_angle_B() : protocols::branch_angle::BranchCoef1
• b1_bond_angle_C() : protocols::branch_angle::BranchCoef1
• b1_torsion_offset_A() : protocols::branch_angle::BranchCoef1
• b1_torsion_offset_B() : protocols::branch_angle::BranchCoef1
• b1_torsion_offset_C() : protocols::branch_angle::BranchCoef1
• b2_bond_angle_A() : protocols::branch_angle::BranchCoef2
• b2_bond_angle_B() : protocols::branch_angle::BranchCoef2
• b2_bond_angle_C() : protocols::branch_angle::BranchCoef2
• b2_torsion_offset_A() : protocols::branch_angle::BranchCoef2
• b2_torsion_offset_B() : protocols::branch_angle::BranchCoef2
• b2_torsion_offset_C() : protocols::branch_angle::BranchCoef2
• b_is_full_motif_bb_alignment() : protocols::motif_grafting::movers::MotifMatch
• bab_motif() : protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• bab_motifs() : protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• backbone_database() : protocols::loophash::LoopHashLibrary
• backbone_for_moltenres_bbconf() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• backbone_for_resid_bbconf() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• backbone_only() : protocols::match::upstream::BuildSet
• BackboneDB() : protocols::loophash::BackboneDB
• BackboneMover() : protocols::simple_moves::BackboneMover
• BackboneSampler() : protocols::enzdes::BackboneSampler
• BackboneSegment() : protocols::loophash::BackboneSegment
• BackboneTorsionPerturbation() : protocols::hybridization::BackboneTorsionPerturbation
• BackboneTorsionSampler() : protocols::hybridization::BackboneTorsionSampler
• backrub() : protocols::dna::DesignProteinBackboneAroundDNA
• backrub_move() : protocols::flexpep_docking::FlexPepDockingProtocol
• BackrubDDMover() : protocols::protein_interface_design::movers::BackrubDDMover
• BackrubMover() : protocols::backrub::BackrubMover
• BackrubSegment() : protocols::backrub::BackrubSegment
• BackrubSidechainMover() : protocols::backrub::BackrubSidechainMover
• backtrack() : protocols::coarse_rna::CoarseRNA_LoopCloser
• backward_check() : protocols::motifs::Motif
• backward_jump() : protocols::motifs::Motif
• bad() : protocols::jd2::InnerJob , protocols::jd2::Job
• BalancedKicMover() : protocols::kinematic_closure::BalancedKicMover
• BANGLE_MIN() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• BANGLE_SD() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• barcode_extend_stems() : protocols::LoopRebuild
• barrier() : protocols::optimize_weights::IterativeOptEDriver , protocols::pmut_scan::PointMutScanDriver
• base() : protocols::dna::DNAParameters
• base_atr_score() : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• base_only() : protocols::dna::RestrictDesignToProteinDNAInterface
• base_rep_score() : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• base_state() : protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler
• base_weight() : protocols::topology_broker::weights::ConstAbinitioMoverWeight
• BaseArchiveManager() : protocols::jd2::archive::BaseArchiveManager
• BaseBinMapUpdater() : protocols::stepwise::screener::BaseBinMapUpdater
• BaseCentroidScreener() : protocols::stepwise::screener::BaseCentroidScreener
• BaseJobDistributor() : protocols::jobdist::BaseJobDistributor
• baseline() : protocols::simple_filters::DeltaFilter , protocols::simple_filters::RelativePoseFilter
• baseline_checkpointing_filename() : protocols::simple_filters::Sigmoid
• baseline_val() : protocols::simple_filters::RelativePoseFilter
• basepair() : protocols::dna::DNAParameters
• basepairs_begin() : protocols::dna::DNAParameters
• basepairs_end() : protocols::dna::DNAParameters
• BasePairStep() : protocols::farna::BasePairStep
• BasePairStepLibrary() : protocols::farna::BasePairStepLibrary
• BasePairStepSequence() : protocols::farna::BasePairStepSequence
• BasePairType() : protocols::farna::BasePairType
• bases_begin() : protocols::dna::DNAParameters
• bases_end() : protocols::dna::DNAParameters
• basestep() : protocols::dna::DNAParameters
• basesteps_begin() : protocols::dna::DNAParameters
• basesteps_end() : protocols::dna::DNAParameters
• BaseTabooPerturber() : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber
• BasicCDRClusterSet() : protocols::antibody::clusters::BasicCDRClusterSet
• BasicCmdLineInit() : protocols::rpc::BasicCmdLineInit
• BasicInit() : protocols::rpc::BasicInit
• BasicJob() : protocols::jobdist::BasicJob
• BasicJumpClaimer() : protocols::topology_broker::BasicJumpClaimer
• BasicSimAnnealerRepacker() : protocols::pack_daemon::BasicSimAnnealerRepacker
• Batch() : protocols::jd2::archive::Batch
• batch() : protocols::jd2::archive::Batch , protocols::jd2::JobDistributor
• batch_apply() : protocols::relax::FastRelax
• batch_set_xyz() : protocols::environment::ProtectedConformation
• batch_underflow() : protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::MPIArchiveJobDistributor , protocols::jd2::JobDistributor
• batches() : protocols::jd2::archive::BaseArchiveManager
• BatchFeatures() : protocols::features::BatchFeatures
• BatchJobInputter() : protocols::jd2::BatchJobInputter
• BatchNrEvaluator() : protocols::simple_filters::BatchNrEvaluator
• bb() : protocols::dna::DnaInterfaceMinMover , protocols::simple_moves::symmetry::SetupNCSMover , protocols::simple_moves::TaskAwareMinMover
• bb_bb() : protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::TaskAwareScoreTypeFilter
• bb_bins_from_pose() : protocols::toolbox::pose_metric_calculators::RotamerRecovery
• bb_only() : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• bb_pos() : protocols::fldsgn::topology::SS_Info2
• BBClaim() : protocols::topology_broker::claims::BBClaim
• bbconf_for_rotamer() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• bbconf_for_rotamer_on_moltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• BBConRotMover() : protocols::simple_moves::BBConRotMover
• bbdb_range() : protocols::loophash::LoopHashMap
• BBG8T3AMover() : protocols::simple_moves::BBG8T3AMover
• BBGaussianMover() : protocols::simple_moves::BBGaussianMover
• bbgrid() : protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::DownstreamBuilder , protocols::match::upstream::UpstreamBuilder
• bbgrid_set() : protocols::match::downstream::DownstreamBuilder
• bbindices_up_to_date() : protocols::fldsgn::topology::BB_Pos
• bbpos_is_set() : protocols::fldsgn::topology::SS_Info2
• bbs_appropriate_for_definitions() : protocols::make_rot_lib::MakeRotLibMover
• bbtorsion_srfd() : protocols::frag_picker::VallResidue
• BDR() : protocols::forge::components::BDR
• be_lenient() : protocols::kinematic_closure::solution_pickers::FilteredSolutions
• begin() : protocols::abinitio::abscript::ResidueChunkSelection , protocols::abinitio::PairingStatistics , protocols::abinitio::Templates , protocols::dna::DnaChains , protocols::filters::CompoundFilter , protocols::fldsgn::topology::HSSTripletSet , protocols::fldsgn::topology::SS_Base , protocols::fldsgn::topology::StrandPairingSet , protocols::forge::build::BuildManager , protocols::hotspot_hashing::HotspotStubSet , protocols::jumping::JumpSelector , protocols::jumping::JumpSetup , protocols::jumping::ResiduePairJumpSetup , protocols::ligand_docking::MinimizeLigand , protocols::loops::Loops , protocols::motifs::MotifLibrary , protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::MethylNames , protocols::noesy_assign::ResonanceList , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::TryRotamers , protocols::rosetta_scripts::ParsedProtocol , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::topology_broker::TopologyBroker , protocols::wum::SilentStructStore , protocols::wum::WorkUnitQueue
• begin1() : protocols::fldsgn::topology::StrandPairing
• begin2() : protocols::fldsgn::topology::StrandPairing
• begin_chain_pair() : protocols::analysis::PeptideDeriverBasicStreamOutputter , protocols::analysis::PeptideDeriverMarkdownStreamOutputter , protocols::analysis::PeptideDeriverOutputter , protocols::analysis::PeptideDeriverOutputterContainer , protocols::analysis::PeptideDeriverPoseOutputter
• begin_critical_section() : protocols::jd2::BOINCJobDistributor , protocols::jd2::JobDistributor , protocols::jobdist::BaseJobDistributor
• begin_processing() : protocols::match::output::MatchConsolidator , protocols::match::output::MatchOutputter , protocols::match::output::MatchProcessor
• begin_stage() : protocols::abinitio::abscript::AbscriptMover::StageTracker
• begin_structure() : protocols::analysis::PeptideDeriverBasicStreamOutputter , protocols::analysis::PeptideDeriverMarkdownStreamOutputter , protocols::analysis::PeptideDeriverOutputter , protocols::analysis::PeptideDeriverOutputterContainer , protocols::analysis::PeptideDeriverPoseOutputter
• bend() : protocols::fldsgn::topology::Helix
• Berendsen_Integrator() : protocols::md::CartesianMD
• best_assignment() : protocols::pack_daemon::PackDaemon
• best_by_ala_scan() : protocols::seeded_abinitio::SeedFoldTree
• best_entities() : protocols::genetic_algorithm::GeneticAlgorithmBase
• best_fitness_from_current_generation() : protocols::genetic_algorithm::GeneticAlgorithmBase
• best_Kmer_rms() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• best_motifhits() : protocols::motifs::BuildPosition
• best_motifs() : protocols::motifs::BuildPosition
• best_rotamers() : protocols::motifs::BuildPosition
• best_score() : protocols::multistate_design::SingleState
• BestHotspotCstMover() : protocols::protein_interface_design::movers::BestHotspotCstMover
• BestMatchesCollection() : protocols::match::output::BestMatchesCollection
• BestTotalScoreSelector() : protocols::frag_picker::BestTotalScoreSelector
• beta() : protocols::dna::DNABase , protocols::stepwise::sampler::rigid_body::EulerAngles
• beta_turn_distance_cutoff() : protocols::features::BetaTurnDetection
• beta_turn_length() : protocols::features::BetaTurnDetection
• beta_turn_present() : protocols::features::BetaTurnDetection
• beta_turn_type() : protocols::features::BetaTurnDetection
• BetaAlphaBetaMotif() : protocols::fldsgn::topology::BetaAlphaBetaMotif
• BetaAlphaBetaMotifSet() : protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• BetaTurnDetection() : protocols::features::BetaTurnDetection
• BetaTurnDetectionFeatures() : protocols::features::BetaTurnDetectionFeatures
• BetaTurnDetectionFeaturesCreator() : protocols::features::BetaTurnDetectionFeaturesCreator
• bF() : protocols::frag_picker::VallResidue
• BFactor() : protocols::frag_picker::scores::BFactor
• BfactorFittingMover() : protocols::electron_density::BfactorFittingMover
• BfactorMPM() : protocols::match::BfactorMPM
• BfactorMultifunc() : protocols::electron_density::BfactorMultifunc
• bias_energy() : protocols::canonical_sampling::BiasedMonteCarlo
• BiasedFragmentMover() : protocols::nonlocal::BiasedFragmentMover
• BiasedMonteCarlo() : protocols::canonical_sampling::BiasedMonteCarlo
• BiasEnergy() : protocols::canonical_sampling::BiasEnergy
• bIdealLoopClosing() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• bigbin() : protocols::frags::VallData
• bIgnoreSequenceSeparation() : protocols::abinitio::FoldConstraints
• bin_center() : protocols::match::Bool3DGrid
• bin_extrema() : protocols::match::Bool3DGrid
• bin_for_point() : protocols::match::Bool3DGrid
• bin_index_() : protocols::frag_picker::scores::LAMBEGO_Similarity , protocols::frag_picker::scores::TorsionBinSimilarity
• bin_width() : protocols::match::Bool3DGrid
• bind_vec_constraint() : protocols::antibody::AntibodyDatabaseManager
• BindingSiteConstraint() : protocols::constraints_additional::BindingSiteConstraint
• BindingSiteConstraintCreator() : protocols::constraints_additional::BindingSiteConstraintCreator
• BindingStrainFilter() : protocols::protein_interface_design::filters::BindingStrainFilter
• binner() : protocols::match::HitHasher
• bitmask_for_position() : protocols::match::OccupiedSpaceHash
• blanket_assign_state_0() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• block() : protocols::jd2::SingleFileBuffer , protocols::jd2::WriteFileSFB
• block_file() : protocols::jd2::MpiFileBuffer
• BluePrint() : protocols::jd2::parser::BluePrint
• blueprint_cst_definition() : protocols::forge::remodel::RemodelEnzdesCstModule
• BluePrintBDR() : protocols::fldsgn::BluePrintBDR
• Boinc() : protocols::boinc::Boinc
• BoincCurrentPoseObserver() : protocols::boinc::BoincCurrentPoseObserver
• BOINCJobDistributor() : protocols::jd2::BOINCJobDistributor
• boltz_rank() : protocols::simple_moves::GenericMonteCarloMover
• boltzmann() : protocols::canonical_sampling::BiasedMonteCarlo , protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo , protocols::moves::ReplicaExchangeMC , protocols::moves::SimulatedTempering , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::TorsionDOFMover
• BoltzmannFilter() : protocols::protein_interface_design::filters::BoltzmannFilter
• BoltzmannRotamerMover() : protocols::simple_moves::BoltzmannRotamerMover
• bond_angle_atoms() : protocols::backrub::BackrubSegment
• bond_angle_residue_type_param_set() : protocols::branch_angle::BranchAngleOptimizer
• bond_length() : protocols::simple_moves::CutChainMover
• bonus_value() : protocols::hotspot_hashing::HotspotStub
• Bool3DGrid() : protocols::match::Bool3DGrid
• Bool3DGridKinemageWriter() : protocols::match::Bool3DGridKinemageWriter
• boost_closure_cycles() : protocols::forge::remodel::RemodelLoopMover
• boost_closure_stage() : protocols::forge::remodel::RemodelLoopMover
• bootstrapCATrace() : protocols::rbsegment_relax::FragInsertAndAlignMover
• bottom() : protocols::dna::DnaPosition
• bound() : protocols::simple_filters::NonSequentialNeighborsFilter
• bound_struct() : protocols::optimize_weights::DGBindOptEData
• bound_width() : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• bounded() : protocols::relax::AtomCoordinateCstMover
• bounded_protocol() : protocols::frag_picker::FragmentPicker
• BoundedCollector() : protocols::frag_picker::BoundedCollector< StrictWeakOrdering >
• BoundedCollector_CompareTotalScore() : protocols::frag_picker::BoundedCollector_CompareTotalScore
• bounding_box() : protocols::match::downstream::ActiveSiteGrid
• bounding_radius_for_rotamers() : protocols::flexpack::interaction_graph::OTFFlexbbNode
• bounds_check_entity() : protocols::pack_daemon::EntityCorrespondence
• bounds_check_residue() : protocols::pack_daemon::EntityCorrespondence
• bp_motifhits() : protocols::motifs::MotifSearch
• bp_rotamers() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• bQuickTest() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• BranchAngleOptimizer() : protocols::branch_angle::BranchAngleOptimizer
• BranchCoef1() : protocols::branch_angle::BranchCoef1
• BranchCoef2() : protocols::branch_angle::BranchCoef2
• branchopt() : protocols::backrub::BackrubMover
• BranchParam1() : protocols::branch_angle::BranchParam1
• BranchParam2() : protocols::branch_angle::BranchParam2
• Bridge() : protocols::forge::build::Bridge
• bridge_res() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• broadcast_coords() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• broadcast_entity_string() : protocols::pack_daemon::MPIMultistateFitnessFunction
• broadcast_newest_coords() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• broker() : protocols::environment::Environment , protocols::topology_broker::TopologyClaimer
• broker_dofs() : protocols::environment::EnvClaimBroker
• broker_file() : protocols::jd2::archive::Batch
• broker_fold_tree() : protocols::environment::EnvClaimBroker
• BrokeredJumpData() : protocols::environment::EnvClaimBroker::BrokeredJumpData
• broking() : protocols::topology_broker::TopologyBroker
• broking_finished() : protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::environment::ClientMover
• brute_move_large() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• brute_move_small() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• brute_move_small_top25() : protocols::abinitio::MembraneAbinitio
• BruteFunGroupTK() : protocols::kinmatch::BruteFunGroupTK
• buckle() : protocols::dna::DNABasepair
• buf_to_address() : protocols::canonical_sampling::mc_convergence_checks::DataBuffer , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• build() : protocols::ligand_docking::InterfaceBuilder , protocols::ligand_docking::MoveMapBuilder , protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::output::WriteUpstreamCoordinateKinemage , protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::upstream::UpstreamBuilder
• build_and_discard_first_round_hits_at_all_positions() : protocols::match::downstream::ClassicMatchAlgorithm
• build_bond_angle_elements() : protocols::environment::claims::XYZClaim
• build_bond_length_elements() : protocols::environment::claims::XYZClaim
• build_bond_torsion_elements() : protocols::environment::claims::XYZClaim
• build_centroid_loop() : protocols::antibody::H3PerturbCCD , protocols::antibody_legacy::CDRH3Modeler
• build_claims() : protocols::abinitio::abscript::FragmentJumpCM
• build_combined_pose_with_zinc_overlay() : protocols::metal_interface::MatchGrafter
• build_conformer_group() : protocols::match::downstream::LigandConformerBuilder
• build_constraints() : protocols::abinitio::AlternativePairings , protocols::abinitio::StrandConstraints
• build_cst_conformer_jumps() : protocols::jumping::ResiduePairJump
• build_dangle_seq1_3prime() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• build_dangle_seq1_5prime() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• build_dangle_seq2_3prime() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• build_dangle_seq2_5prime() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• build_dangling_ends() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• build_dependent_rotamers() : protocols::flexpack::rotamer_set::FlexbbRotamerSet
• build_design_taskset() : protocols::flxbb::FlxbbDesign
• build_fold_tree() : protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• build_fold_tree_from_claimer() : protocols::topology_broker::TopologyBroker
• build_from_three_coords() : protocols::match::downstream::ClassicMatchAlgorithm
• build_full_model() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• build_fullatom_loop() : protocols::antibody_legacy::CDRH3Modeler
• build_helix() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• build_hits_at_all_positions() : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• build_init_pose() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• build_inverted_rotamers() : protocols::motifs::Motif
• build_loop_with_ccd_closure() : protocols::LoopRebuild
• build_loops() : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover
• build_mover() : protocols::loops::loop_mover::LoopCM
• build_new_residues() : protocols::environment::EnvClaimBroker
• build_on_base_pair() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• build_pair_dis_matrix() : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• build_point() : protocols::match::Matcher
• build_positionOPs() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• build_random_loops() : protocols::LoopRebuild
• build_receptor_peptide_pose() : protocols::analysis::PeptideDeriverFilter
• build_residue_vector_from_fragment() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• build_rotamer() : protocols::motifs::MotifHit
• build_rotamer_list() : protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover
• build_rotamers() : protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::motifs::Motif
• build_rotamers_for_concrete_virt() : protocols::flexpack::rotamer_set::FlexbbRotamerSet
• build_round1_hits_twice() : protocols::match::MatcherTask
• build_set() : protocols::match::upstream::ProteinUpstreamBuilder
• build_sidechain_rotamers() : protocols::jumping::ResiduePairJump
• build_stage() : protocols::loop_modeling::LoopModeler
• build_structures() : protocols::loophash::LoopHashSampler
• build_temperature_list() : protocols::moves::ReplicaExchangeMC
• BuildAlaPose() : protocols::protein_interface_design::movers::BuildAlaPose
• builder_loop() : protocols::jumping::SheetBuilder
• BuildingBlockInterfaceOperation() : protocols::matdes::BuildingBlockInterfaceOperation
• BuildInstruction() : protocols::forge::build::BuildInstruction
• BuildManager() : protocols::forge::build::BuildManager
• BuildPosition() : protocols::motifs::BuildPosition
• BuildPosition_from_Size() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• BuildSet() : protocols::match::upstream::BuildSet
• buildtype() : protocols::jd2::parser::BluePrint
• bulge_chain_closure() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• bulge_chain_closure_complete() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• bulge_chain_closure_legacy() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• bulge_chain_minimize_legacy() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• bulge_variant_decision() : protocols::stepwise::screener::BulgeApplier
• BulgeApplier() : protocols::stepwise::screener::BulgeApplier
• BulgeApplyMover() : protocols::stepwise::modeler::rna::bulge::BulgeApplyMover
• BulgeUnApplyMover() : protocols::stepwise::modeler::rna::bulge::BulgeUnApplyMover
• bump_check() : protocols::flexpack::rotamer_set::FlexbbRotamerSet
• bump_grid() : protocols::match::output::MatchCollisionFilter
• BumpGrid() : protocols::match::BumpGrid
• bundle_parameters() : protocols::helical_bundle::MakeBundleHelix
• bundle_symmetry() : protocols::helical_bundle::parameters::BundleParametersSet
• bundle_symmetry_copies() : protocols::helical_bundle::parameters::BundleParametersSet
• BundleGridSampler() : protocols::helical_bundle::BundleGridSampler
• BundleGridSamplerHelper() : protocols::helical_bundle::BundleGridSamplerHelper
• BundleParameters() : protocols::helical_bundle::parameters::BundleParameters
• BundleParametersSet() : protocols::helical_bundle::parameters::BundleParametersSet
• bundleparametersset_index() : protocols::helical_bundle::PerturbBundle
• BuriedPolarScore() : protocols::sic_dock::BuriedPolarScore
• BuriedUnsatHbondFilter() : protocols::simple_filters::BuriedUnsatHbondFilter
• BuriedUnsatisfiedPolarsCalculator() : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• byte_index_from_doublebin() : protocols::match::Bool3DGrid