- b -

• b1() : core::scoring::FACTSResidueInfo
• 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() : core::scoring::FACTSResidueInfo
• 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
• bab_motif() : protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• bab_motifs() : protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• backbone_backbone_energy() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hackelec::HackElecEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::TwoBodyEnergy
• backbone_burial() : core::scoring::rna::RNA_DataInfo
• backbone_database() : protocols::loophash::LoopHashLibrary
• backbone_exposed() : core::scoring::rna::RNA_DataInfo
• backbone_for_moltenres_bbconf() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• backbone_for_resid_bbconf() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• backbone_only() : protocols::match::upstream::BuildSet
• backbone_sidechain_energy() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hackelec::HackElecEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::TwoBodyEnergy
• backbone_stub_constraint_energy() : core::scoring::constraints::ConstraintEdge
• backbone_torsion_angle_atoms() : core::conformation::Conformation
• BackboneDB() : protocols::loophash::BackboneDB
• BackboneMover() : protocols::simple_moves::BackboneMover
• BackboneSampler() : protocols::enzdes::BackboneSampler
• BackboneSegment() : protocols::loophash::BackboneSegment
• BackboneStubConstraint() : core::scoring::constraints::BackboneStubConstraint
• BackgroundNode() : core::pack::interaction_graph::BackgroundNode< V, E, G >
• BackgroundToFirstClassEdge() : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• 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_deviation() : protocols::loops::loop_closure::ccd::CcdLoopClosureMover
• backward_jump() : protocols::motifs::Motif
• bad() : protocols::jd2::InnerJob , protocols::jd2::Job
• bad_tree() : core::kinematics::EXCN_InvalidFoldTree
• Ball() : core::scoring::packing::Ball
• ball() : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• balls() : core::scoring::packing::PoseBalls
• 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
• base2_xyz() : core::scoring::hbonds::hbtrie::HBAtom
• base_axis_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_centroids() : core::scoring::rna::RNA_CentroidInfo
• base_geometry_height_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_geometry_orientation_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_name() : core::chemical::carbohydrates::CarbohydrateInfo , core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• base_only() : protocols::dna::RestrictDesignToProteinDNAInterface
• Base_pair() : core::scoring::rna::Base_pair
• base_pair_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_pair_score() : core::scoring::dna::DNA_BasePotential
• base_restype_name() : core::chemical::ResidueType
• base_score() : core::scoring::dna::DNA_BasePotential
• Base_stack() : core::scoring::rna::Base_stack
• base_stack_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_stack_axis_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_stagger_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_step_score() : core::scoring::dna::DNA_BasePotential
• base_string() : core::scoring::dna::DNA_BasePotential
• base_stubs() : core::scoring::rna::RNA_CentroidInfo
• base_weight() : protocols::topology_broker::weights::ConstAbinitioMoverWeight
• base_xyz() : core::scoring::hbonds::hbtrie::HBAtom
• BaseEtableEnergy() : core::scoring::etable::BaseEtableEnergy< Derived >
• 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
• basepair_axis_stagger_scaling() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• basepairs_begin() : protocols::dna::DNAParameters
• basepairs_end() : protocols::dna::DNAParameters
• BasePairType() : protocols::rna::BasePairType
• BasePartner() : core::scoring::dna::BasePartner
• baserotamer_data() : core::pack::rotamer_set::ContinuousRotamerSet
• bases_begin() : protocols::dna::DNAParameters
• bases_end() : protocols::dna::DNAParameters
• basestack_axis_scaling() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• basestep() : protocols::dna::DNAParameters
• basesteps_begin() : protocols::dna::DNAParameters
• basesteps_end() : protocols::dna::DNAParameters
• BasicJob() : protocols::jobdist::BasicJob
• BasicSimAnnealerRepacker() : protocols::pack_daemon::BasicSimAnnealerRepacker
• Batch() : protocols::jd2::archive::Batch
• batch() : protocols::jd2::archive::Batch , protocols::jd2::JobDistributor
• batch_apply() : protocols::relax::FastRelax
• batch_get_xyz() : core::conformation::Conformation , core::pose::Pose
• batch_set_xyz() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree , core::pose::Pose
• batch_underflow() : protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::MPIArchiveJobDistributor , protocols::jd2::JobDistributor
• batches() : protocols::jd2::archive::ArchiveManager
• BatchFeatures() : protocols::features::BatchFeatures
• BatchFeaturesCreator() : protocols::features::BatchFeaturesCreator
• BatchJobInputter() : protocols::jd2::BatchJobInputter
• BatchNrEvaluator() : protocols::simple_filters::BatchNrEvaluator
• bb() : protocols::dna::DnaInterfaceMinMover , protocols::simple_moves::symmetry::SetupNCSMover , protocols::simple_moves::TaskAwareMinMover
• bb_acc_avail() : core::scoring::hbonds::HBondResidueMinData
• bb_bb() : protocols::simple_filters::EnergyPerResidueFilter
• bb_bb_boundaries() : core::pack::interaction_graph::SimpleEdge
• bb_bb_carbon_hbond_one_way() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• BB_BB_EnergyInvoker() : core::scoring::etable::BB_BB_EnergyInvoker< Evaluator >
• bb_bbE() : core::pack::interaction_graph::SimpleEdge
• bb_bbE_calced() : core::pack::interaction_graph::SimpleEdge
• bb_bins_from_pose() : protocols::toolbox::pose_metric_calculators::RotamerRecovery
• bb_bounding_sphere() : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• bb_C_index() : core::scoring::methods::ResidueCartBondedParameters
• bb_CA_index() : core::scoring::methods::ResidueCartBondedParameters
• bb_centroid() : core::pack::interaction_graph::SimpleNode
• bb_clones() : core::conformation::symmetry::SymmetryInfo
• bb_don_avail() : core::scoring::hbonds::HBondResidueMinData
• bb_donor_acceptor_check() : core::scoring::hbonds::HBondOptions
• bb_follows() : core::conformation::symmetry::SymmetryInfo
• bb_H_index() : core::scoring::methods::ResidueCartBondedParameters
• bb_is_independent() : core::conformation::symmetry::SymmetryInfo
• bb_N_index() : core::scoring::methods::ResidueCartBondedParameters
• bb_O_index() : core::scoring::methods::ResidueCartBondedParameters
• bb_pair_score() : core::scoring::dssp::Dssp
• bb_pos() : core::scoring::SS_Info , protocols::fldsgn::topology::SS_Info2
• bb_radius() : core::pack::interaction_graph::SimpleNode
• bb_sc_carbon_hbond_one_way() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• bb_stats() : core::scoring::orbitals::OrbitalsStatistics
• BBClaim() : protocols::topology_broker::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
• bbdep_angle_parameters() : core::scoring::methods::ResidueCartBondedParameters
• bbdep_bond_devs() : core::scoring::methods::IdealParametersDatabase
• bbdep_bond_params() : core::scoring::methods::IdealParametersDatabase
• bbdep_chisamples_for_rotamer_chi() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbdep_length_parameters() : core::scoring::methods::ResidueCartBondedParameters
• bbdep_nrchi_sample() : core::pack::dunbrack::BBDepSemiRotamericData< T >
• bbdep_nrchi_score() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• BBDepCartBondedParameters() : core::scoring::methods::BBDepCartBondedParameters
• BBDepNRChiSample() : core::pack::dunbrack::BBDepNRChiSample< P >
• BBDepScoreInterpData() : core::pack::dunbrack::BBDepScoreInterpData
• BBDepSemiRotamericData() : core::pack::dunbrack::BBDepSemiRotamericData< T >
• BBDofs() : protocols::protein_interface_design::movers::BBDofs
• 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
• bbind_chisamples_for_rotamer_chi() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbind_nrchi_sample() : core::pack::dunbrack::BBIndSemiRotamericData< T >
• bbind_nrchi_score() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• BBIndepCartBondedParameters() : core::scoring::methods::BBIndepCartBondedParameters
• bbindices_up_to_date() : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• BBIndNRChiSample() : core::pack::dunbrack::BBIndNRChiSample< P >
• BBIndSemiRotamericData() : core::pack::dunbrack::BBIndSemiRotamericData< T >
• bbpos_is_set() : protocols::fldsgn::topology::SS_Info2
• bbtorsion_srfd() : core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue
• BBTorsionAndAnglesSRFD() : core::fragment::BBTorsionAndAnglesSRFD
• BBTorsionSRFD() : core::fragment::BBTorsionSRFD
• BDR() : protocols::forge::components::BDR
• BDRSegmentInfo() : protocols::forge::components::BDRSegmentInfo
• BeadAdder() : core::coarse::Rule::BeadAdder
• BeadAtom() : core::coarse::Translator::BeadAtom
• begin() : core::coarse::Rule , core::coarse::TranslatorSet , core::fragment::ConstantLengthFragSet , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::OrderedFragSet , core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Library< Books > , core::graph::EdgeList , core::io::raw_data::RawFileData , core::io::silent::SilentFileData , core::kinematics::FoldTree , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap , core::pack::rotamer_set::FixbbRotamerSets , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubset , core::pack::rotamer_set::RotamerSubsets , core::pack::task::TaskFactory , core::scoring::constraints::Constraints , core::scoring::constraints::ResidueConstraints , core::scoring::dssp::StrandPairingSet , core::scoring::EMapVector , 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::JumpSetup , protocols::jumping::JumpSelector , protocols::jumping::ResiduePairJumpSetup , protocols::ligand_docking::MinimizeLigand , protocols::loops::Loops , protocols::motifs::MotifLibrary , protocols::moves::DataMap , 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::ResidueBBDofs , 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() : core::scoring::dssp::StrandPairing , protocols::fldsgn::topology::StrandPairing
• begin2() : protocols::fldsgn::topology::StrandPairing
• begin_const() : core::io::raw_data::RawFileData
• 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
• being_designed() : core::pack::task::ResidueLevelTask , core::pack::task::PackerTask , core::pack::task::ResidueLevelTask_ , core::pack::task::PackerTask_
• being_packed() : core::pack::task::ResidueLevelTask , core::pack::task::PackerTask , core::pack::task::ResidueLevelTask_ , core::pack::task::PackerTask_ , core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo
• bend() : protocols::fldsgn::topology::Helix
• BesselI0() : core::scoring::CenHBPotential
• best_abs_log_norm_ratio() : core::optimization::SimpleDerivCheckResult
• best_assignment() : protocols::pack_daemon::PackDaemon
• best_by_ala_scan() : protocols::seeded_abinitio::SeedFoldTree
• best_cos_theta() : core::optimization::SimpleDerivCheckResult
• best_entities() : protocols::genetic_algorithm::GeneticAlgorithm
• best_fitness_from_current_generation() : protocols::genetic_algorithm::GeneticAlgorithm
• best_Kmer_rms() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• best_motifhits() : protocols::motifs::BuildPosition
• best_motifs() : protocols::motifs::BuildPosition
• best_norm_analytic() : core::optimization::SimpleDerivCheckResult
• best_norm_numeric() : core::optimization::SimpleDerivCheckResult
• best_rotamer_energy() : core::pack::dunbrack::CoarseSingleResidueLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleResidueRotamerLibrary , core::pack::dunbrack::RotamerLibrary , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleLigandRotamerLibrary
• best_rotamers() : protocols::motifs::BuildPosition
• best_score() : protocols::multistate_design::SingleState
• bestenergy() : core::pack::annealer::SimAnnealerBase
• BestHotspotCstMover() : protocols::protein_interface_design::movers::BestHotspotCstMover
• BestMatchesCollection() : protocols::match::output::BestMatchesCollection
• bestrotamer_at_seqpos() : core::pack::annealer::SimAnnealerBase
• BestTotalScoreSelector() : protocols::frag_picker::BestTotalScoreSelector
• beta() : core::pose::Pose , core::scoring::CSA , protocols::dna::DNABase
• beta_components() : core::scoring::dna::DNATorsionPotential
• beta_turn_present() : protocols::features::BetaTurnDetectionFeatures
• beta_turn_type() : protocols::features::BetaTurnDetectionFeatures
• BetaAlphaBetaMotif() : protocols::fldsgn::topology::BetaAlphaBetaMotif
• BetaAlphaBetaMotifSet() : protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• BetaTurnDetectionFeatures() : protocols::features::BetaTurnDetectionFeatures
• BetaTurnDetectionFeaturesCreator() : protocols::features::BetaTurnDetectionFeaturesCreator
• bF() : protocols::frag_picker::VallResidue
• bfac() : core::scoring::packing::PoseBalls
• BFactor() : protocols::frag_picker::scores::BFactor
• BfactorMPM() : protocols::match::BfactorMPM
• bg_node_2_resid() : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• Bi() : core::scoring::FACTSResidueInfo
• BiasedFragmentMover() : protocols::nonlocal::BiasedFragmentMover
• bIdealLoopClosing() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• BigBinConstraint() : core::scoring::constraints::BigBinConstraint
• BigBinConstraintCreator() : core::scoring::constraints::BigBinConstraintCreator
• bIgnoreSequenceSeparation() : protocols::abinitio::FoldConstraints
• bin() : core::scoring::constraints::BigBinConstraint
• bin_angle() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• bin_center() : protocols::match::Bool3DGrid
• bin_extrema() : protocols::match::Bool3DGrid
• bin_for_point() : protocols::match::Bool3DGrid
• bin_index_() : protocols::frag_picker::scores::TorsionBinSimilarity , protocols::frag_picker::scores::LAMBEGO_Similarity
• bin_rotameric_chi() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• bin_width() : protocols::match::Bool3DGrid
• binary_is_up_to_date() : core::pack::dunbrack::RotamerLibrary
• binary_is_up_to_date_02() : core::pack::dunbrack::RotamerLibrary
• binary_is_up_to_date_10() : core::pack::dunbrack::RotamerLibrary
• BinaryProteinSilentStruct() : core::io::silent::BinaryProteinSilentStruct
• BinaryProteinSilentStructCreator() : core::io::silent::BinaryProteinSilentStructCreator
• BinaryRNASilentStruct() : core::io::silent::BinaryRNASilentStruct
• BinaryRNASilentStructCreator() : core::io::silent::BinaryRNASilentStructCreator
• 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() : core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• blanket_reset_alt_state_total_hASAs() : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• blanket_set() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• block() : protocols::jd2::SingleFileBuffer , protocols::jd2::WriteFileSFB
• block_file() : protocols::jd2::MpiFileBuffer
• block_signals() : core::conformation::Conformation
• block_size() : core::graph::ArrayPool< T >
• blocking_signals() : core::conformation::Conformation
• 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
• boltzmann() : protocols::moves::MonteCarlo , protocols::moves::ReplicaExchangeMC , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::TorsionDOFMover , protocols::moves::MonteCarlo
• BoltzmannFilter() : protocols::protein_interface_design::filters::BoltzmannFilter
• bond_angle() : core::conformation::Conformation , core::kinematics::AtomTree
• bond_angle_atoms() : protocols::backrub::BackrubSegment
• bond_angle_central_atoms_to_score() : core::scoring::methods::EnergyMethodOptions
• bond_angle_dof_id() : core::kinematics::AtomTree
• bond_angle_residue_type_param_set() : protocols::branch_angle::BranchAngleOptimizer , core::scoring::methods::EnergyMethodOptions , protocols::branch_angle::BranchAngleOptimizer
• bond_length() : protocols::simple_moves::CutChainMover , core::conformation::Conformation , core::kinematics::AtomTree , protocols::simple_moves::CutChainMover
• bond_length_dof_id() : core::kinematics::AtomTree
• bondangle() : core::chemical::ResidueType , core::scoring::mm::MMBondAngleResidueTypeParam
• bondangle_index() : core::scoring::mm::MMBondAngleResidueTypeParam
• bondangles_for_atom() : core::chemical::ResidueType , core::scoring::mm::MMBondAngleResidueTypeParam
• BondData() : core::chemical::sdf::BondData
• bonded() : core::chemical::AutomorphismIterator
• bonded_neighbor() : core::conformation::Residue , core::chemical::ResidueType
• bonded_neighbor_all_res() : core::conformation::Conformation
• bonded_neighbor_types() : core::chemical::ResidueType
• bonded_orbitals() : core::chemical::ResidueType , core::conformation::Residue
• BondedAtom() : core::kinematics::tree::BondedAtom
• BondID() : core::id::BondID
• bonus_value() : protocols::hotspot_hashing::HotspotStub
• Book() : core::fragment::picking_old::concepts::Book< Pages >
• bookmarks() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• books() : core::fragment::picking_old::concepts::Library< Books >
• 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
• born_radius() : core::scoring::GenBornResidueInfo
• bottom() : protocols::dna::DnaPosition
• bound() : protocols::simple_filters::NonSequentialNeighborsFilter
• bound_struct() : protocols::optimize_weights::DGBindOptEData
• boundary_left() : core::kinematics::FoldTree
• boundary_right() : core::kinematics::FoldTree
• bounded_protocol() : protocols::frag_picker::FragmentPicker
• BoundedCollector() : protocols::frag_picker::BoundedCollector< StrictWeakOrdering >
• BoundedCollector_CompareTotalScore() : protocols::frag_picker::BoundedCollector_CompareTotalScore
• BoundedPriorityQueue() : protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering >
• BoundFunc() : core::scoring::constraints::BoundFunc
• bounding_box() : protocols::match::downstream::ActiveSiteGrid
• bounding_radius_for_rotamers() : protocols::flexpack::interaction_graph::OTFFlexbbNode
• bounds_check() : core::graph::Array0< T >
• 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::MembraneAbinitio , protocols::abinitio::FragmentSampler , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• BR() : core::scoring::FACTSResidueInfo
• bRama_check() : protocols::loops::loop_closure::ccd::CcdLoopClosureMover
• branch_point() : core::chemical::carbohydrates::CarbohydrateInfo
• 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
• BRENT() : core::optimization::BrentLineMinimization
• brent_abs_tolerance() : core::optimization::MinimizerOptions
• BrentLineMinimization() : core::optimization::BrentLineMinimization
• Bridge() : protocols::forge::build::Bridge
• 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::topology_broker::TopologyClaimer
• broker_file() : protocols::jd2::archive::Batch
• broking() : protocols::topology_broker::TopologyBroker
• 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::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• BUFFER() : core::io::serialization::BUFFER
• buffer_signals() : core::conformation::Conformation
• buffering_signals() : core::conformation::Conformation
• build() : protocols::match::upstream::UpstreamBuilder , core::scoring::methods::WaterBuilder , core::chemical::AtomICoor , protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , core::chemical::AtomICoor , core::chemical::orbitals::ICoorOrbitalData , core::chemical::AtomICoor , protocols::ligand_docking::MoveMapBuilder , protocols::match::output::WriteUpstreamCoordinateKinemage , protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::ligand_docking::InterfaceBuilder , protocols::match::upstream::ProteinUpstreamBuilder
• build_atom_ideal() : core::conformation::Residue
• build_bbdep_rotamers() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• build_bbind_rotamers() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• build_centroid_loop() : protocols::antibody::CDRH3Modeler , protocols::antibody2::H3PerturbCCD
• build_conformer_group() : protocols::match::downstream::LigandConformerBuilder
• build_constraints() : protocols::abinitio::StrandConstraints , protocols::abinitio::AlternativePairings
• build_cst_conformer_jumps() : protocols::jumping::ResiduePairJump
• build_dependent_rotamers() : core::pack::rotamer_set::RotamerSet , protocols::flexpack::rotamer_set::FlexbbRotamerSet , core::pack::rotamer_set::RotamerSubset , core::pack::rotamer_set::RotamerSet_
• build_dependent_rotamers_for_concrete() : core::pack::rotamer_set::RotamerSet_
• build_design_taskset() : protocols::flxbb::FlxbbDesign
• build_fake_xyz() : core::kinematics::Stub
• build_fold_tree() : protocols::topology_broker::TopologyBroker
• build_from_three_coords() : protocols::match::downstream::ClassicMatchAlgorithm
• build_fullatom_loop() : protocols::antibody::CDRH3Modeler
• build_hits_at_all_positions() : protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::downstream::ClassicMatchAlgorithm
• build_inverted_rotamers() : protocols::motifs::Motif
• build_jumpres_distmap() : core::kinematics::ShortestPathInFoldTree
• build_loop_with_ccd_closure() : protocols::LoopRebuild
• build_loops() : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover , protocols::comparative_modeling::MultiThreadingMover
• build_on_base_pair() : protocols::rna::RNA_HelixAssembler
• build_optimize_H_rotamers() : core::pack::rotamer_set::RotamerSet_
• build_orbital_xyz() : core::conformation::Residue
• build_pair_dis_matrix() : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• build_peptide_table() : core::kinematics::ShortestPathInFoldTree
• build_placeholders() : core::scoring::FACTSPotential , core::scoring::GenBornPotential
• build_point() : protocols::match::Matcher
• build_positionOPs() : protocols::motifs::MotifSearch , protocols::motifs::LigandMotifSearch
• build_random_loops() : protocols::LoopRebuild
• 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() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::ContinuousRotamerSet , core::pack::rotamer_set::RotamerSubset , core::pack::rotamer_set::RotamerSet , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::rotamer_set::RotamerSets , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::motifs::Motif
• build_rotamers_for_concrete() : core::pack::rotamer_set::RotamerSet_
• build_rotamers_for_concrete_virt() : core::pack::rotamer_set::RotamerSet_ , protocols::flexpack::rotamer_set::FlexbbRotamerSet
• build_sc_only_rotamer() : core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::DoubleLazyEdge
• build_set() : protocols::match::upstream::ProteinUpstreamBuilder
• build_sidechain_rotamers() : protocols::jumping::ResiduePairJump
• build_structures() : protocols::loophash::LoopHashSampler
• build_temperature_list() : protocols::moves::ReplicaExchangeMC
• build_waters() : core::scoring::methods::LKB_ResidueInfo
• BuildAlaPose() : protocols::protein_interface_design::movers::BuildAlaPose
• builder_loop() : protocols::jumping::SheetBuilder
• 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
• bump_check() : core::pack::task::PackerTask , protocols::flexpack::rotamer_set::FlexbbRotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::task::PackerTask_
• bump_check_backbone() : core::scoring::ScoreFunction
• bump_check_full() : core::scoring::ScoreFunction
• bump_energy_backbone() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::ProClosureEnergy
• bump_energy_full() : core::scoring::methods::ProClosureEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::TwoBodyEnergy , core::scoring::etable::BaseEtableEnergy< Derived >
• bump_grid() : protocols::match::output::MatchCollisionFilter
• bump_parameter() : core::scoring::rna::RNA_AtomVDW
• BumpGrid() : protocols::match::BumpGrid
• BumpSelector() : core::pack::rotamer_set::BumpSelector
• BurialEnergy() : core::scoring::methods::BurialEnergy
• BuriedPolarScore() : protocols::sic_dock::BuriedPolarScore
• BuriedUnsatHbondFilter() : protocols::simple_filters::BuriedUnsatHbondFilter
• BuriedUnsatisfiedPolarsCalculator() : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• bx_init() : core::optimization::MinimizerOptions
• byte_index_from_doublebin() : protocols::match::Bool3DGrid