- b -

• B() : core::io::CrystInfo , core::scoring::electron_density::OneGaussianScattering , protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• b1() : core::scoring::FACTSRsdTypeInfo
• 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::FACTSRsdTypeInfo
• 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
• back() : protocols::jd2::JobsContainer
• backbone() : protocols::protein_interface_design::filters::HbondsToResidueFilter
• backbone_aa() : core::chemical::ResidueType , core::conformation::Residue
• backbone_backbone_energy() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::lkball::LK_BallEnergy , core::scoring::methods::TwoBodyEnergy
• backbone_burial() : core::pose::rna::RNA_DataInfo
• backbone_database() : protocols::loophash::LoopHashLibrary
• backbone_exposed() : core::pose::rna::RNA_DataInfo
• backbone_for_moltenres_bbconf() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• backbone_for_resid_bbconf() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• backbone_mover_complex_type_namer() : protocols::simple_moves::BackboneMover
• backbone_only() : protocols::match::upstream::BuildSet
• backbone_sidechain_energy() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::lkball::LK_BallEnergy , core::scoring::methods::TwoBodyEnergy
• backbone_stub_constraint_energy() : core::scoring::constraints::ConstraintEdge
• backbone_stub_linear_constraint_energy() : core::scoring::constraints::ConstraintEdge
• backbone_torsion_angle_atoms() : core::conformation::Conformation
• backbone_torsion_angle_atoms_meta_aramid() : core::conformation::Conformation
• backbone_torsion_angle_atoms_oligourea() : core::conformation::Conformation
• backbone_torsion_angle_atoms_ortho_aramid() : core::conformation::Conformation
• backbone_torsion_angle_atoms_para_aramid() : core::conformation::Conformation
• BackboneDB() : protocols::loophash::BackboneDB
• BackboneGridSampler() : protocols::helical_bundle::BackboneGridSampler
• BackboneGridSamplerHelper() : protocols::helical_bundle::BackboneGridSamplerHelper
• BackboneMover() : protocols::simple_moves::BackboneMover
• BackboneSampler() : protocols::enzdes::BackboneSampler
• BackboneSegment() : protocols::loophash::BackboneSegment
• BackboneStubConstraint() : core::scoring::constraints::BackboneStubConstraint
• BackboneStubLinearConstraint() : core::scoring::constraints::BackboneStubLinearConstraint
• BackboneTorsionPerturbation() : protocols::hybridization::BackboneTorsionPerturbation
• BackboneTorsionSampler() : protocols::hybridization::BackboneTorsionSampler
• BackgroundNode() : core::pack::interaction_graph::BackgroundNode< V, E, G >
• BackgroundToFirstClassEdge() : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• backrub() : protocols::dna::DesignProteinBackboneAroundDNA
• backrub_cdrs() : protocols::antibody::design::GeneralAntibodyModeler
• backrub_move() : protocols::flexpep_docking::FlexPepDockingProtocol
• BackrubDDMover() : protocols::protein_interface_design::movers::BackrubDDMover
• BackrubMover() : protocols::backrub::BackrubMover
• BackrubProtocol() : protocols::backrub::BackrubProtocol
• BackrubSegment() : protocols::backrub::BackrubSegment
• BackrubSidechainMover() : protocols::backrub::BackrubSidechainMover
• backtrack() : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser
• backward_check() : protocols::motifs::Motif
• backward_jump() : protocols::motifs::Motif
• bad() : protocols::jd2::InnerJob , protocols::jd2::Job , protocols::jd3::InnerLarvalJob , protocols::jd3::LarvalJob
• bad_tree() : core::kinematics::EXCN_InvalidFoldTree
• BalancedKicMover() : protocols::kinematic_closure::BalancedKicMover
• 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
• BareMinimumPDEdge() : core::pack::hbonds::BareMinimumPDEdge
• barrier() : protocols::optimize_weights::IterativeOptEDriver , protocols::pmut_scan::PointMutScanDriver
• base() : protocols::dna::DNAParameters
• base2_xyz() : core::scoring::hbonds::hbtrie::HBAtom
• base5index2symbolString() : core::sequence::ABEGOManager
• base_analogue() : core::chemical::ResidueType
• base_atr_score() : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• base_axis_array() : core::pose::rna::RNA_RawBaseBaseInfo
• base_backbone_distance_cutoff() : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_rho_cutoff() : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_z_cutoff() : core::scoring::rna::RNA_LowResolutionPotential
• base_centroids() : core::scoring::rna::RNA_CentroidInfo
• base_geometry_height_array() : core::pose::rna::RNA_RawBaseBaseInfo
• base_geometry_orientation_array() : core::pose::rna::RNA_RawBaseBaseInfo
• base_name() : core::chemical::ResidueType , core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• base_native_bonus() : protocols::legacy_sewing::LegacyAssemblyConstraintsMover
• base_only() : protocols::dna::RestrictDesignToProteinDNAInterface
• base_pair_array() : core::pose::rna::RNA_RawBaseBaseInfo
• base_pair_constraint_energy() : core::scoring::constraints::ConstraintEdge
• base_pair_list() : core::pose::rna::RNA_FilteredBaseBaseInfo
• base_pair_rmsd_cutoff() : protocols::recces::options::RECCES_Options
• base_pair_rotation_mag() : protocols::recces::options::RECCES_Options
• base_pair_score() : core::scoring::dna::DNA_BasePotential
• base_pair_translation_mag() : protocols::recces::options::RECCES_Options
• base_pairs() : core::pose::rna::RNA_SecStruct
• base_property() : core::chemical::ResidueTypeFinder
• base_rep_score() : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• base_residue_types() : core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet
• base_score() : core::scoring::dna::DNA_BasePotential
• base_stack_array() : core::pose::rna::RNA_RawBaseBaseInfo
• base_stack_axis_array() : core::pose::rna::RNA_RawBaseBaseInfo
• base_stack_list() : core::pose::rna::RNA_FilteredBaseBaseInfo
• base_stagger_array() : core::pose::rna::RNA_RawBaseBaseInfo
• base_state() : protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler
• base_step_energy() : core::scoring::methods::DNA_ReferenceEnergy
• base_step_score() : core::scoring::dna::DNA_BasePotential
• base_string() : core::scoring::dna::DNA_BasePotential
• base_stubs() : core::scoring::rna::RNA_CentroidInfo
• base_type() : core::chemical::ResidueTypeFinder
• base_types() : core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes , core::pack::task::operation::RestrictToSpecifiedBaseResidueTypes
• base_weight() : protocols::topology_broker::weights::ConstAbinitioMoverWeight
• base_xyz() : core::scoring::hbonds::hbtrie::HBAtom
• BaseArchiveManager() : protocols::jd2::archive::BaseArchiveManager
• BaseBinMapUpdater() : protocols::stepwise::screener::BaseBinMapUpdater
• BaseCentroidScreener() : protocols::stepwise::screener::BaseCentroidScreener
• BaseEtableEnergy() : core::scoring::etable::BaseEtableEnergy< Derived >
• BaseJobDistributor() : protocols::jobdist::BaseJobDistributor
• baseline() : protocols::calc_taskop_filters::RelativePoseFilter , protocols::simple_filters::DeltaFilter
• baseline_checkpointing_filename() : protocols::calc_taskop_filters::Sigmoid
• baseline_val() : protocols::calc_taskop_filters::RelativePoseFilter
• BasePair() : core::pose::rna::BasePair
• basepair() : protocols::dna::DNAParameters
• basepair_axis_stagger_scaling() : core::pose::rna::RNA_FilteredBaseBaseInfo
• BasePairConstraint() : core::scoring::constraints::BasePairConstraint
• BasePairConstraintCreator() : core::scoring::constraints::BasePairConstraintCreator
• basepairs_begin() : protocols::dna::DNAParameters
• basepairs_end() : protocols::dna::DNAParameters
• BasePairStep() : core::pose::rna::BasePairStep
• BasePairStepLibrary() : core::import_pose::libraries::BasePairStepLibrary
• BasePairStepSequence() : core::import_pose::libraries::BasePairStepSequence
• BasePairType() : core::import_pose::libraries::BasePairType
• BasePartner() : core::scoring::dna::BasePartner
• baserotamer_data() : core::pack::rotamer_set::ContinuousRotamerSet
• bases_begin() : protocols::dna::DNAParameters
• bases_end() : protocols::dna::DNAParameters
• BaseStack() : core::pose::rna::BaseStack
• basestack_axis_scaling() : core::pose::rna::RNA_FilteredBaseBaseInfo
• basestep() : protocols::dna::DNAParameters
• basesteps_begin() : protocols::dna::DNAParameters
• basesteps_end() : protocols::dna::DNAParameters
• BaseTabooPerturber() : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber
• basic_auth_string() : protocols::network::NetworkQueue
• basic_name() : core::chemical::carbohydrates::CarbohydrateInfo
• basic_pcs_equation() : core::scoring::nmr::pcs::PCSSingleSet
• basic_rdc_equation() : core::scoring::nmr::rdc::RDCMultiSet
• BasicCDRClusterSet() : protocols::antibody::clusters::BasicCDRClusterSet
• BasicCmdLineInit() : protocols::rpc::BasicCmdLineInit
• BasicInit() : protocols::rpc::BasicInit
• BasicJob() : protocols::jobdist::BasicJob
• BasicJumpClaimer() : protocols::topology_broker::BasicJumpClaimer
• BasicRotamerLibrarySpecification() : core::chemical::rotamers::BasicRotamerLibrarySpecification
• BasicSimAnnealerRepacker() : protocols::pack_daemon::BasicSimAnnealerRepacker
• Basis() : protocols::legacy_sewing::Basis , protocols::sewing::data_storage::Basis
• basis_map() : protocols::sewing::hashing::BasisMapGenerator
• basis_map_generator() : protocols::sewing::hashing::AlignmentFileGeneratorMover
• basis_pair() : protocols::legacy_sewing::HashEdge
• basis_pair_is_valid() : protocols::sewing::hashing::BasisMapGenerator
• BasisMapGenerator() : protocols::sewing::hashing::BasisMapGenerator
• Batch() : protocols::jd2::archive::Batch
• batch() : protocols::jd2::archive::Batch
• Batch() : protocols::jd2::archive::Batch
• 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 , 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::minimization_packing::TaskAwareMinMover , protocols::symmetry::SetupNCSMover
• bb_acc_avail() : core::scoring::hbonds::HBondResidueMinData
• bb_bb() : protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::TaskAwareScoreTypeFilter
• 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::pose_metric_calculators::RotamerRecovery
• bb_boltz_probs() : protocols::mean_field::FlexBBMeanField
• bb_boltz_probs_per_aa() : protocols::mean_field::FlexBBMeanField
• 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_movable_selector() : protocols::fold_from_loops::NubInitioMover
• bb_N_index() : core::scoring::methods::ResidueCartBondedParameters
• bb_O_index() : core::scoring::methods::ResidueCartBondedParameters
• bb_only() : protocols::constraint_movers::AddConstraintsToCurrentConformationMover
• 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
• bb_stdev() : protocols::recces::options::RECCES_Options
• 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
• 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, N >
• bbdep_length_parameters() : core::scoring::methods::ResidueCartBondedParameters
• bbdep_nrchi_sample() : core::pack::dunbrack::BBDepSemiRotamericData< T, N >
• bbdep_nrchi_score() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• BBDepCartBondedParameters() : core::scoring::methods::BBDepCartBondedParameters
• BBDepNRChiSample() : core::pack::dunbrack::BBDepNRChiSample< P >
• BBDepScoreInterpData() : core::pack::dunbrack::BBDepScoreInterpData< N >
• BBDepSemiRotamericData() : core::pack::dunbrack::BBDepSemiRotamericData< T, N >
• BBDihedralSampler() : protocols::simple_moves::bb_sampler::BBDihedralSampler
• BBDihedralSampler2D() : protocols::simple_moves::bb_sampler::BBDihedralSampler2D
• BBDihedralSampler3D() : protocols::simple_moves::bb_sampler::BBDihedralSampler3D
• BBDihedralSamplerBase() : protocols::simple_moves::bb_sampler::BBDihedralSamplerBase
• BBDihedralSamplerMover() : protocols::simple_moves::BBDihedralSamplerMover
• BBDihedralSamplerND() : protocols::simple_moves::bb_sampler::BBDihedralSamplerND
• BBDofs() : protocols::splice::BBDofs
• bbdofs() : protocols::splice::ResidueBBDofs
• 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_nrchi_sample() : core::pack::dunbrack::BBIndSemiRotamericData< T, N >
• 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, N >
• BBMatching() : protocols::splice::BBMatching
• bbnbrs() : protocols::evolution::NucleotideMutation
• bbpos_is_set() : protocols::fldsgn::topology::SS_Info2
• bbs_appropriate_for_definitions() : protocols::make_rot_lib::MakeRotLibMover
• 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
• be_lenient() : protocols::kinematic_closure::solution_pickers::FilteredSolutions
• become() : protocols::sewing::data_storage::SmartSegment , protocols::sewing::data_storage::SmartSewingResidue
• begin() : core::conformation::Conformation , core::environment::DofPassport , core::fragment::ConstantLengthFragSet , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::MinimalFragSet , core::fragment::OrderedFragSet , core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Library< Books > , 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::pose::Pose , core::scoring::constraints::Constraints , core::scoring::constraints::ResidueConstraints , core::scoring::dssp::StrandPairingSet , core::scoring::EMapVector , core::scoring::rna::RNA_Motif , core::scoring::rna::RNA_Motifs , protocols::abinitio::abscript::ResidueChunkSelection , protocols::abinitio::PairingStatistics , protocols::abinitio::Templates , protocols::constraint_generator::ConstraintsMap , protocols::denovo_design::task_operations::AAFrequencies , 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::pose_metric_calculators::FragQualCalculator , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::TryRotamers , protocols::rosetta_scripts::ParsedProtocol , protocols::splice::ResidueBBDofs , 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
• begin_receptor_partner_pair() : protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter , protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter , protocols::peptide_deriver::PeptideDeriverOutputter , protocols::peptide_deriver::PeptideDeriverOutputterContainer , protocols::peptide_deriver::PeptideDeriverPoseOutputter
• begin_stage() : protocols::abinitio::abscript::AbscriptMover::StageTracker
• begin_structure() : protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter , protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter , protocols::peptide_deriver::PeptideDeriverOutputter , protocols::peptide_deriver::PeptideDeriverOutputterContainer , protocols::peptide_deriver::PeptideDeriverPoseOutputter
• being_designed() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• being_packed() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_ , core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo , core::scoring::MultipoleElecPoseInfo , core::scoring::VdWTinkerPoseInfo
• BenchmarkBuildRotamersMover() : protocols::testing::BenchmarkBuildRotamersMover
• bend() : protocols::fldsgn::topology::Helix
• bend_angle() : protocols::fldsgn::filters::HelixPairingFilter
• bend_level() : protocols::fldsgn::filters::StrandCurvatureByLevels
• Berendsen_Integrator() : protocols::md::CartesianMD
• 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::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_norm_analytic() : core::optimization::SimpleDerivCheckResult
• best_norm_numeric() : core::optimization::SimpleDerivCheckResult
• best_rotamer_energy() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamerLibrary , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::rotamers::SingleBasicRotamerLibrary , core::pack::rotamers::SingleLigandRotamerLibrary , core::pack::rotamers::SingleResidueRotamerLibrary
• best_rotamer_for_residue() : protocols::sewing::hashing::LigandBindingResPlacer
• 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::io::CrystInfo , core::pose::Pose , core::scoring::CSA , protocols::cryst::Spacegroup , protocols::dna::DNABase , protocols::stepwise::sampler::rigid_body::EulerAngles
• beta_aform() : core::chemical::rna::RNA_FittedTorsionInfo
• beta_components() : core::scoring::dna::DNATorsionPotential
• 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
• BetaSheetArchitect() : protocols::denovo_design::architects::BetaSheetArchitect
• BetaTurnDetection() : protocols::features::BetaTurnDetection
• BetaTurnDetectionFeatures() : protocols::features::BetaTurnDetectionFeatures
• bF() : protocols::frag_picker::VallResidue
• bfac() : core::scoring::motif::Xfrag , core::scoring::packing::PoseBalls
• bfac1() : core::scoring::motif::ResPairMotif
• bfac2() : core::scoring::motif::ResPairMotif
• bfactor() : core::pose::PDBInfo
• BFactor() : protocols::frag_picker::scores::BFactor
• BfactorFittingMover() : protocols::electron_density::BfactorFittingMover
• BfactorMPM() : protocols::match::BfactorMPM
• BfactorMultifunc() : protocols::electron_density::BfactorMultifunc
• bfactors() : protocols::hybridization::FragmentBiasAssigner
• bg() : protocols::toolbox::ScoreRmsPoints
• bg_node_2_resid() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• Bi() : core::scoring::FACTSResidueInfo
• bias_energy() : protocols::canonical_sampling::BiasedMonteCarlo
• biased_mainchain_torsions() : core::scoring::bin_transitions::BinTransitionCalculator
• 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
• BigBinConstraint() : core::scoring::constraints::BigBinConstraint
• BigBinConstraintCreator() : core::scoring::constraints::BigBinConstraintCreator
• bIgnoreSequenceSeparation() : protocols::abinitio::FoldConstraints
• bin() : core::scoring::constraints::BigBinConstraint , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• bin0_of_real() : core::scoring::motif::ResPairMotifMetaBinner
• bin_angle() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::SingleResidueDunbrackLibrary
• bin_boundaries_i() : core::scoring::bin_transitions::BinTransitionData
• bin_boundaries_iplus1() : core::scoring::bin_transitions::BinTransitionData
• bin_center() : protocols::match::Bool3DGrid
• bin_definition_exists() : core::scoring::bin_transitions::BinTransitionCalculator
• bin_exists() : core::scoring::bin_transitions::BinTransitionData
• bin_exists_i() : core::scoring::bin_transitions::BinTransitionData
• bin_exists_iplus1() : core::scoring::bin_transitions::BinTransitionData
• bin_extrema() : protocols::match::Bool3DGrid
• bin_for_point() : protocols::match::Bool3DGrid
• bin_index() : core::scoring::motif::MotifHash , core::scoring::motif::XformScore
• bin_index_() : protocols::frag_picker::scores::LAMBEGO_Similarity , protocols::frag_picker::scores::TorsionBinSimilarity
• bin_matches() : core::pack::dunbrack::DunbrackConstraint
• bin_name() : core::select::residue_selector::BinSelector
• bin_params_file_name() : core::select::residue_selector::BinSelector
• bin_params_loaded() : core::scoring::bin_transitions::BinTransitionCalculator
• bin_rotameric_chi() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• bin_transition_data() : core::scoring::bin_transitions::BinTransitionCalculator
• 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
• binary_output() : core::io::silent::SilentFileOptions
• binary_rna_output() : core::import_pose::options::RNA_DeNovoProtocolOptions
• BinaryFragmentStoreBackend() : protocols::indexed_structure_store::BinaryFragmentStoreBackend
• BinarySilentStruct() : core::io::silent::BinarySilentStruct
• BinarySilentStructCreator() : core::io::silent::BinarySilentStructCreator
• bind_vec_constraint() : protocols::antibody::AntibodyDatabaseManager
• binder_selector() : protocols::fold_from_loops::utils::Nub
• binder_weight() : protocols::fold_from_loops::NubInitioMover
• binding() : protocols::residue_optimization::MetapatchEnumeration
• BindingSiteConstraint() : protocols::constraints_additional::BindingSiteConstraint
• BindingSiteConstraintCreator() : protocols::constraints_additional::BindingSiteConstraintCreator
• BindingStrainFilter() : protocols::protein_interface_design::filters::BindingStrainFilter
• binname() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• binname_index_from_string_i() : core::scoring::bin_transitions::BinTransitionData
• binname_index_from_string_iplus1() : core::scoring::bin_transitions::BinTransitionData
• binner() : protocols::match::HitHasher
• BinSelector() : core::select::residue_selector::BinSelector
• binsums_i() : core::scoring::bin_transitions::BinTransitionData
• binsums_iplus1() : core::scoring::bin_transitions::BinTransitionData
• BinTransitionCalculator() : core::scoring::bin_transitions::BinTransitionCalculator
• BinTransitionData() : core::scoring::bin_transitions::BinTransitionData
• bitmask_for_position() : protocols::match::OccupiedSpaceHash
• blank() : core::pose::rna::RNA_SecStruct
• blank_score_terms() : protocols::recces::options::RECCES_Options
• blank_secstruct() : core::pose::rna::RNA_SecStruct
• blanket_assign_state_0() : core::pack::interaction_graph::AnnealableGraphBase , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , 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::MultiplexedAnnealableGraph , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::ResidueArrayAnnealingEvaluator , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , 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 , protocols::denovo_design::components::StructureData
• block_stack() : protocols::recces::options::RECCES_Options
• block_stack_above_res() : core::import_pose::RNA_DeNovoParameters , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• block_stack_below_res() : core::import_pose::RNA_DeNovoParameters , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• blocking_signals() : core::conformation::Conformation
• Blosum62Map() : core::sequence::Blosum62Map
• BluePrint() : protocols::parser::BluePrint
• blueprint_cst_definition() : protocols::forge::remodel::RemodelEnzdesCstModule
• BlueprintArchitect() : protocols::denovo_design::architects::BlueprintArchitect
• BluePrintBDR() : protocols::fldsgn::BluePrintBDR
• BOGUS_ATOM_ID() : core::id::AtomID
• BOGUS_DOF_ID() : core::id::DOF_ID
• BOGUS_NAMED_ATOM_ID() : core::id::NamedAtomID
• BOGUS_STUB_ID() : core::id::StubID
• BOGUS_TORSION_ID() : core::id::TorsionID
• Boinc() : protocols::boinc::Boinc
• BoincCurrentPoseObserver() : protocols::boinc::BoincCurrentPoseObserver
• BOINCJobDistributor() : protocols::jd2::BOINCJobDistributor
• boltz_rank() : protocols::monte_carlo::GenericMonteCarloMover
• boltzman() : protocols::legacy_sewing::LegacyMonteCarloAssemblyMover
• boltzmann() : protocols::canonical_sampling::BiasedMonteCarlo , protocols::evolution::EvolutionaryDynamicsMover , protocols::monte_carlo::GenericMonteCarloMover , protocols::monte_carlo::MonteCarloInterface , protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo , protocols::moves::ReplicaExchangeMC , protocols::simple_moves::TorsionDOFMover
• boltzmann_choice_post_enumerated_minimize() : protocols::stepwise::options::StepWiseBasicOptions
• boltzmann_result() : protocols::monte_carlo::GenericSimulatedAnnealer
• BoltzmannFilter() : protocols::protein_interface_design::filters::BoltzmannFilter
• BoltzmannRotamerMover() : protocols::minimization_packing::BoltzmannRotamerMover
• Bond() : core::chemical::Bond
• bond() : core::chemical::ResidueType
• 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() : core::scoring::methods::EnergyMethodOptions , protocols::branch_angle::BranchAngleOptimizer
• bond_geometry_energy() : core::scoring::constraints::ConstraintEdge
• bond_iterators() : core::chemical::ResidueType
• bond_length() : core::conformation::Conformation , core::kinematics::AtomTree , protocols::simple_moves::CutChainMover
• bond_length_dof_id() : core::kinematics::AtomTree
• bond_name() : core::chemical::Bond
• bond_orientation() : core::conformation::Conformation
• 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
• bonded2() : core::chemical::AutomorphismIterator
• bonded_neighbor() : core::chemical::ResidueType , core::conformation::Residue
• bonded_neighbor_all_res() : core::conformation::Conformation
• bonded_neighbor_iterators() : core::chemical::ResidueType
• bonded_neighbor_types() : core::chemical::ResidueType
• bonded_orbitals() : core::chemical::Atom , core::chemical::ResidueType , core::conformation::Residue
• BondedAtom() : core::kinematics::tree::BondedAtom
• BondedResidueSelector() : core::select::residue_selector::BondedResidueSelector
• BondID() : core::id::BondID
• BondInfo() : protocols::denovo_design::components::BondInfo
• bonus_function() : core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy
• 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
• boolean_parameter() : core::conformation::parametric::ParametrizationCalculator
• boolean_parameter_cop() : core::conformation::parametric::ParametrizationCalculator
• BooleanValuedParameter() : core::conformation::parametric::BooleanValuedParameter
• boost_closure_cycles() : protocols::forge::remodel::RemodelLoopMover
• boost_closure_stage() : protocols::forge::remodel::RemodelLoopMover
• bootstrapCATrace() : protocols::rbsegment_relax::FragInsertAndAlignMover
• born_radius() : core::scoring::GenBornResidueInfo
• both_remnants_would_be_deleted() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• bottom() : protocols::dna::DnaPosition
• bound() : protocols::simple_filters::NonSequentialNeighborsFilter
• bound_struct() : protocols::optimize_weights::DGBindOptEData
• bound_width() : protocols::constraint_movers::AddConstraintsToCurrentConformationMover
• boundary_left() : core::kinematics::FoldTree
• boundary_neighs() : core::scoring::elec::FAElecContextData
• boundary_right() : core::kinematics::FoldTree
• boundbox() : core::scoring::atomic_depth::AtomicDepth
• bounded() : protocols::relax::AtomCoordinateCstMover
• bounded_protocol() : protocols::frag_picker::FragmentPicker
• BoundedCollector() : protocols::frag_picker::BoundedCollector< StrictWeakOrdering >
• BoundedCollector_CompareTotalScore() : protocols::frag_picker::BoundedCollector_CompareTotalScore
• BoundFunc() : core::scoring::constraints::BoundFunc
• bounding_box() : protocols::match::downstream::ActiveSiteGrid
• bounding_radius_for_rotamers() : protocols::flexpack::interaction_graph::OTFFlexbbNode
• boundingatom() : core::scoring::atomic_depth::AtomicDepth
• bounds_check_entity() : protocols::pack_daemon::EntityCorrespondence
• bounds_check_residue() : protocols::pack_daemon::EntityCorrespondence
• bp_motifhits() : protocols::motifs::MotifSearch
• bp_res() : protocols::recces::params::RECCES_Parameters
• bp_rotamers() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• bps_moves() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• bQuickTest() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• BR() : core::scoring::FACTSResidueInfo
• branch_connect_atom_names() : core::chemical::ResidueType
• branch_connect_atoms() : core::chemical::ResidueType
• branch_connection_torsion_angle_atoms() : core::conformation::Conformation
• branch_length() : protocols::evolution::EvolutionaryDynamicsMover
• branch_overlapping_networks() : protocols::hbnet::HBNet
• branch_point() : core::chemical::carbohydrates::CarbohydrateInfo
• branch_variant_type_from_atom_name() : core::chemical::carbohydrates::CarbohydrateInfoManager
• branch_variant_type_from_position() : core::chemical::carbohydrates::CarbohydrateInfoManager
• BranchAngleOptimizer() : protocols::branch_angle::BranchAngleOptimizer
• BranchCoef1() : protocols::branch_angle::BranchCoef1
• BranchCoef2() : protocols::branch_angle::BranchCoef2
• BranchEnergy() : core::scoring::methods::BranchEnergy
• branchopt() : protocols::backrub::BackrubMover
• BranchParam1() : protocols::branch_angle::BranchParam1
• BranchParam2() : protocols::branch_angle::BranchParam2
• breadth_first_connect() : protocols::loop_grower::DensSkeleton
• break_disulfides() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• break_repack_reform() : protocols::minimization_packing::DisulfideOptimizationMover
• break_side() : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• break_side_ramp() : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• breaks_skeleton() : protocols::loop_grower::DensSkeleton
• BRENT() : core::optimization::BrentLineMinimization
• brent_abs_tolerance() : core::optimization::MinimizerOptions
• BrentLineMinimization() : core::optimization::BrentLineMinimization
• Bridge() : protocols::forge::build::Bridge
• bridge_res() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• BridgeChainsMover() : protocols::denovo_design::movers::BridgeChainsMover
• bring_to_origin() : protocols::simple_filters::ResidueDepthCalculator
• broadcast_entity_string() : protocols::pack_daemon::MPIMultistateFitnessFunction
• 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
• btmplt() : protocols::tcr::TCRmodel
• buckle() : protocols::dna::DNABasepair
• buf_to_address() : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• BUFFER() : core::io::serialization::BUFFER
• buffer_limit() : protocols::jd3::pose_outputters::SilentFilePoseOutputSpecification
• buffer_observers() : core::pose::Pose
• buffer_signals() : core::conformation::Conformation
• buffering_signals() : core::conformation::Conformation
• build() : core::chemical::AtomICoor , core::chemical::orbitals::ICoorOrbitalData , core::import_pose::FullModelPoseBuilder , core::scoring::lkball::WaterBuilder , 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_aa_matrix() : protocols::mean_field::AAMatrix
• build_and_discard_first_round_hits_at_all_positions() : protocols::match::downstream::ClassicMatchAlgorithm
• build_and_score_disulfide() : protocols::denovo_design::DisulfidizeMover
• build_atom_ideal() : core::conformation::Residue
• build_backbone_rotamer_clouds() : protocols::simple_moves::WaterBoxMover
• build_base_rotamers() : core::pack::rotamers::SingleLigandRotamerLibrary
• build_bbdep_rotamers() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• 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() : core::import_pose::RNA_HelixAssembler
• build_dangle_seq1_5prime() : core::import_pose::RNA_HelixAssembler
• build_dangle_seq2_3prime() : core::import_pose::RNA_HelixAssembler
• build_dangle_seq2_5prime() : core::import_pose::RNA_HelixAssembler
• build_dangling_ends() : core::import_pose::RNA_HelixAssembler
• build_denovo_backbone_ct_naming_func() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• build_dependent_rotamers() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset , protocols::flexpack::rotamer_set::FlexbbRotamerSet
• build_dependent_rotamers_for_concrete() : core::pack::rotamer_set::RotamerSet_
• build_design_taskset() : protocols::flxbb::FlxbbDesign
• build_fake_xyz() : core::kinematics::Stub
• build_filtered_tp3_water_rotamers() : core::pack::rotamer_set::RotamerSet_
• 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_frame_and_rotate() : core::scoring::MultipoleElecPotential
• build_from_three_coords() : protocols::match::downstream::ClassicMatchAlgorithm
• build_full_model() : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• build_fullatom_loop() : protocols::antibody_legacy::CDRH3Modeler
• build_graft_model() : protocols::tcr::TCRmodel
• build_groupinfo() : core::scoring::elec::GroupElec
• build_helix() : core::import_pose::RNA_HelixAssembler , protocols::helical_bundle::BundleParametrizationCalculator
• build_hits_at_all_positions() : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• build_ideal_segment() : protocols::splice::SpliceIn , protocols::splice::SpliceInAntibody , protocols::splice::SpliceInTail , protocols::splice::SpliceOut , protocols::splice::SpliceOutAntibody , protocols::splice::SpliceOutTail
• build_in_phases() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• build_init_pose() : core::import_pose::RNA_HelixAssembler
• build_initial_pose() : core::io::pose_from_sfr::PoseFromSFRBuilder
• build_inverted_rotamers() : protocols::motifs::Motif
• build_jumpres_distmap() : core::kinematics::ShortestPathInFoldTree
• build_lattice_of_virtuals() : protocols::cryst::MakeLatticeMover
• build_layer_of_virtuals() : protocols::cryst::MakeLayerMover
• build_ligand_atom_xyz_table() : protocols::nmr::pcs::PCSLigandTransformMover
• build_lkboverlap_rotamer_clouds() : protocols::simple_moves::WaterBoxMover
• 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_node2seg() : protocols::denovo_design::components::FoldGraph
• build_on_base_pair() : core::import_pose::RNA_HelixAssembler
• build_optimize_H_rotamers() : core::pack::rotamer_set::RotamerSet_
• build_orbital_xyz() : core::conformation::Residue
• build_output_index() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• build_pair_dis_matrix() : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• build_pdb_info_1_everything_but_temps() : core::io::pose_from_sfr::PoseFromSFRBuilder
• build_pdb_info_2_temps() : core::io::pose_from_sfr::PoseFromSFRBuilder
• build_peptide_table() : core::kinematics::ShortestPathInFoldTree
• build_placeholders() : core::scoring::GenBornPotential
• build_point() : protocols::match::Matcher
• build_polymer() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• build_pose() : core::io::pose_from_sfr::PoseFromSFRBuilder
• build_positionOPs() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• build_pwat_rotamers() : core::pack::rotamer_set::RotamerSubset
• build_random_loops() : protocols::LoopRebuild
• build_receptor_peptide_pose() : protocols::peptide_deriver::PeptideDeriverFilter
• build_residue_vector_from_fragment() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• build_rot_matrix() : protocols::mean_field::RotMatrix
• build_rot_matrix_for_pose() : protocols::mean_field::MeanField
• build_rotamer() : protocols::motifs::MotifHit
• build_rotamer_list() : protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover
• build_rotamers() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::rotamer_set::ContinuousRotamerSet , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubset , 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_round1_hits_twice() : protocols::match::MatcherTask
• build_sc_only_rotamer() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge
• build_seg2node() : protocols::denovo_design::components::FoldGraph
• build_set() : protocols::match::upstream::ProteinUpstreamBuilder
• build_sidechain_rotamers() : protocols::jumping::ResiduePairJump
• build_stage() : protocols::loop_modeler::LoopModeler
• build_structures() : protocols::loophash::LoopHashSampler
• build_temperature_list() : protocols::moves::ReplicaExchangeMC
• build_tensor_matrix() : core::scoring::nmr::pcs::PCSTensor , core::scoring::nmr::rdc::RDCTensor
• build_tp3_water_rotamers() : core::pack::rotamer_set::RotamerSet_
• build_virtualizable_rotatable_water_rotamers() : core::pack::rotamer_set::RotamerSet_
• build_waters() : core::scoring::lkball::LKB_ResidueInfo
• buildable() : core::chemical::ICoorAtomID
• buildAdjacentLists() : protocols::cluster::calibur::Clustering
• BuildAlaPose() : protocols::protein_interface_design::movers::BuildAlaPose
• buildboundary() : core::scoring::atomic_depth::AtomicDepth
• BuildDeNovoBackboneMover() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• builder_loop() : protocols::jumping::SheetBuilder
• builders() : core::scoring::lkball::WaterBuilderForRestype
• BuildingBlockInterfaceOperation() : protocols::matdes::BuildingBlockInterfaceOperation
• BuildInstruction() : protocols::forge::build::BuildInstruction
• BuildManager() : protocols::forge::build::BuildManager
• BuildPhases() : protocols::denovo_design::components::BuildPhases
• BuildPosition() : protocols::motifs::BuildPosition
• BuildPosition_from_Size() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• BuildSet() : protocols::match::upstream::BuildSet
• buildtype() : protocols::parser::BluePrint
• built_atom_vertex() : core::chemical::AtomICoor
• bulge_chain_closure() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• bulge_chain_closure_complete() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• bulge_chain_closure_legacy() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• bulge_chain_minimize_legacy() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• bulge_keyname() : protocols::denovo_design::architects::StrandArchitect
• 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() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamers::SingleResidueRotamerLibrary , core::pack::task::PackerTask , core::pack::task::PackerTask_ , protocols::flexpack::rotamer_set::FlexbbRotamerSet
• bump_check_backbone() : core::scoring::ScoreFunction
• bump_check_full() : core::scoring::ScoreFunction
• bump_energy_backbone() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::ProClosureEnergy , core::scoring::methods::TwoBodyEnergy
• bump_energy_full() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::ProClosureEnergy , core::scoring::methods::TwoBodyEnergy
• bump_filter() : core::pack::rotamers::SingleResidueRotamerLibrary
• bump_grid() : protocols::match::output::MatchCollisionFilter
• bump_parameter() : core::scoring::rna::RNA_AtomVDW
• bump_parameter_rnp() : core::scoring::rna::RNA_AtomVDW
• BumpGrid() : protocols::match::BumpGrid
• BumpSelector() : core::pack::rotamer_set::BumpSelector
• 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
• BundleParametrizationCalculator() : protocols::helical_bundle::BundleParametrizationCalculator
• BundleReporterFilter() : protocols::helical_bundle::BundleReporterFilter
• burial() : core::scoring::motif::Xfrag
• burial_deriv() : core::scoring::elec::FA_GrpElecEnergy
• burial_sigmoid() : core::scoring::membrane::MPHelicalityEnergy , core::scoring::membrane::MPResidueLipophilicityEnergy
• burial_threshold() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions
• Burial_v2Energy() : core::scoring::methods::Burial_v2Energy
• burial_weight() : core::scoring::elec::FA_GrpElecEnergy
• BurialEnergy() : core::scoring::methods::BurialEnergy
• buried_unsatisfied_penalty_burial_threshold() : core::scoring::methods::EnergyMethodOptions
• buried_unsatisfied_penalty_cone_angle_exponent() : core::scoring::methods::EnergyMethodOptions
• buried_unsatisfied_penalty_cone_angle_shift_factor() : core::scoring::methods::EnergyMethodOptions
• buried_unsatisfied_penalty_cone_dist_exponent() : core::scoring::methods::EnergyMethodOptions
• buried_unsatisfied_penalty_cone_dist_midpoint() : core::scoring::methods::EnergyMethodOptions
• buried_unsatisfied_penalty_hbond_energy_threshold() : core::scoring::methods::EnergyMethodOptions
• BuriedSurfaceAreaFilter() : protocols::simple_filters::BuriedSurfaceAreaFilter
• BuriedUnsatHbondFilter() : protocols::simple_filters::BuriedUnsatHbondFilter
• BuriedUnsatisfiedPolarsCalculator() : protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• BuriedUnsatPenalty() : core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty
• BuriedUnsatPenaltyEdge() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdge
• BuriedUnsatPenaltyEdgeData() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdgeData
• BuriedUnsatPenaltyGraph() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph
• BuriedUnsatPenaltyGraphContainer() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphContainer
• BuriedUnsatPenaltyGraphHbond() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond
• BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup
• BuriedUnsatPenaltyGraphOptions() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions
• BuriedUnsatPenaltyNode() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode
• BuriedUnsatPenaltyNodeData() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData
• burunsat_atoms() : protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• bx_init() : core::optimization::MinimizerOptions
• by_aln() : protocols::protein_interface_design::filters::RmsdFilter
• byte_index_from_doublebin() : protocols::match::Bool3DGrid